Author Correction: Early Pastoral Economies and Herding Transitions in Eastern Eurasia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Early Pastoral Economies and Herding Transitions in Eastern Eurasia.

While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.

Radiocarbon dating and cultural dynamics across Mongolia's early pastoral transition.

The emergence of mobile herding lifeways in Mongolia and eastern Eurasia was one of the most crucial economic and cultural transitions in human prehistory. Understanding the process by which this played out, however, has been impeded by the absence of a precise chronological framework for the prehistoric era in Mongolia. One rare source of empirically dateable material useful for understanding eastern Eurasia's pastoral tradition comes from the stone burial mounds and monumental constructions that began to appear across the landscape of Mongolia and adjacent regions during the Bronze Age (ca. 3000-700 BCE). Here, along with presenting 28 new radiocarbon dates from Mongolia's earliest pastoral monumental burials, we synthesise, critically analyse, and model existing dates to present the first precision Bayesian radiocarbon model for the emergence and geographic spread of Bronze Age monument and burial forms. Model results demonstrate a cultural succession between ambiguously dated Afanasievo, Chemurchek, and Munkhkhairkhan traditions. Geographic patterning reveals the existence of important cultural frontiers during the second millennium BCE. This work demonstrates the utility of a Bayesian approach for investigating prehistoric cultural dynamics during the emergence of pastoral economies.

Strain-Stabilized Ceramic-Sulfide Electrolytes.

Ceramic-sulfide solid electrolytes are a promising material system for enabling solid-state batteries. However, one challenge that remains is the discrepancy in the reported electrochemical stability. Recent work has suggested that it may be due to the sensitivity of ceramic sulfides to mechanically induced stability. Small changes in ceramic-sulfide microstructure, for example, have been shown to cause substantial differences in the electrochemical stability. In this work, a rigorous theoretical framework is constructed to enable the simulation of such mechanically induced stability for a generalized constraint mechanism. It is shown that the susceptibility for voltage widening in ceramic sulfides can be significantly influenced by the choice of different decay morphology models. This results in a less intrusive microstructure requirement for improved stability, which stems from the tendency of sulfides to decay via inclusions rather than homogeneously. This predicted decay morphology is experimentally confirmed. Li10 GeP2 S12 is stabilized by a thin amorphous shell, which prior models predict is too thin for stabilization. The generality of this framework is discussed in light of stabilization methods beyond microstructure, such as on the battery cell level. The relation of our picture to the observed lithium metal formation in ceramic sulfides is also discussed.

Advanced sulfide solid electrolyte by core-shell structural design.

Solid electrolyte is critical to next-generation solid-state lithium-ion batteries with high energy density and improved safety. Sulfide solid electrolytes show some unique properties, such as the high ionic conductivity and low mechanical stiffness. Here we show that the electrochemical stability window of sulfide electrolytes can be improved by controlling synthesis parameters and the consequent core-shell microstructural compositions. This results in a stability window of 0.7-3.1 V and quasi-stability window of up to 5 V for Li-Si-P-S sulfide electrolytes with high Si composition in the shell, a window much larger than the previously predicted one of 1.7-2.1 V. Theoretical and computational work explains this improved voltage window in terms of volume constriction, which resists the decomposition accompanying expansion of the solid electrolyte. It is shown that in the limiting case of a core-shell morphology that imposes a constant volume constraint on the electrolyte, the stability window can be further opened up. Advanced strategies to design the next-generation sulfide solid electrolytes are also discussed based on our understanding.

Apical Charge Flux-Modulated In-Plane Transport Properties of Cuprate Superconductors.

For copper-based superconductors, the maximum superconducting transition temperature T_{c,max} of different families measured from experiment can vary from 38 K in La_{2}CuO_{4} to 135 K in HgBa_{2}Ca_{2}Cu_{3}O_{8} at the optimal hole doping concentration. We demonstrate herein, using ab initio computations, a new trend suggesting that the cuprates with stronger out-of-CuO_{2}-plane chemical bonding between the apical anion (O, Cl) and apical cation (e.g., La, Hg, Bi, Tl) are generally correlated with higher T_{c,max} in experiments. We then show the underlying fundamental phenomena of coupled apical charge flux and lattice dynamics when the apical oxygen oscillates vertically. This triggers the charge flux among the apical cation, apical anion, and the in-plane CuO_{4} unit. The effect not only dynamically modulates the site energy of the hole at a given Cu site to control the in-plane charge transfer energy, but also can modulate the in-plane hole hopping integral simultaneously in a dynamic way by the cooperative apical charge fluxes.

