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Testing has been central to our response to the COVID-19 pandemic. However, the accuracy of testing relies on standards, including reference materials, proficiency testing schemes, and information and reporting guidelines. The use of standards is a simple, inexpensive, and effective method to ensure reliable test results that inform clinical and public health decisions. Here we describe the central role of standards during the COVID-19 pandemic, where they have enabled population-scale screening, genomic surveillance and measures of immune protection measures. Given these benefits, the Coronavirus Standards Working Group (CSWG) was formed to coordinate standards in SARS-CoV-2 testing. This network of scientists has developed best-practices, reference materials, and conducted proficiency studies to harmonize laboratory performance. We propose that this coordinated development of standards should be prioritized as a key early step in the public health response to future pandemics that is necessary for reliable, large-scale testing for infectious disease.

Perceived lack of tools, and fears of the sensitivity of DNA data, should not be obstacles

Chapter 15 covers various ethical issues associated with the use of DNA methods for forensic analyses and human rights investigations. Topics include informed consent and storage issues for samples and profiles; data security and privacy; identification of individuals using aggregate data from forensic, genealogical, research, or clinical databases; the burden of the obligation to report incidental findings that are medically actionable; cultural perspectives on genetic information; government misuse of potentially sensitive DNA data; public policy regarding the validity of pattern/experience evidence; and other non-DNA forensic science disciplines.

Relatively little has been reported characterizing cumulative risk associated with co-occurring risk factors for cigarette smoking. The purpose of the present study was to address that knowledge gap in a U.S. nationally representative sample.Data were obtained from 114,426 adults (≥18years) in the U.S. National Survey on Drug Use and Health (years 2011-13). Multiple logistic regression and classification and regression tree (CART) modeling were used to examine risk of current smoking associated with eight co-occurring risk factors (age, gender, race/ethnicity, educational attainment, poverty, drug abuse/dependence, alcohol abuse/dependence, mental illness).Each of these eight risk factors was independently associated with significant increases in the odds of smoking when concurrently present in a multiple logistic regression model. Effects of risk-factor combinations were typically summative. Exceptions to that pattern were in the direction of less-than-summative effects when one of the combined risk factors was associated with generally high or low rates of smoking (e.g., drug abuse/dependence, age ≥65). CART modeling identified subpopulation risk profiles wherein smoking prevalence varied from a low of 11% to a high of 74% depending on particular risk factor combinations. Being a college graduate was the strongest independent predictor of smoking status, classifying 30% of the adult population.These results offer strong evidence that the effects associated with common risk factors for cigarette smoking are independent, cumulative, and generally summative. The results also offer potentially useful insights into national population risk profiles around which U.S. tobacco policies can be developed or refined.

Use of technology (e.g., Internet, cell phones) to allow remote implementation of incentives interventions for health-related behavior change is growing. To our knowledge, there has yet to be a systematic review of this literature reported. The present report provides a systematic review of the controlled studies where technology was used to remotely implement financial incentive interventions targeting substance use and other health behaviors published between 2004 and 2015. For inclusion in the review, studies had to use technology to remotely accomplish one of the following two aims alone or in combination: (a) monitor the target behavior, or (b) deliver incentives for achieving the target goal. Studies also had to examine financial incentives (e.g., cash, vouchers) for health-related behavior change, be published in peer-reviewed journals, and include a research design that allowed evaluation of the efficacy of the incentive intervention relative to another condition (e.g., non-contingent incentives, treatment as usual). Of the 39 reports that met inclusion criteria, 18 targeted substance use, 10 targeted medication adherence or home-based health monitoring, and 11 targeted diet, exercise, or weight loss. All 39 (100%) studies used technology to facilitate remote monitoring of the target behavior, and 26 (66.7%) studies also incorporated technology in the remote delivery of incentives. Statistically significant intervention effects were reported in 71% of studies reviewed. Overall, the results offer substantial support for the efficacy of remotely implemented incentive interventions for health-related behavior change, which have the potential to increase the cost-effectiveness and reach of this treatment approach.

This project compared urban/rural differences in tobacco use, and examined how such differences vary across regions/divisions of the U.S. Using pooled 2012–2013 data from the National Survey on Drug Use and Health (NSDUH), we obtained weighted prevalence estimates for the use of cigarettes, menthol cigarettes, chewing tobacco, snuff, cigars, and pipes. NSDUH also provides information on participants’ residence: rural vs. urban, and Census region and division. Overall, use of cigarettes, chew, and snuff were higher in rural, compared to urban areas. Across all tobacco products, urban/rural differences were particularly pronounced in certain divisions (e.g., the South Atlantic). Effects did not appear to be fully explained by differences in poverty. Going beyond previous research, these findings show that urban/rural differences vary across different types of tobacco products, as well as by division of the country. Results underscore the need for regulatory efforts that will reduce health disparities.

