A Comparison of DNA Extraction Methods using Petunia hybrida Tissues

Extraction of DNA from plant tissue is often problematic, as many plants contain high levels of secondary metabolites that can interfere with downstream applications, such as the PCR. Removal of these secondary metabolites usually requires further purification of the DNA using organic solvents or other toxic substances. In this study, we have compared two methods of DNA purification: the cetyltrimethylammonium bromide (CTAB) method that uses the ionic detergent hexadecyltrimethylammonium bromide and chloroform-isoamyl alcohol and the Edwards method that uses the anionic detergent SDS and isopropyl alcohol. Our results show that the Edwards method works better than the CTAB method for extracting DNA from tissues of Petunia hybrida. For six of the eight tissues, the Edwards method yielded more DNA than the CTAB method. In four of the tissues, this difference was statistically significant, and the Edwards method yielded 27–80% more DNA than the CTAB method. Among the different tissues tested, we found that buds, 4 days before anthesis, had the highest DNA concentrations and that buds and reproductive tissue, in general, yielded higher DNA concentrations than other tissues. In addition, DNA extracted using the Edwards method was more consistently PCR-amplified than that of CTAB-extracted DNA. Based on these results, we recommend using the Edwards method to extract DNA from plant tissues and to use buds and reproductive structures for highest DNA yields.     

Assessing early recruitment dynamics and its demographic consequences among tropical reef fishes: Accommodating variation in recruitment seasonally and longevity

Abstract When settlement of pelagic juveniles of reef fishes is highly and predictably seasonal, annual, end-of-season surveys of surviving recruits (which are commonly used on the Great Barrier Reef) are useful for assessing recruitment dynamics and their demographic effects. However, when settlement is continuous or weakly seasonal, with patterns that vary both between species and within species among years, regular, sometimes year-round, recruitment surveys at intervals linked to short-term settlement dynamics are needed to quantify fluctuations in recruitment strength. Monthly recruitment surveys may be appropriate in the tropical northwest Atlantic, where settlement is often both lunar periodic, and broadly and variably seasonal. Use of a variety of recruit-census methods impedes comparisons of recruitment patterns and their demographic effects, because recruit densities and recruit:adult ratios cannot be directly compared when recruits (because they have widely varying post-settlement ages) have experienced very different levels of early post-settlement mortality. Examining the relationship between changes in adult populations and annual, end-of-season recruitment may be satisfactory for long-lived species with strong settlement seasonality and maturation times of approximately 1 year. However, it is inappropriate for short-lived, rapidly maturing species, particularly those that have broad and variable settlement seasons and whose populations fluctuate substantially throughout the year in response to short-term fluctuations in recruitment. Comparisons of demographic effects of recruitment among species with different longevity require the use of non-arbitrary time scales, such as the time to maturity and the adult half-life.     

Problematic Internet use: an overview

There is wide agreement that the Internet can serve as a tool that enhances well-being. It is more difficult, however, to find consensus around the issue of problematic Internet use. That may be in part because scientific investigation has lagged far behind technological advances and media attention. The diagnostic schemas that have been proposed since 1996, and the screening tools that have been developed, stress similarities with substance use, impulse control disorders, and obsessive-compulsive disorder. Prevalence figures vary as a function of the diagnostic definition used, the age group studied, and whether the surveys were conducted online. Studies suggest high comorbidity rates with mood disorders and, among younger individuals, attention-deficit/hyperactivity disorder. Treatment should address any comorbid conditions present, as those may be causing, or exacerbating, problematic Internet use. Interventions that may specifically target problematic Internet use include cognitive behavioral therapy and selective serotonin reuptake inhibitors, but detailed guidelines must await further studies. For a medium that has so radically changed how we conduct our lives, the Internet’s effects on our psychology remain understudied. More research is needed into the pathophysiology, epidemiology, natural course, and treatment of problematic Internet use. In addition, the more subtle psychological changes, such as disinhibition, that seem to characterize people’s online behavior also deserve attention, even if they cannot be seen as necessarily pathological.     

