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Sickle cell disease is genetic red blood cell disorder transmitted via an autosomal recessive mutation due to valine replacing glutamicacid on the beta globulin chain of the hemoglobin molecule. The disease impacts millions of people worldwide majority living in sub-Saharan Africa and India and impacts approximately 100,000 Americans mostly those of African descent. [2-3] In 2019, two novel treatment agents for sickle cell anemia, crizanlizumab (Adakveo) and voxelotor (Oxbryta) were approved by the United States Food and Drug Administration (US FDA) [7, 8]. Both medications offer sickle cell patients improved control of their disease by reducing sickling of the red blood cells (voxelotor) and the painful effects of vaso-occlusive crises, (crizanlizumab). We studied the effects of crizanlizumab and voxelotor on a population of patients in a sickle cell clinic. Fifty-two charts were reviewed for inclusion in the study; 12 patients were using crizanlizumab and 12 patients were using voxelotor. Eight patients met criteria for evaluation of crizanlizumab and 7 patients for voxelotor. Of all data collected, the only significant difference between baseline measures and post-therapy measures was for voxelotor and hemoglobin levels at baseline and at 3 or more months post therapy. This was a small study which reflects the experience of one clinic; sickle cell providers must continue to address the social determinants of health, psychosocial and psychological needs of their patients in addition to prescribing these novel medications.

Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous autosomes and recombination between them is suppressed via inversions to resolve sexual conflict. The resulting degradation of the Y chromosome gene content creates the need for dosage compensation in the heterogametic sex. Sex chromosome theory also implies a linear process, starting from sex chromosome origin and progressing to heteromorphism. Despite many convergent genomic patterns exhibited by independently evolved sex chromosome systems, and many case studies supporting these theoretical predictions, emerging data provide numerous interesting exceptions to these long-standing theories, and suggest that the remarkable diversity of sex chromosomes is matched by a similar diversity in their evolution. For example, it is clear that sex chromosome pairs are not always derived from homologous autosomes. In addition, both the cause and the mechanism of recombination suppression between sex chromosome pairs remain unclear, and it may be that the spread of recombination suppression is a more gradual process than previously thought. It is also clear that dosage compensation can be achieved in many ways, and displays a range of efficacy in different systems. Finally, the remarkable turnover of sex chromosomes in many systems, as well as variation in the rate of sex chromosome divergence, suggest that assumptions about the inevitable linearity of sex chromosome evolution are not always empirically supported, and the drivers of the birth–death cycle of sex chromosome evolution remain to be elucidated. Here, we concentrate on how the diversity in sex chromosomes across taxa highlights an equal diversity in each stage of sex chromosome evolution.

Accelerated rates of sequence evolution on the X chromosome compared to autosomes, known as Fast-X evolution, have been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast-X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across Poeciliid fish species. The common guppy,Poecilia reticulata, Endler’s guppy,P. wingei, swamp guppy,P. picta, and para guppy,P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. This sex chromosome system is absent in recent outgroups. We combined analyses of sequence divergence and polymorphism data across Poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast-X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast-X evolution, inP. pictaandP. parae, while no change in the rate of evolution of X-linked relative to autosomal genes inP. reticulata. InP. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test different models for the origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast-X and suggests a single, recent origin of the sex chromosome system in this clade.

Heritable variation in a gene’s expression arises from mutations impacting cis- and trans-acting components of its regulatory network. Here, we investigate how trans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with trans-regulatory effects on expression of the same focal gene in Saccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that these trans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of the trans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism, and signal transduction. These data show how genetic changes in diverse types of genes can impact a gene’s expression in trans, revealing properties of trans-regulatory mutations that provide the raw material for trans-regulatory variation segregating within natural populations.

Heritable variation in gene expression is common within species. Much of this variation is due to genetic differences outside of the gene with altered expression and is trans-acting. This trans-regulatory variation is often polygenic, with individual variants typically having small effects, making the genetic architecture and evolution of trans-regulatory variation challenging to study. Consequently, key questions about trans-regulatory variation remain, including the variability of trans-regulatory variation within a species, how selection affects trans-regulatory variation, and how trans-regulatory variants are distributed throughout the genome and within a species. To address these questions, we isolated and measured trans-regulatory differences affecting TDH3 promoter activity among 56 strains of Saccharomyces cerevisiae, finding that trans-regulatory backgrounds varied approximately twofold in their effects on TDH3 promoter activity. Comparing this variation to neutral models of trans-regulatory evolution based on empirical measures of mutational effects revealed that despite this variability in the effects of trans-regulatory backgrounds, stabilizing selection has constrained trans-regulatory differences within this species. Using a powerful quantitative trait locus mapping method, we identified ∼100 trans-acting expression quantitative trait locus in each of three crosses to a common reference strain, indicating that regulatory variation is more polygenic than previous studies have suggested. Loci altering expression were located throughout the genome, and many loci were strain specific. This distribution and prevalence of alleles is consistent with recent theories about the genetic architecture of complex traits. In all mapping experiments, the nonreference strain alleles increased and decreased TDH3 promoter activity with similar frequencies, suggesting that stabilizing selection maintained many trans-acting variants with opposing effects. This variation may provide the raw material for compensatory evolution and larger scale regulatory rewiring observed in developmental systems drift among species.

