Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are “encoded” in the thousands ...of known protein structures, “decoding” them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds—a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to ...design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta’s success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.
The C57BL/6 mouse strain is represented by distinct substrains, increasingly recognized to differ genetically and phenotypically. The current study compared stroke vulnerability among C57BL/6 J (J), ...C57BL/6JEiJ (JEiJ), C57BL/6ByJ (ByJ), C57BL/6NCrl (NCrl), C57BL/6NJ (NJ) and C57BL/6NTac (NTac) substrains, using a model of permanent distal middle cerebral artery and common carotid artery occlusion. Mean infarct volume was nearly two-fold smaller in J, JEiJ and ByJ substrains relative to NCrl, NJ and NTac (N-lineage) mice. This identifies a previously unrecognized confound in stroke studies involving genetically modified strain comparisons if control substrain background were not rigorously matched. Mean infarct size was smaller in females of J and ByJ substrains than in the corresponding males, but there was no sex difference for NCrl and NJ mice. A higher proportion of small infarcts in J and ByJ substrains was largely responsible for both substrain- and sex-dependent differences. These could not be straightforwardly explained by variations in posterior communicating artery patency, MCA anatomy or acute penumbral blood flow deficits. Their larger and more homogeneously distributed infarcts, together with their established use as the common background for many genetically modified strains, may make N-lineage C57BL/6 substrains the preferred choice for future studies in experimental stroke.
Saving Governance-By-Design Mulligan, Deirdre K.; Bamberger, Kenneth A.
California law review,
06/2018, Letnik:
106, Številka:
3
Journal Article
Recenzirano
Governing through technology has proven irresistibly seductive. Everything from the Internet backbone to consumer devices employs technological design to regulate behavior purposefully by promoting ...values such as privacy, security, intellectual property protection, innovation, and freedom of expression. Legal and policy scholarship has discussed individual skirmishes over the political impact of technical choices—from whether intelligence and police agencies can gain access to privately encrypted data to debates over digital rights management. But it has failed to come to terms with the reality that “governance-by-design”—the purposeful effort to use technology to embed values—is becoming a central mode of policymaking, and that our existing regulatory system is fundamentally ill-equipped to prevent that phenomenon from subverting public governance.
Far from being a panacea, governance-by-design has undermined important governance norms and chipped away at our voting, speech, privacy, and equality rights. In administrative agencies, courts, Congress, and international policy bodies, public discussions about embedding values in design arise in a one-off, haphazard way, if at all. Constrained by their structural limitations, these traditional venues rarely explore the full range of other values that design might affect, and often advance, a single value or occasionally pit one value against another. They seldom permit a meta-discussion about when and whether it is appropriate to enlist technology in the service of values at all. And their policy discussions almost never include designers, engineers, and those that study the impact of socio-technical systems on values.
When technology is designed to regulate without such discussions—as it often is—the effects can be even more insidious. The resulting technology often hides government and corporate aims and the fundamental political decisions that have been made. In this way, governance-by-design obscures policy choices altogether. Such choices recede from the political as they become what “is” rather than what politics has determined ought to be.
This Article proposes a detailed framework for saving governance-by-design.
Through four case studies, the Article examines a range of recent battles over the values embedded in technology design and makes the case that we are entering an era of policymaking by “design war.” These four battles, in turn, highlight four recurring dysfunctions of governance-by-design:
First, governance-by-design overreaches by using overbroad technological fixes that lack the flexibility to balance equities and adapt to changing circumstances. Errors and unintended consequences result.
Second, governance-by-design often privileges one or a few values while excluding other important ones, particularly broad human rights.
Third, regulators lack the proper tools for governance-by-design. Administrative agencies, legislatures, and courts often lack technical expertise and have traditional structures and accountability mechanisms that poorly fit the job of regulating technology.
Fourth, governance-by-design decisions that broadly affect the public are often made in private venues or in processes that make technological choices appear inevitable and apolitical.
