Insights into the genetic histories and lifeways of Machu Picchu's occupants.

Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Dispatch from the field II: the mystery of the red and blue Opadometa male (Araneae, Tetragnathidae, Opadometa sarawakensis).

BACKGROUND: Males of Opadometa are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex matching in this genus suggest finding a male in the web of a female, or better yet, mating pairs. NEW INFORMATION: A male Opadometa was observed hanging on a frame line of the web of a female Opadometa sarawakensis, a species for which the male was previously undescribed. This occurred during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description was completed as a course activity.

Exchangeable proton ENDOR as a probe of the redox-active iron center in activated bleomycin and ferric bleomycin.

Activated bleomycin (ABLM) is a drug-Fe(iii)-hydroperoxide complex kinetically competent in DNA attack (via H4' abstraction). This intermediate is relatively stable, but its spontaneous conversion to ferric bleomycin (Fe(iii)·BLM) is poorly characterized because no observable intermediate product accumulates. The Fe(iii)·BLM formed cryophotolytically from ABLM and kept at 77 K was remarkably similar by EPR and ENDOR criteria to Fe(iii)·BLM formed from Fe(iii) + BLM solution. The notable ENDOR criteria were the ENDOR frequencies and features of orientation-selected, strongly hyperfine-coupled, exchangeable protons associated with the environs of the iron within <3.5 Å of paramagnetic Fe(iii) in Fe(iii)·BLM and ABLM. Cryophotolytic conversion of activated bleomycin to its ferric bleomycin product in the frozen solid is a sign that the reaction requires only constrained local proton rearrangements. We have characterized the metal-proton distances and orientations of the protons in that rearrangement, especially noting that these protons are of mechanistic importance in the ambient temperature conversion of ABLM to Fe(iii)·BLM in concert with a directed radical-forming attack on DNA.

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Use and legacy of mercury in the Andes.

Both cinnabar (HgS) and metallic mercury (Hg(0)) were important resources throughout Andean prehistory. Cinnabar was used for millennia to make vermillion, a red pigment that was highly valued in pre-Hispanic Peru; metallic Hg(0) has been used since the mid-16th century to conduct mercury amalgamation, an efficient process of extracting precious metals from ores. However, little is known about which cinnabar deposits were exploited by pre-Hispanic cultures, and the environmental consequences of Hg mining and amalgamation remain enigmatic. Here we use Hg isotopes to source archeological cinnabar and to fingerprint Hg pollution preserved in lake sediment cores from Peru and the Galápagos Islands. Both pre-Inca (pre-1400 AD) and Colonial (1532-1821 AD) archeological artifacts contain cinnabar that matches isotopically with cinnabar ores from Huancavelica, Peru, the largest cinnabar-bearing district in Central and South America. In contrast, the Inca (1400-1532 AD) artifacts sampled are characterized by a unique Hg isotopic composition. In addition, preindustrial (i.e., pre-1900 AD) Hg pollution preserved in lake sediments matches closely the isotopic composition of cinnabar from the Peruvian Andes. Industrial-era Hg pollution, in contrast, is distinct isotopically from preindustrial emissions, suggesting that pre- and postindustrial Hg emissions may be distinguished isotopically in lake sediment cores.

Specific function of the Met-Tyr-Trp adduct radical and residues Arg-418 and Asp-137 in the atypical catalase reaction of catalase-peroxidase KatG.

