High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

Rapid Implementation of an Integrated Large-Scale HIV Counseling and Testing,Malaria, and Diarrhea Prevention Campaign in Rural Kenya

Background

Integrated disease prevention in low resource settings can increase coverage, equity and efficiency in controlling high burden infectious diseases. A public-private partnership with the Ministry of Health, CDC, Vestergaard Frandsen and CHF International implemented a one-week integrated multi-disease prevention campaign.

Method

Residents of Lurambi, Western Kenya were eligible for participation. The aim was to offer services to at least 80% of those aged 15–49. 31 temporary sites in strategically dispersed locations offered: HIV counseling and testing, 60 male condoms, an insecticide-treated bednet, a household water filter for women or an individual filter for men, and for those testing positive, a 3-month supply of cotrimoxazole and referral for follow-up care and treatment.

Findings

Over 7 days, 47,311 people attended the campaign with a 96% uptake of the multi-disease preventive package. Of these, 99.7% were tested for HIV (87% in the target 15–49 age group); 80% had previously never tested. 4% of those tested were positive, 61% were women (5% of women and 3% of men), 6% had median CD4 counts of 541 cell/µL (IQR; 356, 754). 386 certified counselors attended to an average 17 participants per day, consistent with recommended national figures for mass campaigns. Among women, HIV infection varied by age, and was more likely with an ended marriage (e.g. widowed vs. never married, OR.3.91; 95% CI. 2.87–5.34), and lack of occupation. In men, quantitatively stronger relationships were found (e.g. widowed vs. never married, OR.7.0; 95% CI. 3.5–13.9). Always using condoms with a non-steady partner was more common among HIV-infected women participants who knew their status compared to those who did not (OR.5.4 95% CI. 2.3–12.8).

Conclusion

Through integrated campaigns it is feasible to efficiently cover large proportions of eligible adults in rural underserved communities with multiple disease preventive services simultaneously achieving various national and international health development goals.     

Cancer Associated Aberrant Protein O-Glycosylation Can Modify Antigen Processing and Immune Response

Aberrant glycosylation of mucins and other extracellular proteins is an important event in carcinogenesis and the resulting cancer associated glycans have been suggested as targets in cancer immunotherapy. We assessed the role of O-linked GalNAc glycosylation on antigen uptake, processing, and presentation on MHC class I and II molecules. The effect of GalNAc O-glycosylation was monitored with a model system based on ovalbumin (OVA)-MUC1 fusion peptides (+/− glycosylation) loaded onto dendritic cells co-cultured with IL-2 secreting OVA peptide-specific T cell hybridomas. To evaluate the in vivo response to a cancer related tumor antigen, Balb/c or B6.Cg(CB)-Tg(HLA-A/H2-D)2Enge/J (HLA-A2 transgenic) mice were immunized with a non-glycosylated or GalNAc-glycosylated MUC1 derived peptide followed by comparison of T cell proliferation, IFN-γ release, and antibody induction. GalNAc-glycosylation promoted presentation of OVA-MUC1 fusion peptides by MHC class II molecules and the MUC1 antigen elicited specific Ab production and T cell proliferation in both Balb/c and HLA-A2 transgenic mice. In contrast, GalNAc-glycosylation inhibited the presentation of OVA-MUC1 fusion peptides by MHC class I and abolished MUC1 specific CD8+ T cell responses in HLA-A2 transgenic mice. GalNAc glycosylation of MUC1 antigen therefore facilitates uptake, MHC class II presentation, and antibody response but might block the antigen presentation to CD8+ T cells.     

Enhanced in vitro growth of murine fibroblast cells and preimplantation embryos cultured in medium supplemented with an amphipathic peptide.