If we fail to develop new rules of engagement for governance-by-design, substantial and consequential policy choices will be made without effective public participation, purposeful debate, and relevant expertise. Important values will be sacrificed—sometimes inadvertently, because of bad decisions, and sometimes willfully, because decisions will be captured by powerful stakeholders.
To address these critical issues, this Article proposes four rules of engagement. It constructs a framework to help decision makers protect values and democratic processes as they consider regulating by technology. Informed by the examination of skirmishes across the battlefields, as well as relevant Science and Technology Studies (STS), legal, design, and engineering literatures, this framework embraces four overarching imperatives:
1. Design with Modesty and Restraint to Preserve Flexibility
2. Privilege Human and Public Rights
3. Ensure Regulators Possess the Right Tools: Broad Authority and Competence, and Technical Expertise
4. Maintain the Publicness of Policymaking
These rules of engagement offer a way toward surfacing and resolving value disputes in technological design, while proeserving rather than subverting public governance and public values.
The steady rise in prescription opioids such as oxycodone has led to a virulent epidemic of widespread abuse and deaths in the United States; approximately 80% of affected individuals initiate the ...habitual use of oxycodone by using prescription oral oxycodone. Given the importance of drug pharmacokinetics in determining abuse potential, we designed an oral operant oxycodone self‐administration (SA) procedure in rats to model drug intake by most human users/abusers of oxycodone. Key aspects of the model include limited initial drug intake followed by increasing drug concentrations during extended 4‐h sessions on alternating days. Sex and genetic predisposition are major determinants of human opiate abuse. Therefore, we studied females in seven inbred strains (WLI, WMI, LEW, DSS, F344, BN and SHR) and both sexes in three of these strains. All strains increased intake across serially increasing doses (0.025–0.2 mg/ml; p < 0.001): the range of intakes at the final concentration of oxycodone was 0.72 ± 0.17–4.84 ± 1.42 mg/kg (mean ± SEM) ‐ a 6.7‐fold difference across strains. In LEW, WLI and WMI strains, oxycodone intake increased significantly across all sessions in both sexes. However, in LEW and WMI male rats but not WLI, daily oxycodone intake was significantly lower across all 4‐h sessions than females (p < 0.005). The estimated heritability in oxycodone intake was in the range of 0.21–0.41. In summary, our novel operant oral oxycodone SA model captures the strong abuse potential of oral oxycodone and shows dose, sex and strain‐specific drug intake that is significantly dependent on heredity.
Seven inbred strains of rats show different dose‐dependent escalation of operant responses for oral oxycodone.
Autism spectrum disorders (ASD) are associated with an increased incidence of epilepsy and of epileptiform discharges on electroencephalograms. It is unknown whether epileptiform discharges correlate ...with symptoms of ASD. We completed a retrospective chart review of 101 patients with ASD who had overnight electroencephalograms. We looked for a relationship between epileptiform abnormalities and diagnosis, history of regression, communication skills, and other features associated with ASD. There was a higher incidence of epileptiform activity in children with stereotypies and aggressive behavior. The incidence of epileptiform abnormalities was significantly lower in Asperger’s compared with more severe forms of autism. Results suggest that increasing severity of autistic symptoms may be associated with higher likelihood of epileptiform abnormalities. Whether treatment alters outcome is unknown.
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from ...associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual's genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of "missing heritability" in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Phenome-wide association is a novel reverse genetic strategy to analyze genome-to-phenome relations in human clinical cohorts. Here we test this approach using a large murine population segregating ...for ∼5 million sequence variants, and we compare our results to those extracted from a matched analysis of gene variants in a large human cohort. For the mouse cohort, we amassed a deep and broad open-access phenome consisting of ∼4,500 metabolic, physiological, pharmacological and behavioural traits, and more than 90 independent expression quantitative trait locus (QTL), transcriptome, proteome, metagenome and metabolome data sets--by far the largest coherent phenome for any experimental cohort (www.genenetwork.org). We tested downstream effects of subsets of variants and discovered several novel associations, including a missense mutation in fumarate hydratase that controls variation in the mitochondrial unfolded protein response in both mouse and Caenorhabditis elegans, and missense mutations in Col6a5 that underlies variation in bone mineral density in both mouse and human.