Origins of equine dentistry.

From the American West to the steppes of Eurasia, the domestic horse transformed human societies, providing rapid transport, communication, and military power, and serving as an important subsistence animal. Because of the importance of oral equipment for horse riding, dentistry is an essential component of modern horse care. In the open grasslands of northeast Asia, horses remain the primary form of transport for many herders. Although free-range grazing on gritty forage mitigates many equine dental issues, contemporary Mongolian horsemen nonetheless practice some forms of dentistry, including the removal of problematic deciduous teeth and the vestigial first premolar ("wolf tooth"). Here, we present archaezoological data from equine skeletal remains spanning the past 3,200 y, indicating that nomadic dental practices have great antiquity. Anthropogenic modifications to malerupted deciduous central incisors in young horses from the Late Bronze Age demonstrate their attempted removal, coinciding with the local innovation or adoption of horseback riding and the florescence of Mongolian pastoral society. Horse specimens from this period show no evidence of first premolar removal, which we first identify in specimens dating to ca. 750 BCE. The onset of premolar extraction parallels the archaeological appearance of jointed bronze and iron bits, suggesting that this technological shift prompted innovations in dentistry that improved horse health and horse control. These discoveries provide the earliest directly dated evidence for veterinary dentistry, and suggest that innovations in equine care by nomadic peoples ca. 1150 BCE enabled the use of horses for increasingly sophisticated mounted riding and warfare.

Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections.

Baleen has been harvested by indigenous people for thousands of years, as well as collected by whalers as an additional product of commercial whaling in modern times. Baleen refers to the food-filtering system of Mysticeti whales; a full baleen rack consists of dozens of plates of a tough and flexible keratinous material that terminate in bristles. Due to its properties, baleen was a valuable raw material used in a wide range of artefacts, from implements to clothing. Baleen is not widely used today, however, analyses of this biomolecular tissue have the potential to contribute to conservation efforts, studies of genetic diversity and a better understanding of the exploitation and use of Mysticeti whales in past and recent times. Fortunately, baleen is present in abundance in museum natural history collections. However, it is often difficult or impossible to make a species identification of manufactured or old baleen. Here, we propose a new tool for biomolecular identification of baleen based on its main structural component alpha-keratin (the same protein that makes up hair and fingernails). With the exception of minke whales, alpha-keratin sequences are not yet known for baleen whales. We therefore used peptide mass fingerprinting to determine peptidic profiles in well documented baleen and evaluated the possibility of using this technique to differentiate species in baleen samples that are not adequately identified or are unidentified. We examined baleen from ten different species of whales and determined molecular markers for each species, including species-specific markers. In the case of the Bryde's whales, differences between specimens suggest distinct species or sub-species, consistent with the complex phylogeny of the species. Finally, the methodology was applied to 29 fragments of baleen excavated from archaeological sites in Labrador, Canada (representing 1500 years of whale use by prehistoric people), demonstrating a dominance of bowhead whale (Balaena mysticetus) in the archaeological assemblage and the successful application of the peptide mass fingerprinting technique to identify the species of whale in unidentified and partially degraded samples.

DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago.

The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some exploited taxa, though economically important, comprise only a small fraction of these sub-fossil assemblages. Here we reconstruct a comprehensive record of past subsistence economies in Greenland by sequencing ancient DNA from four well-described midden deposits. Our results confirm that the species found in the fossil record, like harp seal and ringed seal, were a vital part of Inuit subsistence, but also add a new dimension with evidence that caribou, walrus and whale species played a more prominent role for the survival of Paleo-Inuit cultures than previously reported. Most notably, we report evidence of bowhead whale exploitation by the Saqqaq culture 4,000 years ago.

Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium.

