Publications

convergent evolution in biosynthesis of cyanogenic defence compounds in plants and insects.	for more than 420 million years, plants, insects and their predators have co-evolved based on a chemical arms race including deployment of refined chemical defence systems by each player. cyanogenic glucosides are produced by numerous plants and by some specialized insects and serve an important role as defence compounds in these intimate interactions. burnet moth larvae are able to sequester cyanogenic glucosides from their food plant as well as to carry out de novo biosynthesis. here we show t ...	21505429
a presynaptic endosomal trafficking pathway controls synaptic growth signaling.	structural remodeling of synapses in response to growth signals leads to long-lasting alterations in neuronal function in many systems. synaptic growth factor receptors alter their signaling properties during transit through the endocytic pathway, but the mechanisms controlling cargo traffic between endocytic compartments remain unclear. nwk (nervous wreck) is a presynaptic f-bar/sh3 protein that regulates synaptic growth signaling in drosophila melanogaster. in this paper, we show that nwk acts ...	21464232
the genomic threading database: a comprehensive resource for structural annotations of the genomes from key organisms.	currently, the genomic threading database (gtd) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. structural annotations are carried out using a modified version of genthreader, a reliable fold recognition method. the gen threader annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs. ...	14681393
ensembl 2004.	the ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. it is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. as well as being one of the leading sources of genome annotation, ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated req ...	14681459
identification, tissue distribution and orexigenic activity of neuropeptide f (npf) in penaeid shrimp.	the neuropeptide fs (npfs) are an invertebrate subgroup of the fmrfamide-like peptides, and are proposed by some to be the homologs of vertebrate neuropeptide y. although there is some information about the identity, tissue distribution and function of npfs in insects, essentially nothing is known about them in crustaceans. we have identified and characterized npf-encoding transcripts from the penaeid shrimp litopenaeus vannamei and melicertus marginatus. two transcripts were identified from eac ...	21430216
genomic analysis in the sting-2 quantitative trait locus for defensive behavior in the honey bee, apis mellifera.	we have sequenced an 81-kb genomic region from the honey bee, apis mellifera, associated with a quantitative trait locus (qtl) sting-2 for aggressive behavior. this sequence represents the first extensive study of the honey-bee genome structure encompassing putative genes in a qtl for a behavioral trait. expression of 13 putative genes, as well as two transcripts that were present in a honey-bee est database, was confirmed through reverse transcription analysis of mrna from the honey-bee head. w ...	14656966
silencing of toll pathway components by direct injection of double-stranded rna into drosophila adult flies.	double-stranded rna (dsrna) gene interference is an efficient method to silence gene expression in a sequence-specific manner. here we show that the direct injection of dsrna can be used in adult drosophila flies to disrupt function of endogenous genes in vivo. as a proof of principle, we have used this method to silence components of a major signaling cascade, the toll pathway, which controls fruit fly resistance to fungal and gram-positive bacterial infections. we demonstrate that the knockout ...	14602922
the evolution of parasite recognition genes in the innate immune system: purifying selection on drosophila melanogaster peptidoglycan recognition proteins.	genes involved in the recognition of parasites by the acquired immune system are often subject to intense selection pressures. in some cases, selection to recognize a diverse range of parasites has resulted in high levels of polymorphism, while elsewhere the protein sequence has changed rapidly under directional selection. we tested whether parasite recognition genes in the innate immune system show similar patterns of evolution. we sequenced seven peptidoglycan recognition protein genes (pgrps) ...	14738318
bimodal regulation of raf by cnk in drosophila.	connector enhancer of ksr (cnk) is a multidomain-containing protein previously identified as a positive regulator of the ras/mapk pathway in drosophila. using transfection experiments and an rnai-based rescue assay in drosophila s2 cells, we demonstrate that cnk has antagonistic properties with respect to raf activity. we show that cnk's n-terminal region contains two domains (sam and cric) that are essential for raf function. unexpectedly, we also report that the c-terminal region of cnk contai ...	14517245
rna binding protein sex-lethal (sxl) and control of drosophila sex determination and dosage compensation.	in the past two decades, scientists have elucidated the molecular mechanisms behind drosophila sex determination and dosage compensation. these two processes are controlled essentially by two different sets of genes, which have in common a master regulatory gene, sex-lethal (sxl). sxl encodes one of the best-characterized members of the family of rna binding proteins. the analysis of different mechanisms involved in the regulation of the three identified sxl target genes (sex-lethal itself, tran ...	12966139
the drosophila dysfusion basic helix-loop-helix (bhlh)-pas gene controls tracheal fusion and levels of the trachealess bhlh-pas protein.	the development of the mature insect trachea requires a complex series of cellular events, including tracheal cell specification, cell migration, tubule branching, and tubule fusion. here we describe the identification of the drosophila melanogaster dysfusion gene, which encodes a novel basic helix-loop-helix (bhlh)-pas protein conserved between caenorhabditis elegans, insects, and humans, and controls tracheal fusion events. the dysfusion protein functions as a heterodimer with the tango bhlh-p ...	12897136
malaria: past problems and future prospects. after more than a decade of neglect, malaria is finally black on the agenda for both biomedical research and public health politics.		12789402
malaria films: motion pictures as a public health tool.	i offer a historical examination of a group of malaria motion pictures, a subset of a larger genre of public health films. the majority of these more than 100 films were produced or coproduced by american and british agencies or production companies since 1940. the material is divided into 5 chronological periods, which include world war ii, the postcolonial or ddt era (1946-1961), and the past 2 decades. the films themselves, i argue, represent a unique record of preventive measures, clinical t ...	12835178