The roles of chance, contingency, and necessity in evolution are unresolved because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select proteins in the B-cell lymphoma-2 (BCL-2) family to acquire protein–protein interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and overwhelmed chance as the primary cause of acquired sequence variation; trajectories launched from phylogenetically distant proteins yielded virtually no common mutations, even under strong and identical selection pressures. Chance arose because many sets of mutations could alter specificity at any timepoint; contingency arose because historical substitutions changed these sets. Our results suggest that patterns of variation in BCL-2 sequences – and likely other proteins, too – are idiosyncratic products of a particular and unpredictable course of historical events., eLife digest One of the most fundamental and unresolved questions in evolutionary biology is whether the outcomes of evolution are predictable. Is the diversity of life we see today the expected result of organisms adapting to their environment throughout history (also known as natural selection) or the product of random chance? Or did chance events early in history shape the paths that evolution could take next, determining the biological forms that emerged under natural selection much later? These questions are hard to study because evolution happened only once, long ago. To overcome this barrier, Xie, Pu, Metzger et al. developed an experimental approach that can evolve reconstructed ancestral proteins that existed deep in the past. Using this method, it is possible to replay evolution multiple times, from various historical starting points, under conditions similar to those that existed long ago. The end products of the evolutionary trajectories can then be compared to determine how predictable evolution actually is. Xie, Pu, Metzger et al. studied proteins belonging to the BCL-2 family, which originated some 800 million years ago. These proteins have diversified greatly over time in both their genetic sequences and their ability to bind to specific partner proteins called co-regulators. Xie, Pu, Metzger et al. synthesized BCL-2 proteins that existed at various times in the past. Each ancestral protein was then allowed to evolve repeatedly under natural selection to acquire the same co-regulator binding functions that evolved during history. At the end of each evolutionary trajectory, the genetic sequence of the resulting BCL-2 proteins was recorded. This revealed that the outcomes of evolution were almost completely unpredictable: trajectories initiated from the same ancestral protein produced proteins with very different sequences, and proteins launched from different ancestral starting points were even more dissimilar. Further experiments identified the mutations in each trajectory that caused changes in coregulator binding. When these mutations were introduced into other ancestral proteins, they did not yield the same change in function. This suggests that early chance events influenced each protein’s evolution in an unpredictable way by opening and closing the paths available to it in the future. This research expands our understanding of evolution on a molecular level whilst providing a new experimental approach for studying evolutionary drivers in more detail. The results suggest that BCL-2 proteins, in all their various forms, are unique products of a particular, unpredictable course of history set in motion by ancient chance events.

Heritable variation in a gene’s expression arises from mutations impactingcis- andtrans-acting components of its regulatory network, with expression variation often derived fromtrans-regulatory mutations within species. Here, we investigate howtrans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations withtrans-regulatory effects on expression of the same focal gene inSaccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that thesetrans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of thetrans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism and signal transduction. Finally, we find that the genomic distribution of these new regulatory mutations significantly overlaps with the genomic distribution oftrans-regulatory variants segregating withinS. cerevisiae.

Dosage compensation balances gene expression between the sexes in systems with diverged heterogametic sex chromosomes. Theory predicts that dosage compensation should rapidly evolve in parallel with the divergence of sex chromosomes to prevent the deleterious effects of dosage imbalances that occur as a result of sex chromosome divergence. Examples of complete dosage compensation, where gene expression of the entire sex chromosome is compensated, are rare and have only been found in relatively ancient sex chromosome systems. Consequently, very little is known about the evolutionary dynamics of complete dosage compensation systems. We recently found the first example of complete dosage compensation in a fish, Poecilia picta. We also found that the Y chromosome degraded substantially in the common ancestor of P. picta and their close relative Poecilia parae. In this study we find that P. parae also have complete dosage compensation, thus complete dosage compensation likely evolved in the short (∼3.7 my) interval after the split of the ancestor of these two species from P. reticulata, but before they diverged from each other. These data suggest that novel dosage compensation mechanisms can evolve rapidly, thus supporting the longstanding theoretical prediction that such mechanisms arise in parallel with rapidly diverging sex chromosomes.SIGNIFICANCE STATEMENTIn species with XY sex chromosomes, females (XX) have as many copies of X-linked genes compared to males (XY), leading to unbalanced expression between the sexes. Theory predicts that dosage compensation mechanisms should evolve rapidly as X and Y chromosomes diverge, but examples of complete dosage compensation in recently diverged sex chromosomes are scarce, making this theory difficult to test. Across Poeciliid species the X and Y chromosomes have recently diversified. Here we find complete dosage compensation evolved rapidly as the X and Y diverged in the common ancestor of Poecilia parae and P. picta, supporting that novel dosage compensation mechanisms can evolve rapidly in tandem with diverging sex chromosomes. These data confirm longstanding theoretical predictions of sex chromosome evolution.