BACKGROUND: Support for early detection of lung cancer has emerged from the National Lung Screening Trial (NLST), in which low-dose computed tomography (LDCT) screening reduced lung cancer mortality by 20 % relative to chest x-ray. The US Preventive Services Task Force (USPSTF) recently recommended annual screening for the high-risk population, concluding that the benefits (life years gained) outweighed harms (false positive findings, abortive biopsy/surgery, radiation exposure). In making their recommendation, the USPSTF noted that the moderate net benefit of screening was dependent on the resolution of most false-positive results without invasive procedures. Circulating biomarkers may serve as a valuable adjunctive tool to imaging. RESULTS: We developed a broad-based proteomics discovery program, integrating liquid chromatography/mass spectrometry (LC/MS) analyses of freshly resected lung tumor specimens (n = 13), lung cancer cell lines (n = 17), and conditioned media collected from tumor cell lines (n = 7). To enrich for biomarkers likely to be found at elevated levels in the peripheral circulation of lung cancer patients, proteins were prioritized based on predicted subcellular localization (secreted, cell-membrane associated) and differential expression in disease samples. 179 candidate biomarkers were identified. Several markers selected for further validation showed elevated levels in serum collected from subjects with stage I NSCLC (n = 94), relative to healthy smoker controls (n = 189). An 8-marker model was developed (TFPI, MDK, OPN, MMP2, TIMP1, CEA, CYFRA 21-1, SCC) which accurately distinguished subjects with lung cancer (n = 50) from high risk smokers (n = 50) in an independent validation study (AUC = 0.775). CONCLUSIONS: Integrating biomarker discovery from multiple sample types (fresh tissue, cell lines and conditioned medium) has resulted in a diverse repertoire of candidate biomarkers. This unique collection of biomarkers may have clinical utility in lung cancer detection and diagnoses.

The genetic prehistory of the New World Arctic.

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.

Identification and characterization of angiogenesis targets through proteomic profiling of endothelial cells in human cancer tissues.

Genomic and proteomic analysis of normal and cancer tissues has yielded abundant molecular information for potential biomarker and therapeutic targets. Considering potential advantages in accessibility to pharmacological intervention, identification of targets resident on the vascular endothelium within tumors is particularly attractive. By employing mass spectrometry (MS) as a tool to identify proteins that are over-expressed in tumor-associated endothelium relative to normal cells, we aimed to discover targets that could be utilized in tumor angiogenesis cancer therapy. We developed proteomic methods that allowed us to focus our studies on the discovery of cell surface/secreted proteins, as they represent key antibody therapeutic and biomarker opportunities. First, we isolated endothelial cells (ECs) from human normal and kidney cancer tissues by FACS using CD146 as a marker. Additionally, dispersed human colon and lung cancer tissues and their corresponding normal tissues were cultured ex-vivo and their endothelial content were preferentially expanded, isolated and passaged. Cell surface proteins were then preferentially captured, digested with trypsin and subjected to MS-based proteomic analysis. Peptides were first quantified, and then the sequences of differentially expressed peptides were resolved by MS analysis. A total of 127 unique non-overlapped (157 total) tumor endothelial cell over-expressed proteins identified from directly isolated kidney-associated ECs and those identified from ex-vivo cultured lung and colon tissues including known EC markers such as CD146, CD31, and VWF. The expression analyses of a panel of the identified targets were confirmed by immunohistochemistry (IHC) including CD146, B7H3, Thy-1 and ATP1B3. To determine if the proteins identified mediate any functional role, we performed siRNA studies which led to previously unidentified functional dependency for B7H3 and ATP1B3.

Arctic sea-ice decline archived by multicentury annual-resolution record from crustose coralline algal proxy.

Northern Hemisphere sea ice has been declining sharply over the past decades and 2012 exhibited the lowest Arctic summer sea-ice cover in historic times. Whereas ongoing changes are closely monitored through satellite observations, we have only limited data of past Arctic sea-ice cover derived from short historical records, indirect terrestrial proxies, and low-resolution marine sediment cores. A multicentury time series from extremely long-lived annual increment-forming crustose coralline algal buildups now provides the first high-resolution in situ marine proxy for sea-ice cover. Growth and Mg/Ca ratios of these Arctic-wide occurring calcified algae are sensitive to changes in both temperature and solar radiation. Growth sharply declines with increasing sea-ice blockage of light from the benthic algal habitat. The 646-y multisite record from the Canadian Arctic indicates that during the Little Ice Age, sea ice was extensive but highly variable on subdecadal time scales and coincided with an expansion of ice-dependent Thule/Labrador Inuit sea mammal hunters in the region. The past 150 y instead have been characterized by sea ice exhibiting multidecadal variability with a long-term decline distinctly steeper than at any time since the 14th century.