ontoblast function: from sequence similarities directly to potential functional annotations by ontology terms.	ontoblast allows one to find information about potential functions of proteins by presenting a weighted list of ontology entries associated with similar sequences from completely sequenced genomes identified in a blast search. it combines, in a single analysis step, the search for sequence similarities in several species with the association of information stored in ontologies. from each identified ontology term a list of genes, which share the functional annotation, can be retrieved. the ontobl ...	12824422
analysis of the plastidic phosphate translocator gene family in arabidopsis and identification of new phosphate translocator-homologous transporters, classified by their putative substrate-binding site.	analysis of the arabidopsis genome revealed the complete set of plastidic phosphate translocator (ppt) genes. the arabidopsis genome contains 16 ppt genes: single copies of genes coding for the triose phosphate/phosphate translocator and the xylulose phosphate/phosphate translocator, and two genes coding for each the phosphoenolpyruvate/phosphate translocator and the glucose-6-phosphate/phosphate translocator. a relatively high number of truncated phosphoenolpyruvate/phosphate translocator genes ...	12644669
dmmyd88 controls dorsoventral patterning of the drosophila embryo.	myd88 is an adapter protein in the signal transduction pathway mediated by interleukin-1 (il-1) and toll-like receptors. a drosophila homologue of myd88 (dmmyd88) was recently shown to be required for the toll-mediated immune response. in drosophila, the toll pathway was originally characterized for its role in the dorsoventral patterning of the embryo. we found that, like toll, dmmyd88 messenger rna is maternally supplied to the embryo. here we report the identification of a new mutant allele o ...	12524523
the flybase database of the drosophila genome projects and community literature.	flybase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model drosophila melanogaster and related species. flybase has primary responsibility for the continual reannotation of the d. melanogaster genome. the ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. a co ...	12519974
genbank.	genbank (r) is a comprehensive sequence database that contains publicly available dna sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. most submissions are made using the bankit (web) or sequin programs and accession numbers are assigned by genbank staff upon receipt. daily data exchange with the embl data library in the uk and the dna data bank ...	12519940
the embl nucleotide sequence database: major new developments.	the embl nucleotide sequence database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. the database is located and maintained at the european bioinformatics institute (ebi) near cambridge, uk. in an international collaboration with ddbj (japan) and genbank (usa), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. webin is the preferred web-based submission system f ...	12519939
the daf-7 tgf-beta signaling pathway regulates chemosensory receptor gene expression in c. elegans.	regulation of chemoreceptor gene expression in response to environmental or developmental cues provides a mechanism by which animals can alter their sensory responses. here we demonstrate a role for the daf-7 tgf-beta pathway in the regulation of expression of a subset of chemoreceptor genes in caenorhabditis elegans. we describe a novel role of this pathway in maintaining receptor gene expression in the adult and show that the daf-4 type ii tgf-beta receptor functions cell-autonomously to modul ...	12464635
the bioperl toolkit: perl modules for the life sciences.	the bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of perl modules available for managing and manipulating life-science information. bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. the bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to ...	12368254
the generic genome browser: a building block for a model organism system database.	the generic model organism system database project (gmod) seeks to develop reusable software components for model organism system databases. in this paper we describe the generic genome browser (gbrowse), a web-based application for displaying genomic annotations and other features. for the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of ...	12368253
cures for the third world's problems: the application of genomics to the diseases plaguing the developing world may have huge medical and economic benefits for those countries and might even prevent armed conflict.		12223456
genome-wide analysis of the odorant-binding protein gene family in drosophila melanogaster.	olfaction is of considerable importance to many insects in behaviors critical for survival and reproduction, including location of food sources, selection of mates, recognition of colony con-specifics, and determination of oviposition sites. an ubiquitous, but poorly understood, component of the insect's olfactory system is a group of odorant-binding proteins (obps) that are present at high concentrations in the aqueous lymph surrounding the dendrites of olfactory receptor neurons. obps are beli ...	12213773
default repression and notch signaling: hairless acts as an adaptor to recruit the corepressors groucho and dctbp to suppressor of hairless.	the dna-binding transcription factor suppressor of hairless [su(h)] functions as an activator during notch (n) pathway signaling, but can act as a repressor in the absence of signaling. hairless (h), a novel drosophila protein, binds to su(h) and has been proposed to antagonize n signaling by inhibiting dna binding by su(h). here we show that, in vitro, h directly binds two corepressor proteins, groucho (gro) and dctbp. reduction of gro or dctbp function enhances h mutant phenotypes and suppress ...	12154126
fourfold faster rate of genome rearrangement in nematodes than in drosophila.	we compared the genome of the nematode caenorhabditis elegans to 13% of that of caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. we detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being approximately 1:1:2. we estimate that the species diverged 50-120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. our estimate of the rearrangement rate, 0.4-1.0 ch ...	12045140
genomics and global health.		11991895
