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At least 847 records · Page 47

High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass

Abstract Switchgrass ( Panicum virgatum L.), a native warm‐season perennial grass, is being considered as a feedstock for biofuel production in the United States. To expedite its genetic improvement and enhance genetic gain per selection cycle, application of marker‐assisted selection is indispensable. A high‐density linkage map was constructed in a pseudo‐F 1 testcross mapping population of AP13×VS16, consisting of 349 progenies. A total of 8,757 single nucleotide polymorphism (SNP) markers generated through genotype‐by‐sequencing (GBS) were used to construct the linkage map. The total map length spans up to 2,540.2 cM with the marker density of one marker in every 0.25–0.34 cM. Spring green‐up (SG), days to flowering (FL), and the vegetative growth period (VP) data were analyzed and used for quantitative trait loci (QTL) mapping. The population showed significant variations and exhibited transgressive segregation for SG, FL, and VP. QTL analyses were performed using trait mean of each year and location along with BLUP (best linear unbiased prediction) values of the traits. A total of 35, 37, and 34 QTL for SG, FL, and VP, respectively, were identified. Phenotypic variability explained by each QTL ranged from 11.29% to 27.85%. The additive genetic effects of individual QTL ranged from −1.81 to 2.40, −6.12 to 7.58, and −16.01 to 6.38 for SG, FL, and VP, respectively. Comparing major QTL regions in the switchgrass genome, 20 candidate genes were identified which were reported to be involved in growth‐, development‐, and flowering‐related traits in switchgrass.

Ali, Shahjahan↗

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗

Observations of plasma distributions during the coordinated data analysis workshop substorms of March 31 to April 1, 1979

On March 31 and April 1, 1979, a sequence of substorms was recorded on the ground. During the entire active period the ISEE 1 and 2 satellites were located in the magnetotail, between 22 R(E) and 12 R(E) from the earth. Observations of plasma distributions made at varying levels of activity during these substorms provide good examples of typical magnetotail responses. While the entire magnetotail undergoes temporal variations during substorm activity, the most obvious effect seen is spatial motion of preexisting plasma regimes; for example, at substorm onset the central plasma sheet contracts. This can cause a spacecraft to move from the plasma sheet into the boundary layer. As the plasma sheet boundary layer almost always comprises streaming plasma, the high-speed flows observed there are not necessarily due to the substorm process. The essential nature of the main plasma regions of the magnetotail is relatively unchanged during high activity.

Huang, C. Y.↗

The Evolution of Sulfide Tolerance in the Cyanobacteria

Understanding how the function of extant microorganisms has recorded both their evolutionary histories and their past interactions with the environment is a stated goal of astrobiology. We are taking a multidisciplinary approach to investigate the diversification of sulfide tolerance mechanisms in the cyanobacteria, which vary both in their degree of exposure to sulfide and in their capacity to tolerate this inhibitor of photosynthetic electron transport. Since conditions were very reducing during the first part of Earth's history and detrital sulfides have been found in Archean sediments, mechanisms conferring sulfide tolerance may have been important for the evolutionary success of the ancestors of extant cyanobacteria. Two tolerance mechanisms have been identified in this group: (1) resistance of photosystem II, the principal target of sulfide toxicity; and (2) maintenance of the ability to fix carbon despite photosystem II inhibition by utilizing sulfide as an electron donor in photosystem I - dependent, anoxygenic photosynthesis. We are presently collecting comparative data on aspects of sulfide physiology for laboratory clones isolated from a variety of habitats. These data will be analyzed within a phylogenetic framework inferred from molecular sequence data collected for these clones to test how frequently different mechanisms of tolerance have evolved and which tolerance mechanism evolved first. In addition, by analyzing these physiological data together with environmental sulfide data collected from our research sites using microelectrodes, we can also test whether the breadth of an organism's sulfide tolerance can be predicted from the magnitude of variation in environmental sulfide concentration it has experienced in its recent evolutionary past and whether greater average sulfide concentration and/or temporal variability in sulfide favors the evolution of a particular mechanism of sulfide tolerance.

