Land use causes genetic differentiation of life-history traits in Bromus hordeaceus

There is increasing evidence that species can evolve rapidly in response to environmental change. However, although land use is one of the key drivers of current environmental change, studies of its evolutionary consequences are still fairly scarce, in particular studies that examine land-use effects across large numbers of populations, and discriminate between different aspects of land use. Here, we investigated genetic differentiation in relation to land use in the annual grass Bromus hordeaceus. A common garden study with offspring from 51 populations from three regions and a broad range of land-use types and intensities showed that there was indeed systematic population differentiation of ecologically important plant traits in relation to land use, in particular due to increasing mowing and grazing intensities. We also found strong land-use-related genetic differentiation in plant phenology, where the onset of flowering consistently shifted away from the typical time of management. In addition, increased grazing intensity significantly increased the genetic variability within populations. Our study suggests that land use can cause considerable genetic differentiation among plant populations, and that the timing of land use may select for phenological escape strategies, particularly in monocarpic plant species.

Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species

Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.

An assessment of obesity and hyperphagia in individuals with Smith-Magenis syndrome

Smith-Magenis syndrome (SMS;OMIM# 182290) is a multiple congenital anomalies and mental retardation syndrome caused by a 3.7- Mb deletion on chromosome 17p11.2 or a mutation in the RAI1 gene. Although the majority of the SMS phenotype has been well described, limited studies are available describing growth patterns in SMS. There is some evidence that individuals with SMS develop obesity. Thus, this study aims to characterize the growth and potential influence of hyperphagia in a cohort of individuals with SMS. A retrospective chart review was conducted of 78 individuals with SMS through Baylor College of Medicine (BCM) at Texas Children¡¯s Hospital (TCH.) All documented height and weight measurements were abstracted and Z-scores (SD units) for height-for-age, length-for-age and BMI-for-age were calculated. Mail-out questionnaires were provided to the corresponding parents of the cohort to assess for the presence of hyperphagia through a validated hyperphagia questionnaire (HQ). Analysis of this data demonstrates that by the age ¡Ý 20 years males with SMS have mean BMI¡¯s in the 85th-90th percentile corresponding to an overweight BMI, and females with SMS had mean BMI¡¯s in the 95th -97th percentile corresponding to an obese BMI. Parents indicated that hyperphagia is present in individuals with SMS as 76% of parent¡¯s report having to lock food away from their child. Females¡¯ age ¡Ý 20 years of age had the highest mean behavior, drive and severity scores as well as the highest BMI. Thus, this study concludes that it appears overweight and obesity, as well as hyperphagia, are present in this cohort of SMS individuals. The results of this study will hopefully enable parents and caregivers of children with SMS to take preventative measures in order to control food related behaviors present in their children as well as to prevent overweight and obesity and the associated negative health consequences.

Towards a treaty instrument on marine genetic resources

Marine genetic resources other than fish and mammals are of increasing commercial interest and importance in genetic engineering, but fail being properly addressed in the law of the sea and in international economic law. The paper analyses the implication of the United Nations Convention on the Law of the Sea, the Convention on Biodiversity, the WTO Agreement on Trade Related Aspects of Intellectual Property Rights and related instruments under the auspices of WIPO. The paper argues that the triangle of these agreements does not adequately address marine genetic resources in particular in the high seas. Neither concerns of protecting biodiversity nor of access and benefit sharing find appropriate answers commensurate to the commercial potential of marine genetic resources. The paper suggests developing an instrument inspired by, and comparable to, the mechanisms developed by the International Treaty on Plant Genetic Resources for Food and Agriculture. The instrument would grant facilitated access to marine genetic resources and offer a more detailed set of rules with respect to the sharing of benefits resulting from their use, thereby addressing the existing legal gaps in a comprehensive way.

Asthma and obesity in children: current evidence and potential systems biology approaches.

Both obesity and asthma are highly prevalent, complex diseases modified by multiple factors. Genetic, developmental, lung mechanical, immunological and behavioural factors have all been suggested as playing a causal role between the two entities; however, their complex mechanistic interactions are still poorly understood and evidence of causality in children remains scant. Equally lacking is evidence of effective treatment strategies, despite the fact that imbalances at vulnerable phases in childhood can impact long-term health. This review is targeted at both clinicians frequently faced with the dilemma of how to investigate and treat the obese asthmatic child and researchers interested in the topic. Highlighting the breadth of the spectrum of factors involved, this review collates evidence regarding the investigation and treatment of asthma in obese children, particularly in comparison with current approaches in 'difficult-to-treat' childhood asthma. Finally, the authors propose hypotheses for future research from a systems-based perspective.