Changes in extracellular action potential detect kainic acid and trimethyltin toxicity in hippocampal slice preparations earlier than do MAP2 density measurements

In vitro electrophysiological techniques for the assessment of neurotoxicity could have several advantages over other methods in current use, including the ability to detect damage at a very early stage, and could further assist in replacing animal experimentation in vivo. We investigated how an electrophysiological parameter, the extracellularly-recorded compound action potential ("population spike", PS) could be used as a marker of in vitro neurotoxicity in the case of two well-known toxic compounds, kainic acid (KA) and trimethyltin (TMT). We compared the use of this electrophysiological endpoint with changes in immunoreactivity for microtubule-associated protein 2 (MAP2), a standard histological test for neurotoxicity. We found that both toxic compounds reliably caused disappearance of the PS, and that such disappearance occurred after only 1 hour of exposure to the drug. By contrast, densitometric measurements of MAP2 immunoreactivity were unaffected by both KA and TMT after such a short exposure time. We conclude that, in the case of KA and TMT, the extracellular PS was abolished at a very early time-point, when MAP2 immunoreactivity levels were still comparable to those of the untreated controls. Electrophysiology could be a reliable and early indicator of neurotoxicity, which could improve our ability to test for neurotoxicity in vitro, thus further replacing the need for in vivo experimentation.     

ADHD and comorbid conduct problems among adolescents: associations with self-esteem and substance use

Attention-deficit/hyperactivity disorder (ADHD) is a common child and adolescent disorder that is associated with negative outcomes (e.g., emotional and behavioral problems, substance use) and is often comorbid with Conduct Problems (CP). Research findings are mixed as to whether youth with ADHD alone or comorbid ADHD/CP suffer from low self-esteem. Research has also shown links between low self-esteem and ADHD (alone and with CP) with substance use; yet, no research has examined the links between self-esteem and substance use in adolescents with ADHD and CP. The current study examined the relation between ADHD with and without comorbid CP and self-esteem, and whether self-esteem moderated the relation between ADHD and ADHD/CP with substance use among adolescents. We hypothesized that adolescents with comorbid ADHD/CP would experience lower self-esteem than adolescents with ADHD alone or with neither disorder and that self-esteem would moderate the association between ADHD, CP, and substance use. Participants were 62 adolescents who completed the laboratory-based study with a parent. Results suggested that adolescents with comorbid ADHD and CP had significantly lower self-esteem than adolescents with ADHD alone or neither disorder. Self-esteem was not significantly different for adolescents with ADHD alone versus those in the control group. There was one marginally significant interaction between ADHD and self-esteem predicting substance use, such that individuals with comorbid ADHD/CP who also had low self-esteem tended to use more substances. Results have implications for treatments that target adolescents with ADHD and comorbid CP, as these adolescents are at risk for many deleterious outcomes.     

Contingent valuation analysis of willingness to pay to reduce childhood obesity

Several recent surveys have asked Americans whether they support policies to reduce childhood obesity. There is reason for skepticism of such surveys because people are not confronted with the tax costs of such policies when they are asked whether they support them. This paper uses contingent valuation (CV), a method frequently used to estimate people's willingness to pay (WTP) for goods or services not transacted in markets, applied to unique survey data from New York State to estimate the willingness to pay to reduce childhood obesity. The willingness to pay data correlate in predictable ways with respondent characteristics. The mean WTP for a 50% reduction in childhood obesity is $46.41 (95% CI: $33.45, $59.15), which implies a total WTP by New York State residents of $690.6 million (95% CI: $497.7, $880.15), which is less than that implied by previous surveys that did not use CV methods but greater than current spending on policies to reduce childhood obesity and greater than the estimated savings in external costs. The findings provide policymakers with useful information about taxpayers' support for, and preferred budget for, anti-obesity policies.     

Inequality among industrial workers in the late 19th century United States

This paper uses the large cross sectional survey of 8544 workers in nine industries (pig iron, bar iron, steel, coal, coke, cottons, woolens, and glass) in the United States and five European countries (Belgium, Great Britain, France, Belgium, and Switzerland) to examine inequality in the industrial working class in the late nineteenth century. The paper looks at incomes, the food budget share (estimated using the Almost Ideal Demand System), and home ownership. The results show regular gradients with the unskilled workers doing less well than semi-skilled and skilled workers. Despite the lack of proprietors, farmers, and other groups with significant income from property, such surveys can be useful in the study of the historical aspects of inequality.     

The prevention of HIV infection in abusers of psychoactive substances as a social behavioral problem

This research has made it possible to outline and illuminate a range of problems which should be solved in planning concrete measures for the prophylaxis of HIV infection among the users of psychoactive substances. Such measures should also include those aimed at preventing children and adolescents from getting accustomed to the use of drugs at an early age, as well as the search of ways for providing adequate and effective information on the consequences of using narcotic drugs, the prevention of passage from single cases of the tentative use of drugs to systematic narcotization, etc.     

Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects

The use of environmental DNA (eDNA) surveys to monitor terrestrial species has been relatively limited, with successful implementations still confined to sampling DNA from natural or artificial water bodies and soil. Sampling water for eDNA depends on proximity to or availability of water, whereas eDNA from soil is limited in its spatial scale due to the large quantities necessary for processing and difficulty in doing so. These challenges limit the widespread use of eDNA in several systems, such as surveying forests for invasive insects. We developed two new eDNA aggregation approaches that overcome the challenges of above‐ground terrestrial sampling and eliminate the dependency on creating or utilizing pre‐existing water bodies to conduct eDNA sampling. The first, “spray aggregation,” uses spray action to remove eDNA from surface substrates and was developed for shrubs and other understorey vegetation, while the second, “tree rolling,” uses physical transfer via a roller to remove eDNA from the surface of tree trunks and large branches. We tested these approaches by surveying for spotted lanternfly, Lycorma delicatula, a recent invasive pest of northeastern USA that is considered a significant ecological and economic threat to forests and agriculture. We found that our terrestrial eDNA surveys matched visual surveys, but also detected L. delicatula presence ahead of visual surveys, indicating increased sensitivity of terrestrial eDNA surveys over currently used methodology. The terrestrial eDNA approaches we describe can be adapted for use in surveying a variety of forest insects and represent a novel strategy for surveying terrestrial biodiversity.     

Development of multifunctional foods

Foods contain various biologically active substances with extent physiological effects. Among them, some substances, such as dietary fibers, polyunsaturated fatty acids, and antioxidants, exert multiple activities. In addition, combinational uses of some components, such as sesamin and α-tocopherol, enhance their biological effects each other. The expression of multiple effect leads to the production of multifunctional foods which prevent the occurrence of various diseases. Furthermore, synergic effects between biologically active substances allow us to decrease the dose of each component, which lead to the improvement of safety and reduction of production cost of multifunctional foods. To use these active components for human health, studies on their adsorption and transportation are important, since distribution of some components, such as tocotrienols, is limited to some tissues. In addition, extent safety studies are essential to use artificially synthesized substances such as 10t, 12c derivative of conjugated linoleic acid for human health.     

Adolescent expectations of early death predict adult risk behaviors

Only a handful of public health studies have investigated expectations of early death among adolescents. Associations have been found between these expectations and risk behaviors in adolescence. However, these beliefs may not only predict worse adolescent outcomes, but worse trajectories in health with ties to negative outcomes that endure into young adulthood. The objectives of this study were to investigate perceived chances of living to age 35 (Perceived Survival Expectations, PSE) as a predictor of suicidal ideation, suicide attempt and substance use in young adulthood. We examined the predictive capacity of PSE on future suicidal ideation/attempt after accounting for sociodemographics, depressive symptoms, and history of suicide among family and friends to more fully assess its unique contribution to suicide risk. We investigated the influence of PSE on legal and illegal substance use and varying levels of substance use. We utilized the National Longitudinal Study of Adolescent Health (Add Health) initiated in 1994-95 among 20,745 adolescents in grades 7-12 with follow-up interviews in 1996 (Wave II), 2001-02 (Wave III) and 2008 (Wave IV; ages 24-32). Compared to those who were almost certain of living to age 35, perceiving a 50-50 or less chance of living to age 35 at Waves I or III predicted suicide attempt and ideation as well as regular substance use (i.e., exceeding daily limits for moderate drinking; smoking ≥ a pack/day; and using illicit substances other than marijuana at least weekly) at Wave IV. Associations between PSE and detrimental adult outcomes were particularly strong for those reporting persistently low PSE at both Waves I and III. Low PSE at Wave I or Wave III was also related to a doubling and tripling, respectively, of death rates in young adulthood. Long-term and wide-ranging ties between PSE and detrimental outcomes suggest these expectations may contribute to identifying at-risk youth.     

Drawing the line on in vitro gametogenesis

In vitro gametogenesis (IVG) might offer numerous research and clinical benefits. Some potential clinical applications of IVG, such as allowing opposite-sex couples experiencing infertility to have genetically related children, have attracted support. Others, such as enabling same-sex reproduction and solo reproduction, have attracted significantly more criticism. In this paper, we examine how different ethical principles might help us to draw lines and distinguish between ethically desirable and undesirable uses of IVG. We discuss the alleged distinction between therapeutic and non-therapeutic uses of assisted reproduction in the context of IVG, and show how it is both problematic to apply in practice and theoretically dubious. We then discuss how the ethical principles of reproductive justice and beneficence apply to IVG for opposite-sex reproduction, same-sex reproduction, and solo reproduction. We suggest that these principles generate strong reasons for the use of IVG for opposite-sex and same-sex reproduction, but not for solo reproduction.     

HUMAN DIGNITY IN INTERNATIONAL POLICY DOCUMENTS: A USEFUL CRITERION FOR PUBLIC POLICY?

