Lower Methylation of the ANGPTL2 Gene in Leukocytes from Post-Acute Coronary Syndrome Patients

DNA methylation is believed to regulate gene expression during adulthood in response to the constant changes in environment. The methylome is therefore proposed to be a biomarker of health through age. ANGPTL2 is a circulating pro-inflammatory protein that increases with age and prematurely in patients with coronary artery diseases; integrating the methylation pattern of the promoter may help differentiate age- vs. disease-related change in its expression. We believe that in a pro-inflammatory environment, ANGPTL2 is differentially methylated, regulating ANGPTL2 expression. To test this hypothesis we investigated the changes in promoter methylation of ANGPTL2 gene in leukocytes from patients suffering from post-acute coronary syndrome (ACS). DNA was extracted from circulating leukocytes of post-ACS patients with cardiovascular risk factors and from healthy young and age-matched controls. Methylation sites (CpGs) found in the ANGPTL2 gene were targeted for specific DNA methylation quantification. The functionality of ANGPTL2 methylation was assessed by an in vitro luciferase assay. In post-ACS patients, C-reactive protein and ANGPTL2 circulating levels increased significantly when compared to healthy controls. Decreased methylation of specific CpGs were found in the promoter of ANGPTL2 and allowed to discriminate age vs. disease associated methylation. In vitro DNA methylation of specific CpG lead to inhibition of ANGPTL2 promoter activity. Reduced leukocyte DNA methylation in the promoter region of ANGPTL2 is associated with the pro-inflammatory environment that characterizes patients with post-ACS differently from age-matched healthy controls. Methylation of different CpGs in ANGPTL2 gene may prove to be a reliable biomarker of coronary disease.     

Energy distribution in the photochemical apparatus of Porphyridium cruentum: Picosecond fluorescence spectroscopy of cells in state 1 and state 2 at 77 K

Excitation energy distribution in Porphyridium cruentum in state 1 and state 2 was investigated by time resolved 77 K fluorescence emission spectroscopy. The fluorescence rise times of phycoerythrin, phycocyanin and allophycocyanin (in cells in state 1 and state 2) were very similar in contrast to the emission from chlorophyll a (Chl a) associated with the two photosystems. In state 2 photosystem II (PSII) Chl a fluorescence emission rose faster than the PSI Chl a emission and decayed more rapidly, and the converse was observed in state 1. These kinetic data support the concept of increased energy transfer from PSII Chl a to PSI Chl a in state 2 in P. cruentum.Abbreviations APC allophycocyanin - Chl a chlorophyll a - PSII photosystem II - PC phycocyanin - PE phycoerythrin     

A Chimeric Ty3/Moloney Murine Leukemia Virus Integrase Protein Is Active In Vivo

This report describes the results of experiments to determine whether chimeras between a retrovirus and portions of Ty3 are active in vivo. A chimera between Ty3 and a Neo^r-marked Moloney murine leukemia virus (M-MuLV) was constructed. The C-terminal domain of M-MuLV integrase (IN) was replaced with the C-terminal domain of Ty3 IN. The chimeric retroviruses were expressed from an amphotrophic envelope packaging cell line. The virus generated was used to infect the human fibrosarcoma cell line HT1080, and cells in which integration had occurred were selected by G418 resistance. Three independently integrated viruses were rescued. In each case, the C-terminal Ty3 IN sequences were maintained and short direct repeats of the genomic DNA flanked the integration site. Sequence analysis of the genomic DNA flanking the insertion did not identify a tRNA gene; therefore, these integration events did not have Ty3 position specificity. This study showed that IN sequences from the yeast retrovirus-like element Ty3 can substitute for M-MuLV IN sequences in the C-terminal domain and contribute to IN function in vivo. It is also one of the first in vivo demonstrations of activity of a retrovirus encoding an integrase chimera. Studies of chimeras between IN species with distinctive integration patterns should complement previous work by expanding our understanding of the roles of nonconserved domains.     

Disease and secondary sexual traits: effects of pneumonia on horn size of bighorn sheep

Secondary sexual traits (e.g., horns and antlers) have ecological and evolutionary importance and are of management interest for game species. Yet, how these traits respond to emerging threats like infectious disease remains underexplored. Infectious pneumonia threatens bighorn sheep (Ovis canadensis) populations across North America and we hypothesized it may also reduce horn growth in male sheep. We assess the effect of pneumonia on horn size in male bighorn sheep using 12 herd datasets from across the western United States that had horn growth and disease data. Disease resulted in 12–35% reduction in increment (yearly) length and 3–13% reduction in total horn length in exposed individuals. The disease effect was prolonged when pathogens continued to circulate in sheep populations. Further, disease likely delays the age at which horns reach ¾-curl and prevents achievement of full-curl. This is further evidenced with 6 of the 12 herds experiencing an increase in average age at harvest following die-off events.     

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo. The pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting RNA motifs with low sequence conservation. We also integrate RNA motif prediction with RNA homolog search, which improves the quality of the RNA motifs significantly. Here, we report the results of applying this pipeline to Firmicute bacteria. Our top-ranking motifs include most known Firmicute elements found in the RNA family database (Rfam). Comparing our motif models with Rfam's hand-curated motif models, we achieve high accuracy in both membership prediction and base-pair–level secondary structure prediction (at least 75% average sensitivity and specificity on both tasks). Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth.     

Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness

Within hosts, RNA viruses form populations that are genetically and phenotypically complex. Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood. Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts. We allowed West Nile virus (WNV) to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality. After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing. We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows. Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts. However, the selective pressures that control WNV populations seem to be bird species-dependent. Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7× more than sparrows, ~3.4× more than robins) and defective genomes (~1.4× greater than sparrows, ~2.7× greater than robins), but the lowest average mutation frequency (about equal to sparrows, ~2.6× lower than robins). Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection. These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations. Taken together, these results reveal important insights into how different hosts may contribute to the emergence of RNA viruses.     

A simple calibration improved the accuracy of the thermal dissipation technique for sap flow measurements in juvenile trees of six species

The thermal dissipation technique is widely used to estimate transpiration of individual trees and forest stands, but there are conflicting reports regarding its accuracy. We compared the rate of water uptake by stems of six tree species in potometers with sap flow (F _S) estimates derived from thermal dissipation sensors to evaluate the accuracy of the technique. To include the full range of xylem anatomies (i.e., diffuse-porous, ring-porous, and tracheid), we used saplings of sweetgum (Liquidambar styraciflua), eastern cottonwood (Populus deltoides), white oak (Quercus alba), American elm (Ulmus americana), shortleaf pine (Pinus echinata), and loblolly pine (Pinus taeda). In almost all instances, estimated F _S deviated substantially from actual F _S, with the discrepancy in cumulative F _S ranging from 9 to 55%. The thermal dissipation technique generally underestimated F _S. There were a number of potential causes of these errors, including species characteristics and probe construction and installation. Species with the same xylem anatomy generally did not show similar relationships between estimated and actual F _S, and the largest errors were in species with diffuse-porous (Populus deltoides, 34%) and tracheid (Pinus taeda, 55%) xylem anatomies, rather than ring-porous species Quercus alba (9%) and Ulmus americana (15%) as we had predicted. New species-specific α and β parameter values only modestly improved the accuracy of F _S estimates. However, the relationship between the estimated and actual F _S was linear in all cases and a simple calibration based on the slope of this relationship reduced the error to 1–4% in five of the species, and to 8% in Liquidambar styraciflua. Our calibration approach compensated simultaneously for variation in species characteristics and sensor construction and use. We conclude that species-specific calibrations can substantially increase the accuracy of the thermal dissipation technique.