Ancient DNA from Guam and the peopling of the Pacific.

Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan's First Neolithic Crops.

This study presents the first directly dated physical evidence of crop remains from the Early Neolithic archaeological layers in Taiwan. Systematic sampling and analysis of macro-plant remains suggested that Neolithic farmers at the Zhiwuyuan (Botanical Garden) site in Taipei, northern Taiwan, had cultivated rice and foxtail millet together at least 4,500 years ago. A more comprehensive review of all related radiocarbon dates suggests that agriculture emerged in Taiwan around 4,800-4,600 cal. BP, instead of the previous claim of 5,000 cal. BP. According to the rice grain metrics from three study sites of Zhiwuyuan, Dalongdong, and Anhe, the rice cultivated in northern and western-central Taiwan was mainly a short-grained type of the japonica subspecies, similar to the discoveries from the southeast coast of mainland China and the middle Yangtze valley. These new findings support the hypothesis that the southeast coast of mainland China was the origin of proto-Austronesian people who brought their crops and other cultural traditions across the Taiwan Strait 4,800 years ago and eventually farther into Island Southeast Asia.

Rice and millet cultivated in Ha Long Bay of Northern Vietnam 4000 years ago.

Research has generally outlined that the Neolithic East Asian farmers expanded into Southeast Asia, leading to substantial social and cultural transformations. However, the associated archaeobotanical evidence until now has been insufficient to clarify the exact timing, dispersal route, and farming package of the emergence of agriculture in Mainland Southeast Asia. To clarify these issues, the micro-plant remains of phytolith and starch from three Neolithic sites in Ha Long Bay were extracted and analyzed. This study validates the earliest evidence of co-cropping in northern Vietnam, involving the cultivation of rice together with foxtail millet at 4000 years BP or slightly earlier. Moreover, the results indicate that at least two patterns of subsistence strategy were practiced simultaneously during the initial farming phase in the region. The Trang Kenh people, a regional variant of the Phung Nguyen cultural group often have been seen as the first farmers in northern Vietnam, and they mainly practiced a cereal-based subsistence strategy with more vital cultural characteristics of southern China origin. Meanwhile, the Ha Long people, mainly composed of indigenous hunter-gatherer descendants, continued to utilize a wide range of their preferred plant resources such as taros, yams, and acorns, while they absorbed and incorporated new elements such as millet and rice into their food system. This study provides solid information to understand the diverse economic systems among different cultural groups in Vietnam.

Validating earliest rice farming in the Indonesian Archipelago.

Preserved ancient botanical evidence in the form of rice phytoliths has confirmed that people farmed domesticated rice (Oryza sativa) in the interior of Sulawesi Island, Indonesia, by at least 3,500 years ago. This discovery helps to resolve a mystery about one of the region's major events in natural and cultural history, by documenting when rice farming spread into Indonesia, ultimately from a source in mainland China. At the Minanga Sipakko site in Sulawesi, preserved leaf and husk phytoliths of rice show the diagnostic morphology of domesticated varieties, and the discarded husks indicate on-site processing of the crops. The phytoliths were contained within an undisturbed, subsurface archaeological layer of red-slipped pottery, a marker for an evidently sudden cultural change in the region that multiple radiocarbon results extend back to 3,500 years ago. The results from Minanga Sipakko allow factual evaluation of previously untested hypotheses about the timing, geographic pattern, and cultural context of the spread of rice farming into Indonesia, as well as the contribution of external immigrants in this process.

Correction: Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures.

[This corrects the article DOI: 10.1371/journal.pone.0039171.].

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

The SGCEdb (http://sgce.cbse.uab.edu) database/interface serves the primary purpose of reporting progress of the Structural Genomics of Caenorhabditis elegans project at the University of Alabama at Birmingham. It stores and analyzes results of experiments ranging from solubility screening arrays to individual protein purification and structure solution. External databases and algorithms are referenced and evaluated for target selection in the human, C.elegans and Pneumocystis carinii genomes. The flexible and reusable design permits tracking of standard and custom experiment types in a scientist-defined sequence. The database coordinates efforts between collaborators and is adaptable to a wide range of biological applications.

Genotype by environment interaction for growth and Dothistroma resistance and clonal connectivity between environments in radiata pine in New Zealand and Australia.

Twenty-eight clonal trials of radiata pine planted across Australia and New Zealand were used to investigate genetic variation and genotype by environment (G×E) interaction for diameter-at-breast-height (DBH), height and Dothistroma resistance (DO_R). The average narrow-sense heritabilities were 0.11, 0.21 and 0.30 while the average broad-sense heritabilities were 0.27, 0.34 and 0.40 for DBH, height and Dothistroma resistance, respectively. Dothistroma resistance was assessed as the percentage of needles that were not affected by Dothistroma needle blight. G×E interactions were analysed using an approximate reduced factor analytic model. Apparent G×E interactions were estimated for DBH, height and Dothistroma resistance. Estimates of G×E interactions and their standard errors were strongly influenced by the level of connectivity between trials, in terms of common clones and common parents. When there was sufficient connectivity between trials (more than 30% common clones between trials), a high level of G×E interaction was found for DBH and height but not for Dothistroma resistance. In two simulated clonal trials planted in two environments, low connectivity between environments resulted in a lower estimated genetic correlation between environments with an increased standard error. These results suggest that the number of clones in common between clonal trials is a key factor for inclusion in future experimental designs for estimating G×E interaction. When designing clonal trials for use in multiple environments for accurately estimating the level of G×E, if the resource for creating connectivity between environments is limited, at least 30% of the clones need to be in common between environments.

Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.

Spontaneous formation of isoaspartyl residues (isoAsp) disrupts the structure and function of many normal proteins. Protein isoaspartyl methyltransferase (PIMT) reverts many isoAsp residues to aspartate as a protein repair process. We have determined the crystal structure of human protein isoaspartyl methyltransferase (HPIMT) complexed with adenosyl homocysteine (AdoHcy) to 1.6-A resolution. The core structure has a nucleotide binding domain motif, which is structurally homologous with the N-terminal domain of the bacterial Thermotoga maritima PIMT. Highly conserved residues in PIMTs among different phyla are placed at positions critical to AdoHcy binding and orienting the isoAsp residue substrate for methylation. The AdoHcy is completely enclosed within the HPIMT and a conformational change must occur to allow exchange with adenosyl methionine (AdoMet). An ordered sequential enzyme mechanism is supported because C-terminal residues involved with AdoHcy binding also form the isoAsp peptide binding site, and a change of conformation to allow AdoHcy to escape would preclude peptide binding. Modeling experiments indicated isoAsp groups observed in some known protein crystal structures could bind to the HPIMT active site.

Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures.

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.

His-tag impact on structure.

Crystallographers are increasingly determining structures of protein constructs that include His tags. Many have taken for granted that these tags have little effect on the native structure. This paper surveys and compares crystal structures with and without His tags. It is observed that actual refined tag residues fitted into density occur in less that 10% of the tagged sequences. However, higher resolution crystals are observed when this occurs. It is shown that these purification tags generally have no significant effect on the structure of the native protein. Resolution and R factors are not affected, but the overall B factors are slightly higher. Additional annotation in the PDB format to make tag definition explicit is suggested.

Crystal structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor.

Reduced pteridines are required for a number of important cellular functions. Trypanosomatid parasites, unlike their mammalian hosts, are pteridine auxotrophs and salvage the precursor pteridines from the host and reduce them to the respective biologically active tetrahydro forms using parasite-encoded enzymes. These enzymes may offer selective drug targets. In Leishmania, pteridine reductase 1 (PTR1), the primary enzyme for reducing pterins, is also responsible for resistance to antifolate drugs. Typically, PTR1 is more active with fully oxidized biopterin and folate than with their reduced counterparts. We have identified an enzyme, TcPTR2 of Trypanosoma cruzi, which though very similar to PTR1 in its primary sequence, can reduce only dihydrobiopterin and dihydrofolate and not oxidized pteridines. The structures of an inhibitor (methotrexate) and a substrate (dihydrofolate) complex of this enzyme demonstrate that the orientation of the substrate and the inhibitor in the active site of TcPTR2 are different from each other. However, the orientation of each ligand is similar to that of the corresponding ligand in Leishmania major PTR1 complexes.

A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A.

We report here the crystal structure of the minimal ligand-binding segment of the Staphylococcus aureus MSCRAMM, clumping factor A. This fibrinogen-binding segment contains two similarly folded domains. The fold observed is a new variant of the immunoglobulin motif that we have called DE-variant or the DEv-IgG fold. This subgroup includes the ligand-binding domain of the collagen-binding S.aureus MSCRAMM CNA, and many other structures previously classified as jelly rolls. Structure predictions suggest that the four fibrinogen-binding S.aureus MSCRAMMs identified so far would also contain the same DEv-IgG fold. A systematic docking search using the C-terminal region of the fibrinogen gamma-chain as a probe suggested that a hydrophobic pocket formed between the two DEv-IgG domains of the clumping factor as the ligand-binding site. Mutagenic substitution of residues Tyr256, Pro336, Tyr338 and Lys389 in the clumping factor, which are proposed to contact the terminal residues (408)AGDV(411) of the gamma-chain, resulted in proteins with no or markedly reduced affinity for fibrinogen.

High-throughput expression of C. elegans proteins.

Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in a structural proteomics initiative because of the high quality of its genome sequence and the availability of its ORFeome, protein-encoding open reading frames (ORFs), in a flexible recombinational cloning format. We developed a robotic pipeline for recombinant protein expression, applying the Gateway cloning/expression technology and utilizing a stepwise automation strategy on an integrated robotic platform. Using the pipeline, we have carried out heterologous protein expression experiments on 10,167 ORFs of C. elegans. With one expression vector and one Escherichia coli strain, protein expression was observed for 4854 ORFs, and 1536 were soluble. Bioinformatics analysis of the data indicates that protein hydrophobicity is a key determining factor for an ORF to yield a soluble expression product. This protein expression effort has investigated the largest number of genes in any organism to date. The pipeline described here is applicable to high-throughput expression of recombinant proteins for other species, both prokaryotic and eukaryotic, provided that ORFeome resources become available.

Crystal structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain.

Cytoskeleton-associated proteins (CAPs) are involved in the organization of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of the CAP-Gly domain of Caenorhabditis elegans F53F4.3 protein, solved by single wavelength sulfur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove.