STUDIES OF CARBON, OXYGEN AND STRONTIUM ISOTOPES IN TOOTH ENAMEL: EVALUATING PALEOENVIRONMENTAL CHANGE IN SOUTH AFRICA AND EXPANDING THE PALEOCLIMATE TOOL KIT

Anthropogenic-driven climate change has and will continue to influence Earth’s ecosystems and environments. Major regional and global climate events have been observed throughout the geological record. We need to determine how natural systems responded to climate in the past and the possible interactions between mammalian species, including humans, and their environment, if we are to have perspective on how natural systems will respond to changes in climate both currently and in the future. Evaluating past climate and environment can be a useful way to evaluate if and how past landscapes, ecosystems and animal-environment interactions may have been influenced by climatic change. Archeological and paleontological sites along the coastal region of southwestern South Africa preserve fossils and artifacts dating to the Pliocene and Pleistocene (within the last 5 million years). These materials indicate that southwestern South Africa was once home to large herbivorous mammalian communities and that hominins lived here since the mid-Pleistocene, at ca. 1 million years ago. However, this region is currently hot and dry and within a cool growing season. Furthermore, this region is within the fynbos biome, a biome with species that date to before the Pliocene, and is today mostly composed of woody, nutrient-poor shrub land. It is unknown how animals survived in the region during the Pliocene and Pleistocene or the composition of past vegetation and its distribution. Here I present an evaluation of animal diet and the climate and environment of southwestern South Africa over the last 5 million years using the carbon (δ13C values) and oxygen (δ18O values) isotopic composition of fossil teeth. I then evaluate the movement of animals for food in southwestern South Africa during the mid-Pleistocene and the distribution of vegetation at this time using strontium isotope ratios (87Sr/86Sr ratios) in the fossil tooth enamel preserved at archeological site Elandsfontein. I then consider the use of triple oxygen isotopes (∆17O) in the fossil record as a way to improve upon the current δ18O method to determine past climate and environmental change by presenting and characterizing ∆17O in modern tooth enamel. I found that herbivores ate vegetation characteristic of a cool growing season during the Pliocene and Pleistocene, therefore southwestern South Africa was within a winter rainfall zone since at least 5 million years ago. The ecosystem and environment of southwestern South Africa would have had to support the annual growth of grass if large mammalian herbivores (specifically grazers) could have survived in this region. Deposits indicative of fluvial environments (during the Pliocene) and spring-fed environments (during the Pleistocene) are preserved at fossil sites in the region. These environments would have been extremely important for the survival of animals in southwestern South Africa. The 87Sr/86Sr ratios of fossil teeth from mid-Pleistocene Elandsfontein suggest that large herbivores not only stayed within southwestern South Africa for food, but that they did not necessarily leave the area surrounding the fossil site. The ∆17O values of modern tooth enamel samples cover a greater span and include more negative values in arid environments than in humid environments, regardless of the oxygen isotopic composition of meteoric water and latitude. This record indicates the future potential of applying triple oxygen isotopes to the fossil record for reconstructing aridity, atmospheric pCO2 and diagenesis

Andean drought and glacial retreat tied to Greenland warming during the last glacial period

Abrupt warming events recorded in Greenland ice cores known as Dansgaard-Oeschger (DO) interstadials are linked to changes in tropical circulation during the last glacial cycle. Corresponding variations in South American summer monsoon (SASM) strength are documented, most commonly, in isotopic records from speleothems, but less is known about how these changes affected precipitation and Andean glacier mass balance. Here we present a sediment record spanning the last ~50 ka from Lake Junín (Peru) in the tropical Andes that has sufficient chronologic precision to document abrupt climatic events on a centennial-millennial time scale. DO events involved the near-complete disappearance of glaciers below 4700 masl in the eastern Andean cordillera and major reductions in the level of Peru’s second largest lake. Our results reveal the magnitude of the hydroclimatic disruptions in the highest reaches of the Amazon Basin that were caused by a weakening of the SASM during abrupt arctic warming. Accentuated warming in the Arctic could lead to significant reductions in the precipitation-evaporation balance of the southern tropical Andes with deleterious effects on this densely populated region of South America

