Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.

Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and14C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

Epipalaeolithic animal tending to Neolithic herding at Abu Hureyra, Syria (12,800-7,800 calBP): Deciphering dung spherulites.

Excavations at Abu Hureyra, Syria, during the 1970s exposed a long sequence of occupation spanning the transition from hunting-and-gathering to agriculture. Dung spherulites preserved within curated flotation samples from Epipalaeolithic (ca. 13,300-11,400 calBP) and Neolithic (ca. 10,600-7,800 calBP) occupations are examined here alongside archaeological, archaeobotanical, and zooarchaeological data to consider animal management, fuel selection, and various uses of dung. Spherulites were present throughout the entire sequence in varying concentrations. Using a new method to quantify spherulites, exclusion criteria were developed to eliminate samples possibly contaminated with modern dung, strengthening observations of ancient human behavior. Darkened spherulites within an Epipalaeolithic 1B firepit (12,800-12,300 calBP) indicate burning between 500-700°C, documenting early use of dung fuel by hunter-gatherers as a supplement to wood, coeval with a dramatic shift to rectilinear architecture, increasing proportions of wild sheep and aurochsen, reduced emphasis on small game, and elevated dung concentrations immediately outside the 1B dwelling. Combined, these observations suggest that small numbers of live animals (possibly wild sheep) were tended on-site by Epipalaeolithic hunter-gatherers to supplement gazelle hunting, raising the question of whether early experiments in animal management emerged contemporaneously with, or pre-date, cultivation. Dung was used to prepare plaster floors during the Neolithic and continued to be burned as a supplemental fuel, indicating that spherulites were deposited via multiple human- and animal-related pathways. This has important implications for interpretations of archaeobotanical assemblages across the region. Spherulite concentrations dropped abruptly during Neolithic 2B (9,300-8,000 calBP) and 2C (8,000-7,800 calBP), when sheep/goat herding surpassed gazelle hunting, possibly corresponding with movement of animals away from the site as herd sizes increased. As hunter-gatherers at Abu Hureyra began interacting with wild taxa in different ways, they set in motion a remarkable transformation in the ways people interacted with animals, plants, and their environment.

Isotope evidence for agricultural extensification reveals how the world's first cities were fed.

This study sheds light on the agricultural economy that underpinned the emergence of the first urban centres in northern Mesopotamia. Using δ13C and δ15N values of crop remains from the sites of Tell Sabi Abyad, Tell Zeidan, Hamoukar, Tell Brak and Tell Leilan (6500-2000 cal bc), we reveal that labour-intensive practices such as manuring/middening and water management formed an integral part of the agricultural strategy from the seventh millennium bc. Increased agricultural production to support growing urban populations was achieved by cultivation of larger areas of land, entailing lower manure/midden inputs per unit area-extensification. Our findings paint a nuanced picture of the role of agricultural production in new forms of political centralization. The shift towards lower-input farming most plausibly developed gradually at a household level, but the increased importance of land-based wealth constituted a key potential source of political power, providing the possibility for greater bureaucratic control and contributing to the wider societal changes that accompanied urbanization.

Recovery from cycling exercise: effects of carbohydrate and protein beverages.

The effects of different carbohydrate-protein (CHO + Pro) beverages were compared during recovery from cycling exercise. Twelve male cyclists (VO(2peak): 65 ± 7 mL/kg/min) completed ~1 h of high-intensity intervals (EX1). Immediately and 120 min following EX1, subjects consumed one of three calorically-similar beverages (285-300 kcal) in a cross-over design: carbohydrate-only (CHO; 75 g per beverage), high-carbohydrate/low-protein (HCLP; 45 g CHO, 25 g Pro, 0.5 g fat), or low-carbohydrate/high-protein (LCHP; 8 g CHO, 55 g Pro, 4 g fat). After 4 h of recovery, subjects performed subsequent exercise (EX2; 20 min at 70% VO(2peak) + 20 km time-trial). Beverages were also consumed following EX2. Blood glucose levels (30 min after beverage ingestion) differed across all treatments (CHO > HCLP > LCHP; p < 0.05), and serum insulin was higher following CHO and HCLP ingestion versus LCHP. Peak quadriceps force, serum creatine kinase, muscle soreness, and fatigue/energy ratings measured pre- and post-exercise were not different between treatments. EX2 performance was not significantly different between CHO (48.5 ± 1.5 min), HCLP (48.8 ± 2.1 min) and LCHP (50.3 ± 2.7 min). Beverages containing similar caloric content but different proportions of carbohydrate/protein provided similar effects on muscle recovery and subsequent exercise performance in well-trained cyclists.

MARCO regulates early inflammatory responses against influenza: a useful macrophage function with adverse outcome.

