Using Ancient Samples in Projection Analysis.

Projection analysis is a tool that extracts information from the joint allele frequency spectrum to better understand the relationship between two populations. In projection analysis, a test genome is compared to a set of genomes from a reference population. The projection's shape depends on the historical relationship of the test genome's population to the reference population. Here, we explore in greater depth the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model), or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model). We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present-day population or not. Second, we compute projections for several published ancient genomes. We compare two Neanderthals and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these five ancient genomes to assess how well the observed projections are recovered

Satellite Climatology of Tropical Cyclone with Concentric Eyewalls

An objective method is developed to identify concentric eyewalls (CEs) for tropical cyclones (TCs) using passive microwave satellite imagery from 1997 to 2014 in the western North Pacific (WNP) and Atlantic (ATL) basin. There are 91 (33) TCs and 113 (50) cases with CE identified in the WNP (ATL). Three CE structural change types are classified as follows: a CE with the inner eyewall dissipated in an eyewall replacement cycle (ERC, 51 and 56% in the WNP and ATL), a CE with the outer eyewall dissipated first and the no eyewall replacement cycle (NRC, 27 and 29% in the WNP and ATL), and a CE structure that is maintained for an extended period (CEM, 23 and 15% in the WNP and ATL). The moat size and outer eyewall width in the WNP (ATL) basin are approximately 20–50% (15–25%) larger in the CEM cases than that in the ERC and NRC cases. Our analysis suggests that the ERC cases are more likely dominated by the internal dynamics, whereas the NRC cases are heavily influenced by the environment condition, and both the internal and environmental conditions are important in the CEM cases. A good correlation of the annual CE TC number and the Oceanic Niño index is found (0.77) in WNP basin, with most of the CE TCs occurring in the warm episodes. In contrast, the El Niño/Southern Oscillation (ENSO) may not influence on the CE formation in the ATL basin. After the CE formation, however, the unfavorable environment that is created by ENSO may reduce the TC intensity quickly during warm episode. The variabilities of structural changes in the WNP basin are larger than that in the ATL basin

Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau

A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau

Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

Background: Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution. Results: H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date. Conclusion: The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster

Pines’ demon observed as a 3D acoustic plasmon in Sr₂RuO₄

Sr2RuO4での「パインズの悪魔」の観測 67年前に予言された金属の奇妙な振る舞いの発見. 京都大学プレスリリース. 2023-08-10.Speak of the Demon: Discovery of strange behavior of new plasmons predicted in the 50s. 京都大学プレスリリース. 2023-09-25.The characteristic excitation of a metal is its plasmon, which is a quantized collective oscillation of its electron density. In 1956, David Pines predicted that a distinct type of plasmon, dubbed a ‘demon’, could exist in three-dimensional (3D) metals containing more than one species of charge carrier. Consisting of out-of-phase movement of electrons in different bands, demons are acoustic, electrically neutral and do not couple to light, so have never been detected in an equilibrium, 3D metal. Nevertheless, demons are believed to be critical for diverse phenomena including phase transitions in mixed-valence semimetals, optical properties of metal nanoparticles, soundarons in Weyl semimetals and high-temperature superconductivity in, for example, metal hydrides. Here, we present evidence for a demon in Sr₂RuO₄ from momentum-resolved electron energy-loss spectroscopy. Formed of electrons in the β and γ bands, the demon is gapless with critical momentum qc = 0.08 reciprocal lattice units and room-temperature velocity v = (1.065 ± 0.12) × 10⁵ m s⁻¹ that undergoes a 31% renormalization upon cooling to 30 K because of coupling to the particle–hole continuum. The momentum dependence of the intensity of the demon confirms its neutral character. Our study confirms a 67-year old prediction and indicates that demons may be a pervasive feature of multiband metals

Childhood Obesity Prevention and Treatment Research (COPTR): Interventions addressing multiple influences in childhood and adolescent obesity