Miller, Scott R.↗

Chuar Group of the Grand Canyon: record of breakup of Rodinia, associated change in the global carbon cycle, and ecosystem expansion by 740 Ma

The Chuar Group (approximately 1600 m thick) preserves a record of extensional tectonism, ocean-chemistry fluctuations, and biological diversification during the late Neoproterozoic Era. An ash layer from the top of the section has a U-Pb zircon age of 742 +/- 6 Ma. The Chuar Group was deposited at low latitudes during extension on the north-trending Butte fault system and is inferred to record rifting during the breakup of Rodinia. Shallow-marine deposition is documented by tide- and wave-generated sedimentary structures, facies associations, and fossils. C isotopes in organic carbon show large stratigraphic variations, apparently recording incipient stages of the marked C isotopic fluctuations that characterize later Neoproterozoic time. Upper Chuar rocks preserve a rich biota that includes not only cyanobacteria and algae, but also heterotrophic protists that document increased food web complexity in Neoproterozoic ecosystems. The Chuar Group thus provides a well-dated, high-resolution record of early events in the sequence of linked tectonic, biogeochemical, environmental, and biological changes that collectively ushered in the Phanerozoic Eon.

NASA Discipline Exobiology↗

Parallel iterative methods for a finite family of sequences of nearly nonexpansive mappings in Hilbert spaces

In this paper, we propose some new parallel iterative methods by the hybrid and shrinking projection to find a common fixed point of a finite family of sequences of nearly nonexpansive mappings in Hilbert spaces when the domain C satisfies diam(C) < ∞. We also give some applications of our main results for the problem of finding a common fixed point of nonexpansive mappings, nonexpansive semi-groups, the problem of finding a common zero point of monotone operators, the system of generalized mixed equilibrium problems and the system of variational inequalities without the condition diam(C) < ∞. Three numerical examples also are given to illustrate the effectiveness of the proposed algorithms.

97 MATHEMATICS AND COMPUTING↗

Massive star evolution and SN 1987A

The evolution of massive stars through hydrogen and helium burning is addressed. A set of stellar evolutionary sequences for mass/solar mass of 15, 20, and 25, and metallicity of 0.002, 0.005, 0.007, 0.010, and 0.20 are presented; semiconvection is restricted to operating slower than the local thermal time scale. Using these sequences, simple models of the massive star content of the LMC are found to agree moderately well with the new observational data of Fitzpatrick and Garmany (1990). LMC supergiants were detected only in their postmain-sequence phases, so that 5-10 times more massive stars are there but not identified as such. It is argued that SN 1987A exhibits the normal evolution of a single star of about 20 solar mases having LMC abundances. Despite the variety of envelope behavior, the structure of the core at collapse is rather similar for the stars of a given mass. Variations due to different rates of mass loss are likely to be larger than those due to composition.

Arnett, David↗

Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles

Photosystem II (PSII) catalyzes the oxidation of water at its active site that harbors a high-valent inorganic Mn 4 CaO x cluster called the oxygen-evolving complex (OEC). Extrinsic subunits generally serve to protect the OEC from reductants and stabilize the structure, but diversity in the extrinsic subunits exists between phototrophs. Recent cryo-electron microscopy experiments have provided new molecular structures of PSII with varied extrinsic subunits. We focus on the extrinsic subunit PsbQ, that binds to the mature PSII complex, and on Psb27, an extrinsic subunit involved in PSII biogenesis. PsbQ and Psb27 share a similar binding site and have a four-helix bundle tertiary structure, suggesting they are related. Here, we use sequence alignments, structural analyses, and binding simulations to compare PsbQ and Psb27 from different organisms. We find no evidence that PsbQ and Psb27 are related despite their similar structures and binding sites. Evolutionary divergence within PsbQ homologs from different lineages is high, probably due to their interactions with other extrinsic subunits that themselves exhibit vast diversity between lineages. This may result in functional variation as exemplified by large differences in their calculated binding energies. Psb27 homologs generally exhibit less divergence, which may be due to stronger evolutionary selection for certain residues that maintain its function during PSII biogenesis which is consistent with their more similar calculated binding energies between organisms. Previous experimental inconsistencies, low confidence binding simulations, and recent structural data suggest that Psb27 is likely to exhibit flexibility that may be an important characteristic of its activity. Furthermore, the analysis provides insight into the functions and evolution of PsbQ and Psb27, and an unusual example of proteins with similar tertiary structures and binding sites that probably serve different roles.