Most proteins assemble into multisubunit complexes1. The persistence of these complexes across evolutionary time is usually explained as the result of natural selection for functional properties that depend on multimerization, such as intersubunit allostery or the capacity to do mechanical work2. In many complexes, however, multimerization does not enable any known function3. An alternative explanation is that multimers could become entrenched if substitutions accumulate that are neutral in multimers but deleterious in monomers; purifying selection would then prevent reversion to the unassembled form, even if assembly per se does not enhance biological function3–7. Here we show that a hydrophobic mutational ratchet systematically entrenches molecular complexes. By applying ancestral protein reconstruction and biochemical assays to the evolution of steroid hormone receptors, we show that an ancient hydrophobic interface, conserved for hundreds of millions of years, is entrenched because exposure of this interface to solvent reduces protein stability and causes aggregation, even though the interface makes no detectable contribution to function. Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers. In a database of hundreds of families of multimers, most show signatures of long-term hydrophobic entrenchment. It is therefore likely that many protein complexes persist because a simple ratchet-like mechanism entrenches them across evolutionary time, even when they are functionally gratuitous. Accumulation of hydrophobic residues at the interface between monomers may favour the maintenance of multimeric protein states during evolution, even if multimerization confers no functional advantage.

Understanding the regulatory mechanisms that control sexually dimorphic gene expression is a key part of understanding the processes that govern the rate of sex chromosome evolution and phenotypic sex differences. Epigenetic modifications play a major role in tissue-specific gene expression regulation and have been hypothesized to dramatically impact the speed of sex chromosome divergence. The guppy sex chromosomes are an emerging model for studying the initial stages of divergence between the X and Y. In this study, we use comparative epigenomics to identify conserved sex-specific DNA methylation patterns in gonad and muscle tissue between the Trinidadian guppy (Poecilia reticulata) and its sister species, Endler’s guppy (Poecilia wingei). We find that the oldest part of the guppy sex chromosome shows a conserved pattern of male hypomethylation, consistent with a key role in testis-specific gene expression. This pattern provides a potential mechanism for theoretical predictions that sex chromosome divergence can occur remarkably quickly in evolutionary time, and without widespread degradation of the Y chromosome gene content. Our cross-species comparative epigenomic analysis also provides a robust comparative framework to understand constraints of epigenetic programming. We observe conserved, testis-specific hypomethylated regions near key autosomal developmental genes and a potentially imprinted locus. These observations are consistent with DNA methylation in testis from other vertebrates, and suggest broad conservation of DNA methylation patterns in these regions. Our comparative framework reveals conserved DNA methylation differences between males and females across two related species, providing novel insights into the relationship between epigenetic and evolutionary processes.

Phenotypic plasticity occurs at a variety of timescales, but little is known about the degree to which plastic responses at different timescales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18 and 24°C until hatch and then held at 18°C for 9 months and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18°C and then acclimated to 5 and 25°C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes was affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.

Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.

Background Royal College cancer data sets ideally should present the pathologist not only with lists of core data items for histopathologic reporting of cancers but also communicate the strengths and limitations of the evidence behind those core items. Within the confines of a text- or proforma-based representation, there is little scope for interaction with or encouragement of scrutiny of the evidence base by the pathologist. Objective Wordclouds can be used to represent textual data in a visual format, highlighting frequency and defined categories of items. We wanted to explore whether the core data items in cancer data sets could be recreated in a more visual and interactive format using a “wordcloud” approach. Methods Using the 2013 data set for histopathology reporting of mucosal malignancies of the pharynx as a test case, we extracted the evidence base cited within the document for a subset of the core data items and updated the evidence by systematic review of the literature from year of publication to present. Results We created an HTML-based wordcloud “within” a head and neck sagittal section shape outline that represents (1) each core data item, (2) the strength of evidence (text size), (3) whether that evidence is direct or inferred (text color), and (4) hyperlinks from each core data item to text-based information for that item and relevant publications from the evidence base. Conclusions We believe the dataset wordcloud might enable easier navigation and clarity of the core data items and better understanding and scrutiny of the evidence base behind them.