Classic examples of pharmacogenomic biomarkers for drug efficacy include genetic variation in the drug target (including its expression level) and drug metabolizing enzymes (DMEs). Recent US FDA approvals of tests for cytochrome P450 2D6/2C9 and uridine diphosphate glucuronsyltransferase (UGT)1A1 have given regulatory endorsement to biomarkers that can improve drug safety by identifying individuals at risk for drug toxicity. Markers that predict risk for disease can identify patients who will have a greater than average benefit from therapy. This creates a new opportunity to enrich clinical trials with patients who are likely to have more events and to achieve earlier drug approval. Markers that predict for risk of cardiovascular, thrombotic and liver diseases may also identify a subset of individuals at substantially elevated risk for adverse drug effects. The adaptive clinical trial design provides a mechanism for incorporating genomic information during clinical trials, while providing sufficient time for diagnostic product development and co-registration with a new drug application. Genetic biomarkers for drug efficacy and adverse

This report describes results from a systematic literature review examining gender differences in U.S. prevalence rates of current use of tobacco and nicotine delivery products and how they intersect with other vulnerabilities to tobacco use. We searched PubMed on gender differences in tobacco use across the years 2004-2014. For inclusion, reports had to be in English, in a peer-reviewed journal or federal government report, report prevalence rates for current use of a tobacco product in males and females, and use a U.S. nationally representative sample. Prevalence rates were generally higher in males than in females across all products. This pattern remained stable despite changes over time in overall prevalence rates. Gender differences generally were robust when intersecting with other vulnerabilities, although decreases in the magnitude of gender differences were noted among younger and older users, and among educational levels and race/ethnic groups associated with the highest or lowest prevalence rates. Overall, these results document a pervasive association of gender with vulnerability to tobacco use that acts additively with other vulnerabilities. These vulnerabilities should be considered whenever formulating tobacco control and regulatory policies.

To examine (1) whether use of a recommended algorithm (Johnson and Bickel, 2008) improves upon conventional statistical model fit (R(2)) for identifying nonsystematic response sets in delay discounting (DD) data, (2) whether removing such data meaningfully effects research outcomes, and (3) to identify participant characteristics associated with nonsystematic response sets.Discounting of hypothetical monetary rewards was assessed among 349 pregnant women (231 smokers and 118 recent quitters) via a computerized task comparing $1000 at seven future time points with smaller values available immediately. Nonsystematic response sets were identified using the algorithm and conventional statistical model fit (R(2)). The association between DD and quitting was analyzed with and without nonsystematic response sets to examine whether the inclusion or exclusion impacts this relationship. Logistic regression was used to examine whether participant sociodemographics were associated with nonsystematic response sets.The algorithm excluded fewer cases than the R(2) method (14% vs. 16%), and was not correlated with logk as is R(2). The relationship between logk and the clinical outcome (spontaneous quitting) was unaffected by exclusion methods; however, other variables in the model were affected. Lower educational attainment and younger age were associated with nonsystematic response sets.The algorithm eliminated data that were inconsistent with the nature of discounting and retained data that were orderly. Neither method impacted the smoking/DD relationship in this data set. Nonsystematic response sets are more likely among younger and less educated participants, who may need extra training or support in DD studies.

Retrievable inferior vena cava (IVC) filter use has increased over 115% since the Food and Drug Administration (FDA) approval in 2009. Likewise, there has been a marked increase in complications related to their increased use. In 2014 the FDA, recognizing both the high rate of new complications and

Objectives We asked whether 35 genetic polymorphisms, previously found to be associated with cardiovascular disease, were associated with myocardial infarction (MI) in the CARE (Cholesterol and Recurrent Events) trial and with coronary heart disease (CHD) in the WOSCOPS (West of Scotland Coronary Prevention Study) trial and whether the risk associated with these polymorphisms could be reduced by pravastatin treatment. Background Identification of genetic polymorphisms associated with CHD may improve assessment of CHD risk and understanding of disease pathophysiology. Methods We tested the association between genotype and recurrent MI in the CARE study and between genotype and primary CHD in the WOSCOPS trial using regression models that adjusted for conventional risk factors: Cox proportional hazards models for the CARE study and conditional logistic regression models for a nested case-control study of the WOSCOPS trial. Results We found that Trp719Arg (rs20455) in KIF6 was associated with coronary events. KIF6 encodes kinesin-like protein 6, a member of the molecular motor superfamily. In placebo-treated patients, carriers of the KIF6 719Arg allele (59.4% of the CARE trial cohort) had a hazard ratio of 1.50 (95% confidence interval [CI] 1.05 to 2.15) in the CARE trial and an odds ratio of 1.55 (95% CI 1.14 to 2.09) in the WOSCOPS trial. Among carriers, the absolute risk reduction by pravastatin was 4.89% (95% CI 1.81% to 7.97%) in the CARE trial and 5.49% (95% CI 3.52% to 7.46%) in the WOSCOPS trial. Conclusions In both the CARE and the WOSCOPS trials, carriers of the KIF6 719Arg allele had an increased risk of coronary events, and pravastatin treatment substantially reduced that risk.