RNA interference characterization of proteins discovered by proteomic analysis of pancreatic cancer reveals function in cell growth and survival.

OBJECTIVES: There is a clear need for better therapeutics and diagnostics for pancreatic cancer. We aimed to discover plasma membrane-associated proteins overexpressed in pancreatic cancer using quantitative proteomics and apply RNA interference (RNAi) to uncover proteins associated with cancer cell survival. METHODS: Cell surface glycoproteins from 5 pancreatic cancer cell lines were isolated, and differential analyses were performed using mass spectrometry and the "normoid" cell line Hs766T as the comparator. For validation, immunohistochemistry was performed on tissues from 10 independent patients and 2 normal donors. Correlation of protein and mRNA expression level was determined, and functional activity characterized using RNAi. RESULTS: Integrin ß6, CD46, tissue factor, and a novel protein, chromosome 14 open reading frame 1, were identified as overexpressed on pancreatic cancer cell lines. Immunohistochemistry demonstrated the 4 targets were overexpressed in 20% to 70% of primary pancreatic tumor specimens. Small interfering RNA knockdown resulted in a reduction of cellular proliferation by inhibiting DNA synthesis, blocking S-phase progression or induction of apoptosis. CONCLUSIONS: By combining a mass spectrometry identification platform and an RNAi validation platform, we have identified a panel of cell surface glycoproteins that not only are overexpressed, but also play a functional role in pancreatic tumor cell survival.

Immune modulator CD70 as a potential cisplatin resistance predictive marker in ovarian cancer.

OBJECTIVE: We have used mass-spectrometry (MS) based proteomics platform to identify cell surface proteins over-expressed on a cisplatin resistant derivative of an ovarian cancer cell line A2780. METHODS: Membrane associated glycoproteins from A2780 and its cisplatin resistant derivative cell line, A2780cis, were processed for liquid chromatography (LC)-MS based analysis. The expression of proteins found at elevated levels in A2780cis cell line was confirmed using flow cytometry and Taqman analysis. The expression of these proteins was further evaluated in unrelated ovarian cancer cell lines using MS analysis and flow cytometry. Immunohistochemical (IHC) analysis was performed using ovarian tumor tissues to evaluate the protein density on the cell surface. Monoclonal antibodies were used in an alamar blue proliferation assay to examine the cytotoxic effects on cell proliferation in resistant cell lines. RESULTS: Six proteins were identified by LC-MS as being over-expressed on cell surface of A2780cis cell line. Mass spectrometry and flow cytometry confirmed the over-expression of CD49f, CD70 and Her-2/neu in other cisplatin resistant ovarian cancer cell lines. Immunohistochemical analysis revealed that only CD70 was expressed at moderate levels in ovarian tumors. When cisplatin resistant ovarian cell lines A2780cis and SKOV-3 were treated with antibody against CD70, there was a significant decrease in cell proliferation. CONCLUSION: Using a MS based proteomics approach we have shown that expression of CD70 is associated with cisplatin resistance in ovarian cancer cell lines. Follow-up examination of these tumor cell line findings in clinical tumor specimens with available pathology staging and cisplatin treatment history is warranted.

Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics.

The accurate mass and time (AMT) tag strategy has been recognized as a powerful tool for high-throughput analysis in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. Due to the complexity of the human proteome, this strategy requires highly accurate mass measurements for confident identifications. We have developed a method of building a reference map that allows relaxed criteria for mass errors yet delivers high confidence for peptide identifications. The samples used for generating the peptide database were produced by collecting cysteine-containing peptides from T47D cells and then fractionating the peptides using strong cationic exchange chromatography (SCX). LC-tandem mass spectrometry (MS/MS) data from the SCX fractions were combined to create a comprehensive reference map. After the reference map was built, it was possible to skip the SCX step in further proteomic analyses. We found that the reference-driven identification increases the overall throughput and proteomic coverage by identifying peptides with low intensity or complex interference. The use of the reference map also facilitates the quantitation process by allowing extraction of peptide intensities of interest and incorporating models of theoretical isotope distribution.