Background and Objective: Evidence suggests that the prevalence of medication nonadherence is greater in medically underserved, low-income communities. There is paucity of qualitative data examining the potential use of mobile health (mHealth) in underserved patients. This study aimed to explore barriers to medication adherence and identify opportunities and challenges for the potential use of mHealth adherence interventions in an underserved population. Methods: A qualitative cross-sectional focus group was conducted. Focus groups were conducted with underserved patients recruited at a federally qualified health center. The Health Belief Model was used as theoretical framework to develop the focus group guide. Audio-recorded data were transcribed and thematically analyzed to identify common themes across the data set. Results: Seventeen patients participated in 4 focus groups. Findings were organized by the following themes: (1) perceived barriers to medication adherence, (2) everyday practices used to improve medication adherence, and (3) perceived benefits and barriers to technology use. Use of text messages seemed beneficial; however, not carrying a phone always was a significant barrier for patients. Some patients expressed willingness to try smartphone applications but stated that they would not be able to afford them. Changes in daily routine and complexity of medication regimens were seen as barriers to medication adherence. Conclusions: Findings underscore the importance of considering diverse experiences when engaging patients in mHealth for medication adherence. Providing patient-centered approaches to assist patients construct their individualized medication adherence strategies may lead to better outcomes.

The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome. Many of these nonreference genes are expressed and we functionally confirmed that two of these genes confer increased resistance to antifungals. Next, we simultaneously measured the growth rates of over 4,500 laboratory strains, each of which lacks a nonessential gene, and 81 natural strains across multiple environments using unique DNA barcode present in each strain. By combining the genome-wide reverse genetic information gained from the gene deletion strains with a genome-wide association analysis from the natural strains, we identified genomic regions associated with fitness variation in natural populations. To experimentally validate a subset of these associations, we used reciprocal hemizygosity tests, finding that while the combined forward and reverse genetic approaches can identify a single causal gene, the phenotypic consequences of natural genetic variation often follow a complicated pattern. The resources and approach provided outline an efficient and reliable route to association mapping in yeast and significantly enhance its value as a model for understanding the genetic mechanisms underlying phenotypic variation and evolution in natural populations.

Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. Although previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated. We find that as sequence divergence increases, cis-regulatory differences do indeed become the dominant type of regulatory difference between species, ultimately becoming a better predictor of expression divergence than trans-regulatory divergence. When both cis- and trans-regulatory differences accumulate for the same gene, they more often have effects in opposite directions than in the same direction, indicating widespread compensatory changes underlying the evolution of gene expression. The frequency of compensatory changes within and between species and the magnitude of effect for the underlying cis- and trans-regulatory differences suggests that compensatory changes accumulate primarily due to selection against divergence in gene expression as a result of weak stabilizing selection on gene expression levels. These results show that cis-regulatory differences and compensatory changes in regulation play increasingly important roles in the evolution of gene expression as time increases.

Objective To identify motivators and barriers to pharmacy student completion of instructor evaluations, and to develop potential strategies to improve the evaluation process. Methods Completed at four Ohio Colleges of Pharmacy, Phase I consisted of a student/faculty survey and Phase II consisted of joint student/faculty focus groups to discuss Phase I data and to problem solve. Results In Phase I, the top three student-identified and faculty-perceived motivators to completion of evaluations were to (1) make the course better, (2) earn bonus points, and (3) improve the instructor's teaching. The top three student-identified barriers to completion of evaluations were having to (1) evaluate multiple instructors, (2) complete several evaluations around the same time, and (3) complete lengthy evaluations. Phase II focus groups identified a number of potential ways to enhance the motivators and reduce barriers, including but not limited to making sure faculty convey to students that the feedback they provide is useful and to provide examples of how student feedback has been used to improve their teaching/the course. Conclusions Students and faculty identified motivators and barriers to completing instructor evaluations and were willing to work together to improve the process.

Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments.

The fabrication of bit-patterned media (BPM) is crucial for new types of hard disk drives. The development of methods for the production of BPM is progressing rapidly. Conventional lithography reaches the limit regarding lateral resolution, and new routes are needed. In this study, we mainly focus on the dependence of the size and shape of magnetic nanodots on the Ar+-ion etching duration, using silica dots as masks. Two-dimensional (2D) arrays of magnetic nanostructures are created using silica-filled diblock-copolymer micelles as templates. After the self-assembly of the micelles into 2D hexagonal arrays, the polymer shell is removed, and the SiO2 cores are utilized to transform the morphology into a (Co/Pt)2-multilayer via ion etching under normal incidence. The number of preparation steps is kept as low as possible to simplify the formation of the nanostructure arrays. High-resolution in situ grazing-incidence small-angle X-ray scattering (GISAXS) investigations are performed during the Ar+-ion etching to monitor and control the fabrication process. The in situ investigation provides information on how the etching conditions can be improved for further ex situ experiments. The GISAXS patterns are compared with simulations. We observe that the dots change in shape from cylindrical to conical during the etching process. The magnetic behavior is studied by utilizing the magneto-optic Kerr effect. The Co/Pt dots exhibit different magnetic behaviors depending on their size, interparticle distance, and etching time. They show ferromagnetism with an easy axis of magnetization perpendicular to the film. A systematic dependence of the coercivity on the dot size is observed.