59 BASIC BIOLOGICAL SCIENCES↗

On the relation of host properties and environment of AGN galaxies across the standard optical diagnostic diagram

ABSTRACT We study the host properties and environment of active galactic nuclei (AGNs) galaxies, taken from SDSS-DR12, across the [O iii]/H β versus [N ii]/H α diagnostic diagram. We select AGN subsamples defined as parallel and perpendicular to the star-forming locus on the BPT diagram based on the Kauffmann et al. and Schawinski et al. criteria. For parallel subsamples we find that AGN host properties exhibit a morphological evolution as they become more distant to the star-forming sequence. The local density environment shows a more evident morphology–density relationship for subsamples mainly formed by Composite and Spiral galaxies than those containing LINERs and Seyferts, where the AGN emission is the dominant source. We also analyse the properties of the five closest AGN neighbours observing no significant differences in the environment, although the AGN host properties of every subsample have noticeable variations. The AGNs belonging to perpendicular subsamples show clear differences on their host properties from left top to right bottom on the diagram. However, the analysis of the local density environment do not reflect strong dependency with the host AGN properties. This result is reinforced by the characteristics of the AGN neighbouring galaxies. These findings suggest that mixed AGN/star-forming galaxies present environmental features more similar to that of non-active galaxies. However, as AGNs at the centre of the more evolved galaxies become the dominant source, the environment tends to provide suitable conditions for the central black hole feeding with an increasing content of gas and likelihood of a higher merger rate.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. Here, by performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. We found that SON and SC35 (also known as SRSF2) localize to the central region of the speckle, whereas MALAT1 and small nuclear (sn)RNAs are enriched at the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed speckle-associated genes could contribute to the observed speckle size variations within a single cell.

Fei, Jingyi↗

Adaptive Evolution of Sphingobium hydrophobicum C1 T in Electronic Waste Contaminated River Sediment

Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1 T , characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1 T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1 T and other Sphingobium strains, numerous C1 T -unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1 T . Moreover, presence of type IV secretion systems may allow strain C1 T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.

comparative genomics↗

Thermal emission spectroscopy of the middle atmosphere

The general objective of this research is to obtain, via remote sensing, simultaneous measurements of the vertical distributions of stratospheric temperature, ozone, and trace constituents that participate in the catalytic destruction of ozone (NO(sub y): NO, NO2, NO3, HNO3, ClONO2, N2O5, HNO4; Cl(sub x): HOCl), and the source gases for the catalytic cycles (H2O, CH4, N2O, CF2Cl2, CFCl3, CCl4, CH3Cl, CHF2Cl, etc.). Data are collected during a complete diurnal cycle in order to test our present understanding of ozone chemistry and its associate catalytic cycles. The instrumentation employed is an emission-mode, balloon-borne, liquid-nitrogen-cooled Michelson interferometer-spectrometer (SIRIS), covering the mid-infrared range with a spectral resolution of 0.020 cm(exp -1). Cryogenic cooling combined with the use of extrinsic silicon photoconductor detectors allows the detection of weak emission features of stratospheric gaseous species. Vertical distributions of these species are inferred from scans of the thermal emission of the limb in a sequence of elevation angles. The fourth SIRIS balloon flight was carried out from Palestine, Texas on September 15-16, 1986 with 9 hours of nighttime data (40 km). High quality data with spectral resolution 0.022 cm(exp -1), were obtained for numerous limb sequences. Fifteen stratospheric species have been identified to date from this flight: five species from the NO(sub y) family (HNO3, NO2, NO, ClONO2, N2O5), plus CO2, O3, H2O, N2O, CH4, CCl3F, CCl2F2, CHF2Cl, CF4, and CCl4. The nighttime values of N2O5, ClONO2, and total odd nitrogen have been measured for the first time, and compared to model results. Analysis of the diurnal variation of N2O5 within the 1984 and 1986 data sets, and of the 1984 ClONO2 measurements, were presented in the literature. The demonstrated ability of SIRIS to measure all the major NO(sub y) species, and therefore to determine the partitioning of the nitrogen family over a continuous diurnal cycle, is a powerful tool in the verification and improvement of photochemical modeling.