novel sodium channel gene mutations in blattella germanica reduce the sensitivity of expressed channels to deltamethrin.	pyrethroid insecticides alter the normal gating of voltage-gated sodium channels in the nervous system. three sodium channel mutations (e434k, c764r, l993f) were recently identified in pyrethroid resistant german cockroach populations. in this report, we show that the l993f mutation decreased sodium channel sensitivity to the pyrethroid, deltamethrin, by five-fold in xenopus oocytes. in contrast, neither e434k nor c764r alone decreased channel sensitivity to deltamethrin. however, e434k or c764r ...	11886779
annotated expressed sequence tags and cdna microarrays for studies of brain and behavior in the honey bee.	to accelerate the molecular analysis of behavior in the honey bee (apis mellifera), we created expressed sequence tag (est) and cdna microarray resources for the bee brain. over 20,000 cdna clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult a. mellifera brains. these sequences were processed to identify 15,311 high-quality ests representing 8912 putative transcripts. putative transcripts were functionally annotated (using the gene ontolog ...	11932240
drosophila euchromatic ltr retrotransposons are much younger than the host species in which they reside.	the recent release of the complete euchromatic genome sequence of drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (tes) within the genome of a higher eukaryote. in this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (ltr) retrotransposons from the sequenced component of the d. melanogaster genome. we report the characterization of 17 ltr retrotransposon families described prev ...	11544196
molecular characterization of two natural hotspots in the drosophila buzzatii genome induced by transposon insertions.	transposable elements (tes) have been implicated in the generation of genetic rearrangements, but their potential to mediate changes in the organization and architecture of host genomes could be even greater than previously thought. here, we describe the naturally occurring structural and nucleotide variation around two te insertions in the genome of drosophila buzzatii. the studied regions correspond to the breakpoints of a widespread chromosomal inversion generated by ectopic recombination bet ...	11483576
molecular characterization of the evolution of phagosomes.	amoeba use phagocytosis to internalize bacteria as a source of nutrients, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in vertebrates, initiate a sustained immune response. by using a large-scale approach to identify and compare the proteome and phosphoproteome of phagosomes isolated from distant organisms, and by comparative analysis over 39 taxa, we identified an 'ancient' core of phagosomal proteins around which the immune functions of this ...	20959821
updating historical maps of malaria transmission intensity in east africa using remote sensing.	remotely sensed imagery has been used to update and improve the spatial resolution of malaria transmission intensity maps in tanzania, uganda, and kenya. discriminant analysis achieved statistically robust agreements between historical maps of the intensity of malaria transmission and predictions based on multitemporal meteorological satellite sensor data processed using temporal fourier analysis. the study identified land surface temperature as the best predictor of transmission intensity. rain ...	23814324
rna interference as a method for target-site screening in the western corn rootworm, diabrotica virgifera virgifera.	to test the efficacy of rna interference (rnai) as a method for target-site screening in diabrotica virgifera virgifera leconte (coleptera: chrysomelidae) larvae, genes were identified and tested for which clear rnai phenotypes had been identified in the coleopteran model, tribolium castaneum. here the cloning of the d. v. vergifera orthologs of laccase 2 (dvvlac2) and chitin synthase 2 (dvvchs2) is reported. injection of dvvlac2-specific double-stranded rna resulted in prevention of post-molt c ...	21067417
pedf - a noninhibitory serpin with neurotrophic activity.	the pigment epithelium-derived factor (pedf) is a glycoprotein with a molecular weight of 50 kda belonging to the noninhibitory serpin family. it regulates several physiological processes, such as stimulation of retinoblastoma cell differentiation into neuron cells, and facilitation of the growth and viability of photoreceptor cells and neurons of the central nervous system. moreover, this factor protects neuronal cells against apoptosis. pedf is not only a neurotrophic factor, but also a natura ...	22649652
pistia stratiotes (jalkumbhi).	pistia stratiotes (family: araceae) is commonly used in ayurvedic medicine. this review article is a compilation of all the updated information on its phytochemical and pharmacological activities, which were performed by different methods. studies indicate that p. stratiotes possesses diuretic, antidiabetic, antidermatophytic, antifungal, and antimicrobial properties. these results are very encouraging and indicate that this plant should be studied more extensively to confirm the reproducibility ...	22228955
avoiding deet through insect gustatory receptors.	deet is the most widely used insect repellent worldwide. in drosophila olfactory receptor neurons (orns), deet is detected through a mechanism employing the olfactory receptor, or83b. however, it is controversial as to whether orns respond directly to deet or whether deet blocks the response to attractive odors. here, we showed that deet suppressed feeding behavior in drosophila, and this effect was mediated by gustatory receptor neurons (grns). deet was potent in suppressing feeding as <0.1% de ...	20797533
molecular cloning, expression profile and 5' regulatory region analysis of two chemosensory protein genes from the diamondback moth, plutella xylostella.	chemosensory proteins play an important role in transporting chemical compounds to their receptors on dendrite membranes. in this study, two full-length cdna codings for chemosensory proteins of plutella xylostella (lepidoptera: plutellidae) were obtained by race-pcr. pxylcsp3 and pxyl-csp4, with genbank accession numbers abm92663 and abm92664, respectively, were cloned and sequenced. the gene sequences both consisted of three exons and two introns. rt-pcr analysis showed that pxyl-csp3 and pxyl ...	21073345
the birds and the bees and the flowers and the trees: lessons from genetic mapping of sex determination in plants and animals.	the ability to identify genetic markers in nonmodel systems has allowed geneticists to construct linkage maps for a diversity of species, and the sex-determining locus is often among the first to be mapped. sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. its importance for organisms might suggest that sex determination is highly conserved. however, genetic studies have shown that sex determination mechanisms, and the genes involved, ...	20855574
