Insights into wild-type and mutant p53 functions provided by genetically engineered mice.

PubMed

Donehower, Lawrence A

2014-06-01

Recent whole-exome sequencing studies of numerous human cancers have now conclusively shown that the TP53 tumor-suppressor gene is the most frequently mutated gene in human cancers. Despite extensive studies of the TP53 gene and its encoded protein (p53), our understanding of how TP53 mutations contribute to cancer initiation and progression remain incomplete. Genetically engineered mice with germline or inducible Trp53 somatic mutations have provided important insights into the mechanisms by which different types of p53 mutation influence cancer development. Trp53 germline mutations that alter specific p53 structural domains or posttranslation modification sites have benefitted our understanding of wild-type p53 functions in a whole organism context. Moreover, genetic approaches to reestablish functional wild-type p53 to p53-deficient tissues and tumors have increased our understanding of the therapeutic potential of restoring functional p53 signaling to cancers. This review outlines many of the key insights provided by the various categories of Trp53 mutant mice that have been generated by multiple genetic engineering approaches. © 2014 WILEY PERIODICALS, INC.

First fossil gravid turtle provides insight into the evolution of reproductive traits in turtles.

PubMed

Zelenitsky, Darla K; Therrien, Franc Ois; Joyce, Walter G; Brinkman, Donald B

2008-12-23

Here we report on the first discovery of shelled eggs inside the body cavity of a fossil turtle and on an isolated egg clutch, both referable to the Cretaceous turtle Adocus. These discoveries provide a unique opportunity to gain insight into the reproductive traits of an extinct turtle and to understand the evolution of such traits among living turtles. The gravid adult and egg clutch indicate that Adocus laid large clutches of rigid-shelled spherical eggs and established their nests near rivers, traits that are shared by its closest living relatives, the soft-shelled turtles. Adocus eggshell, however, was probably more rigid than that of living turtles, based on its great thickness and structure, features that may represent unique adaptations to intense predation or to arid nest environments. In light of the reproductive traits observed in Adocus, the distribution of reproductive traits among turtles reveals that large clutches of rigid-shelled eggs are primitive for hidden-necked turtles (cryptodirans) and that spherical eggs may have evolved independently within this group.

New Insight into the Solar System’s Transition Disk Phase Provided by the Metal-rich Carbonaceous Chondrite Isheyevo

NASA Astrophysics Data System (ADS)

Morris, Melissa A.; Garvie, Laurence A. J.; Knauth, L. Paul

2015-03-01

Many aspects of planet formation are controlled by the amount of gas remaining in the natal protoplanetary disks (PPDs). Infrared observations show that PPDs undergo a transition stage at several megayears, during which gas densities are reduced. Our Solar System would have experienced such a stage. However, there is currently no data that provides insight into this crucial time in our PPD’s evolution. We show that the Isheyevo meteorite contains the first definitive evidence for a transition disk stage in our Solar System. Isheyevo belongs to a class of metal-rich meteorites whose components have been dated at almost 5 Myr after formation of Ca, Al-rich inclusions, and exhibits unique sedimentary layers that imply formation through gentle sedimentation. We show that such layering can occur via the gentle sweep-up of material found in the impact plume resulting from the collision of two planetesimals. Such sweep-up requires gas densities consistent with observed transition disks (10-12-10-11 g cm-3). As such, Isheyevo presents the first evidence of our own transition disk and provides new constraints on the evolution of our solar nebula.

Variations upon a theme: Australian lizards provide insights into the endocrine control of vertebrate reproductive cycles.