Catalase activity of the dual-function heme enzyme catalase-peroxidase (KatG) depends on several structural elements, including a unique adduct formed from covalently linked side chains of three conserved amino acids (Met-255, Tyr-229, and Trp-107, Mycobacterium tuberculosis KatG numbering) (MYW). Mutagenesis, electron paramagnetic resonance, and optical stopped-flow experiments, along with calculations using density functional theory (DFT) methods revealed the basis of the requirement for a radical on the MYW-adduct, for oxyferrous heme, and for conserved residues Arg-418 and Asp-137 in the rapid catalase reaction. The participation of an oxyferrous heme intermediate (dioxyheme) throughout the pH range of catalase activity is suggested from our finding that carbon monoxide inhibits the activity at both acidic and alkaline pH. In the presence of H(2)O(2), the MYW-adduct radical is formed normally in KatG[D137S] but this mutant is defective in forming dioxyheme and lacks catalase activity. KatG[R418L] is also catalase deficient but exhibits normal formation of the adduct radical and dioxyheme. Both mutants exhibit a coincidence between MYW-adduct radical persistence and H(2)O(2) consumption as a function of time, and enhanced subunit oligomerization during turnover, suggesting that the two mutations disrupting catalase turnover allow increased migration of the MYW-adduct radical to protein surface residues. DFT calculations showed that an interaction between the side chain of residue Arg-418 and Tyr-229 in the MYW-adduct radical favors reaction of the radical with the adjacent dioxyheme intermediate present throughout turnover in WT KatG. Release of molecular oxygen and regeneration of resting enzyme are thereby catalyzed in the last step of a proposed catalase reaction.

Protection of melanized Cryptococcus neoformans from lethal dose gamma irradiation involves changes in melanin's chemical structure and paramagnetism.

Certain fungi thrive in highly radioactive environments including the defunct Chernobyl nuclear reactor. Cryptococcus neoformans (C. neoformans), which uses L-3,4-dihydroxyphenylalanine (L-DOPA) to produce melanin, was used here to investigate how gamma radiation under aqueous aerobic conditions affects the properties of melanin, with the aim of gaining insight into its radioprotective role. Exposure of melanized fungal cell in aqueous suspensions to doses of γ-radiation capable of killing 50 to 80% of the cells did not lead to a detectable loss of melanin integrity according to EPR spectra of melanin radicals. Moreover, upon UV-visible (Xe-lamp) illumination of melanized cells, the increase in radical population was unchanged after γ-irradiation. Gamma-irradiation of frozen cell suspensions and storage of samples for several days at 77 K however, produced melanin modification noted by a reduced radical population and reduced photoresponse. More direct evidence for structural modification of melanin came from the detection of soluble products with absorbance maxima near 260 nm in supernatants collected after γ-irradiation of cells and cell-free melanin. These products, which include thiobarbituric acid (TBA)-reactive aldehydes, were also generated by Fenton reagent treatment of cells and cell-free melanin. In an assay of melanin integrity based on the metal (Bi(+3)) binding capacity of cells, no detectable loss in binding was detected after γ-irradiation. Our results show that melanin in C. neoformans cells is susceptible to some damage by hydroxyl radical formed in lethal radioactive aqueous environments and serves a protective role in melanized fungi that involves sacrificial breakdown.

Superoxide protects Escherichia coli from bleomycin mediated lethality.

Superoxide and its products, especially hydroxyl radical, were recently proposed to be instrumental in cell death following treatment with a wide range of antimicrobials. Surprisingly, bleomycin lethality to Escherichia coli was ameliorated by a genetic deficiency of superoxide dismutase or by furnishing the superoxide generator plumbagin. Rescue by plumbagin was similar in strains containing or lacking recA or with inactive, inducible, or constitutive soxRS regulons. Thus, superoxide interferes with bleomycin cytotoxicity in ways not readily explained by genetic pathways expected to protect from oxidative damage.

Cryogenic photolysis of activated bleomycin to ferric bleomycin.

Activated bleomycin (ABLM) is a drug--Fe(III)-hydroperoxide complex kinetically competent in DNA attack (via H4' abstraction). This intermediate is relatively stable, but its spontaneous conversion to ferric bleomycin (Fe(III).BLM) is poorly characterized because no observable intermediate product accumulates. Light was shown to trigger ABLM attack on DNA in liquid at -30 degrees C, so ABLM was irradiated (at its 350 nm ligand-to-metal charge-transfer transition) at 77 K to stabilize possible intermediates. ABLM photolysis (quantum yield, Phi = 0.005) generates two kinds of product: Fe(III).BLM (with no detectable intermediate) and one or more minor (1-2%) radical O-Fe-BLM byproduct, photostable at 77 K. Adding DNA, even without its target H4', increases the quantum yield of ABLM conversion >10-fold while suppressing the observed radical yield. Since cryogenic solid-phase reactions can entail only constrained local rearrangement, the reaction(s) converting ABLM to Fe(III).BLM must be similarly constrained.