BACKGROUND Many patients remain without a diagnosis despite extensive medical evaluation. The Undiagnosed Diseases Network (UDN) was established to apply a multidisciplinary model in the evaluation of the most challenging cases and to identify the biologic characteristics of newly discovered diseases. The UDN, which is funded by the National Institutes of Health, was formed in 2014 as a network of seven clinical sites, two sequencing cores, and a coordinating center. Later, a central biorepository, a metabolomics core, and a model organisms screening center were added. METHODS We evaluated patients who were referred to the UDN over a period of 20 months. The patients were required to have an undiagnosed condition despite thorough evaluation by a health care provider. We determined the rate of diagnosis among patients who subsequently had a complete evaluation, and we observed the effect of diagnosis on medical care. RESULTS A total of 1519 patients (53% female) were referred to the UDN, of whom 601 (40%) were accepted for evaluation. Of the accepted patients, 192 (32%) had previously undergone exome sequencing. Symptoms were neurologic in 40% of the applicants, musculoskeletal in 10%, immunologic in 7%, gastrointestinal in 7%, and rheumatologic in 6%. Of the 382 patients who had a complete evaluation, 132 received a diagnosis, yielding a rate of diagnosis of 35%. A total of 15 diagnoses (11%) were made by clinical review alone, and 98 (74%) were made by exome or genome sequencing. Of the diagnoses, 21% led to recommendations regarding changes in therapy, 37% led to changes in diagnostic testing, and 36% led to variant-specific genetic counseling. We defined 31 new syndromes. CONCLUSIONS The UDN established a diagnosis in 132 of the 382 patients who had a complete evaluation, yielding a rate of diagnosis of 35%. (Funded by the National Institutes of Health Common Fund.)

Insulin/Insulin-like growth factor signaling regulates homeostasis and growth in mammals, and is implicated in diseases from diabetes to cancer. In Drosophila melanogaster, as in other invertebrates, multiple Insulin-Like Peptides (DILPs) are encoded by a family of related genes. To assess DILPs' physiological roles, we generated small deficiencies that uncover single or multiple dilps, generating genetic loss-of-function mutations. Deletion of dilps1-5 generated homozygotes that are small, severely growth-delayed, and poorly viable and fertile. These animals display reduced metabolic activity, decreased triglyceride levels and prematurely activate autophagy, indicative of ''starvation in the midst of plenty,'' a hallmark of Type I diabetes. Furthermore, circulating sugar levels are elevated in Df [dilp1-5] homozygotes during eating and fasting. In contrast, Df[dilp6] or Df[dilp7] animals showed no major metabolic defects. We discuss physiological differences between mammals and insects that may explain the unexpected survival of lean, 'diabetic' flies.diabetes ͉ DILP ͉ Drosophila insulin receptor ͉ insect physiology ͉ trehalose

Homeobox genes specify cell fate and positional identity in embryos throughout the animal kingdom. Paradoxically, although each has a specific function in vivo, the in vitro DNA-binding specificities of homeodomain proteins are overlapping and relatively weak. A current model is that homeodomain proteins interact with cofactors that increase specificity in vivo. Here we use a native binding site for the homeodomain protein Fushi tarazu (Ftz) to isolate Ftz-F1, a protein of the nuclear hormone-receptor superfamily and a new Ftz cofactor. Ftz and Ftz-F1 are present in a complex in Drosophila embryos. Ftz-F1 facilitates the binding of Ftz to DNA, allowing interactions with weak-affinity sites at concentrations of Ftz that alone bind only high-affinity sites. Embryos lacking Ftz-F1 display ftz-like pair-rule cuticular defects. This phenotype is a result of abnormal ftz function because it is expressed but fails to activate downstream target genes. Cooperative interaction between homeodomain proteins and cofactors of different classes may serve as a general mechanism to increase HOX protein specificity and to broaden the range of target sites they regulate.