PubMed

Jones, Susan M

2017-04-01

Australian lizards exhibit a broad array of different reproductive strategies and provide an extraordinary diversity and range of models with which to address fundamental problems in reproductive biology. Studies on lizards have frequently led to new insights into hormonal regulatory pathways or mechanisms of control, but we have detailed knowledge of the reproductive cycle in only a small percentage of known species. This review provides an overview and synthesis of current knowledge of the hormonal control of reproductive cycles in Australian lizards. Agamid lizards have provided useful models with which to test hypotheses about the hormonal regulation of the expression of reproductive behaviors, while research on viviparous skinks is providing insights into the evolution of the endocrine control of gestation. However, in order to better understand the potential risks that environmental factors such as climate change and endocrine disrupting chemicals pose to our fauna, better knowledge is required of the fundamental characteristics of the reproductive cycle in a broader range of lizard species. Copyright © 2015 Elsevier Inc. All rights reserved.

Geophysical insights on the GIA process provided by high-quality constraints from peripheral regions: An outlook on perspectives from North America and from the Mediterranean basin

NASA Astrophysics Data System (ADS)

Roy, K.; Peltier, W. R.

2017-12-01

Our understanding of the Earth-Ice-Ocean interactions that have accompanied the large glaciation-deglaciation process characteristic of the last half of the Pleistocene has benefited significantly from the development of high-quality models of the Glacial Isostatic Adjustment (GIA) process. These models provide fundamental insight on the large changes in sea level and land ice cover over this time period, as well as key constraints on the viscosity structure of the Earth's interior. Their development has benefited from the recent availability of high-quality constraints from regions of forebulge collapse. In particular, over North America, the joint use of high-quality sea level data from the U.S. East coast, together with the vast network of precise space-geodetic observations of crustal motion existing over most of the interior of the continent, has led to the latest ICE-7G_NA (VM7) model (Roy & Peltier, GJI, 2017). In this paper, exciting opportunities provided by such high-quality observations related to the GIA process will be discussed, not only in the context of the continuing effort to refine global models of this phenomenon, but also in terms of the fundamental insight they may provide on outstanding issues in high-pressure geophysics, paleoclimatology or hydrogeology. Specific examples where such high-quality observations can be used (either separately, or using a combination of independent sources) will be presented, focusing particularly on constraints from the North American continent and from the Mediterranean basin. This work will demonstrate that, given the high-quality of currently available constraints on the GIA process, considerable further geophysical insight can be obtained based upon the use of spherically-symmetric models of the viscosity structure of the planet.

Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights.

PubMed

Jiang, Chao; Caccamo, Paul D; Brun, Yves V

2015-04-01

How Darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating "evolutionary thinking" into bacterial cell biology in the genomic era. © 2015 WILEY Periodicals, Inc.

The Clean Energy Manufacturing Analysis Center (CEMAC): Providing Analysis and Insights on Clean Technology Manufacturing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Nicholi S

The U.S. Department of Energy's Clean Energy Manufacturing Analysis Center (CEMAC) provides objective analysis and up-to-date data on global supply chains and manufacturing of clean energy technologies. Policymakers and industry leaders seek CEMAC insights to inform choices to promote economic growth and the transition to a clean energy economy.

Dust emission mechanisms in the central Sahara: new insights from remote field observations

NASA Astrophysics Data System (ADS)

Allen, C.; Washington, R.; Engelstaedter, S.

2013-12-01

North Africa is the world's largest source of mineral aerosol (dust). The Fennec Project, an international consortium led by the University of Oxford, is the first project to systematically instrument the remote central Sahara Desert. These observations have, among others, provided new insights into the atmospheric mechanisms of dust emission. Bordj Badji Mokhtar, in south-west Algeria, is within kilometres of the centre of the global mean summer dust maximum. The site, operated by Fennec partners ONM Algerie, has been heavily instrumented since summer 2011. During the Intensive Observation Period (IOP) in June 2011, four main emission mechanisms were observed and documented: cold pool outflows, low level jets (LLJs), monsoon surges and dry convective plumes. Establishing the relative importance of dust emission mechanisms has been a long-standing research goal. A detailed partitioning exercise of dust events during the IOP shows that 45% of the dust over BBM was generated by local emission in cold pool outflows, 14% by LLJs and only 2% by dry convective plumes. 27% of the dust was advected to the site rather than locally emitted and 12% of the dust was residual or ';background' dust. The work shows the primacy of cold pool outflows for dust emission in the region and also the important contribution of dust advection. In accordance with long-held ideas, the cube of wind speed is strongly correlated with dust emission. Surprisingly however, particles in long-range advection (>500km) were found to be larger than locally emitted dust. Although a clear LLJ wind structure is evident in the mean diurnal cycle during the IOP (12m/s peak winds at 935hPa between 04-05h), LLJs are only responsible for a relatively small amount of dust emission. There is significant daily variability in LLJ strength; the strongest winds are produced by a relatively small number of events. The position and strength of the Saharan Heat Low is strongly associated with the development (or