Genetic markers for stallion fertility - lessons from humans and mice

Our knowledge on the many aspects of mammalian reproduction in general and equine reproduction in particular has greatly increased during the last 15 years. Advances in the understanding of the physiology, cell biology, and biochemistry of reproduction have facilitated genetic analyses of fertility. Currently, there are more than 200 genes known that are involved in the production of fertile sperm cells. The completion of a number of mammalian genome projects will aid in the investigation of these genes in different species. Great progress has been made in the understanding of genetic aberrations that lead to male infertility. Additionally, the first genetic mechanisms are being discovered that contribute to the quantitative variation of fertility traits in fertile male animals. As artificial insemination (AI) represents a widespread technology in horse breeding, semen quality traits may eventually become an additional selection criterion for breeding stallions. Current research activities try to identify genetic markers that correlate to these semen quality traits. Here, we will review the current state of genetic research in male fertility and offer some perspectives for future research in horses.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

The domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data and modern genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication.

Linking altered central pain processing and genetic polymorphism to drug efficacy in chronic low back pain.

BACKGROUND Inability to predict the therapeutic effect of a drug in individual pain patients prolongs the process of drug and dose finding until satisfactory pharmacotherapy can be achieved. Many chronic pain conditions are associated with hypersensitivity of the nervous system or impaired endogenous pain modulation. Pharmacotherapy often aims at influencing these disturbed nociceptive processes. Its effect might therefore depend on the extent to which they are altered. Quantitative sensory testing (QST) can evaluate various aspects of pain processing and might therefore be able to predict the analgesic efficacy of a given drug. In the present study three drugs commonly used in the pharmacological management of chronic low back pain are investigated. The primary objective is to examine the ability of QST to predict pain reduction. As a secondary objective, the analgesic effects of these drugs and their effect on QST are evaluated. METHODS/DESIGN In this randomized, double blinded, placebo controlled cross-over study, patients with chronic low back pain are randomly assigned to imipramine, oxycodone or clobazam versus active placebo. QST is assessed at baseline, 1 and 2 h after drug administration. Pain intensity, side effects and patients' global impression of change are assessed in intervals of 30 min up to two hours after drug intake. Baseline QST is used as explanatory variable to predict drug effect. The change in QST over time is analyzed to describe the pharmacodynamic effects of each drug on experimental pain modalities. Genetic polymorphisms are analyzed as co-variables. DISCUSSION Pharmacotherapy is a mainstay in chronic pain treatment. Antidepressants, anticonvulsants and opioids are frequently prescribed in a "trial and error" fashion, without knowledge however, which drug suits best which patient. The present study addresses the important need to translate recent advances in pain research to clinical practice. Assessing the predictive value of central hypersensitivity and endogenous pain modulation could allow for the implementation of a mechanism-based treatment strategy in individual patients. TRIAL REGISTRATION Clinicaltrials.gov, NCT01179828.

Implications of Longterm Diameter-Limit Harvesting: Effects on Radial Growth of Red Spruce (Picea rubens) and Genetic Diversity of White Pine (Pinus strobus)