This report describes a systematic literature review of voucher and related monetary-based contingency management (CM) interventions for substance use disorders (SUDs) over 5.2 years (November 2009 through December 2014). Reports were identified using the search engine PubMed, expert consultations, and published bibliographies. For inclusion, reports had to (a) involve monetary-based CM; (b) appear in a peer-reviewed journal; (c) include an experimental comparison condition; (d) describe an original study; (e) assess efficacy using inferential statistics; (f) use a research design allowing treatment effects to be attributed to CM. Sixty-nine reports met inclusion criteria and were categorized into 7 research trends: (1) extending CM to special populations, (2) parametric studies, (3) extending CM to community clinics, (4) combining CM with pharmacotherapies, (5) incorporating technology into CM, (6) investigating longer-term outcomes, (7) using CM as a research tool. The vast majority (59/69, 86%) of studies reported significant (p < 0.05) during-treatment effects. Twenty-eight (28/59, 47%) of those studies included at least one follow-up visit after CM was discontinued, with eight (8/28, 29%) reporting significant (p < 0.05) effects. Average effect size (Cohen’s d) during treatment was 0.62 (95% CI: 0.54, 0.70) and post-treatment it was 0.26 (95% CI: 0.11, 0.41). Overall, the literature on voucher-based CM over the past 5 years documents sustained growth, high treatment efficacy, moderate to large effect sizes during treatment that weaken but remain evident following treatment termination, and breadth across a diverse set of SUDs, populations, and settings consistent with and extending results from prior reviews.

This paper examines how the human demand on bioproductive lands, as measured by the Ecological Footprint, is distributed across the globe using methods commonly used to measure the distribution of income. Measuring the distribution of natural resource use will be necessary to achieve an economy that is sustainable, just and efficient. Currently, different nations place different demands on the environment, i.e. the Ecological Footprint is not evenly distributed across the globe. Calculation of the Gini coefficient for total Ecological Footprint and its components explains the sources of inequality in overall resource use. Calculation of the Atkinson index shows how inequality in the Ecological Footprint is related to the inequality of income, and environmental intensity.

INTRODUCTION The present study examines whether use of machine-estimated high-nicotine/tar-yield (full-flavor) cigarettes predicts greater risk of nicotine dependence after controlling for the influence of potential confounding factors in US nationally representative samples. METHODS Data were obtained from multiple years of the National Survey on Drug Use and Health (NSDUH). Nicotine dependence was measured by (1) the Nicotine Dependence Syndrome Scale and (2) latency to first cigarette after waking. Associations between use of high-nicotine/tar-yield cigarettes and risk for nicotine dependence were examined using multiple logistic regression. RESULTS The odds of nicotine dependence were reliably greater among users of high- compared to lower-nicotine/tar-yield cigarettes even after adjusting for sociodemographic and other smoking characteristics (Ps < .0001). This relationship was (1) generally graded across differing nicotine/tar-yield cigarettes, (2) discernible across two definitions of nicotine dependence and multiple NSDUH survey years, and (3) observed among adult and adolescent smokers. CONCLUSION Use of high-nicotine/tar-yield cigarettes is associated with increased odds of nicotine dependence, a relationship that has important tobacco regulatory implications. Whether the widespread marketing and availability of high-nicotine/tar-yield cigarettes is increasing risk of nicotine dependence among US smokers warrants further research. IMPLICATIONS This study adds additional empirical evidence to the relation of machine measured high-yield cigarettes and likelihood of nicotine dependence, and draws some implications in regards to regulation.

Introduction Individuals with lower socioeconomic status (SES) are at increased risk for cigarette smoking. Less research has been conducted characterizing the relationship between SES and risk of using of other tobacco products. The present study examined SES as a risk factor for smokeless tobacco (ST) use in a US nationally representative sample, utilizing data from the 2012 National Survey on Drug Use and Health. Methods Odds were generated for current cigarette smoking and ST use among adults (≥18 years) based on SES markers (educational attainment, income, blue-collar employment, and unemployment) after controlling for the influence of demographics and other substance dependence. Results Odds of current cigarette smoking increased as a graded, inverse function of educational attainment as well as lower income and being unemployed. Odds of current ST use also increased as a function of lower educational attainment, although not in the linear manner seen with cigarette smoking. Odds of ST use but not cigarette smoking also increased with blue-collar employment. In contrast to patterns seen with cigarette smoking, ST use did not change in relation to income or unemployment. Conclusions Markers of SES are significantly associated with odds of cigarette smoking and ST use, but which indicators are predictive and the shape of their relationship to use differs across the two tobacco products.