Lung macrophages use the scavenger receptor MARCO to bind and ingest bacteria, particulate matter, and post cellular debris. We investigated the role of MARCO in influenza A virus (IAV) pneumonia. In contrast to higher susceptibility to bacterial infection, MARCO(-/-) mice had lower morbidity and mortality from influenza pneumonia than wild-type (WT) mice. The early course of influenza in MARCO(-/-) lungs was marked by an enhanced but transient neutrophilic inflammatory response and significantly lower viral replication compared with the WT mice. At later time points, no significant differences in lung histopathology or absolute numbers of T lymphocyte influx were evident. Uptake of IAV by WT and MARCO(-/-) bronchoalveolar lavage macrophages in vitro was similar. By LPS coadministration, we demonstrated that rapid neutrophil and monocyte influx during the onset of influenza suppressed viral replication, indicating a protective role of early inflammation. We hypothesized that the presence of increased basal proinflammatory post cellular debris in the absence of scavenging function lowered the inflammatory response threshold to IAV in MARCO(-/-) mice. Indeed, MARCO(-/-) mice showed increased accumulation of proinflammatory oxidized lipoproteins in the bronchoalveolar lavage early in the infection process, which are the potential mediators of the observed enhanced inflammation. These results indicate that MARCO suppresses a protective early inflammatory response to influenza, which modulates viral clearance and delays recovery.

First direct evidence of chalcolithic footwear from the near eastern highlands.

In 2008, a well preserved and complete shoe was recovered at the base of a Chalcolithic pit in the cave of Areni-1, Armenia. Here, we discuss the chronology of this find, its archaeological context and its relevance to the study of the evolution of footwear. Two leather samples and one grass sample from the shoe were dated at the Oxford Radiocarbon Accelerator Unit (ORAU). A third leather sample was dated at the University of California-Irvine Accelerator Mass Spectrometry Facility (UCIAMS). The R_Combine function for the three leather samples provides a date range of 3627-3377 Cal BC (95.4% confidence interval) and the calibrated range for the straw is contemporaneous (3627-3377 Cal BC). The shoe was stuffed with loose, unfastened grass (Poaceae) without clear orientation which was more than likely used to maintain the shape of the shoe and/or prepare it for storage. The shoe is 24.5 cm long (European size 37), 7.6 to 10 cm wide, and was made from a single piece of leather that wrapped around the foot. It was worn and shaped to the wearer's right foot, particularly around the heel and hallux where the highest pressure is exerted in normal gait. The Chalcolithic shoe provides solid evidence for the use of footwear among Old World populations at least since the Chalcolithic. Other 4th millennium discoveries of shoes (Italian and Swiss Alps), and sandals (Southern Israel) indicate that more than one type of footwear existed during the 4th millennium BC, and that we should expect to discover more regional variations in the manufacturing and style of shoes where preservation conditions permit.

Selective impairment in dendritic cell function and altered antigen-specific CD8+ T-cell responses in diet-induced obese mice infected with influenza virus.

There is a clear link between obesity and metabolic disorders; however, little is known about the effect of obesity on immune function, particularly during an infection. We have previously reported that diet-induced obese mice are more susceptible to morbidity and mortality during influenza infection than lean mice. Obese mice displayed aberrant innate immune responses characterized by minimal induction of interferon (IFN)-alpha/beta, delayed expression of pro-inflammatory cytokines and chemokines, and impaired natural killer cell cytotoxicity. To further examine the abnormal immune response of diet-induced obese mice, we analysed the cellularity of their lungs during influenza virus infection. We found delayed mononuclear cell entry with a marked decrease in dendritic cells (DCs) throughout the infection. Given the critical role of the DC in activating the cell-mediated immune response, we also analysed the functional capacity of DCs from obese mice. We found that, while obesity did not interfere with antigen uptake and migration, it did impair DC antigen presentation. This was probably attributable to an altered cytokine milieu, as interleukin (IL)-2, IL-12, and IL-6 were differentially regulated in the obese mice. Overall, this did not impact the total number of virus-specific CD8(+) T cells that were elicited, but did affect the number and frequency of CD3(+) and CD8(+) T cells in the lung. Thus, obesity interferes with cellular responses during influenza infection, leading to alterations in the T-cell population that ultimately may be detrimental to the host.

Diet-induced obese mice have increased mortality and altered immune responses when infected with influenza virus.

Obesity is associated with an impaired immune response, an increased susceptibility to bacterial infection, and a chronic increase in proinflammatory cytokines such as IL-6 and TNFalpha. However, few studies have examined the effect of obesity on the immune response to viral infections. Because infection with influenza is a leading cause of morbidity and mortality worldwide, we investigated the effect of obesity on early immune responses to influenza virus exposure. Diet-induced obese and lean control C57BL/6 mice were infected with influenza A/PR8/34, and lung pathology and immune responses were examined at d 0 (uninfected), 3, and 6, postinfection. Following infection, diet-induced obese mice had a significantly higher mortality rate than the lean controls and elevated lung pathology. Antiviral and proinflammatory cytokine mRNA production in the lungs of the infected mice was markedly different between obese and lean mice. IFNalpha and beta were only minimally expressed in the infected lungs of obese mice and there was a notable delay in expression of the proinflammatory cytokines IL-6 and TNFalpha. Additionally, obese mice had a substantial reduction in NK cell cytotoxicity. These data indicate that obesity inhibits the ability of the immune system to appropriately respond to influenza infection and suggests that obesity may lead to increased morbidity and mortality from viral infections.