For over 3 centuries, diameter-limit harvesting has been a predominant logging method in the northeastern United States. Silvicultural theory asserts that such intensively selective harvesting can lead to genetic degradation. A decrease in softwood productivity has recently been reported in Maine - has a long history of dysgenic selection degraded the genetic resources of Maine softwoods, contributing to a decrease in growth and productivity? This study examines two aspects of potential implications of diameter-limit harvesting: effects on residual phenotypes of red spruce and impacts on genetic diversity of white pine. Radial growth of residual red spruce trees in stands experiencing 50 years of fixed diameter-limit harvesting was measured using annual increment rings and compared with residual red spruce trees in positive selection stands. Trees remaiaing after several rounds of diameter-limit harvesting exhibited sigdicantl y smaller radial sizes throughout their lives, and displayed significantly slower growth rates for the first 80 years of measured growth. These results strongly suggest that the largest and fastest-growing genotypes and their respective gene complexes determining good radial growth have been removed from the diameter-limit stand. Dysgenic selection can be observed in fixed diarneter-limit stands, resulting in a diminished genetic resource and decreased residual stand value. To examine more direct genetic implications of long-term diameter-limit harvesting, microsatellite DNA markers were implemented to study genetic diversity of eastern white pine in Maine. Three age groups of trees were studied: mature trees older than 200 years, juvenile trees 5-30 years old, and embryos. Trees were genotyped at 10 microsatellite loci. Overall genetic diversity levels of eastern white pine in Maine were extremely high, with an average observed heterozygosity of 0.762. Genetic differentiation was minimal among and between all three age groups, although an excess of heterozygotes was shown in the mature and juvenile groups that was not reflected in the embryo group, which actually had a slight heterozygote deficiency. Allele frequencies did not differ significantly between age groups, but did reveal more rare and low frequency alleles in the embryo groups than in the mature group. Overall, low frequency alleles comprise the largest portion of alleles in the sample population, with no common alleles evident overall. These results suggest that significant genetic degradation has either not occurred for white pine, or that the results of dysgenic selection have not yet emerged. It is clear, however, that selective harvesting could result in a loss of low frequency alleles, which are a primary reserve of evolutionary potential in a species. Implications of these studies affect industrial forestry, regional economics, and ecological concerns for the northeast. Long-term diameter-limit harvesting can lead to a degradation of residual phenotypes, and an overall decrease in stand quality. Potentially, a loss of low frequency, locally adapted alleles could result in a decrease of allelic richness and degradation of the regidnal genetic resource. Decreased genetic variation can lead to seriously limited evolutionary potential of species and ecosystems, particularly in rapidly changing environments. Based on these findings, I recommend a reassessment of any harvesting prescription that includes fixed diameter-limit removals, particularly for species that have low natural genetic diversity levels or a limited natural range, such as red spruce. Maintenance of a healthy genetic reserve can avoid effects of dysgenic harvesting.

Adiposity and the perilipin gene: The role of single locus and multilocus variation, obesity-related quantitative traits, and disease-related phenotypes in the Atherosclerosis Risk in Communities (ARIC) study

Obesity is a complex multifactorial disease and is a public health priority. Perilipin coats the surface of lipid droplets in adipocytes and is believed to stabilize these lipid bodies by protecting triglyceride from early lipolysis. This research project evaluated the association between genetic variation within the human perilipin (PLIN) gene and obesity-related quantitative traits and disease-related phenotypes in Non-Hispanic White (NHW) and African American (AA) participants from the Atherosclerosis Risk in Communities (ARIC) Study. ^ Multivariate linear regression, multivariate logistic regression, and Cox proportional hazards models evaluated the association between single gene variants (rs2304794, rs894160, rs8179071, and rs2304795) and multilocus variation (rs894160 and rs2304795) within the PLIN gene and both obesity-related quantitative traits (body weight, body mass index [BMI], waist girth, waist-to-hip ratio [WHR], estimated percent body fat, and plasma total triglycerides) and disease-related phenotypes (prevalent obesity, metabolic syndrome [MetS], prevalent coronary heart disease [CHD], and incident CHD). Single variant analyses were stratified by race and gender within race while multilocus analyses were stratified by race. ^ Single variant analyses revealed that rs2304794 and rs894160 were significantly related to plasma triglyceride levels in all NHWs and NHW women. Among AA women, variant rs8179071 was associated with triglyceride levels and rs2304794 was associated with risk-raising waist circumference (>0.8 in women). The multilocus effects of variants rs894160 and rs2304795 were significantly associated with body weight, waist girth, WHR, estimated percent body fat, class II obesity (BMI ≥ 35 kg/m2), class III obesity (BMI ≥ 35 kg/m2), and risk-raising WHR (>0.9 in men and >0.8 in women) in AAs. Variant rs2304795 was significantly related to prevalent MetS among AA males and prevalent CHD in NHW women; multilocus effects of the PLIN gene were associated with prevalent CHD among NHWs. Rs2304794 was associated with incident CHD in the absence of the MetS among AAs. These findings support the hypothesis that variation within the PLIN gene influences obesity-related traits and disease-related phenotypes. ^ Understanding these effects of the PLIN genotype on the development of obesity can potentially lead to tailored health promotion interventions that are more effective. ^