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sidhu, Navdeep S.; University of Göttingen, Tammannstrasse 4, 37077 Göttingen; Schreiber, Kathrin

2014-05-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However,more » the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.« less

Genetic Determinants of Epigenetic Patterns: Providing Insight into Disease.

PubMed

Cazaly, Emma; Charlesworth, Jac; Dickinson, Joanne L; Holloway, Adele F

2015-03-26

The field of epigenetics and our understanding of the mechanisms that regulate the establishment, maintenance and heritability of epigenetic patterns continue to grow at a remarkable rate. This information is providing increased understanding of the role of epigenetic changes in disease, insight into the underlying causes of these epigenetic changes and revealing new avenues for therapeutic intervention. Epigenetic modifiers are increasingly being pursued as therapeutic targets in a range of diseases, with a number of agents targeting epigenetic modifications already proving effective in diseases such as cancer. Although it is well established that DNA mutations and aberrant expression of epigenetic modifiers play a key role in disease, attention is now turning to the interplay between genetic and epigenetic factors in complex disease etiology. The role of genetic variability in determining epigenetic profiles, which can then be modified by environmental and stochastic factors, is becoming more apparent. Understanding the interplay between genetic and epigenetic factors is likely to aid in identifying individuals most likely to benefit from epigenetic therapies. This goal is coming closer to realization because of continual advances in laboratory and statistical tools enabling improvements in the integration of genomic, epigenomic and phenotypic data.

Characteristics of Kodak Insight, an F-speed intraoral film.

PubMed

Ludlow, J B; Platin, E; Mol, A

2001-01-01

This study reports film speed, contrast, exposure latitude, resolution, and response to processing solution depletion of Kodak Insight intraoral film. Densitometric curves were generated by using International Standards Organization protocol. Additional curves were generated for Ultra-speed, Ektaspeed Plus, and Insight films developed in progressively depleted processing solutions. Eight observers viewed images of a resolution test tool for maximum resolution assessment. Images of an aluminum step-wedge were reviewed to determine useful exposure latitude. Insight's sensitivity in fresh automatic processor solutions places it in the F-speed group. An average gradient of 1.8 was found with all film types. Insight provided 93% of the useful exposure latitude of Ektaspeed Plus film. Insight maintained contrast in progressively depleted processing solutions. Like Ektaspeed Plus, Insight was able to resolve at least 20 line-pairs per millimeter. Under International Standards Organization conditions, Insight required only 77% of the exposure of Ektaspeed Plus film. Insight film provided stable contrast in depleted processing solutions.

Formative Observation of Teaching: Focusing Peer Assistance on Teachers' Developmental Goals

ERIC Educational Resources Information Center

Drew, Steve; Phelan, Liam; Lindsay, Katherine; Carbone, Angela; Ross, Bella; Wood, Kayleen; Stoney, Susan; Cottman, Caroline

2017-01-01

Peer observation of teaching can provide valuable insights into effective educational practices. By adopting a developmental focus, peer observation can also provide insights into how practices might be enhanced and, importantly, how enhancements in practices might be aligned to teachers' development goals. However, a review of peer observation of…

New Insight into Polar Stratospheric Cloud Processes from A-Train Observations

NASA Astrophysics Data System (ADS)

Pitts, M. C.; Poole, L. R.