Current developments in biomedicine are presenting us with difficult ethical decisions and raising complex policy questions about how to regulate these new developments. Particularly vexing for governments have been issues related to human embryo experimentation. Because some of the most promising biomedical developments, such as stem cell research and nuclear somatic transfer, involve such experimentation, several international bodies have drafted documents aimed to provide guidance to governments when developing biomedical science policy. Here I focus on two such documents: the Council of Europe's Convention for the Protection of Human Rights and Dignity of the Human Being and the Additional Protocol to the Convention for the Protection of Human Rights and Dignity of the Human Being. I argue that by using human dignity as a criterion to determine the permissibility of particular human embryo research practices, these documents cannot aid in identifying research that would be contrary to human dignity. Thus, they fail to guide public policy on embryo experimentation. Their use of human dignity as a criterion makes their task of offering guidance unfeasible because the concept as used in these documents is too vague and is applied in contradictory ways. I discuss the main goals of these documents and their claims in relation to human embryo research. I then discuss how they have influenced public policy in several countries. Finally, I show that although these Council of Europe treaties attempt to serve as public policy guides in the area of embryo research, they fail to do so.     

Assessing the public health impacts of legalizing recreational cannabis use: the US experience

The sale of cannabis for adult recreational use has been made legal in nine US states since 2012, and nationally in Uruguay in 2013 and Canada in 2018. We review US research on the effects of legalization on cannabis use among adults and adolescents and on cannabis‐related harms; the impact of legalizing adult recreational use on cannabis price, availability, potency and use; and regulatory policies that may increase or limit adverse effects of legalization. The legalization of recreational cannabis use in the US has substantially reduced the price of cannabis, increased its potency, and made cannabis more available to adult users. It appears to have increased the frequency of cannabis use among adults, but not so far among youth. It has also increased emergency department attendances and hospitalizations for some cannabis‐related harms. The relatively modest effects on cannabis use to date probably reflect restrictions on the number and locations of retail cannabis outlets and the constraints on commercialization under a continued federal prohibition of cannabis. Future evaluations of legalization should monitor: cannabis sales volumes, prices and content of tetrahydrocannabinol; prevalence and frequency of cannabis use among adolescents and adults in household and high school surveys; car crash fatalities and injuries involving drivers who are cannabis‐impaired; emergency department presentations related to cannabis; the demand for treatment of cannabis use disorders; and the prevalence of regular cannabis use among vulnerable young people in mental health services, schools and the criminal justice system. Governments that propose to legalize and regulate cannabis use need to fund research to monitor the impacts of these policy changes on public health, and take advantage of this research to develop ways of regulating can­nabis use that minimize adverse effects on public health.     

Efficient Modeling and Active Learning Discovery of Biological Responses

High throughput and high content screening involve determination of the effect of many compounds on a given target. As currently practiced, screening for each new target typically makes little use of information from screens of prior targets. Further, choices of compounds to advance to drug development are made without significant screening against off-target effects. The overall drug development process could be made more effective, as well as less expensive and time consuming, if potential effects of all compounds on all possible targets could be considered, yet the cost of such full experimentation would be prohibitive. In this paper, we describe a potential solution: probabilistic models that can be used to predict results for unmeasured combinations, and active learning algorithms for efficiently selecting which experiments to perform in order to build those models and determining when to stop. Using simulated and experimental data, we show that our approaches can produce powerful predictive models without exhaustive experimentation and can learn them much faster than by selecting experiments at random.     

Optimal surveillance strategy for invasive species management when surveys stop after detection

Invasive species are a cause for concern in natural and economic systems and require both monitoring and management. There is a trade‐off between the amount of resources spent on surveying for the species and conducting early management of occupied sites, and the resources that are ultimately spent in delayed management at sites where the species was present but undetected. Previous work addressed this optimal resource allocation problem assuming that surveys continue despite detection until the initially planned survey effort is consumed. However, a more realistic scenario is often that surveys stop after detection (i.e., follow a “removal” sampling design) and then management begins. Such an approach will indicate a different optimal survey design and can be expected to be more efficient. We analyze this case and compare the expected efficiency of invasive species management programs under both survey methods. We also evaluate the impact of mis‐specifying the type of sampling approach during the program design phase. We derive analytical expressions that optimize resource allocation between monitoring and management in surveillance programs when surveys stop after detection. We do this under a scenario of unconstrained resources and scenarios where survey budget is constrained. The efficiency of surveillance programs is greater if a “removal survey” design is used, with larger gains obtained when savings from early detection are high, occupancy is high, and survey costs are not much lower than early management costs at a site. Designing a surveillance program disregarding that surveys stop after detection can result in an efficiency loss. Our results help guide the design of future surveillance programs for invasive species. Addressing program design within a decision‐theoretic framework can lead to a better use of available resources. We show how species prevalence, its detectability, and the benefits derived from early detection can be considered.     

