Zinc isotopes from archaeological bones provide reliable trophic level information for marine mammals

In marine ecology, dietary interpretations of faunal assemblages often rely on nitrogen isotopes as the main or only applicable trophic level tracer. We investigate the geographic variability and trophic level isotopic discrimination factors of bone zinc 66Zn/64Zn ratios (δ66Zn value) and compared it to collagen nitrogen and carbon stable isotope (δ15N and δ13C) values. Focusing on ringed seals (Pusa hispida) and polar bears (Ursus maritimus) from multiple Arctic archaeological sites, we investigate trophic interactions between predator and prey over a broad geographic area. All proxies show variability among sites, influenced by the regional food web baselines. However, δ66Zn shows a significantly higher homogeneity among different sites. We observe a clear trophic spacing for δ15N and δ66Zn values in all locations, yet δ66Zn analysis allows a more direct dietary comparability between spatially and temporally distinct locations than what is possible by δ15N and δ13C analysis alone. When combining all three proxies, a more detailed and refined dietary analysis is possible

Strontium and Oxygen Isotope Analyses Reveal Late Cretaceous Shark Teeth in Iron Age Strata in the Southern Levant

Skeletal remains in archaeological strata are often assumed to be of similar ages. Here we show that combined Sr and O isotope analyses can serve as a powerful tool for assessing fish provenance and even for identifying fossil fish teeth in archaeological contexts. For this purpose, we established a reference Sr and O isotope dataset of extant fish teeth from major water bodies in the Southern Levant. Fossil shark teeth were identified within Iron Age cultural layers dating to 8–9th century BCE in the City of David, Jerusalem, although the reason for their presence remains unclear. Their enameloid 87Sr/86Sr and δ18OPO4 values [0.7075 ± 0.0001 (1 SD, n = 7) and 19.6 ± 0.9‰ (1 SD, n = 6), respectively], are both much lower than values typical for modern marine sharks from the Mediterranean Sea [0.7092 and 22.5–24.6‰ (n = 2), respectively]. The sharks’ 87Sr/86Sr are also lower than those of rain- and groundwater as well as the main soil types in central Israel (≥0.7079). This indicates that these fossil sharks incorporated Sr (87Sr/86Sr ≈ 0.7075) from a marine habitat with values typical for Late Cretaceous seawater. This scenario is in line with the low shark enameloid δ18OPO4 values reflecting tooth formation in the warm tropical seawater of the Tethys Ocean. Age estimates using 87Sr/86Sr stratigraphy place these fossil shark teeth at around 80-million-years-old. This was further supported by their taxonomy and the high dentine apatite crystallinity, low organic carbon, high U and Nd contents, characteristics that are typical for fossil specimens, and different from those of archaeological Gilthead seabream (Sparus aurata) teeth from the same cultural layers and another Chalcolithic site (Gilat). Chalcolithic and Iron Age seabream enameloid has seawater-like 87Sr/86Sr of 0.7091 ± 0.0001 (1 SD, n = 6), as expected for modern marine fish. Fossil shark and archaeological Gilthead seabream teeth both preserve original, distinct enameloid 87Sr/86Sr and δ18OPO4 signatures reflecting their different aquatic habitats. Fifty percent of the analysed Gilthead seabream teeth derive from hypersaline seawater, indicating that these seabreams were exported from the hypersaline Bardawil Lagoon in Sinai (Egypt) to the Southern Levant since the Iron Age period and possibly even earlier

Subarctic climate for the earliest Homo sapiens in Europe

Acknowledgments The re-excavation of Bacho Kiro Cave was jointly conducted by the National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia and the Department of Human Evolution at the MPI-EVA. We would like to thank the National Museum of Natural History (Sofia), the Archaeology Department at the New Bulgarian University (Sofia), the Regional Museum of History in Gabrovo, and the History Museum in Dryanovo for assistance on this project and the opportunity to study the Bacho Kiro Cave faunal material. We would like to thank M. Trost, S. Hesse, M. Kaniecki, and P. Dittmann (MPI-EVA) for technical assistance during stable isotope sample preparation. S. Steinbrenner is thanked for technical assistance with TC/EA-IRMS maintenance. Thanks are also due to H. Temming and U. Schwarz (MPI-EVA) for the production of microCT scans and replicas of the sample materials. We would also like to acknowledge the assistance of to D. Veres with taking OSL samples. Last but not least we would like to thank the handling editor, S. Ortman, as well as three anonymous reviewers for their thoughtful comments that greatly improved this manuscript. Funding: The field work was financed by the Max Planck Society. The stable isotope work was funded by the Max Planck Society as part of S.P.’s doctoral project. S.P. was supported by the Max Planck Society and the University of Aberdeen. K.B. was supported by a Philip Leverhulme Prize from The Leverhulme Trust (PLP-2019-284). N.B.’s work was supported as part of a grant by the German Research Foundation (“PALÄODIET” Project 378496604). V.A. was supported by a grant from the Foundation for Science and Technology, Portugal (IF/01157/2015/CP1308/CT0002). Author contributions: The study was devised by S.P., K.B., S.P.M., J.-J.H., and T.T. Archaeological excavation was undertaken by N.S. and T.T. in collaboration with Z.R. and S.P.M. who all contributed contextual information. V.A. collected sedimentological data at the site and untertook micromorphological investigations that provided information on site formation for this study. Zooarchaeological and paleontological analyses were performed by G.M.S. and R.S. OSL dating was carried out by T.L. Radiocarbon dating and recalibration of radiocarbon dates were conducted by H.F. MC-ICPMS analysis was conducted by N.B. and S.P. Sampling, sample processing for oxygen and strontium stable isotope analysis, and TC/EA-IRMS analysis were carried out by S.P. Code and data analyses were written and conducted by S.P. N.-H.T. consulted on statistical analysis and coding. S.P. wrote the paper with input from all authors. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.Peer reviewedPublisher PD