2016-12-01

Polar stratospheric clouds (PSCs) play essential roles in the chemical depletion of stratospheric ozone at high latitudes. Heterogeneous reactions occurring on PSC particles, primarily supercooled ternary (H2SO4-H2O-HNO3) solution (STS) droplets, convert stable chlorine reservoir species to highly reactive ozone-destructive forms. Also, sedimentation and evaporation of large nitric acid trihydrate (NAT) particles irreversibly redistributes odd nitrogen and prolongs ozone depletion by slowing the reformation of stable chlorine reservoirs. Even after three decades of research, significant gaps in our understanding of PSC processes still exist, particularly concerning NAT nucleation and the extent to which chlorine is activated on cold background aerosol prior to PSC formation. These uncertainties limit our ability to represent PSCs accurately in global models and call into question predictions of ozone recovery in a changing climate. PSC observations from the A-Train satellite constellation have stimulated a number of new research activities that have both extended and challenged our knowledge of PSC processes and modeling capabilities. Specifically, the CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) lidar on the CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations) satellite is providing information on PSC morphology and composition in unprecedented detail, while the Microwave Limb Sounder (MLS) on the Aura satellite is providing nearly coincident measurements of gas-phase HNO3 and H2O, the major constituents of all PSC particles. The combined analyses of these datasets enable better PSC composition discrimination and provide valuable new insight into processes such as PSC-catalyzed chlorine activation and PSC particle growth kinetics. The more than ten years of CALIOP and MLS measurements have uniquely captured the primary aspects of the seasonal and multi-year variability of PSCs in the Arctic and Antarctic and are enabling the

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics

PubMed Central

Lin, Yuling; Min, Jiumeng; Lai, Ruilian; Wu, Zhangyan; Chen, Yukun; Yu, Lili; Cheng, Chunzhen; Jin, Yuanchun; Tian, Qilin; Liu, Qingfeng; Liu, Weihua; Zhang, Chengguang; Lin, Lixia; Hu, Yan; Zhang, Dongmin; Thu, Minkyaw; Zhang, Zihao; Liu, Shengcai; Zhong, Chunshui; Fang, Xiaodong; Wang, Jian; Yang, Huanming

2017-01-01

Abstract Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, “Honghezi,” was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3΄H, ANR, and UFGT) and contracted (PAL, CHS, and F3΄5΄H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics. PMID:28368449

Basic Science Simulations Provide New Insights to Aid Hydrogen Gas Turbine Development (Fact Sheet), NREL Highlights, Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2011-11-01

Massive first-principles simulation provides insight into flame anchoring in a hydrogen-rich jet in cross-flow. When gas turbine designers want to use gasified biomass for stationary power generation, they are faced with a challenge: bio-derived syngas typically contains significant amounts of hydrogen, which is far more reactive than the methane that is the traditional gas turbine fuel. This reactivity leads to a safety design issue, because with hydrogen-rich fuels a flame may anchor in the fuel injection section of the combustor instead of the downstream design point. In collaboration with Jacqueline Chen of Sandia National Laboratories and Andrea Gruber of SINTEF,more » a Norwegian energy think tank, the National Renewable Energy Laboratory (NREL) is carrying out fundamental simulations to provide new insight into the physics of flame anchoring in canonical 'jet in cross-flow' configurations using hydrogen-rich fuels. To deal with the large amount and complexity of the data, the combustion scientists also teamed up with computer scientists from across the U.S. Department of Energy's laboratories to develop novel ways to analyze the data. These simulations have shown that fine-scale turbulence structures formed at the jet boundary provide particularly intense mixing between the fuel and air, which then enters a quiescent region formed downstream of the jet in a separate, larger turbulent structure. This insight explains the effect that reducing the wall-normal velocity of the fuel jet causes the flame to blow off; with the aid of the simulation, we now understand this counterintuitive result because reducing the wall-normal velocity would reduce the intensity of the mixing as well as move the quiescent region farther downstream. NREL and its research partners are conducting simulations that provide new insight into the physics of flame anchoring in canonical 'jet in cross-flow' configurations using hydrogen-rich fuels. Simulation results explain the mechanism

New insight into the comparative power of quality-control rules that use control observations within a single analytical run.