In natural environments, organisms must cope with complex combinations of abiotic stressors. Here, we use threespine stickleback (Gasterosteus aculeatus) to examine how changes in salinity affect tolerance of high temperatures. Threespine stickleback inhabit a range of environments that vary in both salinity and thermal stability making this species an excellent system for investigating interacting stressors. We examined the effects of environmental salinity on maximum thermal tolerance (CTMax) and 70 kDa heat shock protein (hsp70) gene expression using divergent stickleback ecotypes from marine and freshwater habitats. In both ecotypes, the CTMax of fish acclimated to 20 ppt was significantly higher compared to fish acclimated to 2 ppt. The effect of salinity acclimation on the expression of hsp70-1 and hsp70-2 was similar in both the marine and freshwater stickleback ecotype. There were differences in the expression profiles of hsp70-1 and hsp70-2 during heat shock, with hsp70-2 being induced earlier and to a higher level compared to hsp70-1. These data suggest that the two hsp70 isoforms may have functionally different roles in the heat shock response. Lastly, acute salinity challenge coupled with heat shock revealed that the osmoregulatory demands experienced during the heat shock response have a larger effect on the hsp70 expression profile than does the acclimation salinity.

Objective There is a growing interest in using natural language processing (NLP) for healthcare-associated infections (HAIs) monitoring. A French project consortium, SYNODOS, developed a NLP solution for detecting medical events in electronic medical records for epidemiological purposes. The objective of this study was to evaluate the performance of the SYNODOS data processing chain for detecting HAIs in clinical documents. Materials and methods The collection of textual records in these hospitals was carried out between October 2009 and December 2010 in three French University hospitals (Lyon, Rouen and Nice). The following medical specialties were included in the study: digestive surgery, neurosurgery, orthopedic surgery, adult intensive-care units. Reference Standard surveillance was compared with the results of automatic detection using NLP. Sensitivity on 56 HAI cases and specificity on 57 non-HAI cases were calculated. Results The accuracy rate was 84% (n = 95/113). The overall sensitivity of automatic detection of HAIs was 83.9% (CI 95%: 71.7–92.4) and the specificity was 84.2% (CI 95%: 72.1–92.5). The sensitivity varies from one specialty to the other, from 69.2% (CI 95%: 38.6–90.9) for intensive care to 93.3% (CI 95%: 68.1–99.8) for orthopedic surgery. The manual review of classification errors showed that the most frequent cause was an inaccurate temporal labeling of medical events, which is an important factor for HAI detection. Conclusion This study confirmed the feasibility of using NLP for the HAI detection in hospital facilities. Automatic HAI detection algorithms could offer better surveillance standardization for hospital comparisons.

In all vertebrates studied to date, CO

Gene expression noise is an evolvable property of biological systems that describes differences in gene expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by natural selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for theTDH3gene inSaccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns that are consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.

In all vertebrates studied to date, CO2 excretion depends on the enzyme carbonic anhydrase (CA) that catalyses the rapid conversion of HCO3− to CO2 at the gas-exchange organs. The largest pool of CA is present within red blood cells (RBC) and, in some vertebrates, plasma-accessible CA (paCA) isoforms participate in CO2 excretion. However, teleost fishes typically do not have paCA at the gills and CO2 excretion is reliant entirely on RBC CA; a strategy that is not possible in icefishes. As the result of a natural knockout, Antarctic icefishes (Channichthyidae) are the only known vertebrates that do not express haemoglobin (Hb) as adults, and largely lack RBC in the circulation (haematocrit

From seasonal variation in the color of butterfly wings to trees bending toward the light, organisms often change in response to their environment. These changes, known as phenotypic plasticity, can result from differences in how genes are expressed among environments. Mutations causing environment-specific changes in gene expression provide raw material for phenotypic plasticity, but their frequency, effect size, and direction of effects among environments are not well understood. This study shows that mutations in the promoter of a yeast metabolic gene often display environment-dependent effects on gene expression and that these environment-dependent effects have been shaped by selection in natural populations.

Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single-nucleotide mutations in the Saccharomyces cerevisiae TDH3 promoter (PTDH3) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild-type allele. Comparing the effects of these mutations with the effects of 30 PTDH3 polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response in PTDH3 activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.

Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single nucleotide mutations in theSaccharomyces cerevisiae TDH3promoter (PTDH3) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild type allele. Comparing the effects of these mutations to the effects of 30PTDH3polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response inPTDH3activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, however, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.Significance StatementFrom seasonal variation in the color of butterfly wings to trees bending toward the light, organisms often change in response to their environment. These changes, known as phenotypic plasticity, can result from differences in how genes are expressed among environments. Mutations causing environment-specific changes in gene expression provide raw material for phenotypic plasticity, but their frequency, effect size and direction of effects among environments are not well understood. This study shows that mutations in the promoter of a yeast metabolic gene often display environment-dependent effects on gene expression and that these environment-dependent effects have been shaped by selection in natural populations.