We examined whether impulsiveness moderates response to financial incentives for cessation among pregnant smokers. All participants were randomized to either a condition wherein financial incentives were delivered contingent on smoking abstinence or to a control condition wherein incentives were delivered independent of smoking status. The study was conducted in two steps: First, we examined associations between baseline impulsiveness scores and abstinence at late pregnancy and 24-weeks postpartum as part of a planned prospective study of this topic using data from a recently completed, randomized controlled clinical trial (N = 118). Next, to increase statistical power, we conducted a second analysis collapsing results across that recent trial and two prior trials involving the same contingent incentive and control conditions (N = 236). Impulsivity was assessed using a delay discounting (DD) of hypothetical monetary rewards task in all three trials and Barratt Impulsiveness Scale (BIS) in the most recent trial. Neither DD nor BIS predicted antepartum or postpartum smoking status in the single or combined trials. Receiving abstinence-contingent incentives, lower baseline smoking rate (cigs/day), and a history of quit attempts pre-pregnancy predicted greater odds of antepartum abstinence across the single and combined trials. No variable predicted postpartum abstinence across the single and combined trials, although a history of antepartum quit attempts and receiving abstinence-contingent incentives predicted in the single and combined trials, respectively. Overall, this study provides no evidence that impulsiveness as assessed by DD or BIS moderates response to this treatment approach while underscoring a substantial association of smoking rate and prior quit attempts with abstinence across the contingent incentives and control treatment conditions.

Strong evidence of linkage to late-onset Alzheimer disease (LOAD) has been observed on chromosome 10, which implicates a wide region and at least one disease-susceptibility locus. Although significant associations with several biological candidate genes on chromosome 10 have been reported, these findings have not been consistently replicated, and they remain controversial. We performed a chromosome 10–specific association study with 1,412 gene-based single-nucleotide polymorphisms (SNPs), to identify susceptibility genes for developing LOAD. The scan included SNPs in 677 of 1,270 known or predicted genes; each gene contained one or more markers, about half (48%) of which represented putative functional mutations. In general, the initial testing was performed in a white case-control sample from the St. Louis area, with 419 LOAD cases and 377 age-matched controls. Markers that showed significant association in the exploratory analysis were followed up in several other white case-control sample sets to confirm the initial association. Of the 1,397 markers tested in the exploratory sample, 69 reached significance (P

Comparisons of DNA polymorphism within species to divergence between species enables the discovery of molecular adaptation in evolutionarily constrained genes as well as the differentiation of weak from strong purifying selection. The extent to which weak negative and positive darwinian selection have driven the molecular evolution of different species varies greatly, with some species, such as Drosophila melanogaster, showing strong evidence of pervasive positive selection, and others, such as the selfing weed Arabidopsis thaliana, showing an excess of deleterious variation within local populations. Here we contrast patterns of coding sequence polymorphism identified by direct sequencing of 39 humans for over 11,000 genes to divergence between humans and chimpanzees, and find strong evidence that natural selection has shaped the recent molecular evolution of our species. Our analysis discovered 304 (9.0%) out of 3,377 potentially informative loci showing evidence of rapid amino acid evolution. Furthermore, 813 (13.5%) out of 6,033 potentially informative loci show a paucity of amino acid differences between humans and chimpanzees, indicating weak negative selection and/or balancing selection operating on mutations at these loci. We find that the distribution of negatively and positively selected genes varies greatly among biological processes and molecular functions, and that some classes, such as transcription factors, show an excess of rapidly evolving genes, whereas others, such as cytoskeletal proteins, show an excess of genes with extensive amino acid polymorphism within humans and yet little amino acid divergence between humans and chimpanzees.

Nearly one in eight US women will develop breast cancer in their lifetime. Most breast cancer is not associated with a hereditary syndrome, occurs in postmenopausal women, and is estrogen and progesterone receptor-positive. Estrogen exposure is an epidemiologic risk factor for breast cancer and estrogen is a potent mammary mitogen. We studied single nucleotide polymorphisms (SNPs) in estrogen receptors in 615 healthy subjects and 1011 individuals with histologically confirmed breast cancer, all from New York City. We analyzed 13 SNPs in the progesterone receptor gene (PGR), 17 SNPs in estrogen receptor 1 gene (ESR1), and 8 SNPs in the estrogen receptor 2 gene (ESR2). We observed three common haplotypes in ESR1 that were associated with a decreased risk for breast cancer [odds ratio (OR), ∼ O.4; 95% confidence interval (CI), 0.2–0.8; P < 0.01]. Another haplotype was associated with an increased risk of breast cancer (OR, 2.1; 95% CI, 1.2–3.8; P < 0.05). A unique risk haplotype was present in ∼7% of older Ashkenazi Jewish study subjects (OR, 1.7; 95% CI, 1.2–2.4; P < 0.003). We narrowed the ESR1 risk haplotypes to the promoter region and first exon. We define several other haplotypes in Ashkenazi Jews in both ESR1 and ESR2 that may elevate susceptibility to breast cancer. In contrast, we found no association between any PGR variant or haplotype and breast cancer. Genetic epidemiology study replication and functional assays of the haplotypes should permit a better understanding of the role of steroid receptor genetic variants and breast cancer risk.

