An amphioxus orthologue of the estrogen receptor that does not bind estradiol: Insights into estrogen receptor evolution

<p>Abstract</p> <p>Background</p> <p>The origin of nuclear receptors (NRs) and the question whether the ancestral NR was a liganded or an unliganded transcription factor has been recently debated. To obtain insight into the evolution of the ligand binding ability of estrogen receptors (ER), we comparatively characterized the ER from the protochordate amphioxus (<it>Branchiostoma floridae</it>), and the ER from lamprey (<it>Petromyzon marinus</it>), a basal vertebrate.</p> <p>Results</p> <p>Extensive phylogenetic studies as well as signature analysis allowed us to confirm that the amphioxus ER (amphiER) and the lamprey ER (lampER) belong to the ER group. LampER behaves as a "classical" vertebrate ER, as it binds to specific DNA Estrogen Responsive Elements (EREs), and is activated by estradiol (E₂), the classical ER natural ligand. In contrast, we found that although amphiER binds EREs, it is unable to bind E₂and to activate transcription in response to E₂. Among the 7 natural and synthetic ER ligands tested as well as a large repertoire of 14 cholesterol derivatives, only Bisphenol A (an endocrine disruptor with estrogenic activity) bound to amphiER, suggesting that a ligand binding pocket exists within the receptor. Parsimony analysis considering all available ER sequences suggest that the ancestral ER was not able to bind E₂and that this ability evolved specifically in the vertebrate lineage. This result does not support a previous analysis based on ancestral sequence reconstruction that proposed the ancestral steroid receptor to bind estradiol. We show that biased taxonomic sampling can alter the calculation of ancestral sequence and that the previous result might stem from a high proportion of vertebrate ERs in the dataset used to compute the ancestral sequence.</p> <p>Conclusion</p> <p>Taken together, our results highlight the importance of comparative experimental approaches vs ancestral reconstructions for the evolutionary study of endocrine systems: comparative analysis of extant ERs suggests that the ancestral ER did not bind estradiol and that it gained the ability to be regulated by estradiol specifically in the vertebrate lineage, before lamprey split.</p

AutoML4ETC: Automated Neural Architecture Search for Real-World Encrypted Traffic Classification

Deep learning (DL) has been successfully applied to encrypted network traffic classification in experimental settings. However, in production use, it has been shown that a DL classifier's performance inevitably decays over time. Re-training the model on newer datasets has been shown to only partially improve its performance. Manually re-tuning the model architecture to meet the performance expectations on newer datasets is time-consuming and requires domain expertise. We propose AutoML4ETC, a novel tool to automatically design efficient and high-performing neural architectures for encrypted traffic classification. We define a novel, powerful search space tailored specifically for the near real-time classification of encrypted traffic using packet header bytes. We show that with different search strategies over our search space, AutoML4ETC generates neural architectures that outperform the state-of-the-art encrypted traffic classifiers on several datasets, including public benchmark datasets and real-world TLS and QUIC traffic collected from the Orange mobile network. In addition to being more accurate, AutoML4ETC's architectures are significantly more efficient and lighter in terms of the number of parameters. Finally, we make AutoML4ETC publicly available for future research.Comment: 14 pages, 13 figure

Voluntary Medical Male Circumcision: A Qualitative Study Exploring the Challenges of Costing Demand Creation in Eastern and Southern Africa

BACKGROUND: This paper proposes an approach to estimating the costs of demand creation for voluntary medical male circumcision (VMMC) scale-up in 13 countries of eastern and southern Africa. It addresses two key questions: (1) what are the elements of a standardized package for demand creation? And (2) what challenges exist and must be taken into account in estimating the costs of demand creation? METHODS AND FINDINGS: We conducted a key informant study on VMMC demand creation using purposive sampling to recruit seven people who provide technical assistance to government programs and manage budgets for VMMC demand creation. Key informants provided their views on the important elements of VMMC demand creation and the most effective funding allocations across different types of communication approaches (e.g., mass media, small media, outreach/mobilization). The key finding was the wide range of views, suggesting that a standard package of core demand creation elements would not be universally applicable. This underscored the importance of tailoring demand creation strategies and estimates to specific country contexts before estimating costs. The key informant interviews, supplemented by the researchers' field experience, identified these issues to be addressed in future costing exercises: variations in the cost of VMMC demand creation activities by country and program, decisions about the quality and comprehensiveness of programming, and lack of data on critical elements needed to "trigger the decision" among eligible men. CONCLUSIONS: Based on this study's findings, we propose a seven-step methodological approach to estimate the cost of VMMC scale-up in a priority country, based on our key assumptions. However, further work is needed to better understand core components of a demand creation package and how to cost them. Notwithstanding the methodological challenges, estimating the cost of demand creation remains an essential element in deriving estimates of the total costs for VMMC scale-up in eastern and southern Africa

Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm

The evolution of vertebrates from an ancestral chordate was accompanied by the acquisition of a predatory lifestyle closely associated to the origin of a novel anterior structure, the highly specialized head. While the vertebrate head mesoderm is unsegmented, the paraxial mesoderm of the earliest divergent chordate clade, the cephalochordates (amphioxus), is fully segmented in somites. We have previously shown that fibroblast growth factor signalling controls the formation of the most anterior somites in amphioxus; therefore, unravelling the fibroblast growth factor signalling downstream effectors is of crucial importance to shed light on the evolutionary origin of vertebrate head muscles. By using a comparative RNA sequencing approach and genetic functional analyses, we show that several transcription factors, such as Six1/2, Pax3/7 and Zic, act in combination to ensure the formation of three different somite populations. Interestingly, these proteins are orthologous to key regulators of trunk, and not head, muscle formation in vertebrates. Contrary to prevailing thinking, our results suggest that the vertebrate head mesoderm is of visceral and not paraxial origin and support a multistep evolutionary scenario for the appearance of the unsegmented mesoderm of the vertebrates new 'head'