Insulin receptors are abundant in the central nervous system, but their roles remain elusive. Here we show that the insulin receptor functions in axon guidance. The Drosophila insulin receptor (DInR) is required for photoreceptor-cell (R-cell) axons to find their way from the retina to the brain during development of the visual system. DInR functions as a guidance receptor for the adapter protein Dock/Nck. This function is independent of Chico, the Drosophila insulin receptor substrate (IRS) homolog.

Background The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus , a seed feeder of the family Lygaeidae. Results The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus ’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes. Electronic supplementary material The online version of this article (10.1186/s13059-019-1660-0) contains supplementary material, which is available to authorized users.

The Drosophila fushi tarazu (ftz) upstream element is an enhancer-like element that is required for the correct expression of fez in developing embryos and that directs transcription from a minimal promoter in a ftz-like seven-striped pattern. Using a deletion analysis, we have identified several independent c/s-regulatory elements in the upstream element. A distal enhancer directs fusion gene expression in seven stripes primarily in the mesoderm. A more complex proximal enhancer contains a mesodermally active element and a second element with which it interacts to generate seven stripes in the ectoderm. Striped expression directed by each enhancer is ftz-dependent, and each contains binding sites for purified ftz homeo domain. We suggest that ftz protein acts in combination with germ layer-restricted transcription factors directly and positively to regulate the transcription of its own gene. The development of a complex organism from a fertilized egg requires the differential expression of genetic information in a temporally and spatially restricted fashion. This differential expression is frequently regulated at the level of transcription initiation (for reviews, see Maniatis et al. 1987;Mitchell and Tjian 1989). In such cases, cis-acting DNA sequences mediate interactions between trans-acting protein factors and RNA polymerase II or the "general transcription machinery" to activate transcription. Promoter elements, located close to the transcription start site, are required for efficient initiation and positioning of the start site, whereas upstream regulatory elements or enhancers act to increase the rate of transcription from a given promoter. Enhancers are characterized by their abilities to (1) stimulate transcription over large and varying distances, (2) act in an orientation-independent fashion, and (3) stimulate transcription of heterologous promoters (Serfling et al. 1985). For both viral and cellular genes, discrete cisacting regulatory elements have been identified that direct transcription in a cell type-restricted fashion. Although some cell type-specific enhancers have been studied in detail (Atchison 1988), only a small number have been examined in their native cellular environments in transgenic animals (Posakony et al. 1985;Garabedian et al. 1986;Hammer et al. 1987; Pinkert et al. 1987; Johnson et al. 1989;Logan et al. 1989). Much of what we know about enhancer function comes from studies of viral model systems. Analysis of the wellcharacterized viral SV40 enhancers suggests that the basic building blocks of enhancers are short "enhansons" that correspond to the binding sites for transacting factors (Ondek et al. 1988}. Different enhancer motifs may be active in different cell types, suggesting that the availability of cell type-specific transcription factors may control the specificity of enhancer activation {Schirm et al. 1987). Given the complexity of promoter and enhancer elements, it is possible to construct a scenario in which transcriptional specificity is determined by the combinatoria...

Background: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in humanmade structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.

Despite the importance of insulin signaling pathways in human disease, initial concerns that insect physiology and sugar metabolism differ enough from humans that flies would not model human disease hampered research in this area. However, during the past 10–15 years, evidence has accumulated that flies can indeed model various aspects of diabetes and related human disorders. This cluster of diseases impact insulin and insulin signaling pathways, fields which have been discussed in many excellent review articles in recent years. In this chapter, we restrict our focus to specific examples of diabetes-related disease models in Drosophila, discussing the advantages and limitations of these models in light of physiological similarities and differences between insects and mammals. We discuss features of metabolism and sugar regulation that are shared between flies and mammals, and specific Drosophila models for Type 1 and Type 2 diabetes, Metabolic syndrome, and related abnormalities including insulin resistance and heart disease. We conclude that fly models for diabetes and related disorders enhance our ability to identify genes and discern functional interactions that can be exploited for disease intervention.