While clinical trials of medications often use a double-blind procedure, the integrity of the blind and its relationship to treatment outcome is seldom examined. In this review, 73 double-blind, placebo-controlled clinical trials of the nicotine replacement therapies (NRTs) in smoking cessation were identified. Seventeen articles were found that assessed blindness integrity, demonstrating major variations in the assessment, analysis, and reporting of blindness integrity. Although 12 studies found that subjects accurately judged treatment assignment at a rate significantly above chance, the available literature does not permit definitive conclusions about blindness integrity. Recommendations for the assessment, analysis, and reporting of blindness integrity are made.

Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein-coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein-coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.

Coccidioides posadasii sp. nov., formerly known as non-California (non-CA) Coccidioides immi- tis, is described. Phylogenetic analyses using single nucleotide polymorphisms, genes, and microsatellites show that C. posadasii represents a divergent, genet- ically recombining monophyletic clade. Coccidioides posadasii can be distinguished from C. immitis by nu- merous DNA polymorphisms, and we show how ei- ther of two microsatellite loci may be used as diag- nostic markers for this species. Growth experiments show that C. posadasii has significantly slower growth rates on high-salt media when compared with C. im- mitis, suggesting that other phenotypic characters may exist.

We investigated three potential predictors (educational attainment, prepregnancy smoking rate, and delay discounting [DD]) of spontaneous quitting among pregnant smokers. These predictors were examined alone and in combination with other potential predictors using study-intake assessments from controlled clinical trials examining the efficacy of financial incentives for smoking cessation and relapse prevention. Data from 349 pregnant women (231 continuing smokers and 118 spontaneous quitters) recruited from the greater Burlington, VT, area contributed to this secondary analysis, including psychiatric/sociodemographic characteristics, smoking characteristics, and performance on a computerized DD task. Educational attainment, smoking rate, and DD values were each significant predictors of spontaneous quitting in univariate analyses. A model examining those three predictors together retained educational attainment as a main effect and revealed a significant interaction of DD and smoking rate (i.e., DD was a significant predictor at lower but not higher smoking rates). A final model considering all potential predictors, included education, the interaction of DD and smoking rate, and five additional predictors (i.e., stress ratings, the belief that smoking during pregnancy will "greatly harm my baby," age of smoking initiation, marital status, and prior quit attempts during pregnancy). The study presented here contributes new knowledge on predictors of spontaneous quitting among pregnant smokers with substantive practical implications for reducing smoking during pregnancy.

Smoking prevalence is unevenly distributed in the U.S. population, with those with mental illness, other substance use disorders, and lower socioeconomic status being especially vulnerable. Less research has been conducted on the association between these same vulnerabilities and smokeless tobacco (ST) use. The present study examined cigarette and ST use among adolescents and adults who met diagnostic criteria for major depressive disorder in the National Survey on Drug Use and Health (NSDUH). Utilizing the most recent (2011) NSDUH, we compared odds for current cigarette smoking and ST use among adolescents and adults meeting criteria for past-year major depressive disorder to the general population, after adjusting for potential confounding influences of sociodemographic and other substance use characteristics. Analyses were conducted to examine sex as a moderator of the relation between major depressive disorder and tobacco use. Odds for current cigarette smoking among those classified with major depressive disorder were increased among adolescents (OR = 1.33, 95% CI [1.05, 1.69], p = .021) and adults (OR = 1.70, 95% CI [1.47, 1.97], p < .0005), and odds for current ST use did not differ among adolescents (OR = 0.90, 95% CI [0.54, 1.49], p = .678) and were lower among adults (OR = 0.68, 95% CI [0.51, 0.91], p = .010). Sex was not a significant moderator in adolescents or adults. Major depressive disorder is associated with increased risk for smoking but not ST use among adolescents and adults further demonstrating heterogeneity in predictors of vulnerability to use of different tobacco products.

Histoplasma capsulatum has a worldwide distribution but is particularly concentrated in the midwestern United States and throughout Central and South America. Genetic differences between isolates resident in separate parts of the world have been reported, but the relationship between the isolates and the level of migration between different endemic foci has not been clear. In this study we used multilocus genotypes based on amplified polymorphic loci and one microsatellite to quantify the level of genetic differentiation occurring between North and South American populations of H. capsulatum. Significant genetic differentiation occurred between isolates obtained from Indiana and Alabama, and a marked division was seen between the Indiana population and the Class 1 isolates from St. Louis. Strong genetic differentiation occurred between the two North American populations and the Colombian population. This study supports the separation of North and South American H. capsulatum into different species, which has been proposed under the phylogenetic species concept.

