A Simple PCR–RFLP Method for Genetic Phase Determination in Compound Heterozygotes

When susceptibility to diseases is caused by cis-effects of multiple alleles at adjacent polymorphic sites, it may be difficult to assess with confidence the genetic phase and identify individuals carrying the risk haplotype. Experimental assessment of genetic phase is still challenging and most population studies use statistical approaches to infer haplotypes given the observed genotypes. While these statistical approaches are powerful and have been proven very useful in large scale genetic population studies, they may be prone to errors in studies with small sample size, especially in the presence of compound heterozygotes. Here, we describe a simple and novel approach using the popular PCR–RFLP based strategy to assess the genetic phase in compound heterozygotes. We apply this method to two extensively studied SNPs in two clustered immune-related genes: The −308 (G > A) and the +252 (A > G) SNPs of the tumor necrosis factor (TNF) alpha and the lymphotoxin alpha (LTA) genes, respectively. Using this method, we successfully determined the genetic phase of these two SNPs in known compound heterozygous individuals and in every sample tested. We show that the A allele of TNF −308 is carried on the same chromosome as the LTA +252(G) allele

EFFECTS OF JOINT PRODUCT MANAGEMENT STRATEGIES ON E.COLI 0157:H7 AND FEEDLOT PROFITS

The objective of this study was to determine the effect of Escherichia coli 0157:H7 on feedlot profits. Fecal samples from 711 feedlot pens in 73 feedlots in Nebraska, Kansas, Oklahoma, and Texas were tested for E. coli 0157:H7. Average daily gain and feed-to-gain ratios were computed for each feedlot pen, and managers from each feedlot provided information on various feedlot management practices. Cattle performance and E. coli 0157:H7 prevalence are both affected by feedlot management practices. The indirect effect of E. coli 0157:H7 on potential feedlot profits was determined by measuring the effects of management practices on E. coli 0157:H7 levels and cattle performance. Management practices that affect cattle performance were identified using ordinary least squares regressions. A negative binomial regression was used to identify management practices that affect E. coli 0157:H7 prevalence. Certain feedlot management practices were identified that have a joint impact on cattle performance and E. coli 0157:H7 prevalence. Using predatory insects to control flies, controlling for stray dogs, foxes, and coyotes in feed areas, removing manure from pens during finishing, and including tallow in the ration were management strategies associated with higher feedlot profits and lower E. coli 0157:H7 prevalence. Using mobile sprinklers for dust control and including alfalfa or sorghum hay or silage in the ration were associated with lower E. coli 0157:H7 prevalence and lower feedlot profits. Increasing days between cleaning water tanks and restricting movement of horses were associated with higher feedlot profits and higher E. coli 0157:H7 levels. Controlling for stray cats in feed areas and including liquid protein in the ration were associated with lower feedlot profits and higher E. coli 0157:H7 levels. These specific management strategies, which were not robust through a sensitivity analysis, should be interpreted with caution. The general categories of management strategies, however, were robust and consistent with past researchLivestock Production/Industries,

Treatment algorithm for infants diagnosed with spinal muscular atrophy through newborn screening

Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by the degeneration of alpha motor neurons in the spinal cord, leading to muscular atrophy. SMA is caused by deletions or mutations in the survival motor neuron 1 gene (SMN1). In humans, a nearly identical copy gene, SMN2, is present. Because SMN2 has been shown to decrease disease severity in a dose-dependent manner, SMN2 copy number is predictive of disease severity. To develop a treatment algorithm for SMA-positive infants identified through newborn screening based upon SMN2 copy number. A working group comprised of 15 SMA experts participated in a modified Delphi process, moderated by a neutral third-party expert, to develop treatment guidelines. The overarching recommendation is that all infants with two or three copies of SMN2 should receive immediate treatment (n = 13). For those infants in which immediate treatment is not recommended, guidelines were developed that outline the timing and appropriate screens and tests to be used to determine the timing of treatment initiation. The identification SMA affected infants via newborn screening presents an unprecedented opportunity for achievement of maximal therapeutic benefit through the administration of treatment pre-symptomatically. The recommendations provided here are intended to help formulate treatment guidelines for infants who test positive during the newborn screening process

Optical map of the genotype A1 WB C6 Giardia lamblia genome isolate

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Molecular and Biochemical Parasitology 180 (2011): 112-114, doi:10.1016/j.molbiopara.2011.07.008.The Giardia lamblia genome consists of 12 Mb divided among 5 chromosomes ranging in size from approximately 1 to 4 Mb. The assembled contigs of the genotype A1 isolate, WB, were previously mapped along the 5 chromosomes on the basis of hybridization of plasmid clones representing the contigs to chromosomes separated by PFGE. In the current report, we have generated an MluI optical map of the WB genome to improve the accuracy of the physical map. This has allowed us to correct several assembly errors and to better define the extent of the subtelomeric regions that are not included in the genome assembly.This work was funded in part by the Woods Hole Center for Oceans and Human Health, jointly funded by the National Science Foundation (OCE-0430724) and the National Institute for Environmental Health Sciences (P50 ES012742)