Identification of protein remains in archaeological potsherds by proteomics.

We demonstrate here the possibility of identifying proteins trapped in few milligrams of the clay matrix of a 1200-1400 AD Iñupiat potsherd fragment from Point Barrow, Alaska, by a dedicated proteomics approach. The four main steps of a proteomics analysis, (i) protein extraction from biological samples, (ii) protein hydrolysis using a hydrolase enzyme, (iii) nanoLC, nanoESI MS, and MS/MS analysis of the generated peptides, and (iv) protein identification using protein databank proceeded from genomic data, have been optimized for archeological remains. Briefly our procedure starts by grinding the potsherds, extraction with 1% trifluoroacetic acid, digestion with excess of trypsin, nanoLC, nanoESI FT-ICR analysis, and data mining by homology search. The developed conditions were evaluated on protein extracts from remains obtained by heated muscle tissues and blubbers of different seal and whale species, these samples representing the main diet sources of the Eskimo population. Most of the proteins were identified by sequence homology to other species due to the lack of cetacean and pinniped proteins in the databanks. More interestingly, two proteins, myoglobin and hemoglobin, respectively, identified in muscle tissue samples and blubber samples highlight several specific peptides of cetacean and pinniped species; these peptides are significant to prove the presence of these marine species in the analyzed samples. Based on the developed methodology and on protein identification results obtained from the heated seal/whale muscle tissues and blubbers, the analysis of the clay matrix of a 1200-1400 AD Iñupiat potsherd fragment from Point Barrow was investigated. The described method succeeds in identifying four peptides corresponding to the harbor seal myoglobin (species Phoca vitulina) with a measured mass accuracy better than 1 ppm (MS and MS/MS experiments) including one specific peptide of the cetacean and pinniped species and one specific peptide of the seal species. These results highlight, for the first time, a methodology able to identify proteins from a few milligrams of archeological potsherd buried for years; the obtained results confirm the presence of a seal muscle tissue protein in this Punuk potsherd.

Use of an immunoaffinity-mass spectrometry-based approach for the quantification of protein biomarkers from serum samples of lung cancer patients.

It is a challenging task to verify and quantify potential biomarkers expressed at elevated levels in sera from cancer patients. An immunoaffinity-mass spectrometry-based approach has been developed using antibodies to enrich proteins of interest from sera followed by mass spectrometry-based quantification. Antibodies specific to the protein of interest were immobilized to hydrazide resin via the carbohydrate moiety on the Fc region of the antibody. Captured proteins were eluted, reduced, alkylated, and digested with trypsin. Peptides were analyzed by LC coupled with multiple reaction monitoring approach, and quantification was achieved by the addition of stable isotope-labeled (heavy) standard peptides. Using this methodology, we were able to achieve a linear response from 15 to 250 ng/ml for carcinoembryonic antigen (CEA), a known tumor biomarker. Moreover we observed elevated levels of CEA in sera samples from lung cancer patients that to our knowledge is the first time that circulating CEA has been detected by mass spectrometry-based analysis. This approach was further applied to potential protein biomarkers discovered from tumor cell lines and tumor tissues. A linear response was obtained from a multiplex spiking experiment in normal human sera for secretory leukocyte peptidase inhibitor (4-500 ng/ml), tissue factor pathway inhibitor (TFPI) (42-1000 ng/ml), tissue factor pathway inhibitor 2 (TFPI2) (2-250 ng/ml), and metalloproteinase inhibitor 1 (TIMP1) (430-1000 ng/ml). A replicate experiment for a single concentration value yielded a relative coefficient of variation better than 11% for TFPI, secretory leukocyte peptidase inhibitor, and TFPI2. The expression level of the proteins in lung cancer patient sera was assayed by an immunoaffinity-multiple reaction monitoring method, and the results were comparable with those obtained from ELISA. This immunoaffinity-mass spectrometry-based quantification approach thus provides a specific and accurate assay for verifying the expression of potential biomarkers in patient serum samples especially for those proteins for which the necessary reagents for ELISA development are unavailable.

The genome sequence of the filamentous fungus Neurospora crassa.

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.