Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

SummaryBackgroundEnhancers are genomic cis-regulatory sequences that integrate spatiotemporal signals to control gene expression. Enhancer activity depends on the combination of bound transcription factors as well as—in some cases—the arrangement and spacing of binding sites for these factors. Here, we examine evolutionary changes to the sequence and structure of sparkling, a Notch/EGFR/Runx-regulated enhancer that activates the dPax2 gene in cone cells of the developing Drosophila eye.ResultsDespite functional and structural constraints on its sequence, sparkling has undergone major reorganization in its recent evolutionary history. Our data suggest that the relative strengths of the various regulatory inputs into sparkling change rapidly over evolutionary time, such that reduced input from some factors is compensated by increased input from different regulators. These gains and losses are at least partly responsible for the changes in enhancer structure that we observe. Furthermore, stereotypical spatial relationships between certain binding sites (“grammar elements”) can be identified in all sparkling orthologs—although the sites themselves are often recently derived. We also find that low binding affinity for the Notch-regulated transcription factor Su(H), a conserved property of sparkling, is required to prevent ectopic responses to Notch in noncone cells.ConclusionsRapid DNA sequence turnover does not imply either the absence of critical cis-regulatory information or the absence of structural rules. Our findings demonstrate that even a severely constrained cis-regulatory sequence can be significantly rewired over a short evolutionary timescale

Structure, Function, and Evolution of a Signal-Regulated Enhancer.

Enhancers are cis-regulatory elements that control the level, timing, and cell-type specificity of gene expression. Despite the central role that enhancers play in transcriptional regulation, the rules that govern their composition and organization are poorly understood. To elucidate the relationship between enhancer structure and function, we performed an in-depth analysis of a signal-regulated enhancer in D. melanogaster, the D-Pax2 sparkling (spa) enhancer. This enhancer drives cone cell-specific expression in the Drosophila eye, where D-Pax2 is required for cone cell fate specification. Although twelve transcription factor binding sites have been previously identified within spa, we have found that those sites are not sufficient for cone cell-specific gene expression. We have identified novel regulatory sequences within spa that are essential for enhancer function in vivo, revealing significant complexity in the regulatory circuitry of this enhancer. We also found that binding site organization is tightly linked to function in spa; rearrangements of the regulatory elements within spa can affect both the levels and patterning of gene expression. These data indicate that organizational rules constrain spa structure. However, evolutionary comparisons show that the sequence and structure of spa are evolving rapidly, suggesting that some aspects of spa structure are flexible. Our results shed light on the highly combinatorial nature of enhancer regulation, as well as the complex structural rules that govern enhancer function in vivo.Ph.D.Cell and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/76017/1/rogersci_1.pd

InnoVoting: How Democracy Is Being Reshaped By Women\u27s Innovative Voting Activism & Candidacy

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Prognostic Significance of Growth Kinetics in Newly Diagnosed Glioblastomas Revealed by Combining Serial Imaging with a Novel Biomathematical Model

Glioblastomas (GBMs) are the most aggressive primary brain tumors characterized by their rapid proliferation and diffuse infiltration of the brain tissue. Survival patterns in patients with GBM have been associated with a number of clinico-pathologic factors, including age and neurological status, yet a significant quantitative link to in vivo growth kinetics of each glioma has remained elusive. Exploiting a recently developed tool for quantifying glioma net proliferation and invasion rates in individual patients using routinely available magnetic resonance images (MRIs), we propose to link these patient-specific kinetic rates of biological aggressiveness to prognostic significance. Using our biologically-based mathematical model for glioma growth and invasion, examination of serial pre-treatment MRIs of 32 GBM patients allowed quantification of these rates for each patient’s tumor. Survival analyses revealed that even when controlling for standard clinical parameters (e.g., age, KPS) these model-defined parameters quantifying biologically aggressiveness (net proliferation and invasion rates) were significantly associated with prognosis. One hypothesis generated was that the ratio of the actual survival time after whatever therapies were employed to the duration of survival predicted (by the model) without any therapy would provide a “Therapeutic Response Index” (TRI) of the overall effectiveness of the therapies. The TRI may provided important information, not otherwise available, as to the effectiveness of the treatments in individual patients. To our knowledge, this is the first report indicating that dynamic insight from routinely obtained pre-treatment imaging may be quantitatively useful in characterizing survival of individual patients with GBM. Such a hybrid tool bridging mathematical modeling and clinical imaging may allow for statifying patients for clinical studies relative to their pretreatment biological aggressiveness

Essential role of Notch signaling in effector memory CD8+ T cell–mediated airway hyperresponsiveness and inflammation

Adoptive transfer of in vivo–primed CD8+ T cells or in vitro–generated effector memory CD8+ T (TEFF) cells restores airway hyperresponsiveness (AHR) and airway inflammation in CD8-deficient (CD8−/−) mice. Examining transcription levels, there was a strong induction of Notch1 in TEFF cells compared with central memory CD8+ T cells. Treatment of TEFF cells with a γ-secretase inhibitor (GSI) strongly inhibited Notch signaling in these cells, and after adoptive transfer, GSI-treated TEFF cells failed to restore AHR and airway inflammation in sensitized and challenged recipient CD8−/− mice, or to enhance these responses in recipient wild-type (WT) mice. These effects of GSI were also associated with increased expression of the Notch ligand Delta1 in TEFF cells. Treatment of sensitized and challenged WT mice with Delta1-Fc resulted in decreased AHR and airway inflammation accompanied by higher levels of interferon γ in bronchoalveolar lavage fluid. These results demonstrate a role for Notch in skewing the T cell response from a T helper (Th)2 to a Th1 phenotype as a consequence of the inhibition of Notch receptor activation and the up-regulation of the Notch ligand Delta1. These data are the first to show a functional role for Notch in the challenge phase of CD8+ T cell–mediated development of AHR and airway inflammation, and identify Delta1 as an important regulator of allergic airway inflammation