Epigenetic mechanisms such as changes in DNA methylation have the potential to affect the resilience of species to climate change, but little is known about the response of the methylome to changes in environmental temperature in animals. Using reduced representation bisulfite sequencing, we assessed the effects of development temperature and adult acclimation temperature on DNA methylation levels in threespine stickleback (Gasterosteus aculeatus). Across all treatments, we identified 2130 differentially methylated cytosines distributed across the genome. Both increases and decreases in temperature during development and with thermal acclimation in adults increased global DNA methylation levels. Approximately 25% of the differentially methylated regions (DMRs) responded to both developmental temperature and adult thermal acclimation, and 50 DMRs were common to all treatments, demonstrating a core response of the epigenome to thermal change at multiple time scales. We also identified differentially methylated loci that were specific to a particular developmental or adult thermal response, which could facilitate the accumulation of epigenetic variation between natural populations that experience different thermal regimes. These data demonstrate that thermal history can have long-lasting effects on the epigenome, highlighting the role of epigenetic modifications in the response to temperature change across multiple time scales.

Background: For patients with atrial fibrillation (AF), early treatment is essential to prevent serious complications such as stroke. Several randomized clinical trials have shown that rate-control may be as effective as rhythm-control medications, whereas the latter have serious side effects. Little evidence exists, however, about which class of rate-control medication—β-blockers (BBs) or calcium channel blockers (CCBs)—may be superior. Objective: The objective was to compare the long-term persistence on BBs versus CCBs in nonelderly adult patients with AF. Methods: A longitudinal retrospective cohort study for patients 40 to 60 years old with newly diagnosed AF (identified by ICD-9 code 427.31) was performed using data from Ohio Medicaid physician, institutional, and pharmacy claims from January 2006 through June 2011. A Cox proportional hazard regression, with time to change out of rate-control therapy as the dependent variable, was estimated to compare persistence on (proxy for effectiveness of) rate-control medication across drug classes. A propensity-score analysis was used to control for selection bias. Additional covariates included age, development of heart failure, and medication adherence. Results: Out of 1239 patients included in the cohort, 1016 received a BB; 223 received a CCB. Over time, patients on CCBs were significantly more likely to switch out of rate-control therapy (hazard ratio = 1.89; 95% CI = 1.14-3.09) than patients on BBs. Conclusions: Evidence suggests that nonelderly AF patients, when prescribed rate-control therapy, persist longer on BBs than CCBs. Because this is the first long-term study comparing the 2 drug classes in the nonelderly population, further research is suggested.

We apply advanced X-ray diffraction techniques at synchrotron microfocus beamlines in order to study the local ultrastructure of biogenic calcite with high spatial and angular resolution. Specifically, we investigate individual calcitic prisms extracted from Pinna nobilis mollusk shells with an aim to shed additional light on the structural aspects of organic/inorganic interfaces. We use annealing at elevated temperatures to destroy intracrystalline organics and measure the same prisms before and after annealing to achieve deeper understanding of the internal organization of these nanobiocomposites. Complementary nanoindentation measurements (also performed before and after annealing) allow us to elucidate the role of intracrystalline organics in increased hardness in pristine prisms and hardness reduction after annealing. We found that removal of intracrystalline organics during annealing facilitates generation of well-oriented lattice defects, which reduce the (006) diffraction intensity and are respons...

Genetic variants identified by mapping are biased toward large phenotypic effects because of methodologic challenges for detecting genetic variants with small phenotypic effects. Recently, bulk segregant analysis combined with next-generation sequencing (BSA-seq) was shown to be a powerful and cost-effective way to map small effect variants in natural populations. Here, we examine the power of BSA-seq for efficiently mapping small effect mutations isolated from a mutagenesis screen. Specifically, we determined the impact of segregant population size, intensity of phenotypic selection to collect segregants, number of mitotic generations between meiosis and sequencing, and average sequencing depth on power for mapping mutations with a range of effects on the phenotypic mean and standard deviation as well as relative fitness. We then used BSA-seq to map the mutations responsible for three ethyl methanesulfonate−induced mutant phenotypes in Saccharomyces cerevisiae. These mutants display small quantitative variation in the mean expression of a fluorescent reporter gene (−3%, +7%, and +10%). Using a genetic background with increased meiosis rate, a reliable mating type marker, and fluorescence-activated cell sorting to efficiently score large segregating populations and isolate cells with extreme phenotypes, we successfully mapped and functionally confirmed a single point mutation responsible for the mutant phenotype in all three cases. Our simulations and experimental data show that the effects of a causative site not only on the mean phenotype, but also on its standard deviation and relative fitness should be considered when mapping genetic variants in microorganisms such as yeast that require population growth steps for BSA-seq.