This paper examines the relationship between scale and distribution issues. It is argued that since achieving a sustainable scale requires economic activity to stay within biophysical limits, considerations of equity should not be limited to the distribution of monetary measures such as income, but should include the distribution of scarce environmental services as well. In order to make this point this paper examines how differences in diet across populations lead to inequality in the distribution of environmental impact. First, the distribution of food consumption across the world’s population is examined using national data. Next, ecological footprints are estimated in order to ascertain how differences in diet affect the distribution of environmental impact. The results show that the meat-intensive diet enjoyed by many in the industrialized world leads to a greater degree of inequality in the use of environmental services than is apparent from examination of the distribution of food consumption across countries.

In this Round Table, the application of several methods of molecular typing were discussed in reference to four important pathogenic fungi: Coccidioides immitis , Histoplasma capsulatum , Candida albicans and Paracoccidioides brasiliensis . Among the different methods the following were discussed: restriction fragment length polymorphisms (RFLP), single nucleotide polymorphisms, random amplie ed polymorphic DNA (RAPD), polymerase chain reaction (PCR)-RFLP and microsatellites. By means of these methods, several important biological questions related to speciation, mode of reproduction and population genetics could be approached. The basic information obtained from this approach has implications in the understanding of these pathogenic fungi in relation to their behavior and the development of pathogenic features, such as resistance to antimicrobials and virulence factors used for colonization of mammalian hosts. The knowledge obtained from these studies could also be used for the development of innovative diagnostic methods, as well as for novel therapeutic approaches and production of vaccines.

Coccidioides immitis causes coccidioidomycosis, a fungal disease of both immuno-compromised and otherwise healthy people; it is capable of causing large epidemics and the disease is often refractory to chemotherapy. To quantify the magnitude of population differentiation and estimate levels of gene flow in C. immitis, multilocus genotypes were scored for 20-25 clinical isolates from each of Bakersfield (California), Tucson (Arizona), and San Antonio (Texas). The molecular markers used were PCR products with polymorphic restriction endonuclease sites, found and characterized in a previous study of the Tucson population. The data show very highly significant differences in allele frequencies between all three populations, and suggest very low levels of migration between populations. One isolate in the San Antonio sample was an outlier, showing the California-specific allele at all four of the loci distinguishing the two populations, and subsequent inquiries indicated that the infection had indeed been acquired in California. Thus, genetic information can be used to infer the geographical origin of a fungal infection.

A set of eleven biallelic and three multiallelic molecular markers have been developed to analyze populations of Histoplasma capsulatum. All markers are amplified by polymerase chain reaction (PCR) and can be readily scored using minimal amounts of template DNA. The 11 biallelic loci have polymorphic restriction endonuclease sites or small insertions or deletions which may be assessed by agarose gel electrophoresis. These markers are inherited in an unambiguous manner and are ideal for assessing structure and gene flow within US populations of H. capsulatum, but are monomorphic in non-US populations. Both length and sequence variation are present in the multiallelic loci, which can be scored by direct sequencing, polyacrylamide gel electrophoresis, or single-strand conformation polymorphism (SSCP): As they are hypervariable, the multiallelic loci can be used to type isolates and to assess the level of genetic variation within populations. Preliminary results indicate that the three multiallelic markers presented are sufficient to distinguish isolates at the individual level and are polymorphic in both US and non-US populations. This collection of molecular markers will be a useful tool in population and epidemiology studies of H. capsulatum.

A sample of 30 clinical isolates of Histoplasma capsulatum was analyzed to determine (i) whether genetic exchange is important in the life cycle of this fungus and (ii) whether distinct subpopulations which correlate with disease severity or host immune status exist. Eleven biallelic molecular markers were developed, with the frequency of the least common allele at each molecular locus ranging from 10 to 50%. Every isolate had a different, unique multilocus genotype. Data analysis indicated that frequent recombination occurs within the Indianapolis, Ind., population. There were no associations between isolates from the immunocompromised population or from those with different clinical manifestations of histoplasmosis.

Coronary heart disease (CHD) often presents suddenly with little warning. Traditional risk factors are inadequate to identify the asymptomatic high-risk individuals. Early identification of patients with subclinical coronary artery disease using noninvasive imaging modalities would allow the early adoption of aggressive preventative interventions. Currently, it is impractical to screen the entire population with noninvasive coronary imaging tools. The use of relatively simple and inexpensive genetic markers of increased CHD risk can identify a population subgroup in which benefit of atherosclerotic imaging modalities would be increased despite nominal cost and radiation exposure. Additionally, genetic markers are fixed and need only be measured once in a patient’s lifetime, can help guide therapy selection, and may be of utility in family counseling.