Preliminary studies on the proliferative effects of lytic peptides were carried out using NIH 3T3 murine fibroblast cells and human lymphocytes. Cells were cultured in various concentrations of three different amphipathic peptides (SB-37, Shiva-1, and Vishnu), and enhanced proliferation was determined by uptake of 3H-thymidine with treated cells compared with control cultures. Enhanced proliferation of 3T3 cells was observed in cultures containing 50 microM or less SB-37. The primary study consisted of 263 four-cell- to eight-cell-stage mouse embryos from naturally bred mice and incubated in Whitten's medium containing 0.2, 1, or 10 microM of the amino terminus of an amphipathic cecropin B analog (Vishnu) or in Whitten's medium alone. Embryos were cultured to the hatched blastocyst stage, and effect of treatment was determined by the rate of growth to that stage of development. Statistical analysis revealed that culture in all three levels of Vishnu significantly accelerated in vitro growth of these stages of preimplantation embryos compared with controls. These results indicate that Vishnu promotes increased cleavage rates of embryos in vitro. A growth factor receptor clustering mechanism of action is proposed. This peptide may have some potential as an embryo culture medium additive to enhance in vitro growth rate.     

Two optical coherence tomography systems detect topical gold nanoshells in hair follicles,sweat ducts and measure epidermis

Optical coherence tomography (OCT) is an established imaging technology for in vivo skin investigation. Topical application of gold nanoshells (GNS) provides contrast enhancement in OCT by generating a strong hyperreflective signal from hair follicles and sweat glands, which are the natural skin openings. This study explores the utility of 150 nm diameter GNS as contrast agent for OCT imaging. GNS was massaged into skin and examined in four skin areas of 11 healthy volunteers. A commercial OCT system and a prototype with 3 μm resolution (UHR‐OCT) were employed to detect potential benefits of increased resolution and variability in intensity generated by the GNS. In both OCT‐systems GNS enhanced contrast from hair follicles and sweat ducts. Highest average penetration depth of GNS was in armpit 0.64 mm ± SD 0.17, maximum penetration depth was 1.20 mm in hair follicles and 15 to 40 μm in sweat ducts. Pixel intensity generated from GNS in hair follicles was significantly higher in UHR‐OCT images (P = .002) and epidermal thickness significantly lower 0.14 vs 0.16 mm (P = .027). This study suggests that GNSs are interesting candidates for increasing sensitivity in OCT diagnosis of hair and sweat gland disorders and demonstrates that choice of OCT systems influences results.      

Profound afternoon depression of ecosystem production and nighttime decline of respiration in a macrophyte-rich,shallow lake

Small, shallow lakes with dense growth of submerged macrophytes are extremely abundant worldwide, but have remained grossly understudied although open water oxygen measurements should be suitable to determine diel fluctuations and test drivers of ecosystem metabolism during the day. We measured the temporal and spatial variability of environmental conditions as well as net ecosystem production (NEP) and respiration (R) in a small, shallow Swedish lake with dense charophyte stands by collecting data from oxygen-, pH-, temperature- and light-sensors across horizontal and vertical gradients during different periods between April and June in 3 years. We found reproducible diel oxygen patterns and daily metabolic rates. The charophyte canopy accounted for almost all primary production and respiration of the ecosystem. Two novel discoveries—profound afternoon depression of production and nighttime decline of respiration—occurred on virtually every day. Extensive increase of oxygen-, temperature- and pH-levels and depletion of dissolved inorganic carbon (DIC) and CO₂ concentrations could account for maximum NEP-rates before noon and afternoon depression with low NEP-rates. Ecosystem respiration declined during the night to 24–70% of rates at sunset, probably because of depletion of respiratory substrates. Afternoon depression of photosynthesis should be widespread in numerous habitats with dense growth of macrophytes, periphyton, or phytoplankton implying that daily photosynthesis and growth are restricted and species with efficient DIC use may have an advantage.     