Domestic Content Restrictions: The Buy American Act and Complementary Provisions of Federal Law

This report provides an overview of the Buy American Act, Trade Agreements Act, Berry Amendment (including its former specialty metals provision), and Buy America Act, specifically highlighting the commonalities and differences among them. The report also lists other federal domestic content restrictions codified in the U.S. Code

screening for transthyretin amyloid cardiomyopathy in everyday practice

Abstract Transthyretin amyloid cardiomyopathy (ATTR-CM) is a life-threatening, progressive, infiltrative disease caused by the deposition of transthyretin amyloid fibrils in the heart, and can often be overlooked as a common cause of heart failure. Delayed diagnosis due to lack of disease awareness and misdiagnosis results in a poorer prognosis. Early accurate diagnosis is therefore key to improving patient outcomes, particularly in the context of both the recent approval of tafamidis in some countries (including the United States) for the treatment of ATTR-CM, and of other promising therapies under development. With the availability of scintigraphy as an inexpensive, noninvasive diagnostic tool, the rationale to screen for ATTR-CM in high-risk populations of patients is increasingly warranted. Here the authors propose a framework of clinical scenarios in which screening for ATTR-CM is recommended, as well as diagnostic "red flags" that can assist in its diagnosis among the wider population of patients with heart failure

Lipid changes due to fenofibrate treatment are not associated with changes in DNA methylation patterns in the GOLDN study

Fenofibrate lowers triglycerides (TG) and raises high density lipoprotein cholesterol (HDLc) in dyslipidemic individuals. Several studies have shown genetic variability in lipid responses to fenofibrate treatment. It is, however, not known whether epigenetic patterns are also correlated with the changes in lipids due to fenofibrate treatment. The present study was therefore undertaken to examine the changes in DNA methylation among the participants of Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study. A total of 443 individuals were studied for epigenome-wide changes in DNA methylation, assessed using the Illumina Infinium HumanMethylation450 array, before and after a 3-week daily treatment with 160 mg of fenofibrate. The association between the change in DNA methylation and changes in TG, HDLc, and low-density lipoprotein cholesterol (LDLc) were assessed using linear mixed models adjusted for age, sex, baseline lipids, and study center as fixed effects and family as a random effect. Changes in DNA methylation were not significantly associated with changes in TG, HDLc, or LDLc after 3 weeks of fenofibrate for any CpG. CpG changes in genes known to be involved in fenofibrate response, e.g., PPAR-α, APOA1, LPL, APOA5, APOC3, CETP, and APOB, also did not show evidence of association. In conclusion, changes in lipids in response to 3-week treatment with fenofibrate were not associated with changes in DNA methylation. Studies of longer duration may be required to detect treatment-induced changes in methylation

Geopolitics at the margins? Reconsidering genealogies of critical geopolitics

Critical geopolitics has become one of the most vibrant parts of political geography. However it remains a particularly western way of knowing which has been much less attentive to other traditions of thinking. This paper engages with Pan-Africanism, and specifically the vision of the architect of post-colonial Tanzania, Julius Nyerere, to explore this overlooked contribution to critical engagements with geopoli- tics. Pan-Africanism sought to forge alternative post-colonial worlds to the binary geopolitics of the Cold War and the geopolitical economy of neo-colonialism. The academic division of labour has meant that these ideas have been consigned to African studies rather than being drawn into wider debates around the definitions of key disciplinary concepts. However Nyerere’s continental thinking can be seen as a form of geopolitical imagination that challenges dominant neo-realist projections, and which still has much to offer contemporary political geography

Genome- and CD4\u3csup\u3e+\u3c/sup\u3e T-Cell Methylome-Wide Association Study of Circulating Trimethylamine-N-Oxide in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN)

Background: Trimethylamine-N-oxide (TMAO), an atherogenic metabolite species, has emerged as a possible new risk factor for cardiovascular disease. Animal studies have shown that circulating TMAO levels are regulated by genetic and environmental factors. However, large-scale human studies have failed to replicate the observed genetic associations, and epigenetic factors such as DNA methylation have never been examined in relation to TMAO levels. Methods and results: We used data from the family-based Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) to investigate the heritable determinants of plasma TMAO in humans. TMAO was not associated with other plasma markers of cardiovascular disease, e.g. lipids or inflammatory cytokines. We first estimated TMAO heritability at 27%, indicating a moderate genetic influence. We used 1000 Genomes imputed data (n = 626) to estimate genome-wide associations with TMAO levels, adjusting for age, sex, family relationships, and study site. The genome-wide study yielded one significant hit at the genome-wide level, located in an intergenic region on chromosome 4. We subsequently quantified epigenome-wide DNA methylation using the Illumina Infinium array on CD4þ Tcells. We tested for association of methylation loci with circulating TMAO (n = 847), adjusting for age, sex, family relationships, and study site as the genome-wide study plus principal components capturing CD4þ T-cell purity. Upon adjusting for multiple testing, none of the epigenetic findings were statistically significant. Conclusions: Our findings contribute to the growing body of evidence suggesting that neither genetic nor epigenetic factors play a critical role in establishing circulating TMAO levels in humans