PubMed

Parvin, C A

1993-03-01

The error detection characteristics of quality-control (QC) rules that use control observations within a single analytical run are investigated. Unlike the evaluation of QC rules that span multiple analytical runs, most of the fundamental results regarding the performance of QC rules applied within a single analytical run can be obtained from statistical theory, without the need for simulation studies. The case of two control observations per run is investigated for ease of graphical display, but the conclusions can be extended to more than two control observations per run. Results are summarized in a graphical format that offers many interesting insights into the relations among the various QC rules. The graphs provide heuristic support to the theoretical conclusions that no QC rule is best under all error conditions, but the multirule that combines the mean rule and a within-run standard deviation rule offers an attractive compromise.

ISS observations offer insights into plant function

DOE PAGES

Stavros, E. Natasha; Schimel, David; Pavlick, Ryan; ...

2017-06-22

Technologies on the International Space Station will provide ~1 year of synchronous observations of ecosystem composition, structure and function, in 2018. Here, we discuss these instruments and how they can be used to constrain global models and improve our understanding of the current state of terrestrial ecosystems.

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

PubMed Central

2011-01-01

Background Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. Results 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. Conclusions Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens. PMID:21247460

High content analysis provides mechanistic insights on the pathways of toxicity induced by amine-modified polystyrene nanoparticles.

PubMed

Anguissola, Sergio; Garry, David; Salvati, Anna; O'Brien, Peter J; Dawson, Kenneth A

2014-01-01

The fast-paced development of nanotechnology needs the support of effective safety testing. We have developed a screening platform measuring simultaneously several cellular parameters for exposure to various concentrations of nanoparticles (NPs). Cell lines representative of different organ cell types, including lung, endothelium, liver, kidney, macrophages, glia, and neuronal cells were exposed to 50 nm amine-modified polystyrene (PS-NH2) NPs previously reported to induce apoptosis and to 50 nm sulphonated and carboxyl-modified polystyrene NPs that were reported to be silent. All cell lines apart from Raw 264.7 executed apoptosis in response to PS-NH2 NPs, showing specific sequences of EC50 thresholds; lysosomal acidification was the most sensitive parameter. Loss of mitochondrial membrane potential and plasma membrane integrity measured by High Content Analysis resulted comparably sensitive to the equivalent OECD-recommended assays, allowing increased output. Analysis of the acidic compartments revealed good cerrelation between size/fluorescence intensity and dose of PS-NH2 NPs applied; moreover steatosis and phospholipidosis were observed, consistent with the lysosomal alterations revealed by Lysotracker green; similar responses were observed when comparing astrocytoma cells with primary astrocytes. We have established a platform providing mechanistic insights on the response to exposure to nanoparticles. Such platform holds great potential for in vitro screening of nanomaterials in highthroughput format.

Flow-mediated dilation: can new approaches provide greater mechanistic insight into vascular dysfunction in preeclampsia and other diseases?

PubMed

Weissgerber, Tracey L

2014-11-01

Endothelial dysfunction is a key feature of preeclampsia and may contribute to increased cardiovascular disease risk years after pregnancy. Flow-mediated dilation (FMD) is a non-invasive endothelial function test that predicts cardiovascular event risk. New protocols allow researchers to measure three components of the FMD response: FMD, low flow-mediated constriction, and shear stimulus. This review encourages researchers to think beyond "low FMD" by examining how these three components may provide additional insights into the mechanisms and location of vascular dysfunction. The review then examines what FMD studies reveal about vascular dysfunction in preeclampsia while highlighting opportunities to gain greater mechanistic insight from new protocols. Studies using traditional protocols show that FMD is low in mid-pregnancy prior to preeclampsia, at diagnosis, and for 3 years post-partum. However, FMD returns to normal by 10 years post-partum. Studies using new protocols are needed to gain more mechanistic insight.

A six-gene phylogeny provides new insights into choanoflagellate evolution.