The radiolytic preparation of sub-nanometer sized CdS clusters in LTL-type zeolite crystals in suspension is reported. The growing process of CdS in the zeolite crystals using a γ-ray irradiator (low dose rate) and a pulse electron accelerator (high dose rate) is followed by UV-vis spectroscopy. The pulse electron accelerator equipped with a transient absorption setup allowed the real-time capturing of CdS formed in the zeolite suspension. Two distinct stages during the formation of sub-nanometer sized CdS clusters in the LTL-type zeolite are identified: (i) fast formation of dispersed small oligomers exhibiting a well-defined sharp absorption peak, which is shifted from 292 to 350 nm in the course of the growth process, and (ii) formation of interconnected CdS clusters along the zeolite channels by diffusion-assisted process. Additionally, the presence of sub-nanometer sized CdS clusters in the zeolite channels is confirmed by transmission electron microscopy (TEM). The sub-nanometer sized CdS clusters formed in the LTL-type zeolite suspension exhibit good stability under hydrous conditions, and no coalesce in the presence of water is observed.

Summary Background: A full-text search tool was introduced into the daily practice of Léon Bérard Center (France), a health care facility devoted to treatment of cancer. This tool was integrated into the hospital information system by the IT department having been granted full autonomy to improve the system. Objectives: To describe the development and various uses of a tool for full-text search of computerized patient records. Methods: The technology is based on Solr, an open-source search engine. It is a web-based application that processes HTTP requests and returns HTTP responses. A data processing pipeline that retrieves data from different repositories, normalizes, cleans and publishes it to Solr, was integrated in the information system of the Leon Bérard center. The IT department developed also user interfaces to allow users to access the search engine within the computerized medical record of the patient. Results: From January to May 2013, 500 queries were launched per month by an average of 140 different users. Several usages of the tool were described, as follows: medical management of patients, medical research, and improving the traceability of medical care in medical records. The sensitivity of the tool for detecting the medical records of patients diagnosed with both breast cancer and diabetes was 83.0%, and its positive predictive value was 48.7% (gold standard: manual screening by a clinical research assistant). Conclusion: The project demonstrates that the introduction of full-text-search tools allowed practitioners to use unstructured medical information for various purposes. Citation: Biron P; Metzger MH; Pezet C; Sebban C; Barthuet E; Durand T. An information retrieval system for computerized patient records in the context of a daily hospital practice: the example of the Léon Bérard Cancer Center (France)Appl Clin Inf 2014; 5: 191–205http://dx.doi.org/10.4338/ACI-2013-08-CR-0065

The orientation distribution of cellulose microfibrils in the plant cell wall is a key parameter for understanding anisotropic plant growth and mechanical behavior. However, precisely visualizing cellulose orientation in the plant cell wall has ever been a challenge due to the small size of the cellulose microfibrils and the complex network of polymers in the plant cell wall. X-ray diffraction is one of the most frequently used methods for analyzing cellulose orientation in single cells and plant tissues, but the interpretation of the diffraction images is complex. Traditionally, circular or square cells and Gaussian orientation of the cellulose microfibrils have been assumed to elucidate cellulose orientation from the diffraction images. However, the complex tissue structures of common model plant systems such as Arabidopsis or aspen (Populus) require a more sophisticated approach. We present an evaluation procedure which takes into account the precise cell geometry and is able to deal with complex microfibril orientation distributions. The evaluation procedure reveals the entire orientation distribution of the cellulose microfibrils, reflecting different orientations within the multi-layered cell wall. By analyzing aspen wood and Arabidopsis stems we demonstrate the versatility of this method and show that simplifying assumptions on geometry and orientation distributions can lead to errors in the calculated microfibril orientation pattern. The simulation routine is intended to be used as a valuable tool for nanostructural analysis of plant cell walls and is freely available from the authors on request.

International audience; Objective. To propose an original method of benchmarking regions based on their prevalence of healthcare-associated infections (HAIs) and to identify regions with unusual results. Design. To study between-region variability with a three-level hierarchical logistic regression model and a Bayesian non-parametric method. Setting. French 2006 national HAIs point prevalence survey. Participants. A total of 336 858 patients from 2289 healthcare facilities in 27 regions. Patients with an imported HAI (1% of the data, 20.7% of infected patients), facilities with

Objective To describe pharmacy preceptors' use of Facebook and compare the perspectives of those with and without Facebook profiles regarding student–preceptor relationships. Methods A survey was sent electronically to pharmacy practice preceptors ( n = 2523) at four colleges of pharmacy asking them to provide their opinions on the student–preceptor Facebook relationship. If respondents answered "yes" to having a Facebook profile, they were asked 12 questions. If respondents answered "no", they were asked two questions. Demographic data were collected from all the respondents. Two reminder emails were sent before the survey closed after 24 days. Results Of the 612 total respondents (response rate=24.3%), 413 preceptors (67%) currently maintain a Facebook page, while 199 (33%) do not. The majority of those with a Facebook profile (93%) use it for social networking, 27% use it for professional networking or campaigning, and 6% use it to collaborate with colleagues. Fifty-four percent of the preceptors with a Facebook profile are not friends with students on Facebook, while 46% are, although 10% of responders do limit what the student can view on their profile. Responses were highly varied when asked how they would handle a "friend request," including accept it right away, after some thought, or simply decline it. Conclusion As the use of these social media sites increases, the need arises for preceptors to discuss and/or clearly define the appropriateness of social networking relationships without compromising the line between the personal and professional relationships with pharmacy students.

