Influence of Nitrogen Rate and Sampling Date on Soil Analysis Values of Highbush Blueberries

Three studies were conducted on nitrogen (N) fertilization effects on soil of highbush blueberries in Arkansas. Objectives included: 1) determination of varying N rate effects on the standard soil analysis variables, 2) determination of date of soil sampling effects on soil analyses, 3) evaluation of the interactions of N rate and time of sampling, and 4) determination of changes in soil content over years. This research was done in two of the more important highbush blueberry production areas in Arkansas: the Arkansas River Valley where blueberries are grown on sandy loam soils, and northwest Arkansas where production is more common on silt loam soils. This information provides greater insight into the soil dynamics of highbush blueberry plantings in Arkansas and can be used to increase precision of fertility and other soil property recommendations provided to growers

Teneurins and Teneurin C-Terminal Associated Peptide (TCAP) in Metabolism: What’s Known in Fish?

Teneurins have well established roles in function and maintenance of the central nervous systems of vertebrates. In addition, teneurin c-terminal associated peptide (TCAP), a bioactive peptide found on the c-terminal portion of teneurins, has been shown to regulate glucose metabolism. Although, the majority of research conducted on the actions of teneurins and TCAPs has strictly focused on neurological systems in rodents, TCAP was first identified in rainbow trout after screening trout hypothalamic cDNA. This suggests a conserved functional role of TCAP across vertebrates, however, the current depth of literature on teneurins and TCAPs in fish is limited. In addition, the overall function of TCAP in regulating metabolism is unclear. This review will highlight work that has been conducted specifically in fish species in relation to the teneurin system and metabolism in order to identify areas of research that are needed for future work

A comparison of sexual dimorphism and range of variation in Papio cynocephalus and Gorilla gorilla dentition

The dentitions of 48 baboons ( Papio cynocephalus ) and 242 gorillas ( Gorilla gorilla ) are compared metrically and the baboons are found to have a greater range of variation, and greater sexual dimorphism than the gorillas. This is explained in terms of the different ecologies of these species: life on the African savannah, with its sharp seasonal changes in available food, seems to have given selective advantage to broader niches than life in the rain forest. Further, the historic continuity of the savannah has provided fewer chances for allopatric speciation than the rain forest. These contrasts between forest and savannah speciation should provide insights into hominid evolution. In trying to judge whether australopithecines, probable savannah residents, can be lumped into one or several species, based upon dental variability, a comparison with baboons should be more informative than the now frequently used contrast with gorillas.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41597/1/10329_2006_Article_BF02381794.pd

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations

IL1B-CGTC haplotype is associated with colorectal cancer in admixed individuals with increased African ancestry

Single-nucleotide polymorphisms (SNPs) in cytokine genes can affect gene expression and thereby modulate inflammation and carcinogenesis. However, the data on the association between SNPs in the interleukin 1 beta gene (IL1B) and colorectal cancer (CRC) are conflicting. We found an association between a 4-SNP haplotype block of the IL1B (-3737C/-1464G/-511T/-31C) and CRC risk, and this association was exclusively observed in individuals with a higher proportion of African ancestry, such as individuals from the Coastal Colombian region (odds ratio, OR 2.06; 95% CI 1.31–3.25; p < 0.01). Moreover, a significant interaction between this CRC risk haplotype and local African ancestry dosage was identified in locus 2q14 (p = 0.03). We conclude that Colombian individuals with high African ancestry proportions at locus 2q14 harbour more IL1B-CGTC copies and are consequently at an increased risk of CRC. This haplotype has been previously found to increase the IL1B promoter activity and is the most frequent haplotype in African Americans. Despite of limitations in the number of samples and the lack of functional analysis to examine the effect of these haplotypes on CRC cell lines, our results suggest that inflammation and ethnicity play a major role in the modulation of CRC risk

Evaluating the use of ABBA-BABA statistics to locate introgressed loci

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson’s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f ̂ d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f ̂ d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f ̂ d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak’s hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ~1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding

Enhancing discovery of genetic variants for posttraumatic stress disorder through integration of quantitative phenotypes and trauma exposure information

Background Posttraumatic stress disorder (PTSD) is heritable and a potential consequence of exposure to traumatic stress. Evidence suggests that a quantitative approach to PTSD phenotype measurement and incorporation of lifetime trauma exposure (LTE) information could enhance the discovery power of PTSD genome-wide association studies (GWASs). Methods A GWAS on PTSD symptoms was performed in 51 cohorts followed by a fixed-effects meta-analysis (N = 182,199 European ancestry participants). A GWAS of LTE burden was performed in the UK Biobank cohort (N = 132,988). Genetic correlations were evaluated with linkage disequilibrium score regression. Multivariate analysis was performed using Multi-Trait Analysis of GWAS. Functional mapping and annotation of leading loci was performed with FUMA. Replication was evaluated using the Million Veteran Program GWAS of PTSD total symptoms. Results GWASs of PTSD symptoms and LTE burden identified 5 and 6 independent genome-wide significant loci, respectively. There was a 72% genetic correlation between PTSD and LTE. PTSD and LTE showed largely similar patterns of genetic correlation with other traits, albeit with some distinctions. Adjusting PTSD for LTE reduced PTSD heritability by 31%. Multivariate analysis of PTSD and LTE increased the effective sample size of the PTSD GWAS by 20% and identified 4 additional loci. Four of these 9 PTSD loci were independently replicated in the Million Veteran Program. Conclusions Through using a quantitative trait measure of PTSD, we identified novel risk loci not previously identified using prior case-control analyses. PTSD and LTE have a high genetic overlap that can be leveraged to increase discovery power through multivariate methods