PubMed

Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

2017-02-01

Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity

PubMed Central

Selengut, Jeremy D.; Harkins, Derek M.; Patra, Kailash P.; Moreno, Angelo; Lehmann, Jason S.; Purushe, Janaki; Sanka, Ravi; Torres, Michael; Webster, Nicholas J.; Vinetz, Joseph M.; Matthias, Michael A.

2012-01-01

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness

Using Health Provider Insights to Inform Pediatric HIV Disclosure: A Qualitative Study and Practice Framework from Kenya

PubMed Central

John-Stewart, Grace; Shah, Brandi; Wamalwa, Dalton; Maleche-Obimbo, Elizabeth; Kelley, Maureen

2014-01-01

Abstract Optimal pediatric HIV disclosure impacts illness and developmental experiences while improving access to timely treatment. However, disclosure rates in high HIV prevalence countries remain low and there are limited data on best practices. We conducted a qualitative study of disclosure practices and interviewed healthcare providers from five pediatric HIV clinics in Kenya. We identified themes central to disclosure practices, rationale for approaches, barriers to implementing disclosure, and creative strategies to overcome challenges. We used these insights to develop a practice-based framework for disclosure that is sensitive to practical challenges. Overall, providers had limited training but extensive experience in disclosure, endorsed individualized disclosure practices, invested substantial time on disclosure despite clinical burden, and noted adverse outcomes associated with unplanned or abrupt disclosure. Providers advocated for an approach to disclosure that is child-centered but respects caregiver fears and values. Caregiver support was provided to enable caregivers to be the person who ultimately disclosed HIV status to children. Unplanned or abrupt disclosure to children was reported to have severe and persistent adverse impact and was a stimulus to accelerate disclosure in scenarios when providers believed children may be suspecting their diagnosis. Based on these expert insights, the framework we developed incorporates concurrent evaluation of child and caregiver readiness, identifies cues to prompt disclosure discussions, includes caregiver education and support, and utilizes a gradual approach of unveiling HIV diagnosis to the child. PMID:25216105

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

PubMed Central

Smith, Jeramiah J; Kuraku, Shigehiro; Holt, Carson; Sauka-Spengler, Tatjana; Jiang, Ning; Campbell, Michael S; Yandell, Mark D; Manousaki, Tereza; Meyer, Axel; Bloom, Ona E; Morgan, Jennifer R; Buxbaum, Joseph D; Sachidanandam, Ravi; Sims, Carrie; Garruss, Alexander S; Cook, Malcolm; Krumlauf, Robb; Wiedemann, Leanne M; Sower, Stacia A; Decatur, Wayne A; Hall, Jeffrey A; Amemiya, Chris T; Saha, Nil R; Buckley, Katherine M; Rast, Jonathan P; Das, Sabyasachi; Hirano, Masayuki; McCurley, Nathanael; Guo, Peng; Rohner, Nicolas; Tabin, Clifford J; Piccinelli, Paul; Elgar, Greg; Ruffier, Magali; Aken, Bronwen L; Searle, Stephen MJ; Muffato, Matthieu; Pignatelli, Miguel; Herrero, Javier; Jones, Matthew; Brown, C Titus; Chung-Davidson, Yu-Wen; Nanlohy, Kaben G; Libants, Scot V; Yeh, Chu-Yin; McCauley, David W; Langeland, James A; Pancer, Zeev; Fritzsch, Bernd; de Jong, Pieter J; Zhu, Baoli; Fulton, Lucinda L; Theising, Brenda; Flicek, Paul; Bronner, Marianne E; Warren, Wesley C; Clifton, Sandra W; Wilson, Richard K; Li, Weiming

2013-01-01

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms. PMID:23435085

Flow-mediated Dilation: Can New Approaches Provide Greater Mechanistic Insight into Vascular Dysfunction in Preeclampsia and Other Diseases?

PubMed Central

Weissgerber, Tracey L.