Symptoms associated with victimization in patients with schizophrenia and related disorders

Background: Patients with psychoses have an increased risk of becoming victims of violence. Previous studies have suggested that higher symptom levels are associated with a raised risk of becoming a victim of physical violence. There has been, however, no evidence on the type of symptoms that are linked with an increased risk of recent victimization. Methods: Data was taken from two studies on involuntarily admitted patients, one national study in England and an international one in six other European countries. In the week following admission, trained interviewers asked patients whether they had been victims of physical violence in the year prior to admission, and assessed symptoms on the Brief Psychiatric Rating Scale (BPRS). Only patients with a diagnosis of schizophrenia or related disorders (ICD-10 F20–29) were included in the analysis which was conducted separately for the two samples. Symptom levels assessed on the BPRS subscales were tested as predictors of victimization. Univariable and multivariable logistic regression models were fitted to estimate adjusted odds ratios. Results: Data from 383 patients in the English sample and 543 patients in the European sample was analysed. Rates of victimization were 37.8% and 28.0% respectively. In multivariable models, the BPRS manic subscale was significantly associated with victimization in both samples. Conclusions: Higher levels of manic symptoms indicate a raised risk of being a victim of violence in involuntary patients with schizophrenia and related disorders. This might be explained by higher activity levels, impaired judgement or poorer self-control in patients with manic symptoms. Such symptoms should be specifically considered in risk assessments

Camera Trap Images used in "Identifying Animal Species in Camera Trap Images using Deep Learning and Citizen Science"

All images were downloaded from Zooniverse and have been resized to 330x330 pixels.This dataset provides the camera trap images used in "Identifying Animal Species in Camera Trap Images using Deep Learning and Citizen Science" as well as meta-data about the images. The Snapshop Serengeti collection includes 6,163,870 images in JPG format. The Snapshot Wisconsin collection includes 497,204 images in JPG format. The Camera CATalogue collection include 506,241 images in JPG format. Excluded are the images for the dataset "Elephant Expedition" which will be published separately outside DRUM. Also excluded are images of humans due to privacy reasons.This study was partially supported by the NSF under award IIS 1619177The development of the Zooniverse platform was partially supported by a Global Impact Award from Google.We also acknowledge support from STFC under grant ST/N003179/1.EE was funded by the University of Oxford’s Hertford College Mortimer May fund

Expression of an S phase-stabilized version of the CDK inhibitor Dacapo can alter endoreplication

In developing organisms, divergence from the canonical cell division cycle is often necessary to ensure the proper growth, differentiation, and physiological function of a variety of tissues. An important example is endoreplication, in which endocycling cells alternate between G and S phase without intervening mitosis or cytokinesis, resulting in polyploidy. Although significantly different from the canonical cell cycle, endocycles use regulatory pathways that also function in diploid cells, particularly those involved in S phase entry and progression. A key S phase regulator is the Cyclin E-Cdk2 kinase, which must alternate between periods of high (S phase) and low (G phase) activity in order for endocycling cells to achieve repeated rounds of S phase and polyploidy. The mechanisms that drive these oscillations of Cyclin E-Cdk2 activity are not fully understood. Here, we show that the Drosophila Cyclin E-Cdk2 inhibitor Dacapo (Dap) is targeted for destruction during S phase via a PIP degron, contributing to oscillations of Dap protein accumulation during both mitotic cycles and endocycles. Expression of a PIP degron mutant Dap attenuates endocycle progression but does not obviously affect proliferating diploid cells. A mathematical model of the endocycle predicts that the rate of destruction of Dap during S phase modulates the endocycle by regulating the length of G phase. We propose from this model and our in vivo data that endo S phase-coupled destruction of Dap reduces the threshold of Cyclin E-Cdk2 activity necessary to trigger the subsequent G-S transition, thereby influencing endocycle oscillation frequency and the extent of polyploidy

Identification of plasma lipid biomarkers for prostate cancer by lipidomics and bioinformatics

Background: Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer. Methodology/Principal Findings: Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient's age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer. Conclusions/Significance: Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy

'A tragedy as old as history':Medical responses to infertility and artificial insemination by donor in 1950s Britain

This chapter will explore how the infertile patient was characterized, perceived, and treated by the medical profession in 1950s England and Scotland. Such was the concern that this subject engendered in postwar Britain that a Departmental Committee was appointed in 1958 (known as the Feversham Committee) to investigate infertility and its treatment through artificial insemination. The written and oral evidence submitted by medical witnesses to that Committee offers rich insights into medical thinking and practice, and into the complex sociomedical politics and ethical anxieties which surrounded the topic. The testimony of legal and religious witnesses will also be explored to a more limited extent in order to offer some context to medical understandings and treatments of infertility. It will be considered how women’s bodies, personalities, and even agency in proactively seeking motherhood through artificial insemination were heavily pathologized in medical and religious discourses, but also how the men involved – husbands, sperm donors and even doctors – did not escape this tendency to pathologize