Polymorphisms in the pituitary growth hormone gene and its receptor associated with coronary artery disease in a predisposed cohort from India

We investigated the promoter polymorphisms of the pituitary growth hormone gene (GH1) and exon 3 deletion polymorphism (GHRd3) in its receptor gene (GHR) in 299 angiographically proven patients with coronary artery disease (CAD) and 231 asymptomatic controls enrolled in the ongoing Indian Atherosclerosis Research Study. Real time PCR based analysis of the GHR variant showed significant association of the GHRd3 deletion allele with CAD (OR 0.48, 95% CI: 0.30–0.76, P = 0.0014) and a dominant model of inheritance (Akaike information criterion = 482). The deletion allele showed significant association with high plasma HDL-c levels (P = 0.001). Sequencing of the proximal promoter region of GH1 revealed 12 novel polymorphisms and a TAGA haplotype constituted by the functional SNPs rs2005171, rs11568828, rs2005172 and rs6171, that showed significant association with CAD alone (adjusted OR of 3.31 (95% CI = 1.33–8.29, P = 0.011) and in CAD patients with diabetes (P = 0.019). Mean standardized height was associated with three of the four haplotype-tagging SNPs in the cohort (P ≤ 0.03). Eleven of the 12 polymorphic promoter SNPs contributed to 14.7% of variation in height in females in the whole dataset (P = 0.029). CAD patients with history of stroke exhibited marginally significantly lower mean height as compared to rest of the cohort (P < 0.006). In conclusion, genetic polymorphisms in the GHR gene and its ligand, GH1, may modulate the risk of CAD in the Asian Indian population.     

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms. The process can be equally applied to individual sequence reads from traditional Sanger capillary electrophoresis sequences, newer technologies such as 454 pyrosequencing, or sequence assemblies derived from one or more of these data types. It includes the analysis of both coding and non-coding genes, whether full-length or, as is often the case for shotgun metagenomics, fragmentary. The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation value hierarchy established through extensive manual curation. The functional annotation attributes assigned by this system include gene name, gene symbol, GO terms, EC numbers, and JCVI functional role categories.     

Influence of calcium, potassium, and magnesium on Cornus florida L. density and resistance to dogwood anthracnose

Dogwood anthracnose, a major disease of Cornus florida L., has caused heavy mortality of C. florida in eastern United States forests. Disease severity and rate of infection have been shown to vary with several environmental factors, but the link between soil cation availability and anthracnose has not been examined. We hypothesized that soil cation availability, particularly calcium (Ca), potassium (K), and magnesium (Mg), would influence dogwood survival from anthracnose. In forested stands, positive correlations between soil Ca, K, and Mg saturation and C. florida stem density and basal area were found. The effect of these cations at four levels (0, 50, 100, and 200%) of a standard nursery fertilization rate on C. florida seedling survival and resistance to dogwood anthracnose was tested. Although most of the seedlings died after one season of exposure to dogwood anthracnose, seedlings that had lower inputs of Ca and K cations showed higher levels of disease severity sooner than seedlings in other treatments, suggesting that these nutrients play a role in C. florida survival from anthracnose. Magnesium treatment levels did not appear to have an effect on C. florida disease severity or mortality.     

Allelopathy in black walnut (Juglans nigraL.) alley cropping. II. Effects of juglone on hydroponically grown corn (Zea maysL.) and soybean (Glycine maxL. Merr.) growth and physiology

We conducted an experiment to investigate the effects of juglone (5-hydroxy-1, 4-napthoquinone) on the growth and physiology of hydroponically grown corn (Zea mays L.) and soybean (Glycine max L. Merr.) seedlings. Three different concentrations of juglone (10^-6 M, 10^-5 M, and 10^-4 M) along with a control were applied. Within 3 days, juglone exhibited significant inhibitory effects on all measured variables including shoot and root relative growth rates (RGR_s and RGR_r), leaf photosynthesis (P_net), transpiration (E), stomatal conductance (g_s), and leaf and root respiration. In general, soybean was found to be more sensitive to juglone than corn. RGR_r was the most inhibited variable for both species, and reductions of 86.5 and 99% were observed in corn and soybean, respectively, with 10_-4 M juglone concentrations. Among the physiological variables measured, P_net showed the greatest impact of toxicity though the other physiological parameters were also impacted. We conclude that both corn and soybean are sensitive to juglone and observed growth reductions in corn and soybean in black walnut alley cropping may partly be due to juglone phytotoxicity. Determination of actual phytotoxicity will require quantification of soil solution juglone levels, particularly in areas where soil solid-phase levels are high in close proximity to trees.     

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea

Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.     