a novel predicted bromodomain-related protein affects coordination between meiosis and spermiogenesis in drosophila and is required for male meiotic cytokinesis.	temporal coordination of meiosis with spermatid morphogenesis is crucial for successful generation of mature sperm cells. we identified a recessive male sterile drosophila melanogaster mutant, mitoshell, in which events of spermatid morphogenesis are initiated too early, before meiotic onset. premature mitochondrial aggregation and fusion lead to an aberrant mitochondrial shell around premeiotic nuclei. despite successful meiotic karyokinesis, improper mitochondrial localization in mitoshell tes ...	20491580
influence of global climate change on chemical fate and bioaccumulation: the role of multimedia models.	multimedia environmental fate models are valuable tools for investigating potential changes associated with global climate change, particularly because thermodynamic forcing on partitioning behavior as well as diffusive and nondiffusive exchange processes are implicitly considered. similarly, food-web bioaccumulation models are capable of integrating the net effect of changes associated with factors such as temperature, growth rates, feeding preferences, and partitioning behavior on bioaccumulat ...	23136071
discover: a feature-based discriminative method for motif search in complex genomes.	identifying transcription factor binding sites (tfbss) encoding complex regulatory signals in metazoan genomes remains a challenging problem in computational genomics. due to degeneracy of nucleotide content among binding site instances or motifs, and intricate 'grammatical organization' of motifs within cis-regulatory modules (crms), extant pattern matching-based in silico motif search methods often suffer from impractically high false positive rates, especially in the context of analyzing larg ...	19478006
identification and characterization of the doublesex gene of nasonia.	the doublesex (dsx) gene of the parasitic wasp nasonia vitripennis is described and characterized. differential splicing of dsx transcripts has been shown to induce somatic sexual differentiation in diptera and lepidoptera, but not yet in other insect orders. two spliceforms of nasonia dsx mrna are differentially expressed in males and females. in addition, in a gynandromorphic line that produces haploids (normally males) with full female phenotypes, these individuals show the female spliceform, ...	19523063
the insect chemoreceptor superfamily in drosophila pseudoobscura: molecular evolution of ecologically-relevant genes over 25 million years.	the insect chemoreceptor superfamily, consisting of the odorant receptor (or) and gustatory receptor (gr) families, exhibits patterns of evolution ranging from highly conserved proteins to lineage-specific gene subfamily expansions when compared across insect suborders and orders. here their evolution across the timespan of 25 million years is examined which yield orthologous divergences ranging from 5-50%. they also reveal the beginnings of lineage-specific gene subfamilies as multiple duplicat ...	19613461
mutations and polymorphisms in gusb gene in mucopolysaccharidosis vii (sly syndrome).	mucopolysaccharidosis vii (mps vii; sly syndrome) is an autosomal recessive disorder caused by a deficiency of beta-glucuronidase (gus, ec 3.2.1.31; gusb). gus is required to degrade glycosaminoglycans (gags), including heparan sulfate (hs), dermatan sulfate (ds), and chondroitin-4,6-sulfate (cs). accumulation of undegraded gags in lysosomes of affected tissues leads to mental retardation, short stature, hepatosplenomegaly, bone dysplasia, and hydrops fetalis. we summarize information on the 49 ...	19224584
review: thermal preference in drosophila.	environmental temperature strongly affects physiology of ectotherms. small ectotherms, like drosophila, cannot endogenously regulate body temperature so must rely on behavior to maintain body temperature within a physiologically permissive range. here we review what is known about drosophila thermal preference. work on thermal behavior in this group is particularly exciting because it provides the opportunity to connect genes to neuromolecular mechanisms to behavior to fitness in the wild.	20161211
distance threshold for the effect of urban agriculture on elevated self-reported malaria prevalence in accra, ghana.	irrigated urban agriculture (ua), which has helped alleviate poverty and increase food security in rapidly urbanizing sub-saharan africa, may inadvertently support malaria vectors. previous studies have not identified a variable distance effect on malaria prevalence from ua. this study examines the relationships between self-reported malaria information for 3,164 women surveyed in accra, ghana, in 2003, and both household characteristics and proximity to sites of ua. malaria self-reports are ass ...	19346373
priority, invisibility and eradication: the history of smallpox and the brazilian public health agenda.		19367347
plant nhx cation/proton antiporters.	although physiological and biochemical data since long suggested that na(+)/h(+) and k(+)/h(+) antiporters are involved in intracellular ion and ph regulation in plants, it has taken a long time to identify genes encoding antiporters that could fulfil these roles. genome sequencing projects have now shown that plants contain a very large number of putative cation/proton antiporters, the function of which is only beginning to be studied. the intracellular nhx transporters constitute the first cat ...	19794841
control of the postmating behavioral switch in drosophila females by internal sensory neurons.	mating induces changes in the receptivity and egg-laying behavior in drosophila females, primarily due to a peptide pheromone called sex peptide which is transferred with the sperm into the female reproductive tract during copulation. whereas sex peptide is generally believed to modulate fruitless-gal4-expressing neurons in the central nervous system to produce behavioral changes, we found that six to eight sensory neurons on the reproductive tract labeled by both ppk-gal4 and fruitless-gal4 can ...	19249273
dual role of wingless signaling in stem-like hematopoietic precursor maintenance in drosophila.	in drosophila, blood development occurs in a specialized larval hematopoietic organ, the lymph gland (lg), within which stem-like hemocyte precursors or prohemocytes differentiate to multiple blood cell types. here we show that components of the wingless (wg) signaling pathway are expressed in prohemocytes. loss- and gain-of-function analysis indicates that canonical wg signaling is required for maintenance of prohemocytes and negatively regulates their differentiation. wg signals locally in a s ...	19460351