Spatial and temporal aspects of synaptic plasticity

The notion that changes in synaptic efficacy underlie learning and memory processes is now widely accepted even if definitive proof of the synaptic plasticity and memory hypothesis is still lacking. When learning occurs, patterns of neural activity representing the occurrence of events cause changes in the strength of synaptic connections within the brain. Reactivation of these altered connections constitutes the experience of memory for these events and for other events with which they may be associated. These statements summarize a long-standing theory of memory formation that we refer to as the synaptic plasticity and memory hypothesis. Since activity-dependent synaptic plasticity is induced at appropriate synapses during memory formation, and is both necessary and sufficient for the information storage, we can speculate that a methodological study of the synapse will help us understand the mechanism of learning. Random events underlie a wide range of biological processes as diverse as genetic drift and molecular diffusion, regulation of gene expression and neural network function. Additionally spatial variability may be important especially in systems with nonlinear behavior. Since synapse is a complex biological system we expect that stochasticity as well as spatial gradients of different enzymes may be significant for induction of plasticity. ^ In that study we address the question "how important spatial and temporal aspects of synaptic plasticity may be". We developed methods to justify our basic assumptions and examined the main sources of variability of calcium dynamics. Among them, a physiological method to estimate the number of postsynaptic receptors as well as a hybrid algorithm for simulating postsynaptic calcium dynamics. Additionally we studied how synaptic geometry may enhance any possible spatial gradient of calcium dynamics and how that spatial variability affect plasticity curves. Finally, we explored the potential of structural synaptic plasticity to provide a metaplasticity mechanism specific for the synapse. ^

Genetic variability and the hypothalamic control of energy balance

Background. Obesity is a major health problem throughout the industrialized world. Despite numerous attempts to curtail the rapid growth of obesity, its incidence continues to rise. Therefore, it is crucial to better understand the etiology of obesity beyond the concept of energy balance.^ Aims. The first aim of this study was to first investigate the relationship between eating behaviors and body size. The second goal was to identify genetic variation associated with eating behaviors. Thirdly, this study aimed to examine the joint relationships between eating behavior, body size and genetic variation.^ Methods. This study utilized baseline data ascertained in young adults from the Training Interventions and Genetics of Exercise (TIGER) Study. Variables assessed included eating behavior (Emotional Eating Scale, Eating Attitudes Test-26, and the Block98 Food Frequency Questionnaire), body size (body mass index, waist and hip circumference, waist/hip ratio, and percent body fat), genetic variation in genes implicated related to the hypothalamic control of energy balance, and appropriate covariates (age, gender, race/ethnicity, smoking status, and physical activity. For the genetic association analyses, genotypes were collapsed by minor allele frequency, and haplotypes were estimated for each gene. Additionally, Bayesian networks were constructed in order to determine the relationships between genetic variation, eating behavior and body size.^ Results. We report that the EAT-26 score, Caloric intake, percent fat, fiber intake, HEAT index, and daily servings of vegetables, meats, grains, and fats were significantly associated with at least one body size measure. Multiple SNPs in 17 genes and haplotypes from 12 genes were tested for their association with body size. Variation within both DRD4 and HTR2A was found to be associated with EAT-26 score. In addition, variation in the ghrelin gene (GHRL) was significantly associated with daily Caloric intake. A significant interaction between daily servings of grains and the HEAT index and variation within the leptin receptor gene (LEPR) was shown to influence body size.^ Conclusion. This study has shown that there is a substantial genetic component to eating behavior and that genetic variation interacts with eating behavior to influence body size.^

Role of obesity, weight gain, physical activity, and polymorphisms in the mTOR pathway and the risk of renal cell carcinoma

The interplay between obesity, physical activity, weight gain and genetic variants in mTOR pathway have not been studied in renal cell carcinoma (RCC). We examined the associations between obesity, weight gain, physical activity and RCC risk. We also analyzed whether genetic variants in the mTOR pathway could modify the association. Incident renal cell carcinoma cases and healthy controls were recruited from the University of Texas MD Anderson Cancer Center in Houston, Texas. Cases and controls were frequency-matched by age (±5 years), ethnicity, sex, and county of residence. Epidemiologic data were collected via in-person interview. A total of 577 cases and 593 healthy controls (all white) were included. One hundred ninety-two (192) SNPs from 22 genes were available and their genotyping data were extracted from previous genome-wide association studies. Logistic regression and regression spline were performed to obtain odds ratios. Obesity at age 20, 40, and 3 years prior to diagnosis/recruitment, and moderate and large weight gain from age 20 to 40 were each significantly associated with increased RCC risk. Low physical activity was associated with a 4.08-fold (95% CI: 2.92-5.70) increased risk. Five single nucleotide polymorphisms (SNPs) were significantly associated with RCC risk and their cumulative effect increased the risk by up to 72% (95% CI: 1.20-2.46). Strata specific effects for weight change and genotyping cumulative groups were observed. However, no interaction was suggested by our study. In conclusion, energy balance related risk factors and genetic variants in the mTOR pathway may jointly influence susceptibility to RCC. ^