Cross-resistance to antibiotics of Escherichia coli adapted to benzalkonium chloride or exposed to stress-inducers

AIMS: To study the effects of adaptation and stress on the resistance to benzalkonium chloride (BC) and cross-resistance to antibiotics in Escherichia coli. METHODS AND RESULTS: Precultivation of E. coli ATCC 11775 and E. coli DSM 682 in the presence of subinhibitory concentrations of BC or stress inducers (salicylate, chenodeoxycholate and methyl viologen) resulted in higher minimum inhibitory concentration (MIC) of BC and chloramphenicol (CHL). Adaptation to growth in sixfold of the initial MIC of BC resulted in stable BC resistance and enhanced tolerance to several antibiotics and ethidium bromide (EtBr). The MIC of CHL increased more than 10-fold for both strains. Enhanced efflux of EtBr in adapted E. coli ATCC 11775 indicated that the observed resistance was due to efflux. Changes in outer membrane protein profiles were detected in the BC-adapted cells. There were no indications of lower membrane permeability to BC. CONCLUSIONS: Induction of stress response or gradual adaptation to BC or CHL results in acquired cross-tolerance between BC and antibiotics in E. coli. Enhanced efflux was one of the observed differences in adapted cells. SIGNIFICANCE AND IMPACT OF THE STUDY: Provided not taking due precautions, extensive use of disinfectants could lead to emergence of antibiotic-resistant isolates.     

Coastal ecosystems on a tipping point: Global warming and parasitism combine to alter community structure and function

Mounting evidence suggests that the transmission of certain parasites is facilitated by increasing temperatures, causing their host population to decline. However, no study has yet addressed how temperature and parasitism may combine to shape the functional structure of a whole host community in the face of global warming. Here, we apply an outdoor mesocosm approach supported by field surveys to elucidate this question in a diverse intertidal community of amphipods infected by the pathogenic microphallid trematode, Maritrema novaezealandensis. Under present temperature (17°C) and level of parasitism, the parasite had little impact on the host community. However, elevating the temperature to 21°C in the presence of parasites induced massive structural changes: amphipod abundances decreased species‐specifically, affecting epibenthic species but leaving infaunal species largely untouched. In effect, species diversity dropped significantly. In contrast, four degree higher temperatures in the absence of parasitism had limited influence on the amphipod community. Further elevating temperatures (19–25°C) and parasitism, simulating a prolonged heat‐wave scenario, resulted in an almost complete parasite‐induced extermination of the amphipod community at 25°C. In addition, at 19°C, just two degrees above the present average, a similar temperature–parasite synergistic impact on community structure emerged as seen at 21°C under lower parasite pressure. The heat‐wave temperature of 25°C per se affected the amphipod community in a comparable way: species diversity declined and the infaunal species were favoured at the expense of epibenthic species. Our experimental findings are corroborated by field data demonstrating a strong negative relationship between current amphipod species richness and the level of Maritrema parasitism across 12 sites. Hence, owing to the synergistic impact of temperature and parasitism, our study predicts that coastal amphipod communities will deteriorate in terms of abundance and diversity in face of anticipated global warming, functionally changing them to be dominated by infaunal species.     

Land‐atmosphere exchange of methane from soil thawing to soil freezing in a high‐Arctic wet tundra ecosystem

The land‐atmosphere exchange of methane (CH₄) and carbon dioxide (CO₂) in a high‐Arctic wet tundra ecosystem (Rylekærene) in Zackenberg, north‐eastern Greenland, was studied over the full growing season and until early winter in 2008 and from before snow melt until early winter in 2009. The eddy covariance technique was used to estimate CO₂ fluxes and a combination of the gradient and eddy covariance methods was used to estimate CH₄ fluxes. Small CH₄ bursts were observed during spring thawing 2009, but these existed during short periods and would not have any significant effect on the annual budget. Growing season CH₄ fluxes were well correlated with soil temperature, gross primary production, and active layer thickness. The CH₄ fluxes remained low during the entire autumn, and until early winter. No increase in CH₄ fluxes were seen as the soil started to freeze. However, in autumn 2008 there were two CH₄ burst events that were highly correlated with atmospheric turbulence. They were likely associated with the release of stored CH₄ from soil and vegetation cavities. Over the measurement period, 7.6 and 6.5 g C m^?2 was emitted as CH₄ in 2008 and in 2009, respectively. Rylekærene acted as a C source during the warmer and wetter measurement period 2008, whereas it was a C sink for the colder and drier period of 2009. Wet tundra ecosystems, such as Rylekærene may thus play a more significant role for the climate in the future, as temperature and precipitation are predicted to increase in the high‐Arctic.