Andean drought and glacial retreat tied to Greenland warming during the last glacial period

Abrupt warming events recorded in Greenland ice cores known as Dansgaard-Oeschger (DO) interstadials are linked to changes in tropical circulation during the last glacial cycle. Corresponding variations in South American summer monsoon (SASM) strength are documented, most commonly, in isotopic records from speleothems, but less is known about how these changes affected precipitation and Andean glacier mass balance. Here we present a sediment record spanning the last ~50 ka from Lake Junín (Peru) in the tropical Andes that has sufficient chronologic precision to document abrupt climatic events on a centennial-millennial time scale. DO events involved the near-complete disappearance of glaciers below 4700 masl in the eastern Andean cordillera and major reductions in the level of Peru’s second largest lake. Our results reveal the magnitude of the hydroclimatic disruptions in the highest reaches of the Amazon Basin that were caused by a weakening of the SASM during abrupt arctic warming. Accentuated warming in the Arctic could lead to significant reductions in the precipitation-evaporation balance of the southern tropical Andes with deleterious effects on this densely populated region of South America

U-Th dating of lake sediments: Lessons from the 700 ka sediment record of Lake Junín, Peru

Deep sediment cores from long-lived lake basins are fundamental records of paleoenvironmental history, but the power of these reconstructions has been often limited by poor age control. Uranium-thorium (U-Th) dating has the potential to fill a gap in current geochronological tools available for such sediment archives. We present our systematic approach to U-Th date carbonate-rich sediments from the ∼100 m drill core from Lake Junín, Peru. The results form the foundation of an age-depth model spanning ∼700 kyrs. High uranium concentrations (0.3–4 ppm) of these sediments allow us to date smaller amounts of material, giving us the opportunity to improve sample selection by avoiding detrital contamination, the greatest factor limiting the success of previous U-Th dating efforts in other lake basins. Despite this advantage, the dates from 174 analyses on 55 bulk carbonate samples reveal significant scatter that cannot be resolved with traditional isochrons, suggesting that at least some of the sediments have not remained closed systems. To understand the source of noise in the geochronological data, we first apply threshold criteria that screen samples by their U/Th ratio, reproducibility, and δ²³⁴U_(initial) value. We then compare these results with facies types, trace element concentrations, carbonate and total organic carbon content, color reflectance, mineralogy, and ostracode shell color to investigate the causes of open system behavior. Alongside simulations of the isotopic evolution of our samples, we find that the greatest impediment to U-Th dating of these sediments is not detrital contamination, but rather post-depositional remobilization of uranium. Examining U-Th data in these contexts, we identify samples that have likely experienced the least amount of alteration, and use dates from those samples as constraints for the age-depth model. Our work has several lessons for future attempts to U-Th date lake sediments, namely that geologic context is equally as important as the accuracy and precision of analytical measurements. In addition, we caution that significant geologic scatter may remain undetected if not for labor intensive tests of reproducibility achieved through replication. As a result of this work, the deep sediment core from Lake Junín is the only continuous record in the tropical Andes spanning multiple glacial cycles that is constrained entirely by independent radiometric dates

Stable isotope ecology of Cape dune mole-rats (Bathyergus suillus) from Elandsfontein, South Africa: implications for C4 vegetation and hominin paleobiology in the Cape Floral Region

The archaeological and paleontological records from the west coast of South Africa have potential to provide insights into ecosystem dynamics in the region during the mid Pleistocene. Although the fossil record suggests an ecosystem quite different than that of the region today, we understand little about the ecological factors that contributed to this disparity. The site of Elandsfontein (EFT) dates to between 1.0 and 0.6 million years ago (Ma), preserves in situ lithic and faunal materials found in direct association with each other, and provides the rare opportunity to examine the relationship between hominin behavioural variability and landscape heterogeneity in a winter rainfall ecosystem. In this study, we examine the stable carbon isotopic composition of a large sample (n = 81) of Cape dune mole-rats (Bathyergus suillus) and contemporaneous large mammals (> 6 kg; n = 194) from EFT. We find that δ13C values of B. suillus are significantly different to those of contemporaneous large mammals from EFT indicating a significant presence of plants utilizing the C4 photosynthetic pathway during the mid-Pleistocene, in contrast to present C3 dominated ecosystems along the west coast of South Africa. Additionally, we find that artifact density at EFT localities is positively correlated with δ13C values in B. suillus enamel suggesting that evidence of more intense hominin occupation may be associated with the presence of more C4 vegetation. Lastly, we hypothesize that this unique distribution of vegetation 1) provided abundant resources for both hominin and non-hominin taxa and 2) may have concentrated hominin and animal behavior in certain places on the ancient landscape

Importance of pre-analytical steps for transcriptome and RT-qPCR analyses in the context of the phase II randomised multicentre trial REMAGUS02 of neoadjuvant chemotherapy in breast cancer patients

<p>Abstract</p> <p>Background</p> <p>Identification of predictive markers of response to treatment is a major objective in breast cancer. A major problem in clinical sampling is the variability of RNA templates, requiring accurate management of tumour material and subsequent analyses for future translation in clinical practice. Our aim was to establish the feasibility and reliability of high throughput RNA analysis in a prospective trial.</p> <p>Methods</p> <p>This study was conducted on RNA from initial biopsies, in a prospective trial of neoadjuvant chemotherapy in 327 patients with inoperable breast cancer. Four independent centres included patients and samples. Human U133 GeneChips plus 2.0 arrays for transcriptome analysis and quantitative RT-qPCR of 45 target genes and 6 reference genes were analysed on total RNA.</p> <p>Results</p> <p>Thirty seven samples were excluded because <it>i) </it>they contained less than 30% malignant cells, or <it>ii) </it>they provided RNA Integrity Number (RIN) of poor quality. Among the 290 remaining cases, taking into account strict quality control criteria initially defined to ensure good quality of sampling, 78% and 82% samples were eligible for transcriptome and RT-qPCR analyses, respectively. For RT-qPCR, efficiency was corrected by using standard curves for each gene and each plate. It was greater than 90% for all genes. Clustering analysis highlighted relevant breast cancer phenotypes for both techniques (ER+, PR+, HER2+, triple negative). Interestingly, clustering on trancriptome data also demonstrated a "centre effect", probably due to the sampling or extraction methods used in on of the centres. Conversely, the calibration of RT-qPCR analysis led to the centre effect withdrawing, allowing multicentre analysis of gene transcripts with high accuracy.</p> <p>Conclusions</p> <p>Our data showed that strict quality criteria for RNA integrity assessment and well calibrated and standardized RT-qPCR allows multicentre analysis of genes transcripts with high accuracy in the clinical context. More stringent criteria are needed for transcriptome analysis for clinical applications.</p

Stable isotopic composition of fossil mammal teeth and environmental change in southwestern South Africa during the Pliocene and Pleistocene