2015-01-01

Endothelial dysfunction is a key feature of preeclampsia, and may contribute to increased cardiovascular disease risk years after pregnancy. Flow-mediated dilation (FMD) is a non-invasive endothelial function test that predicts cardiovascular event risk. New protocols allow researchers to measure three components of the FMD response: FMD, low flow-mediated constriction and the shear stimulus. This review encourages researchers to think beyond “low FMD” by examining how these three components may provide additional insights into the mechanisms and location of vascular dysfunction. The review then examines what FMD studies reveal about vascular dysfunction in preeclampsia, while highlighting opportunities to gain greater mechanistic insight from new protocols. Studies using traditional protocols show that FMD is low in mid-pregnancy prior to preeclampsia, at diagnosis, and for three years post-partum. However, FMD returns to normal by ten years post-partum. Studies using new protocols are needed to gain more mechanistic insight. PMID:25182159

Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby.

PubMed

MacDonald, A J; Fitzsimmons, N N; Chambers, B; Renfree, M B; Sarre, S D

2014-03-01

The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been isolated on several islands off the Western Australian and South Australian coastlines for between 10,000 and 13,000 years. Here, we combine analyses of autosomal, Y-linked and X-linked microsatellite loci to investigate genetic variation in populations of this species on two islands (Kangaroo Island, South Australia and Garden Island, Western Australia). All measures of diversity were higher for the larger Kangaroo Island population, in which genetic variation was lowest at Y-linked markers and highest at autosomal markers (θ=3.291, 1.208 and 0.627 for autosomal, X-linked and Y-linked data, respectively). Greater relatedness among females than males provides evidence for male-biased dispersal in this population, while sex-linked markers identified genetic lineages not apparent from autosomal data alone. Overall genetic diversity in the Garden Island population was low, especially on the Y chromosome where most males shared a common haplotype, and we observed high levels of inbreeding and relatedness among individuals. Our findings highlight the utility of this approach for management actions, such as the selection of animals for translocation or captive breeding, and the ecological insights that may be gained by combining analyses of microsatellite markers on sex chromosomes with those derived from autosomes.

Working wonders? investigating insight with magic tricks.

PubMed

Danek, Amory H; Fraps, Thomas; von Müller, Albrecht; Grothe, Benedikt; Ollinger, Michael

2014-02-01

We propose a new approach to differentiate between insight and noninsight problem solving, by introducing magic tricks as problem solving domain. We argue that magic tricks are ideally suited to investigate representational change, the key mechanism that yields sudden insight into the solution of a problem, because in order to gain insight into the magicians' secret method, observers must overcome implicit constraints and thus change their problem representation. In Experiment 1, 50 participants were exposed to 34 different magic tricks, asking them to find out how the trick was accomplished. Upon solving a trick, participants indicated if they had reached the solution either with or without insight. Insight was reported in 41.1% of solutions. The new task domain revealed differences in solution accuracy, time course and solution confidence with insight solutions being more likely to be true, reached earlier, and obtaining higher confidence ratings. In Experiment 2, we explored which role self-imposed constraints actually play in magic tricks. 62 participants were presented with 12 magic tricks. One group received verbal cues, providing solution relevant information without giving the solution away. The control group received no informative cue. Experiment 2 showed that participants' constraints were suggestible to verbal cues, resulting in higher solution rates. Thus, magic tricks provide more detailed information about the differences between insightful and noninsightful problem solving, and the underlying mechanisms that are necessary to have an insight. Copyright © 2013 Elsevier B.V. All rights reserved.

Insights into the use of time-lapse GPR data as observations for inverse multiphase flow simulations of DNAPL migration

USGS Publications Warehouse

Johnson, R.H.; Poeter, E.P.