urban vegetation cover and vegetation change in accra, ghana: connection to housing quality.	the objectives are to (1) quantify, map, and analyze vegetation cover distributions and changes across accra, ghana, for 2002 and 2010; and (2) examine the statistical relationship between vegetation cover and a housing quality index (hqi) for 2000 at the neighborhood level. pixel-level vegetation cover maps derived using threshold classification of 2002 and 2010 quickbird normalized difference vegetation index images have very high overall accuracies and yield an estimate of 5.9 percent vegetat ...	24293703
the discerning predator: decision rules underlying prey classification by a mosquito-eating jumping spider.	evarcha culicivora is an east african jumping spider that feeds indirectly on vertebrate blood by choosing blood-fed female anopheles mosquitoes as prey. previous studies have shown that this predator can identify its preferred prey even when restricted to using only visual cues. here, we used lures and virtual mosquitoes to investigate the optical cues underlying this predator's prey-choice behaviour. we made lures by dissecting and then reconstructing dead mosquitoes, combining the head plus t ...	22675186
impact of indoor residual spraying with lambda-cyhalothrin on malaria parasitemia and anemia prevalence among children less than five years of age in an area of intense, year-round transmission in malawi.	little is known about the impact of indoor residual spraying (irs) in areas with intense malaria transmission such as sub-saharan africa. in malawi, irs with lambda-cyhalothrin has been applied annually in an area of intense year-long transmission since 2007. we evaluated the impact of irs on parasitemia and anemia prevalence in children less than five years of age by using a cross-sectional household survey conducted in 2009, six months after the second irs spray round. we measured malaria para ...	22665608
function and composition of male accessory gland secretions in anopheles gambiae: a comparison with other insect vectors of infectious diseases.	human malaria, a major public health burden in tropical and subtropical countries, is transmitted exclusively by the bite of a female anopheles mosquito. malaria control strategies aimed at inducing sexual sterility in natural vector populations are an attractive alternative to the use of insecticides. however, despite their importance as disease vectors, limited information is available on the molecular mechanisms regulating fertility in anopheles mosquitoes. in the major malaria vector, an. ga ...	22943543
an insight into the sialotranscriptome of triatoma rubida (hemiptera: heteroptera).	the kissing bug triatoma rubida (uhler, 1894) is found in southwestern united states and parts of mexico where it is found infected with trypanosoma cruzi, invades human dwellings and causes allergies from their bites. although the protein salivary composition of several triatomine species is known, not a single salivary protein sequence is known from t. rubida. furthermore, the salivary diversity of related hematophagous arthropods is very large probably because of the immune pressure from thei ...	22679863
the genetics of sex chromosomes: evolution and implications for hybrid incompatibility.	heteromorphic sex chromosomes, where one sex has two different types of sex chromosomes, face very different evolutionary consequences than do autosomes. two important features of sex chromosomes arise from being present in only one copy in one of the sexes: dosage compensation and the meiotic silencing of sex chromosomes. other differences arise because sex chromosomes spend unequal amounts of time in each sex. thus, the impact of evolutionary processes (mutation, selection, genetic drift, and ...	23025408
connecting the dots between health, poverty and place in accra, ghana.	west africa has a rapidly growing population, an increasing fraction of which lives in urban informal settlements characterized by inadequate infrastructure and relatively high health risks. little is known, however, about the spatial or health characteristics of cities in this region or about the spatial inequalities in health within them. in this article we show how we have been creating a data-rich field laboratory in accra, ghana, to connect the dots between health, poverty, and place in a l ...	24532846
plasmodium falciparum, anaemia and cognitive and educational performance among school children in an area of moderate malaria transmission: baseline results of a cluster randomized trial on the coast of kenya.	studies have typically investigated health and educational consequences of malaria among school-aged children in areas of high malaria transmission, but few have investigated these issues in moderate transmission settings. this study investigates the patterns of and risks for plasmodium falciparum and anaemia and their association with cognitive and education outcomes on the kenyan coast, an area of moderate malaria transmission.	22950512
where's the money? inversions, genes, and the hunt for genomic targets of selection.		22491888
bombyx mori transcription factors: genome-wide identification, expression profiles and response to pathogens by microarray analysis.	transcription factors are present in all living organisms, and play vital roles in a wide range of biological processes. studies of transcription factors will help reveal the complex regulation mechanism of organisms. so far, hundreds of domains have been identified that show transcription factor activity. here, 281 reported transcription factor domains were used as seeds to search the transcription factors in genomes of bombyx mori l. (lepidoptera: bombycidae) and four other model insects. over ...	22943524
the global crisis of malaria: report on a yale conference.	an international conference, "the global crisis of malaria: lessons of the past and future prospects," met at yale university, november 7-9, 2008. the symposium was organized by professor frank snowden and sponsored by the provost's office, the macmillan center, the program in the history of science and history of medicine, and the section of the history of medicine at the yale school of medicine. it brought together experts on malaria from a variety of disciplines, countries, and experiences--p ...	19325942
a regulator of dscam mutually exclusive splicing fidelity.	the down syndrome cell adhesion molecule (dscam) gene has essential roles in neural wiring and pathogen recognition in drosophila melanogaster. dscam encodes 38,016 distinct isoforms via extensive alternative splicing. the 95 alternative exons in dscam are organized into clusters that are spliced in a mutually exclusive manner. the exon 6 cluster contains 48 variable exons and uses a complex system of competing rna structures to ensure that only one variable exon is included. here we show that t ...	21188797