Exploration of genetic susceptibility to pancreatic cancer: A GWAS approach

Pancreatic cancer is the 4th most common cause for cancer death in the United States, accompanied by less than 5% five-year survival rate based on current treatments, particularly because it is usually detected at a late stage. Identifying a high-risk population to launch an effective preventive strategy and intervention to control this highly lethal disease is desperately needed. The genetic etiology of pancreatic cancer has not been well profiled. We hypothesized that unidentified genetic variants by previous genome-wide association study (GWAS) for pancreatic cancer, due to stringent statistical threshold or missing interaction analysis, may be unveiled using alternative approaches. To achieve this aim, we explored genetic susceptibility to pancreatic cancer in terms of marginal associations of pathway and genes, as well as their interactions with risk factors. We conducted pathway- and gene-based analysis using GWAS data from 3141 pancreatic cancer patients and 3367 controls with European ancestry. Using the gene set ridge regression in association studies (GRASS) method, we analyzed 197 pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Using the logistic kernel machine (LKM) test, we analyzed 17906 genes defined by University of California Santa Cruz (UCSC) database. Using the likelihood ratio test (LRT) in a logistic regression model, we analyzed 177 pathways and 17906 genes for interactions with risk factors in 2028 pancreatic cancer patients and 2109 controls with European ancestry. After adjusting for multiple comparisons, six pathways were marginally associated with risk of pancreatic cancer ( P < 0.00025): Fc epsilon RI signaling, maturity onset diabetes of the young, neuroactive ligand-receptor interaction, long-term depression (Ps < 0.0002), and the olfactory transduction and vascular smooth muscle contraction pathways (P = 0.0002; Nine genes were marginally associated with pancreatic cancer risk (P < 2.62 × 10−5), including five reported genes (ABO, HNF1A, CLPTM1L, SHH and MYC), as well as four novel genes (OR13C4, OR 13C3, KCNA6 and HNF4 G); three pathways significantly interacted with risk factors on modifying the risk of pancreatic cancer (P < 2.82 × 10−4): chemokine signaling pathway with obesity ( P < 1.43 × 10−4), calcium signaling pathway (P < 2.27 × 10−4) and MAPK signaling pathway with diabetes (P < 2.77 × 10−4). However, none of the 17906 genes tested for interactions survived the multiple comparisons corrections. In summary, our current GWAS study unveiled unidentified genetic susceptibility to pancreatic cancer using alternative methods. These novel findings provide new perspectives on genetic susceptibility to and molecular mechanisms of pancreatic cancer, once confirmed, will shed promising light on the prevention and treatment of this disease. ^

AN ASSESSMENT OF KNOWLEDGE AND ATTITUDES OF GENETIC COUNSELING SERVICES IN U.S. HTCs

Hemophilia is a hereditary bleeding disorder which requires lifelong specialized care. A network of Hemophilia Treatment Centers (HTCs) exists to meet the medical needs of patients affected by hemophilia. Genetic counseling services are an integral part of the HTC model of care; however, many HTCs do not have genetic counselors on staff. As a result, the duty to provide these services must fall to other healthcare providers within the HTC. To assess the knowledge and attitudes of these providers we developed a 49 question survey that was distributed electronically to hematologists and nurses at U.S. HTCs. The survey consisted of a three sections: demographic information, knowledge of hemophilia genetics, and attitudes towards genetic services. A total of 111 complete responses were received and analyzed. The average knowledge score among all participants was 74.8% with a total of 81 participants receiving a passing score of 70% or above. Thirty participants scored below 70% in the knowledge section. In general, attitude scores were high indicating that the majority of hematologists and nurses in HTCs feel confident in their ability to provide genetic counseling services. Over 90% of participants reported that they have some form of access to genetic counseling services at their center. Hematologists and nurses practicing in U.S. HTCs demonstrate sufficient knowledge of the genetics of hemophilia, and they generally feel confident in their ability to provide genetic counseling services to their patients. While their knowledge is sufficient, the average knowledge score was lower than 75%. Certain questions covering new genetic technologies and testing practices were more commonly missed than questions asking about more basic aspects of hemophilia genetics, such as inheritance and carrier testing. Finally, many clinics report having access to a counselor, but it is oftentimes a hematologist or nurse who is providing genetic counseling services to patients. Given the inconsistency in knowledge among providers coupled with the high confidence in one’s ability to counsel patients, it leaves room to question whether information about the genetics of hemophilia is being communicated to patients in the most appropriate and accurate manner.