Developmental cell-cell communication pathways in the cephalochordate amphioxus: actors and functions

The laboratory of H.E. was supported by the CNRS and the ANR16-CE12-0008-01 and S.B. by the Institut Universitaire de France. The laboratory of I.M.L.S. is currently supported by Wellcome Trust ISSF grant 204821/Z/16/ZDuring embryonic development, cells of metazoan embryos need to communicate in order to construct the correct bodyplan. To do so, they use several signals that usually act through interactions between ligands and receptors. Interestingly, only a few pathways are known to be fundamental during animal development, and they are usually found in all the major metazoan clades, raising the following question: how have evolution of the actors and of the functions of these pathways participated in the appearance of the current diversity of animal morphologies? The chordate lineage comprises vertebrates, their sister group the urochordates, and the cephalochordates (i.e. amphioxus). Urochordates are quite derived relative to the chordate ancestor, whereas cephalochordates and vertebrates share many morphological traits. Thus, comparing embryonic development between vertebrates and cephalochordates should give us some insight into the ancestral characters present in chordates and into the morphological evolution in this clade. However, while much is known about the function of different signalling pathways in vertebrates, data are still scarce in the literature for cephalochordates. In this review, we summarize the current state of the field concerning the expression of actors and the function of the major cell-cell communication pathways, including Hedgehog (Hh), Notch, Nuclear Receptor (NR), Receptor Tyrosine Kinase (RTK), Transforming Growth Factor-β (TGF-β) and Wingless/Int (Wnt), in amphioxus.Publisher PDFPeer reviewe

Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ~40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0452883)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0752291)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0723667)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0928414)National Science Foundation (U.S.). Polar Program (ANT-0732665)United States. Environmental Protection Agency (Star Fellowship)Woods Hole Oceanographic Institution. Ocean Life InstituteCenter for Microbial Oceanography: Research and EducationCenter for Environmental Bioinorganic Chemistr

Synthetic computed tomography for low-field magnetic resonance-only radiotherapy in head-and-neck cancer using residual vision transformers

BACKGROUND AND PURPOSE Synthetic computed tomography (sCT) scans are necessary for dose calculation in magnetic resonance (MR)-only radiotherapy. While deep learning (DL) has shown remarkable performance in generating sCT scans from MR images, research has predominantly focused on high-field MR images. This study presents the first implementation of a DL model for sCT generation in head-and-neck (HN) cancer using low-field MR images. Specifically, the use of vision transformers (ViTs) was explored. MATERIALS AND METHODS The dataset consisted of 31 patients, resulting in 196 pairs of deformably-registered computed tomography (dCT) and MR scans. The latter were obtained using a balanced steady-state precession sequence on a 0.35T scanner. Residual ViTs were trained on 2D axial, sagittal, and coronal slices, respectively, and the final sCTs were generated by averaging the models' outputs. Different image similarity metrics, dose volume histogram (DVH) deviations, and gamma analyses were computed on the test set (n = 6). The overlap between auto-contours on sCT scans and manual contours on MR images was evaluated for different organs-at-risk using the Dice score. RESULTS The median [range] value of the test mean absolute error was 57 [37-74] HU. DVH deviations were below 1% for all structures. The median gamma passing rates exceeded 94% in the 2%/2mm analysis (threshold = 90%). The median Dice scores were above 0.7 for all organs-at-risk. CONCLUSIONS The clinical applicability of DL-based sCT generation from low-field MR images in HN cancer was proved. High sCT-dCT similarity and dose metric accuracy were achieved, and sCT suitability for organs-at-risk auto-delineation was shown

A prospective analysis of circulating saturated and monounsaturated fatty acids and risk of non-Hodgkin lymphoma

Circulating saturated (SFA) and monounsaturated fatty acids (MUFA), which are predominantly derived from endogenous metabolism, may influence non-Hodgkin lymphoma (NHL) risk by modulating inflammation or lymphocyte membrane stability. However, few biomarker studies have evaluated NHL risk associated with these fats. We conducted a prospective study of 583 incident NHL cases and 583 individually matched controls with archived pre-diagnosis red blood cell (RBC) specimens in the Nurses\u27 Health Study (NHS) and Health Professionals Follow-up Study (HPFS). RBC membrane fatty acid levels were measured using gas chromatography. Using multivariable logistic regression, we estimated odds ratios (OR) and 95% confidence intervals (CI) for risk of NHL and major NHL subtypes including T cell NHL (T-NHL), B cell NHL (B-NHL) and three individual B-NHLs: chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma. RBC SFA and MUFA levels were not associated with NHL risk overall. However, RBC very long chain SFA levels (VLCSFA; 20:0, 22:0, 23:0) were inversely associated with B-NHLs other than CLL/SLL; ORs (95% CIs) per standard deviation (SD) increase in level were 0.81 (0.70, 0.95) for 20:0, 0.82 (0.70, 0.95) for 22:0, and 0.82 (0.70, 0.96) for 23:0 VLCSFA. Also, both VLCSFA and MUFA levels were inversely associated with T-NHL [ORs (95% CIs) per SD: VLCSFA, 0.63 (0.40, 0.99); MUFA, 0.63 (0.40, 0.99)]. The findings of inverse associations for VLCSFAs with B-NHLs other than CLL/SLL and for VLCSFA and MUFA with T-NHL suggest an influence of fatty acid metabolism on lymphomagenesis