High-elevation ground-layer plant community composition across environmental gradients in spruce-fir forests

We examined the influence of vegetation structure and soil chemistry on post-adelgid, ground-layer plant communities in high-elevation forests of the southern Appalachian Mountains. Specifically, we hypothesized that post-disturbance community composition and diversity would vary along a gradient of soil acidity and other soil characteristics influenced by acid deposition. Ground-layer vegetation and soils were sampled on 60 randomly located nested vegetation plots in the spruce-fir (Picea abies) zone of Great Smoky Mountains National Park, TN and NC, USA. To capture a range of deposition levels, plot placement was stratified based on modeled acid deposition classes. Ordination and multiple regression results showed that ground-layer composition and diversity were negatively associated with acidity of the A horizon and the presence of ericaceous shrubs (i.e., Rhododendron spp.). A strong correspondence between soil acidity and ericaceous shrub cover was also observed, suggesting that soil acidity may be, in conjunction with overstory disturbance resulting from chronic acid deposition and adelgid induced mortality, an important driver of ericaceous shrub thicket expansion. Slow-decaying, acidic ericaceous litter may also induce a positive feedback resulting in enhanced acidification.     

Exposure to 16O-particle radiation causes aging-like decrements in rats through increased oxidative stress, inflammation and loss of autophagy

Exposing young rats to particles of high energy and charge (HZE particles), a ground-based model for exposure to cosmic rays, enhances indices of oxidative stress and inflammation, disrupts the functioning of neuronal communication, and alters cognitive behaviors. Even though exposure to HZE particles occurs at low fluence rates, the cumulative effects of long-term exposure result in molecular changes similar to those seen in aged animals. In the present study, we assessed markers of autophagy, a dynamic process for intracellular degradation and recycling of toxic proteins and organelles, as well as stress and inflammatory responses, in the brains of Sprague-Dawley rats irradiated at 2 months of age with 5 and 50 cGy and 1 Gy of ionizing oxygen particles ((16)O) (1000 MeV/n). Compared to nonirradiated controls, exposure to (16)O particles significantly inhibited autophagy function in the hippocampus as measured by accumulation of ubiquitin inclusion bodies such as P62/SQSTM1, autophagosome marker microtubule-associated protein 1 beta light chain 3 (MAP1B-LC3), beclin1 and proteins such as mammalian target of rapamycin (mTOR). The molecular changes measured at short (36 h) and long (75 days) intervals after (16)O-particle exposure indicate that the loss of autophagy function occurred shortly after exposure but was recovered via inhibition of mTOR. However, HZE-particle radiation caused significant sustained loss of protein kinase C alpha (PKC-α), a key G protein modulator involved in neuronal survival and functions of neuronal trophic factors. Exposure to (16)O particles also caused substantial increases in the levels of nuclear factor kappa B (NF-κB) and glial fibrillary acidic protein (GFAP), indicating glial cell activation 75 days after exposure. This is the first report to show the molecular effects of (16)O-particle radiation on oxidative stress, inflammation and loss of autophagy in the brain of young rats.     

Inhibition of colon cancer cell growth and antioxidant activity of bioactive compounds from Poncirus trifoliata (L.) Raf

Recently several plant derived natural compounds have been screened for their anticancer activity in order to identify putative compounds with novel structures or mechanism of action. In the present study, fruits of Poncirus trifoliata were extracted with acetone and loaded onto silica gel column chromatography. The column was eluted with different solvents to obtain two bioactive compounds. The purity of compounds was analyzed by HPLC and their structures were identified by 1H and 13C NMR experiments as beta-sitosterol and 2-hydroxy-1,2,3-propanetricarboxylic acid 2-methyl ester (HPCME). beta-Sitosterol, HPCME, and trolox were tested for their antioxidant capacity by oxygen radical absorbance capacity (ORAC) measurement. Further, these compounds were tested for their inhibition of cancer cell proliferation and apoptosis using human colon cancer cell line (HT-29). These results were compared with the corresponding activity on non-cancerous (COS-1 fibroblast) cells. Cell proliferation and induction of apoptosis were determined by MTT assay and nuclear staining. The MTT assay indicated that both the compounds exhibited differential inhibition at various concentrations. Significant arrest of cell growth was observed with beta-sitosterol even at low concentration such as 0.63 microM in 48 h and none of the compounds exerted any apparent cytostatic effects on the non-cancerous COS-1 fibroblast cells. Growth inhibition assay suggested the potential use of bioactive compounds as cancer chemopreventive and therapeutic agents. This is the first report on HPCME isolation and identification from Rutaceae family and beta-sitosterol from P. trifoliata.     

Analyses of the microbial diversity across the human microbiome

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max), and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ"), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.