Fetal alcohol spectrum disorders (FASD) are the leading preventable neurodevelopmental disorders and two hallmark symptoms of FASD are abnormal behavior, and cognitive and learning deficits. The ...severity of alcohol's teratogenic effects on the developing brain is influenced by genetics and sex. We previously identified recombinant inbred BXD mouse strains that show differential vulnerability to ethanol-induced cell death in the developing hippocampus, a brain region important in learning and memory. The present study aimed to test the hypothesis that strains with increased vulnerability to ethanol-induced cell death in the hippocampus have concomitant deficits in multiple hippocampal-related behaviors during adolescence.
The current study evaluated the effects of developmental ethanol exposure on adolescent behavior in two BXD strains that show high cell death (BXD48a, BXD100), two that show low cell death (BXD60, BXD71), and the two parental strains (C57BL/6 J (B6), DBA/2 J (D2)). On postnatal day 7, male and female neonatal pups were treated with ethanol (5.0 g/kg) or saline given in two equal doses 2 h apart. Adolescent behavior was assessed across multiple behavioral paradigms including the elevated plus maze, open field, Y-maze, and T-maze.
Our results demonstrate that the effects of developmental ethanol exposure on adolescent behavioral responses are highly dependent on strain. The low cell death strains, BXD60 and BXD71, showed minimal effect of ethanol exposure on all behavioral measures but did present sex differences. The parental -B6 and D2-strains and high cell death strains, BXD48a and BXD100, showed ethanol-induced effects on activity-related or anxiety-like behaviors. Interestingly, the high cell death strains were the only strains that showed a significant effect of postnatal ethanol exposure on hippocampal-dependent spatial learning and memory behaviors.
Overall, we identified effects of ethanol exposure, strain, and/or sex on multiple behavioral measures. Interestingly, the strains that showed the most effects of postnatal ethanol exposure on adolescent behavior were the BXD strains that show high ethanol-induced cell death in the neonatal hippocampus, consistent with our hypothesis. Additionally, we found evidence for interactions among strain and sex, demonstrating that these factors have a complex effect on alcohol responses and that both are important considerations.
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•Exposure to bisphenol A (BPA) in Drosophila melanogaster impacted behavior, axon guidance, and neuroblast development.•BPA-exposure caused mutant phenotypes in w1118 flies.•BPA ...either had no significant impact or exhibited rescue effects in the Fragile X syndrome (FXS) Drosophila model.•BPA exposure increased embryonic-to-pupal lethality in w1118 flies, but had no impact on early lethality of FXS flies.
Bisphenol A (BPA) is a ubiquitous environmental chemical that has been linked to behavioral differences in children and shown to impact critical neurodevelopmental processes in animal models. Though data is emerging, we still have an incomplete picture of how BPA disrupts neurodevelopment; in particular, how its impacts may vary across different genetic backgrounds. Given the genetic tractability of Drosophila melanogaster, they present a valuable model to address this question. Fruit flies are increasingly being used for assessment of neurotoxicants because of their relatively simple brain structure and variety of measurable behaviors. Here we investigated the neurodevelopmental impacts of BPA across two genetic strains of Drosophila—w1118 (control) and the Fragile X Syndrome (FXS) model—by examining both behavioral and neuronal phenotypes. We show that BPA induces hyperactivity in larvae, increases repetitive grooming behavior in adults, reduces courtship behavior, impairs axon guidance in the mushroom body, and disrupts neural stem cell development in the w1118 genetic strain. Remarkably, for every behavioral and neuronal phenotype examined, the impact of BPA in FXS flies was either insignificant or contrasted with the phenotypes observed in the w1118 strain. This data indicates that the neurodevelopmental impacts of BPA can vary widely depending on genetic background and suggests BPA may elicit a gene-environment interaction with Drosophila fragile X mental retardation 1 (dFmr1)—the ortholog of human FMR1, which causes Fragile X Syndrome and is associated with autism spectrum disorder.
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