comparative genomic analysis of the odorant-binding protein family in 12 drosophila genomes: purifying selection and birth-and-death evolution.	chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. the insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (or), the gustatory receptor (gr), and the odorant-binding protein (obp) families. members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.	18039354
molecular evolution of glutathione s-transferases in the genus drosophila.	as classical phase ii detoxification enzymes, glutathione s-transferases (gsts) have been implicated in insecticide resistance and may have evolved in response to toxins in the niche-defining feeding substrates of drosophila species. we have annotated the gst genes of the 12 drosophila species with recently sequenced genomes and analyzed their molecular evolution. gene copy number variation is attributable mainly to unequal crossing-over events in the large delta and epsilon clusters. within the ...	18039872
phylogenetic and genomewide analyses suggest a functional relationship between kayak, the drosophila fos homolog, and fig, a predicted protein phosphatase 2c nested within a kayak intron.	a gene located within the intron of a larger gene is an uncommon arrangement in any species. few of these nested gene arrangements have been explored from an evolutionary perspective. here we report a phylogenetic analysis of kayak (kay) and fos intron gene (fig), a divergently transcribed gene located in a kay intron, utilizing 12 drosophila species. the evolutionary relationship between these genes is of interest because kay is the homolog of the proto-oncogene c-fos whose function is modulate ...	18039871
the ribosomal protein genes and minute loci of drosophila melanogaster.	mutations in genes encoding ribosomal proteins (rps) have been shown to cause an array of cellular and developmental defects in a variety of organisms. in drosophila melanogaster, disruption of rp genes can result in the 'minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. while more than 50 minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown ...	17927810
contrasting infection strategies in generalist and specialist wasp parasitoids of drosophila melanogaster.	although host-parasitoid interactions are becoming well characterized at the organismal and cellular levels, much remains to be understood of the molecular bases for the host immune response and the parasitoids' ability to defeat this immune response. leptopilina boulardi and l. heterotoma, two closely related, highly infectious natural parasitoids of drosophila melanogaster, appear to use very different infection strategies at the cellular level. here, we further characterize cellular level dif ...	17967061
fraganchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring.	a glycosylphosphatidylinositol (gpi) anchor is a common but complex c-terminal post-translational modification of extracellular proteins in eukaryotes. here we investigate the problem of correctly annotating gpi-anchored proteins for the growing number of sequences in public databases. we developed a computational system, called fraganchor, based on the tandem use of a neural network (nn) and a hidden markov model (hmm). firstly, nn selects potential gpi-anchored proteins in a dataset, then hmm ...	17893077
high-resolution genome-wide dissection of the two rules of speciation in drosophila.	postzygotic reproductive isolation is characterized by two striking empirical patterns. the first is haldane's rule--the preferential inviability or sterility of species hybrids of the heterogametic (xy) sex. the second is the so-called large x effect--substitution of one species's x chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. although the first rule has been well-established, the second rule remains controvers ...	17850182
novel point mutations in the german cockroach para sodium channel gene are associated with knockdown resistance (kdr) to pyrethroid insecticides.	knockdown resistance (kdr) to pyrethroid insecticides has been attributed to point mutations in the para sodium channel gene in more than a half dozen insect pest species. in this study, we identified two novel para mutations in five highly resistant kdr-type german cockroach strains. the two mutations, from glutamic acid (e434) to lysine (k434) and from cysteine (c764) to arginine (r764), respectively, are located in the first intracellular linker connecting domains i and ii. e434k is located n ...	10899465
attachment of het-a sequences to chromosomal termini in drosophila melanogaster may occur by different mechanisms.	drosophila telomeres contain arrays of the retrotransposonlike elements het-a and tart. their transposition to broken chromosomal termini has been implicated in chromosome healing and telomere elongation. the het-a element is attached by its 3' end, which contains the promoter. to monitor the behavior of het-a elements, we used the yellow gene with terminal deficiencies consisting of breaks in the yellow promoter region that result in the y-null phenotype. attachment of the het-a element provide ...	11003659
retrotransposition of the i factor, a non-long terminal repeat retrotransposon of drosophila, generates tandem repeats at the 3' end.	non-long terminal repeat (ltr) retrotransposons or lines transpose by reverse transcription of an rna intermediate and are thought to use the 3' hydroxyl of a chromosomal cleavage to initiate synthesis of the first strand of the cdna. many of them terminate in a poly(da) sequence at the 3' end of the coding strand although some, like the i factor of drosophila melanogaster, have 3' ends formed by repeats of the trinucleotide taa. we report results showing that i factor transcripts end a few nucl ...	10871395
activation of drosophila sodium channels promotes modification by deltamethrin. reductions in affinity caused by knock-down resistance mutations.	kdr and super-kdr are mutations in houseflies and other insects that confer 30- and 500-fold resistance to the pyrethroid deltamethrin. they correspond to single (l1014f) and double (l1014f+m918t) mutations in segment iis6 and linker ii(s4-s5) of na channels. we expressed drosophila para na channels with and without these mutations and characterized their modification by deltamethrin. all wild-type channels can be modified by <10 nm deltamethrin, but high affinity binding requires channel openin ...	10694259
genetic localization of a drosophila melanogaster resistance gene to a parasitoid wasp and physical mapping of the region.	drosophila melanogaster larvae usually react against eggs of the parasitoid wasp leptopilina boulardi by surrounding them with a multicellular melanotic capsule. the genetic determinism of this response has been studied previously using susceptible (non-capsule-forming) and resistant (capsule-forming) strains. the results suggest that differences in their encapsulation response involve a single gene, resistance to leptopilina boulardi (rlb), with two alleles, the resistant one being dominant. rl ...	10330127