Kunde, V. G.↗

The orbital record in stratigraphy

Orbital signals are being discovered in pre-Pleistocene sediments. Due to their hierarchical nature these cycle patterns are complex, and the imprecision of geochronology generally makes the assignment of stratigraphic cycles to specific orbital cycles uncertain, but in sequences such as the limnic Newark Group under study by Olsen and pelagic Cretaceous sequence worked on by our Italo-American group the relative frequencies yield a definitive match to the Milankovitch hierarchy. Due to the multiple ways in which climate impinges on depositional systems, the orbital signals are recorded in a multiplicity of parameters, and affect different sedimentary facies in different ways. In platform carbonates, for example, the chief effect is via sea-level variations (possibly tied to fluctuating ice volume), resulting in cycles of emergence and submergence. In limnic systems it finds its most dramatic expression in alternations of lake and playa conditions. Biogenic pelagic oozes such as chalks and the limestones derived from them display variations in the carbonate supplied by planktonic organisms such as coccolithophores and foraminifera, and also record variations in the aeration of bottom waters. Whereas early studies of stratigraphic cyclicity relied mainly on bedding variations visible in the field, present studies are supplementing these with instrumental scans of geochemical, paleontological, and geophysical parameters which yield quantitative curves amenable to time-series analysis; such analysis is, however, limited by problems of distorted time-scales. My own work has been largely concentrated on pelagic systems. In these, the sensitivity of pelagic organisms to climatic-oceanic changes, combined with the sensitivity of botton life to changes in oxygen availability (commonly much more restricted in the Past than now) has left cyclic patterns related to orbital forcing. These systems are further attractive because (1) they tend to offer depositional continuity, and (2) presence of abundant microfossils yields close ties to geochronology. A tantalizing possibility that stratigraphy may yield a record of orbital signals unrelated to climate has turned up in magnetic studies of our Cretaceous core. Magnetic secular variations here carry a strong 39 ka periodicity, corresponding to the theoretical obliquity period of that time - Does the obliquity cycle perhaps have some direct influence on the magnetic field?

Fischer, Alfred G.↗

Oxygen and Magnesium Isotopic Compositions of Asteroidal Materials Returned from Itokawa by the Hayabusa Mission

The Hayabusa spacecraft made two touchdowns on the surface of Asteroid 25143 Itokawa on November 20th and 26th, 2005. The Asteroid 25143 Itokawa is classified as an S-type asteroid and inferred to consist of materials similar to ordinary chondrites or primitive achondrites [1]. Near-infrared spectroscopy by the Hayabusa spacecraft proposed that the surface of this body has an olivine-rich mineral assemblage potentially similar to that of LL5 or LL6 chondrites with different degrees of space weathering [2]. The spacecraft made the reentry into the Earth s atmosphere on June 12th, 2010 and the sample capsule was successfully recovered in Australia on June 13th, 2010. Although the sample collection processes on the Itokawa surface had not been made by the designed operations, more than 1,500 grains were identified as rocky particles in the sample curation facility of JAXA, and most of them were judged to be of extraterrestrial origin, and definitely from Asteroid Itokawa on November 17th, 2010 [3]. Although their sizes are mostly less than 10 microns, some larger grains of about 100 microns or larger were also included. The mineral assembly is olivine, pyroxene, plagioclase, iron sulfide and iron metal. The mean mineral compositions are consistent with the results of near-infrared spectroscopy from Hayabusa spacecraft [2], but the variations suggest that the petrologic type may be smaller than the spectroscopic results. Several tens of grains of relatively large sizes among the 1,500 grains will be selected by the Hayabusa sample curation team for preliminary examination [4]. Each grain will be subjected to one set of preliminary examinations, i.e., micro-tomography, XRD, XRF, TEM, SEM, EPMA and SIMS in this sequence. The preliminary examination will start from the last week of January 2011. Therefore, samples for isotope analyses in this study will start from the last week of February 2011. By the time of the LPSC meeting we will have measured the oxygen and magnesium isotopic composition of several grains. We will present the first results from the isotope analyses that will have been performed.