A multi-proxy approach to exploring Homo sapiens’ arrival, environments and adaptations in Southeast Asia

The capability of Pleistocene hominins to successfully adapt to different types of tropical forested environments has long been debated. In order to investigate environmental changes in Southeast Asia during a critical period for the turnover of hominin species, we analysed palaeoenvironmental proxies from five late Middle to Late Pleistocene faunas. Human teeth discoveries have been reported at Duoi U’Oi, Vietnam (70–60 ka) and Nam Lot, Laos (86–72 ka). However, the use of palaeoproteomics allowed us to discard the latter, and, to date, no human remains older than ~ 70 ka are documented in the area. Our findings indicate that tropical rainforests were highly sensitive to climatic changes over that period, with significant fluctuations of the canopy forests. Locally, large-bodied faunas were resilient to these fluctuations until the cooling period of the Marine Isotope Stage 4 (MIS 4; 74–59 ka) that transformed the overall biotope. Then, under strong selective pressures, populations with new phenotypic characteristics emerged while some other species disappeared. We argue that this climate-driven shift offered new foraging opportunities for hominins in a novel rainforest environment and was most likely a key factor in the settlement and dispersal of our species during MIS 4 in SE Asia

Dietary soy and meat proteins induce distinct physiological and gene expression changes in rats

This study reports on a comprehensive comparison of the effects of soy and meat proteins given at the recommended level on physiological markers of metabolic syndrome and the hepatic transcriptome. Male rats were fed semi-synthetic diets for 1 wk that differed only regarding protein source, with casein serving as reference. Body weight gain and adipose tissue mass were significantly reduced by soy but not meat proteins. The insulin resistance index was improved by soy, and to a lesser extent by meat proteins. Liver triacylglycerol contents were reduced by both protein sources, which coincided with increased plasma triacylglycerol concentrations. Both soy and meat proteins changed plasma amino acid patterns. The expression of 1571 and 1369 genes were altered by soy and meat proteins respectively. Functional classification revealed that lipid, energy and amino acid metabolic pathways, as well as insulin signaling pathways were regulated differently by soy and meat proteins. Several transcriptional regulators, including NFE2L2, ATF4, Srebf1 and Rictor were identified as potential key upstream regulators. These results suggest that soy and meat proteins induce distinct physiological and gene expression responses in rats and provide novel evidence and suggestions for the health effects of different protein sources in human diets

Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level

Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC) can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that subclasses were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC

Analyzing ChIP-chip Data Using Bioconductor

Analyzing ChIP-chip Data Using Bioconducto

Sighting acute myocardial infarction through platelet gene expression

© 2019, The Author(s). Acute myocardial infarction is primarily due to coronary atherosclerotic plaque rupture and subsequent thrombus formation. Platelets play a key role in the genesis and progression of both atherosclerosis and thrombosis. Since platelets are anuclear cells that inherit their mRNA from megakaryocyte precursors and maintain it unchanged during their life span, gene expression profiling at the time of an acute myocardial infarction provides information concerning the platelet gene expression preceding the coronary event. In ST-segment elevation myocardial infarction (STEMI), a gene-by-gene analysis of the platelet gene expression identified five differentially expressed genes: FKBP5, S100P, SAMSN1, CLEC4E and S100A12. The logistic regression model used to combine the gene expression in a STEMI vs healthy donors score showed an AUC of 0.95. The same five differentially expressed genes were externally validated using platelet gene expression data from patients with coronary atherosclerosis but without thrombosis. Platelet gene expression profile highlights five genes able to identify STEMI patients and to discriminate them in the background of atherosclerosis. Consequently, early signals of an imminent acute myocardial infarction are likely to be found by platelet gene expression profiling before the infarction occurs

Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways

Meiotic DNA double-strand breaks (DSBs) initiate crossover (CO) recombination, which is necessary for accurate chromosome segregation, but DSBs may also repair as non-crossovers (NCOs). Multiple recombination pathways with specific intermediates are expected to lead to COs and NCOs. We revisited the mechanisms of meiotic DSB repair and the regulation of CO formation, by conducting a genome-wide analysis of strand-transfer intermediates associated with recombination events. We performed this analysis in a SK1 × S288C Saccharomyces cerevisiae hybrid lacking the mismatch repair (MMR) protein Msh2, to allow efficient detection of heteroduplex DNAs (hDNAs). First, we observed that the anti-recombinogenic activity of MMR is responsible for a 20% drop in CO number, suggesting that in MMR–proficient cells some DSBs are repaired using the sister chromatid as a template when polymorphisms are present. Second, we observed that a large fraction of NCOs were associated with trans–hDNA tracts constrained to a single chromatid. This unexpected finding is compatible with dissolution of double Holliday junctions (dHJs) during repair, and it suggests the existence of a novel control point for CO formation at the level of the dHJ intermediate, in addition to the previously described control point before the dHJ formation step. Finally, we observed that COs are associated with complex hDNA patterns, confirming that the canonical double-strand break repair model is not sufficient to explain the formation of most COs. We propose that multiple factors contribute to the complexity of recombination intermediates. These factors include repair of nicks and double-stranded gaps, template switches between non-sister and sister chromatids, and HJ branch migration. Finally, the good correlation between the strand transfer properties observed in the absence of and in the presence of Msh2 suggests that the intermediates detected in the absence of Msh2 reflect normal intermediates