Novel, cross-restricted, conserved, and immunodominant Cytotoxic T Lymphocyte epitopes in slow progressors in HIV Type 1 infection

HIV-specific cytotoxic T lymphocytes (CTLs) play an important role in the immune response to HIV infection. Long-term nonprogressors (LTNPs) or slow progressors (SPs) in HIV infection may make qualitatively different CTL responses compared to those generated by seropositive individuals who progress to disease at a faster rate. The class I molecule HLA-B*57 has been identified as one restriction element overrepresented in SP groups studied, and, together with the closely related molecule HLA-B*58, occurs commonly in ethnic groups where HTV is most prevalent. In this study, we have identified five new HLA-B*57-restricted CTL epitopes recognized by SP donors, one of which is also HLA-B*5801 restricted. These HLA-B*57-restricted responses represent the dominant HIV-specific CTL response in each of the SP donors tested. These and other such epitopes may be an important component in future vaccine design

The UK register of HIV seroconverters: Methods and analytical issues

A Register of HIV-infected persons who have had a negative antibody test within 3 years of their first antibody positive test (seroconverters) is being set up in the UK to monitor the distribution of times from HIV seroconversion to AIDS (the incubation period) and to death. It will also provide a national resource for use by those designing studies in this group of individuals. Clinicians caring for HIV-positive persons in Genito-Urinary Medicine, Infectious Disease and other departments throughout the UK were asked to participate by providing information on eligible subjects. Most laboratories undertaking HIV antibody testing were also contacted and asked to provide the name of the attending clinician for all seroconverters identified through the HIV laboratory reporting systems of the PHLS Communicable Disease Surveillance Centre (CDSC) and the Scottish Centre for Infection and Environmental Health (SCIEH) and for any other seroconverters known to them but not identified by CDSC or SCIEH. Data items sought for the Register include: sex, ethnic group, probable route of HIV transmission, annual CD4 counts, details of therapy and prophylaxis prescribed, AIDS-defining events and vital status. Follow up information is collected annually. Wherever possible, all seroconverters known to a clinic have been identified, whether currently alive or dead, either from clinic records or laboratory reporting or both. The objective is to establish and update a complete register of seroconverters on a long-term basis to provide reliable estimates of the incubation period on which future projections of AIDS cases in the UK can be made

Agricultural Turns, Geographical Turns: Retrospect and Prospect.

It is accepted that British rural geography has actively engaged with the ‘cultural turn’, leading to a resurgence of research within the sub-discipline. However, a reading of recent reviews suggests that the cultural turn has largely, if not completely, bypassed those geographers interested in the agricultural sector. Farming centred engagements with notions of culture have been relatively limited compared with those concerned with the non-agricultural aspects of rural space. Indeed, agricultural geography represents something of an awkward case in the context of the disciplinary turn to culture, a situation that demands further exposition. In seeking explanation, it becomes evident that research on the farm sector is more culturally informed than initially appears. This paper argues that there have been both interesting and important engagements between agricultural geography and cultural perspectives over the past decade. The paper elaborates four specific areas of research which provide evidence for concern about the ‘culture’ within agriculture. The future contribution that culturally informed perspectives in geographical research can bring to agricultural issues is outlined by way of conclusion

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action.With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs

Historical ecology, human niche construction and landscape in pre-Columbian Amazonia: a case study of the geoglyph builders of Acre, Brazil

This paper applies concepts from the fields of historical ecology and human niche construction theory to interpret archaeological and palaeoecological data from the Brazilian state of Acre, southwest Amazonia, where modern deforestation has revealed hundreds of pre-Columbian monumental earthworks called 'geoglyphs', largely built between ca. 2000–650 cal. BP (calibrated years before present). Our main objective was to move away from the debate which currently dominates Amazonian archaeology over large- vs. small-scale pre-Columbian environmental impacts, and instead offer a more nuanced interpretation of human-environment interactions in our specific study area. Despite the difficulties presented by working with an incomplete regional archaeological dataset, interpreting our findings in light of these theoretical frameworks allowed us to re-think landscape history and ask new questions about a possible relationship between anthropogenic forests, symbolic capital and monument building in our particular study area

Amazon Basin forest pyrogenic carbon stocks: First estimate of deep storage

Amazon Basin forest soils contain considerable soil organic carbon stocks; however, the contribution of soil pyrogenic carbon (PyC) to the total is unknown. PyC is derived from local fires (historical and modern) and external inputs via aeolian deposition. To establish an initial estimate of PyC stocks in non-terra preta forest with no known history of fire, to assess site and vertical variability, as well as to determine optimal sampling design, we sampled 37 one hectare forest plots in the Amazon Basin and analysed PyC via hydrogen pyrolysis of three individual samples per plot and of bulked samples to 200 cm depth. Using our data and published total organic carbon stocks, we present the first field-based estimate of total PyC stock for the Amazon Basin of 1.10 Pg over 0–30 cm soil depth, and 2.76 Pg over 0–100 cm soil depth. This is up to 20 times higher than previously assumed. Three individual samples per 1 ha are sufficient to capture the site variability of PyC in our plots. PyC showed significant, large-scale variability among plots. To capture 50% of the PyC in 200 cm soil profiles, soil must be sampled to a depth of at least 71 cm. PyC represents a significant (11%) portion of total organic carbon in soil profiles 0–200 cm depth. This finding highlights the potentially important role that historical fire has played in modifying soil C stocks. Our data suggest that PyC is an important carbon pool for long-term storage, involved in millennial scale biogeochemical cycling, particularly in the subsurface soil

Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation.

Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global suitability model of highly pathogenic avian influenza (HPAI) H5N1 and demonstrate that reliable predictions can be obtained at global scale. Best predictions are obtained using spatial predictor variables describing host distributions, rather than land use or eco-climatic spatial predictor variables, with a strong association with domestic duck and extensively raised chicken densities. Our results also support a more systematic use of spatial cross-validation in large-scale disease suitability modelling compared to standard random cross-validation that can lead to unreliable measure of extrapolation accuracy. A global suitability model of the H5 clade 2.3.4.4 viruses, a group of viruses that recently spread extensively in Asia and the US, shows in comparison a lower spatial extrapolation capacity than the HPAI H5N1 models, with a stronger association with intensively raised chicken densities and anthropogenic factors

CD8+ T-cell responses to Theileria parva are preferentially directed to a single dominant antigen: Implications for parasite strain-specific immunity

Although immunodominance of CD8+ T-cell responses is a well-recognised feature of viral infections, its role in responses to more antigenically complex pathogens is less clear. In previous studies we have observed that CD8+ T-cell responses to Theileria parva exhibit different patterns of parasite strain specificity in cattle of different MHC genotypes. In the current study, we demonstrated that animals homozygous for the A10 and A18 MHC haplotypes have detectable responses to only one of 5 T. parva antigens. Over 60% of the responding T cells from the A18+ and A10+ animals recognised defined epitopes in the Tp1 and Tp2 antigens, respectively. Comparison of T-cell receptor β chain expression profiles of CD8+ T-cell lines and CD8+ T cells harvested ex vivo confirmed that the composition of the T-cell lines was representative of the in vivo memory CD8+ T-cell populations. Analysis of the Tp1 and Tp2 antigens revealed sequence polymorphism, which was reflected by differential recognition by T-cell lines. In conclusion, we have demonstrated a profound immunodominance in the CD8+ T-cell response to T. parva, which we propose is a major determinant of the parasite strain specificity of the response and hence immune protection