Yurimoto, H↗

THEMIS Observations of Directly-Driven Pi2 Pulsations

The THEMIS tail seasons have provided an unprecedented opportunity to examine the causal relationship between midtail plasma flows and low latitude Pi2 pulsations. We present several events where multiple THEMIS spacecraft observed magnetotail flow bursts which were followed up to several minutes later by ground Pi2 pulsations. We find good agreement with the waveforms of the flow bursts and flank Pi2, in agreement with the hypothesis that Pi2 at low-latitude on the flank are directly-driven by periodic variations in the flow bursts. For at least I event we are able to follow the Pi2 impulses from the periodic flow bursts on the nightside. to ground Pi2 at the flanks, and finally through the dayside magnetosphere as observed by GOES. We further place the physical mechanism generating these Pi2 into the context of sub storm onset. We conclude by discussing the sequence and coupling of events that are necessary to explain the correlation, and the constraints this places on models of transient magnetospheric transport.

Kepko, L.↗

Local Estimators for Spacecraft Formation Flying

A formation estimation architecture for formation flying builds upon the local information exchange among multiple local estimators. Spacecraft formation flying involves the coordination of states among multiple spacecraft through relative sensing, inter-spacecraft communication, and control. Most existing formation flying estimation algorithms can only be supported via highly centralized, all-to-all, static relative sensing. New algorithms are needed that are scalable, modular, and robust to variations in the topology and link characteristics of the formation exchange network. These distributed algorithms should rely on a local information-exchange network, relaxing the assumptions on existing algorithms. In this research, it was shown that only local observability is required to design a formation estimator and control law. The approach relies on breaking up the overall information-exchange network into sequence of local subnetworks, and invoking an agreement-type filter to reach consensus among local estimators within each local network. State estimates were obtained by a set of local measurements that were passed through a set of communicating Kalman filters to reach an overall state estimation for the formation. An optimization approach was also presented by means of which diffused estimates over the network can be incorporated in the local estimates obtained by each estimator via local measurements. This approach compares favorably with that obtained by a centralized Kalman filter, which requires complete knowledge of the raw measurement available to each estimator.

Fathpour, Nanaz↗

Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense )

The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.

59 BASIC BIOLOGICAL SCIENCES↗

Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Intraspecific trait variation within natural populations (i.e. intra-population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource-limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. Here, we propose that during invasion, IPTV and its relative change in response to key resource enrichment may increase with the resource deficit of invaded sites, and that this relationship may facilitate plant invasions into resource-limited environments. We analyzed the invasion trend, IPTV and its response to water enrichment, and moisture variability among populations of an annual grass Brachypodium hybridum in California, United States. We incorporated a genotyping-by-sequencing approach, a common garden experiment that had two water level treatments, and public plant and climate databases. Our hypothesis was supported by the observation that for populations that invaded sites with higher spring moisture deficit, both their seed biomass IPTV (for the water-enriched treatment only) and relative change of the IPTV across water treatments were larger when examined in the common garden experiment. A generally north to south spreading direction was found in these B. hybridum populations, towards a drier and warmer climate exhibiting higher moisture deficit for plant growth. Our results suggest a role for interactions between IPTV (rather than trait means) and environmental resource availability in promoting plant invasions, providing new insights into the significance of IPTV in shaping plant geographic distributions.

54 ENVIRONMENTAL SCIENCES↗