Influence of HAART on Alternative Reading Frame Immune Responses over the Course of HIV-1 Infection

Background: Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8(+) T cells on the virus has already been observed in vitro. HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo. Methodology/Principal findings: In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance: These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.

Chemically Resolved Particle Fluxes Over Tropical and Temperate Forests

Chemically resolved submicron (PM1) particlemass fluxes were measured by eddy covariance with a high resolution time-of-flight aerosolmass spectrometer over temperate and tropical forests during the BEARPEX-07 and AMAZE-08 campaigns. Fluxes during AMAZE-08 were small and close to the detection limit (<1 ng m−2 s−1) due to low particle mass concentrations (<1 μg m−3). During BEARPEX-07, concentrations were five times larger, with mean mid-day deposition fluxes of −4.8 ng m−2 s−1 for total nonrefractory PM1 (Vex,PM1 = −1 mm s−1) and emission fluxes of +2.6 ng m−2 s−1 for organic PM1 (Vex,org = +1 mm s−1). Biosphere–atmosphere fluxes of different chemical components are affected by in-canopy chemistry, vertical gradients in gas-particle partitioning due to canopy temperature gradients, emission of primary biological aerosol particles, and wet and dry deposition. As a result of these competing processes, individual chemical components had fluxes of varying magnitude and direction during both campaigns. Oxygenated organic components representing regionally aged aerosol deposited, while components of fresh secondary organic aerosol (SOA) emitted. During BEARPEX-07, rapid incanopy oxidation caused rapid SOA growth on the timescale of biosphere-atmosphere exchange. In-canopy SOA mass yields were 0.5–4%. During AMAZE-08, the net organic aerosol flux was influenced by deposition, in-canopy SOA formation, and thermal shifts in gas-particle partitioning.Wet deposition was estimated to be an order ofmagnitude larger than dry deposition during AMAZE-08. Small shifts in organic aerosol concentrations from anthropogenic sources such as urban pollution or biomass burning alters the balance between flux terms. The semivolatile nature of the Amazonian organic aerosol suggests a feedback in which warmer temperatures will partition SOA to the gas-phase, reducing their light scattering and thus potential to cool the region.

Modern and fossil corals from Palmyra and Christmas islands

The relationship between decadal to centennial changes in ocean circulation and climate is difficult to discern using the sparse and discontinuous instrumental record of climate and, as such, represents a large uncertainty in coupled ocean-atmosphere general circulation models. We present new modern and fossil coral radiocarbon (D14C) records from Palmyra (6°N, 162°W) and Christmas (2°N, 157°W) islands to constrain central tropical Pacific ocean circulation changes during the last millennium. Seasonally to annually resolved coral D14C measurements from the 10th, 12th-17th, and 20th centuries do not contain significant interannual to decadal-scale variations, despite large changes in coral d18O on these timescales. A centennial-scale increase in coral radiocarbon from the Medieval Climate Anomaly (~900-1200 AD) to the Little Ice Age (~1500-1800) can be largely explained by changes in the atmospheric D14C, as determined with a box model of Palmyra mixed layer D14C. However, large 12th century depletions in Palmyra coral D14C may reflect as much as a 100% increase in upwelling rates and/or a significant decrease in the D14C of higher-latitude source waters reaching the equatorial Pacific during this time. SEM photos reveal evidence for minor dissolution and addition of secondary aragonite in the fossil corals, but our results suggest that coral D14C is only compromised after moderate to severe diagenesis for these relatively young fossil corals.

Stable isotope record of benthic and planktonic foraminifera in sediment cores of ODP Leg 177, Southern Ocean

While onboard ship during Leg 177, we used variations in sediment physical properties (mainly percent color reflectance) in conjunction with biomagnetostratigraphy to correlate among sites and predict the position of marine isotope stages (MISs) (e.g., see fig. F11 in Shipboard Scientific Party, 1999, p. 45). Our working assumption was that physical properties of Leg 177 sediments are controlled mainly by variations in carbonate content. Previous studies of Southern Ocean sediment cores have shown that carbonate concentrations are relatively high during interglacial stages and low during glacial stages at sites located within the Polar Frontal Zone (PFZ). Today, the PFZ marks a lithologic boundary in underlying sediment separating calcareous oozes to the north and silica-rich facies to the south (Hays et al., 1976). Although there is debate whether the position of the "physical" PFZ actually moved during glacial-interglacial cycles (Charles and Fairbanks, 1990; Matsumoto et al., 2001), the "biochemical" PFZ, as expressed by the CaCO3/opal boundary in sediments, certainly migrated north during glacials and south during interglacials. This gave rise to lithologic variations that are useful for stratigraphic correlation. At Leg 177 sites located north of the PFZ and at sublysoclinal depths, we expected the same pattern of carbonate variation because cores in the Atlantic basin are marked by increased carbonate dissolution during glacial periods and increased preservation during interglacials (Crowley, 1985).