This paper builds on the optimal city size literature by examining factors that influence location benefits and costs. Total population, population density, employment type, and networking are evaluated using ordinary least squares. Results indicate that population density may play a more significant role in predicting average location benefits and average location costs than population.

Fungal model organisms are widely used because, in general, they are less expensive to maintain under laboratory conditions than are members of the two other higher eukaryotic kingdoms, the animals and plants. Ascomycetes have been the most popular fungi with geneticists and molecular developmental biologists, beginning with Neurospora and recently with Saccharomyces and Aspergillus. Fungal molecular evolution studies of 18S ribosomal RNA and DNA have recently produced a robust phylogeny of ascomycetes, and molecular genetic studies of fungal development are unraveling the pathway of spore production. We wondered if systematists and developmental biologists were taking advantage of each other's knowledge (...)

The striking similarity between the first two human immunodeficiency virus type 1 (HIV-1) isolates Lai/LAV (formerly LAV, isolated at the Pasteur Institute) and Lai/IIIB (formerly HTLV-IIIB, reported to be isolated from a pooled culture at the Laboratory of Tumor Cell Biology (LTCB) of the National Cancer Institute) provoked considerable controversy in light of the high level of variability found among subsequent HIV-1 isolates. In November 1990, the Office of Scientific Integrity at the National Institutes of Health commissioned our group to analyse archival samples established at the Pasteur Institute and LTCB between 1983 and 1985. Retrospective analyses have shown that contamination of a culture derived from patient BRU by one from patient LAI was responsible for the provenance of HIV-1 Lai/LAV; the contaminated culture (M2T-/B) was sent to LTCB in September 1983. Our goals were to determine which HIV-1 variants were present in the samples and the sequence diversity among HIV-1 isolates from the earliest stages of the AIDS epidemic. We examined archival specimens and report here the detection of six novel HIV-1 sequences in the cultures used to establish the pool: none is closely related to HIV-1 Lai/IIIB. A sample derived from patient LAI contained variants of both HIV-1 Lai/IIIB and HIV-1 Lai/LAV, and a sequence identical to a variant of HIV-1 Lai/IIIB was detected in the contaminated M2T-/B culture. We conclude that the pool, and probably another LTCB culture, MoV, were contaminated between October 1983 and early 1984 by variants of HIV-1 Lai from the M2T-/B culture. Therefore, the origin of the HIV-1 Lai/IIIB isolate also was patient LAI.

For over two decades, substantial National efforts have been directed toward ­reducing blood cholesterol levels of the American population with the intent of reducing the burden of cardiovascular events. This initiative was initially prompted by the successful results of the Lipid Research Clinic-Coronary Primary Prevention Trial (LRC-CPPT) that first proved reducing LDL-C resulted in a statistically ­significant reduction in cardiovascular events [2]. Since then an abundance of monotherapy cholesterol-lowering drug trials have consistently reported an approximate 25% relative risk reduction (RRR) for cardiovascular events [3].

Nucleotide sequences obtained from regions of the ribosomal DNA repeat were compared by phylogenetic methods and combined with a statistical evaluation to clarify the relationships among the genera Cystofilobasidium, Filobasidium (F.) and Filobasidiella (Fl.), to assess the affinity of Filobasidiella neoformans and Filobasidiella depauperata, and to compare the varieties of Fl. neoformans. With appropriate primers, the nuclear 18S, 5.8S and internal transcribed spacer (ITS) regions of the ribosomal RNA genes (rDNA) of 10 strains were amplified with the polymerase chain reaction. The resulting DNA products were compared by digestion with endonucleases and analysis of restriction fragments. Single strands of the 5.8S rDNA and ITS regions were subsequently sequenced by the dideoxy method. Statistical support for the phylogeny inferred from parsimony analysis of aligned 5.8S rDNA sequences was determined by bootstrapping. There were no nucleotide substitutions in this region, nor in the ITS, among strains of ...

Balancing selection is potentially an important biological force for maintaining advantageous genetic diversity in populations, including variation that is responsible for long-term adaptation to the environment. By serving as a means to maintain genetic variation, it may be particularly relevant to maintaining phenotypic variation in natural populations. Nevertheless, its prevalence and specific targets in the human genome remain largely unknown. We have analyzed the patterns of diversity and divergence of 13,400 genes in two human populations using an unbiased single-nucleotide polymorphism data set, a genome-wide approach, and a method that incorporates demography in neutrality tests. We identified an unbiased catalog of genes with signatures of long-term balancing selection, which includes immunity genes as well as genes encoding keratins and membrane channels; the catalog also shows enrichment in functional categories involved in cellular structure. Patterns are mostly concordant in the two populations, with a small fraction of genes showing population-specific signatures of selection. Power considerations indicate that our findings represent a subset of all targets in the genome, suggesting that although balancing selection may not have an obvious impact on a large proportion of human genes, it is a key force affecting the evolution of a number of genes in humans.