toll receptor-mediated drosophila immune response requires dif, an nf-kappab factor.	the induction of immunity genes in drosophila has been proposed to be dependent on dorsal, dif, and relish, the nf-kappab-related factors. here we provide genetic evidence that dif is required for the induction of only a subset of antimicrobial peptide genes. the results show that the presence of dif without dorsal is sufficient to mediate the induction of drosomycin and defensin. we also demonstrate that dif is a downstream component of the toll signaling pathway in activating the drosomycin ex ...	10197979
uncoupling integrin adhesion and signaling: the betaps cytoplasmic domain is sufficient to regulate gene expression in the drosophila embryo.	integrin cell surface receptors are ideally suited to coordinate cellular differentiation and tissue assembly during embryogenesis, as they can mediate both signaling and adhesion. we show that integrins regulate gene expression in the intact developing embryo by identifying two genes that require integrin function for their normal expression in drosophila midgut endodermal cells. we determined the relative roles of integrin adhesion versus signaling in the regulation of these integrin target ge ...	10090729
analysis of two cosmid clones from chromosome 4 of drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences.	chromosome 4 from drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. these include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of p-element transgenes. as part of a larger project to understand these properties, we are assembling a physical map of this chromosome. here we report the sequence of two cosmids representing approximately 5% of the polytenized region. both cosm ...	10022978
deriving meteorological variables across africa for the study and control of vector-borne disease: a comparison of remote sensing and spatial interpolation of climate.	this paper presents the results of an investigation into the utility of remote sensing (rs) using meteorological satellites sensors and spatial interpolation (si) of data from meteorological stations, for the prediction of spatial variation in monthly climate across continental africa in 1990. information from the advanced very high resolution radiometer (avhrr) of the national oceanic and atmospheric administration's (noaa) polar-orbiting meteorological satellites was used to estimate land surf ...	10203175
comparative study of total hydroperoxides and antioxidant defense system in the indian tropical tasar silkworm, antheraea mylitta, in diapausing and non-diapausing generations.	in the present study, the total hydroperoxides, catalase, glutathione-s-transferase, and ascorbic acid contents were determined in different developmental stages of the non-diapause and the diapause generation of the tropical tasar silkworm, antheraea mylitta drury (lepidoptera: saturniidae). the results showed stage-specific significantly higher levels of total hydroperoxides, catalase, and ascorbic acid contents in the non-diapause as compared to the diapause generation (p < 0.05). however, a ...	24786341
gustatory receptors: not just for good taste.	a recent study has found that a drosophila gustatory receptor is required for thermotaxis. with other fly gustatory receptors having been shown to act in the detection of co2, nutrients in the brain, and light, the roles of the so-called 'gustatory receptors' clearly go way beyond peripheral detection of non-volatile chemicals.	24156814
the genomic distribution of sex-biased genes in drosophila serrata: x chromosome demasculinization, feminization, and hyperexpression in both sexes.	the chromosomal distribution of genes with sex-biased expression is often nonrandom, and in species with xy sex chromosome systems, it is common to observe a deficit of x-linked male-biased genes and an excess of x-linked female-biased genes. one explanation for this pattern is that sex-specific selection has shaped the gene content of the x. alternatively, the deficit of male-biased and excess of female-biased genes could be an artifact of differences between the sexes in the global expression ...	24084777
impact of intermittent preventive anti-malarial treatment on the growth and nutritional status of preschool children in rural senegal (west africa).	negative consequences of malaria might account for seasonality in nutritional status in children in the sahel. we report the impact of a randomized, double-blind, placebo-controlled trial of seasonal intermittent preventive anti-malarial treatment on growth and nutritional status in 1,063 senegalese preschool children. a combination of artesunate and sulfadoxine-pyrimethamine was given monthly from september to november. in the intervention arm, mean weight gain was significantly greater (122.9 ...	17827352
bedraggled, a putative transporter, influences the tissue polarity complex during the r3/r4 fate decision in the drosophila eye.	the tissue polarity pathway is required for the establishment of epithelial polarity in a variety of vertebrate and invertebrate organs. core tissue polarity proteins act in a dynamically regulated complex to direct the polarization of the drosophila eye. we report the identification and characterization of bedraggled (bdg), a novel gene that regulates one output of the tissue polarity pathway--the establishment of the r3/r4 photoreceptor fates. bdg encodes a novel, putative transporter protein ...	17890365
the animal in the genome: comparative genomics and evolution.	comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; ...	18192189
the ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records.	unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the cambrian explosion. because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (ediacaran) to very deep (mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. here, we show using a range of molecular clock methods that t ...	18192191
rewarding the fruits of young labor.		18172516
selenoproteinless animals: selenophosphate synthetase sps1 functions in a pathway unrelated to selenocysteine biosynthesis.	proteins containing the 21st amino acid, selenocysteine (sec), have been described in all three domains of life, but the composition of selenoproteomes in organisms varies significantly. here, we report that aquatic arthropods possess many selenoproteins also detected in other animals and unicellular eukaryotes, and that most of these proteins were either lost or replaced with cysteine-containing homologs in insects. as a result of this selective selenoproteome reduction, fruit flies and mosquit ...	18156471
diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833t>c: a possible role for gene conversion.	homozygosity or compound heterozygosity for the c.833t>c transition (p.i278 t) in the cystathionine beta-synthase (cbs) gene represents the most common cause of pyridoxine-responsive homocystinuria in western eurasians. however, the frequency of the pathogenic c.833c allele, as observed in healthy newborns from several european countries (q(c.833c) approximately equals 3.3 x 10(-3)), is approximately 20-fold higher than expected on the basis of the observed number of symptomatic homocystinuria p ...	17072863
insights into social insects from the genome of the honeybee apis mellifera.	here we report the genome sequence of the honeybee apis mellifera, a key model for social behaviour and essential to global ecology through pollination. compared with other sequenced insect genomes, the a. mellifera genome has high a+t and cpg contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, rna interference and dna methylation genes, among others. furthermore, a. mellifera has fewer genes for innate immunity, detoxification ...	17073008
the importance of smelly feet and stinky cheese.		17038719
recurrent replacement of mtdna and cryptic hybridization between two sibling bat species myotis myotis and myotis blythii.	the two sibling bat species myotis myotis and myotis blythii occur in sympatry over wide areas of southern and central europe. morphological, ecological and previous genetic evidence supported the view that the two species constitute two well-differentiated groups, but recent phylogenetic analyses have shown that the two species share some mtdna haplotypes when they occur in sympatry. in order to see whether some genetic exchange has occurred between the two species, we sequenced a highly variab ...	17018432
discovery and characterization of two nimrod superfamily members in anopheles gambiae.	anti-bacterial proteins in mosquitoes are known to play an important modulatory role on immune responses to infections with human pathogens including malaria parasites. in this study we characterized two members of the anopheles gambiae nimrod superfamily, namely agnimb2 and ageater. we confirm that current annotation of the an. gambiae genome incorrectly identifies agnimb2 and ageater as a single gene, agap009762. through in silico and experimental approaches, it has been shown that agnimb2 is ...	24428830
identification and characteristics of the structural gene for the drosophila eye colour mutant sepia, encoding pda synthase, a member of the omega class glutathione s-transferases.	the eye colour mutant sepia (se1) is defective in pda {6-acetyl-2-amino-3,7,8,9-tetrahydro-4h-pyrimido[4,5-b]-[1,4]diazepin-4-one or pyrimidodiazepine} synthase involved in the conversion of 6-ptp (2-amino-4-oxo-6-pyruvoyl-5,6,7,8-tetrahydropteridine; also known as 6-pyruvoyltetrahydropterin) into pda, a key intermediate in drosopterin biosynthesis. however, the identity of the gene encoding this enzyme, as well as its molecular properties, have not yet been established. here, we identify and ch ...	16712527
the peptidoglycan recognition proteins (pgrps).	peptidoglycan recognition proteins (pgrps) are innate immunity molecules present in insects, mollusks, echinoderms, and vertebrates, but not in nematodes or plants. pgrps have at least one carboxy-terminal pgrp domain (approximately 165 amino acids long), which is homologous to bacteriophage and bacterial type 2 amidases. insects have up to 19 pgrps, classified into short (s) and long (l) forms. the short forms are present in the hemolymph, cuticle, and fat-body cells, and sometimes in epidermal ...	16930467
computational prediction of micrornas encoded in viral and other genomes.	we present an overview of selected computational methods for microrna prediction. it is especially aimed at viral mirna detection. as the number of micrornas increases and the range of genomes encoding mirnas expands, it seems that these small regulators have a more important role than has been previously thought. most micrornas have been detected by cloning and northern blotting, but experimental methods are biased towards abundant micrornas as well as being time-consuming. computational detect ...	17057374
modelling insecticide-binding sites in the voltage-gated sodium channel.	a homology model of the housefly voltage-gated sodium channel was developed to predict the location of binding sites for the insecticides fenvalerate, a synthetic pyrethroid, and ddt an early generation organochlorine. the model successfully addresses the state-dependent affinity of pyrethroid insecticides, their mechanism of action and the role of mutations in the channel that are known to confer insecticide resistance. the sodium channel was modelled in an open conformation with the insecticid ...	16475981
dilimot: discovery of linear motifs in proteins.	discovery of protein functional motifs is critical in modern biology. small segments of 3-10 residues play critical roles in protein interactions, post-translational modifications and trafficking. dilimot (discovery of linear motifs) is a server for the prediction of these short linear motifs within a set of proteins. given a set of sequences sharing a common functional feature (e.g. interaction partner or localization) the method finds statistically over-represented motifs likely to be responsi ...	16845024
a proprotein convertase-inhibiting serpin with an endoplasmic reticulum targeting signal from branchiostoma lanceolatum, a close relative of vertebrates.	lancelets are considered to take a key position in the evolution of lineages leading to vertebrates. herein, a serpin from the lancelet branchiostoma lanceolatum, bl-spn1, was identified that inhibits the pcs (proprotein convertases) pc1/3 and furin. the inhibitor forms sds-stable complexes with either of its targets. analysis of the inhibitor/furin reaction products by mass spectroscopy assigns the enzyme's cleavage position c-terminally to met-met-lys-arg downward arrow in the reactive site lo ...	16445382
the evolution of hexapod engrailed-family genes: evidence for conservation and concerted evolution.	phylogenetic analyses imply that multiple engrailed-family gene duplications occurred during hexapod evolution, a view supported by previous reports of only a single engrailed-family gene in members of the grasshopper genus schistocerca and in the beetle tribolium castaneum. here, we report the cloning of a second engrailed-family gene from schistocerca gregaria and present evidence for two engrailed-family genes from four additional hexapod species. we also report the existence of a second engr ...	16790405