Incorporating sacrificial cross-links into polymers represents an exciting new avenue for the development of self-healing materials, but it is unclear to what extent their spatial arrangement is important for this functionality. In this respect, self-healing biological materials, such as mussel byssal threads, can provide important chemical and structural insights. In this study, we employ in situ small-angle X-ray scattering (SAXS) measurements during mechanical deformation to show that byssal threads consist of a partially crystalline protein framework capable of large reversible deformations via unfolding of tightly folded protein domains. The long-range structural order is destroyed by stretching the fiber but reappears rapidly after removal of load. Full mechanical recovery, however, proceeds more slowly, suggesting the presence of strong and slowly reversible sacrificial cross-links. One likely role of the highly ordered elastic framework is to bring sacrificial binding sites back into register upon stress release, facilitating bond reformation and self-repair.

Objectives This study examined social media use by pharmacy faculty members and their strategies for Facebook friending of students. Additional objectives included determining faculty members' opinions regarding e-professionalism, how they responded to e-professionalism transgressions, and their use of social media for teaching, learning, and professional interests. Methods A 32-item questionnaire was sent to 358 pharmacy faculty members at five schools via a web-based survey tool. Results One hundred and fifty-nine faculty members completed the questionnaire for a 44.4% response rate. Almost 65% ( N =103) of the respondents use Facebook. The most common (37.6%, N =38) Facebook-friending philosophy was not to accept any student friend requests. Half ( N =27) of the faculty members who have viewed student profiles noticed an e-professionalism transgression. Fifty-nine (50.1%) faculty members responded that they were either likely or very likely to use social media for teaching. A little less than half (46.6%, N =54) of the respondents reported using social media for professional networking purposes. Conclusions A majority of pharmacy faculty members have an online social media presence, with Facebook being the most common application. Strategies for Facebook-friending students varied, but in general they were very conservative. The majority does not accept any Facebook friend requests from students, or accepts them only when students have graduated. Most faculty members agreed that social media connections with students might compromise the instructor–student relationship boundary. It is important that higher education faculty adapt to the paradigm and examine the appropriate contexts of use for professional, educational, and networking purposes.

The budding yeastSaccharomyces cerevisiaeis the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of natural phenotypic variation is limited by the inefficiency of association mapping owing to strong and complex population structure. To facilitate association mapping, we analyzed 190 high-quality genomes of diverse strains, including 85 newly sequenced ones, to uncover yeast’s population structure that varies substantially among genomic regions. We identified 181 yeast genes that are absent from the reference genome and demonstrated their expression and role in important functions such as drug resistance. We then simultaneously measured the growth rates of over 4500 lab strains each deficient of a nonessential gene and 81 natural strains across multiple environments using unique DNA barcode present in each strain. We combined the genome-wide reverse genetic information with genome-wide association analysis to determine potential genomic regions of importance to environmental adaptations, and for a subset experimentally validated their role by reciprocal hemizygosity tests. The resources provided permit efficient and reliable association mapping in yeast and significantly enhances its value as a model for understanding the genetic mechanisms of phenotypic polymorphism and evolution.

Phenotypic plasticity is thought to facilitate the colonization of novel environments and shape the direction of evolution in colonizing populations. However, the relative prevalence of various predicted patterns of changes in phenotypic plasticity following colonization remains unclear. Here, we use a whole-transcriptome approach to characterize patterns of gene expression plasticity in the gills of a freshwater-adapted and a saltwater-adapted ecotype of threespine stickleback (Gasterosteus aculeatus) exposed to a range of salinities. The response of the gill transcriptome to environmental salinity had a large shared component common to both ecotypes (2159 genes) with significant enrichment of genes involved in transmembrane ion transport and the restructuring of the gill epithelium. This transcriptional response to freshwater acclimation is induced at salinities below two parts per thousand. There was also differentiation in gene expression patterns between ecotypes (2515 genes), particularly in processes important for changes in the gill structure and permeability. Only 508 genes that differed between ecotypes also responded to salinity and no specific processes were enriched among this gene set, and an even smaller number (87 genes) showed evidence of changes in the extent of the response to salinity acclimation between ecotypes. No pattern of relative expression dominated among these genes, suggesting that neither gains nor losses of plasticity dominated the changes in expression patterns between the ecotypes. These data demonstrate that multiple patterns of changes in gene expression plasticity can occur following colonization of novel habitats.