Obesity is a major public health problem affecting more than 12 million (~17%)U.S. children. The scientific community agrees that tackling this problem must begin in childhood to reduce risk of subsequent development of cardiovascular diseases and other chronic diseases. The Childhood Obesity Prevention and Treatment Research (COPTR) Consortium, initiated by the National Institutes of Health (NIH), is conducting intervention studies to prevent obesity in pre-schoolers and treat overweight or obese 7–13 year olds. Four randomized controlled trials plan to enroll a total of 1,700 children and adolescents (~ 50% female, 70% minorities), and are testing innovative multi-level and multi-component interventions in multiple settings involving primary care physicians, parks and recreational centers, family advocates, and schools. For all the studies, the primary outcome measure is body mass index; secondary outcomes, moderators and mediators of intervention include diet, physical activity, home and neighborhood influences, and psychosocial factors. COPTR is being conducted collaboratively among four participating field centers, a coordinating center, and NIH project offices

Brute-Force Mapmaking with Compact Interferometers: A MITEoR Northern Sky Map from 128 MHz to 175 MHz

We present a new method for interferometric imaging that is ideal for the large fields of view and compact arrays common in 21 cm cosmology. We first demonstrate the method with the simulations for two very different low-frequency interferometers, the Murchison Widefield Array and the MIT Epoch of Reionization (MITEoR) experiment. We then apply the method to the MITEoR data set collected in 2013 July to obtain the first northern sky map from 128 to 175 MHz at ∼2° resolution and find an overall spectral index of −2.73 ± 0.11. The success of this imaging method bodes well for upcoming compact redundant low-frequency arrays such as Hydrogen Epoch of Reionization Array. Both the MITEoR interferometric data and the 150 MHz sky map are available at http://space.mit.edu/home/tegmark/omniscope.html.National Science Foundation (U.S.) (AST-0908848)National Science Foundation (U.S.) (AST-1105835)National Science Foundation (U.S.) (AST-1440343

Real-time PCR-based assay to quantify the relative amount of human and mouse tissue present in tumor xenografts

<p>Abstract</p> <p>Background</p> <p>Xenograft samples used to test anti-cancer drug efficacies and toxicities in vivo contain an unknown mix of mouse and human cells. Evaluation of drug activity can be confounded by samples containing large amounts of contaminating mouse tissue. We have developed a real-time quantitative polymerase chain reaction (qPCR) assay using TaqMan technology to quantify the amount of mouse tissue that is incorporated into human xenograft samples.</p> <p>Results</p> <p>The forward and reverse primers bind to the same DNA sequence in the human and the mouse genome. Using a set of specially designed fluorescent probes provides species specificity. The linearity and sensitivity of the assay is evaluated using serial dilutions of single species and heterogeneous DNA mixtures. We examined many xenograft samples at various in vivo passages, finding a wide variety of human:mouse DNA ratios. This variation may be influenced by tumor type, number of serial passages in vivo, and even which part of the tumor was collected and used in the assay.</p> <p>Conclusions</p> <p>This novel assay provides an accurate quantitative assessment of human and mouse content in xenograft tumors. This assay can be performed on aberrantly behaving human xenografts, samples used in bioinformatics studies, and periodically for tumor tissue frequently grown by serial passage in vivo.</p

Seasonal melting and the formation of sedimentary rocks on Mars, with predictions for the Gale Crater mound

A model for the formation and distribution of sedimentary rocks on Mars is proposed. The rate-limiting step is supply of liquid water from seasonal melting of snow or ice. The model is run for a O(10^2) mbar pure CO2 atmosphere, dusty snow, and solar luminosity reduced by 23%. For these conditions snow only melts near the equator, and only when obliquity >40 degrees, eccentricity >0.12, and perihelion occurs near equinox. These requirements for melting are satisfied by 0.01-20% of the probability distribution of Mars' past spin-orbit parameters. Total melt production is sufficient to account for aqueous alteration of the sedimentary rocks. The pattern of seasonal snowmelt is integrated over all spin-orbit parameters and compared to the observed distribution of sedimentary rocks. The global distribution of snowmelt has maxima in Valles Marineris, Meridiani Planum and Gale Crater. These correspond to maxima in the sedimentary-rock distribution. Higher pressures and especially higher temperatures lead to melting over a broader range of spin-orbit parameters. The pattern of sedimentary rocks on Mars is most consistent with a Mars paleoclimate that only rarely produced enough meltwater to precipitate aqueous cements and indurate sediment. The results suggest intermittency of snowmelt and long globally-dry intervals, unfavorable for past life on Mars. This model makes testable predictions for the Mars Science Laboratory rover at Gale Crater. Gale Crater is predicted to be a hemispheric maximum for snowmelt on Mars.Comment: Submitted to Icarus. Minor changes from submitted versio