The past 5 million years mark a global change from the warmer, more stable climate of the Pliocene to the initiation of glacial-interglacial cycles during the Pleistocene. Marine core sediment records located off the coast of southwestern Africa indicate aridification and intensified upwelling in the Benguela Current over the Pliocene and Pleistocene. However, few terrestrial records document environmental change in southwestern Africa over this time interval. Here we synthesize new and published carbon and oxygen isotope data of the teeth from large mammals (>6 kg) at Langebaanweg (~5 million years ago, Ma), Elandsfontein (1.0 – 0.6 Ma), and Hoedjiespunt (0.35 – 0.20 Ma), to evaluate environmental change in southwestern Africa between the Pliocene and Pleistocene. The majority of browsing and grazing herbivores from these sites yield enamel 13 C values within the range expected for animals with a pure C3 diet, however some taxa have enamel 13C values that suggest the presence of small amounts C4 grasses at times during the Pleistocene. Considering that significant amounts of C4 grasses require a warm growing season, these results indicate that the winter rainfall zone, characteristic of the region today, could have been in place for the past 5 million years. The average 18O value of the herbivore teeth increases ~4.4‰ between Langebaanweg and Elandsfontein for all taxa except suids. This increase may solely be a function of a change in hydrology between the fluvial system at Langebaanweg and the spring-fed environments at Elandsfontein, or a combination of factors that include depositional context, regional circulation and global climate. However, an increase in regional aridity or global cooling between the early Pliocene and mid-Pleistocene cannot explain the entire increase in enamel 18O values. Spring-fed environments like those at Elandsfontein may have 75 provided critical resources for mammalian fauna in the mid-Pleistocene within an increasingly arid southwestern Africa ecosystem

Lack of Protection following Passive Transfer of Polyclonal Highly Functional Low-Dose Non-Neutralizing Antibodies

Recent immune correlates analysis from the RV144 vaccine trial has renewed interest in the role of non-neutralizing antibodies in mediating protection from infection. While neutralizing antibodies have proven difficult to induce through vaccination, extra-neutralizing antibodies, such as those that mediate antibody-dependent cellular cytotoxicity (ADCC), are associated with long-term control of infection. However, while several non-neutralizing monoclonal antibodies have been tested for their protective efficacy in vivo, no studies to date have tested the protective activity of naturally produced polyclonal antibodies from individuals harboring potent ADCC activity. Because ADCC-inducing antibodies are highly enriched in elite controllers (EC), we passively transferred highly functional non-neutralizing polyclonal antibodies, purified from an EC, to assess the potential impact of polyclonal non-neutralizing antibodies on a stringent SHIV-SF162P3 challenge in rhesus monkeys. Passive transfer of a low-dose of ADCC inducing antibodies did not protect from infection following SHIV-SF162P3 challenge. Passively administered antibody titers and gp120-specific, but not gp41-specific, ADCC and antibody induced phagocytosis (ADCP) were detected in the majority of the monkeys, but did not correlate with post infection viral control. Thus these data raise the possibility that gp120-specific ADCC activity alone may not be sufficient to control viremia post infection but that other specificities or Fc-effector profiles, alone or in combination, may have an impact on viral control and should be tested in future passive transfer experiments

HIV-1 Protease and Reverse Transcriptase Control the Architecture of Their Nucleocapsid Partner

The HIV-1 nucleocapsid is formed during protease (PR)-directed viral maturation, and is transformed into pre-integration complexes following reverse transcription in the cytoplasm of the infected cell. Here, we report a detailed transmission electron microscopy analysis of the impact of HIV-1 PR and reverse transcriptase (RT) on nucleocapsid plasticity, using in vitro reconstitutions. After binding to nucleic acids, NCp15, a proteolytic intermediate of nucleocapsid protein (NC), was processed at its C-terminus by PR, yielding premature NC (NCp9) followed by mature NC (NCp7), through the consecutive removal of p6 and p1. This allowed NC co-aggregation with its single-stranded nucleic-acid substrate. Examination of these co-aggregates for the ability of RT to catalyse reverse transcription showed an effective synthesis of double-stranded DNA that, remarkably, escaped from the aggregates more efficiently with NCp7 than with NCp9. These data offer a compelling explanation for results from previous virological studies that focused on i) Gag processing leading to nucleocapsid condensation, and ii) the disappearance of NCp7 from the HIV-1 pre-integration complexes. We propose that HIV-1 PR and RT, by controlling the nucleocapsid architecture during the steps of condensation and dismantling, engage in a successive nucleoprotein-remodelling process that spatiotemporally coordinates the pre-integration steps of HIV-1. Finally we suggest that nucleoprotein remodelling mechanisms are common features developed by mobile genetic elements to ensure successful replication