Hagfish embryos again: the end of a long drought

Hagfishes have long held a key place in discussions of early vertebrate evolution. Frustratingly, one basis for such discussions -- namely hagfish embryology -- is very incompletely known, because the embryos of these animals are notoriously difficult to obtain. Fortunately, a recent publication on a Far Eastern hagfish describes a workable procedure for obtaining embryos and then uses this precious material to show that the hagfish neural crest arises by cell delamination as in other vertebrates -- and not by epithelial outpouchings from the wall of the neural tube as previously claimed. Importantly, because hagfish embryos should now be available on a regular basis, the way is open for additional morphological and developmental genetic investigations to help evaluate existing evolutionary scenarios and perhaps suggest new ones.     

Child Mortality Estimation: Appropriate Time Periods for Child Mortality Estimates from Full Birth Histories

Background

Child mortality estimates from complete birth histories from Demographic and Health Surveys (DHS) surveys and similar surveys are a chief source of data used to track Millennium Development Goal 4, which aims for a reduction of under-five mortality by two-thirds between 1990 and 2015. Based on the expected sample sizes when the DHS program commenced, the estimates are usually based on 5-y time periods. Recent surveys have had larger sample sizes than early surveys, and here we aimed to explore the benefits of using shorter time periods than 5 y for estimation. We also explore the benefit of changing the estimation procedure from being based on years before the survey, i.e., measured with reference to the date of the interview for each woman, to being based on calendar years.

Methods and Findings

Jackknife variance estimation was used to calculate standard errors for 207 DHS surveys in order to explore to what extent the large samples in recent surveys can be used to produce estimates based on 1-, 2-, 3-, 4-, and 5-y periods. We also recalculated the estimates for the surveys into calendar-year-based estimates. We demonstrate that estimation for 1-y periods is indeed possible for many recent surveys.

Conclusions

The reduction in bias achieved using 1-y periods and calendar-year-based estimation is worthwhile in some cases. In particular, it allows tracking of the effects of particular events such as droughts, epidemics, or conflict on child mortality in a way not possible with previous estimation procedures. Recommendations to use estimation for short time periods when possible and to use calendar-year-based estimation were adopted in the United Nations 2011 estimates of child mortality.     

Development of community metrics to evaluate recovery of Minnesota wetlands

Monitoring wetland recovery requires assessment tools that efficiently and reliably discern ecosystem changes in response to changes in land use. The biological indicator approach pioneered for rivers and streams that uses changes in species assemblages to interpret degradation levels may be a promising monitoring approach for wetlands. We explored how well metrics based on species assemblages related to land use patterns for eight kinds of wetlands in Minnesota. We evaluated land use on site and within 500 m,1000 m, 2500 m and 5000 m of riverine, littoral, and depressional wetlands (n = 116) in three ecoregions. Proportion of agriculture, urban, grassland, forest,and water were correlated with metrics developed from plant, bird, fish, invertebrate, and amphibian community data collected from field surveys. We found79 metrics that relate to land use, including five that may be useful for many wetlands: proportion of wetland birds, wetland bird richness, proportion of insectivorous birds, importance of Carex, importance of invasive perennials. Since very few metrics were significant for even one-half of the wetland types surveyed, our data suggest that monitoring recovery in wetlands with community indicators will likely require different metrics,depending on type and ecoregion. In addition, wetlands within extensively degraded ecoregions may be most problematic for indicator development because biotic degradation is historic and severe. This revised version was published online in July 2006 with corrections to the Cover Date.     

Including individuals with memory impairment in the research process: the importance of scales and response categories used in surveys

Several ethical considerations emerge when conducting research with memory-impaired individuals, including the individuals' ability to comprehend and accurately respond to survey questions. However, little empirical research exists on how to format surveys to decrease cognitive demands, thereby allowing researchers to more accurately survey this population. The current study presents data from structured interviews with 125 community-residing, memory-impaired older adults about their illness experience. The interview contained 14 scales varying in subjectivity, directionality, and response choice content. While objectivity did not affect participants' ability to use the full range of responses, participants with greater cognitive impairment tended to use simpler, dichotomous response categories, especially when questions had bidirectional response choices. Results suggest that memory-impaired individuals can participate in survey research, that such surveys should contain unidirectional frequency/amount items when possible, and that not all memory-impaired individuals will have difficulty completing surveys.