Analysis of polymorphism and divergence in the non-coding portion of the human genome yields crucial information about factors driving the evolution of gene regulation. Candidate cis-regulatory regions spanning more than 15,000 genes in 15 African Americans and 20 European Americans were re-sequenced and aligned to the chimpanzee genome in order to identify potentially functional polymorphism and to characterize and quantify departures from neutral evolution. Distortions of the site frequency spectra suggest a general pattern of selective constraint on conserved non-coding sites in the flanking regions of genes (CNCs). Moreover, there is an excess of fixed differences that cannot be explained by a Gamma model of deleterious fitness effects, suggesting the presence of positive selection on CNCs. Extensions of the McDonald-Kreitman test identified candidate cis-regulatory regions with high probabilities of positive and negative selection near many known human genes, the biological characteristics of which exhibit genome-wide trends that differ from patterns observed in protein-coding regions. Notably, there is a higher probability of positive selection in candidate cis-regulatory regions near genes expressed in the fetal brain, suggesting that a larger portion of adaptive regulatory changes has occurred in genes expressed during brain development. Overall we find that natural selection has played an important role in the evolution of candidate cis-regulatory regions throughout hominid evolution., Author Summary It has been suggested that changes in gene expression may have played a more important role in the evolution of modern humans than changes in protein-coding sequences. In order to identify signatures of natural selection on candidate cis-regulatory regions, we examined single nucleotide polymorphisms obtained from the complete re-sequencing of conserved non-coding sites (CNCs) in the flanking regions of over 15,000 genes in 35 humans. Patterns of allele frequencies in CNCs indicate the presence of both positive and negative selection acting on standing variation within these candidate cis-regulatory regions, particularly for the 5′ and 3′ UTRs of genes. Gene-specific tests comparing levels of polymorphism and divergence identify several genes with strong signatures of selection on candidate cis-regulatory regions and suggest that the biological characteristics of genes subject to selection are different between coding and candidate cis-regulatory regions with respect to gene expression and function. For example, we find stronger signatures of positive selection in candidate cis-regulatory regions near genes expressed in the fetal brain, which we do not observe in a concurrent analysis on protein-coding regions. Our results suggest that both positive and negative selection have acted on candidate cis-regulatory regions and that the evolution of non-coding DNA has played an important role throughout hominid evolution.

We used the polymerase chain reaction (PCR) to amplify specific regions of the nuclear and mitochondrial genomes of fungi using DNA extracted from pure cultures as well as that directly from ectomycorrhizal rootlets. The internal transcribed spacer (ITS) of the nuclear ribosomal repeat unit and a portion of the mitochondrial large subunit ribosomal RNA gene were chosen as target sequences because both exist in high copy number and amplification primers for both discriminate between plant and fungal DNAs. These features provided a sensitivity and specificity sufficient for detection and analysis of a single mycorrhizal rootlet. We evaluated the variations in the amplified products with regard to the length, restriction endonuclease sites, and primary sequence for use in identification of genera, species, and strains of ectomycorrhizal fungi, with particular attention to selected Laccaria species. Accidental contamination of jack pine seedlings by Telephora terrestris was easily recognized. Amplification and direct DNA sequencing of a portion of the ITS were done for three strains of L. bicolor, one of L. laccata, one of L. proximo, and one of T. terrestris. The nucleotide sequence variation was 32% between L. bicolor and T. terrestris, and it ranged from 3 to 5% among the three Laccaria species examined and from 1 to 2% within L. bicolor. The degree of variation observed is sufficient to allow the use of specific oligonucleotides to characterize amplified ITS products. To demonstrate the feasibility of this approach we designed and tested a probe that enabled two isolates of L. bicolor to be distinguished by a single base-pair difference in a filter-based hybridization assay. In combination these methods now provide an important set of tools for the study of mycorrhizal ecology. Key words: internal transcribed spacer, LrDNA gene, mycorrhizal ecology, polymerase chain reaction, rDNA.

Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P < 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P < 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.

sive analysis of gene structure from a limited number of species, primarily humans, mice, fruit flies, yeast, and the bacterium Escherichia coli. The powerful new molecular biological methods have also led to major discoveries in population biology and the study of organismal evolution. Among the many achievements are a better understanding of the evolutionary relationships among the major groups of microorganisms (Woese 1987) and the discovery that apes and humans had a common ancestor as recently as 5 million years ago (Wilson et al. 1989). Despite the profound nature of such discoveries, little data have been generated by molecular biological methods when the world's total biota is considered. Only a small number of individuals and species have been