2007-01-01

Perchloroethylene (PCE) saturations determined from GPR surveys were used as observations for inversion of multiphase flow simulations of a PCE injection experiment (Borden 9??m cell), allowing for the estimation of optimal bulk intrinsic permeability values. The resulting fit statistics and analysis of residuals (observed minus simulated PCE saturations) were used to improve the conceptual model. These improvements included adjustment of the elevation of a permeability contrast, use of the van Genuchten versus Brooks-Corey capillary pressure-saturation curve, and a weighting scheme to account for greater measurement error with larger saturation values. A limitation in determining PCE saturations through one-dimensional GPR modeling is non-uniqueness when multiple GPR parameters are unknown (i.e., permittivity, depth, and gain function). Site knowledge, fixing the gain function, and multiphase flow simulations assisted in evaluating non-unique conceptual models of PCE saturation, where depth and layering were reinterpreted to provide alternate conceptual models. Remaining bias in the residuals is attributed to the violation of assumptions in the one-dimensional GPR interpretation (which assumes flat, infinite, horizontal layering) resulting from multidimensional influences that were not included in the conceptual model. While the limitations and errors in using GPR data as observations for inverse multiphase flow simulations are frustrating and difficult to quantify, simulation results indicate that the error and bias in the PCE saturation values are small enough to still provide reasonable optimal permeability values. The effort to improve model fit and reduce residual bias decreases simulation error even for an inversion based on biased observations and provides insight into alternate GPR data interpretations. Thus, this effort is warranted and provides information on bias in the observation data when this bias is otherwise difficult to assess. ?? 2006 Elsevier B

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

PubMed

Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

2015-02-10

Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae).

PubMed

Gaudeul, Myriam; Rouhan, Germinal; Gardner, Martin F; Hollingsworth, Peter M

2012-01-01

Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.

Sequential structures provide insights into the fidelity of RNA replication.

PubMed

Ferrer-Orta, Cristina; Arias, Armando; Pérez-Luque, Rosa; Escarmís, Cristina; Domingo, Esteban; Verdaguer, Nuria

2007-05-29

RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.

Tackling wicked problems: how theories of agency can provide new insights.

PubMed

Varpio, Lara; Aschenbrener, Carol; Bates, Joanna

2017-04-01

This paper reviews why and how theories of agency can be used as analytical lenses to help health professions education (HPE) scholars address our community's wicked problems. Wicked problems are those that resist clear problem statements, defy traditional analysis approaches, and refuse definitive resolution (e.g. student remediation, assessments of professionalism, etc.). We illustrate how theories of agency can provide new insights into such challenges by examining the application of these theories to one particular wicked problem in HPE: interprofessional education (IPE). After searching the HPE literature and finding that theories of agency had received little attention, we borrowed techniques from narrative literature reviews to search databases indexing a broad scope of disciplines (i.e. ERIC, Web of Science, Scopus, MEDLINE and PubMed) for publications (1994-2014) that: (i) examined agency, or (ii) incorporated an agency-informed analytical perspective. The lead author identified the theories of agency used in these articles, and reviewed the texts on agency cited therein and the original sources of each theory. We identified 10 theories of agency that we considered to be applicable to HPE's wicked problems. To select a subset of theories for presentation in this paper, we discussed each theory in relation to some of HPE's wicked problems. Through debate and reflection, we unanimously agreed on the applicability of a subset of theories for illuminating HPE's wicked problems. This subset is described in this paper. We present four theories of agency: Butler's post-structural formulation; Giddens' sociological formulation; cultural historical activity theory's formulation, and Bandura's social cognitive psychology formulation. We introduce each theory and apply each to the challenges of engaging in IPE. Theories of agency can inform HPE scholarship in novel and generative ways. Each theory offers new insights into the roots of wicked problems and means for

African genetic diversity provides novel insights into evolutionary history and local adaptations.

PubMed

Choudhury, Ananyo; Aron, Shaun; Sengupta, Dhriti; Hazelhurst, Scott; Ramsay, Michèle

2018-05-08

Genetic variation and susceptibility to disease are shaped by human demographic history. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about the origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unraveling the critical role of events like migration and admixture and environment factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa is providing historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers.

PubMed

Wang, Jun; Bonnesen, Peter V; Rangel, E; Vallejo, E; Sanchez-Castillo, Ariadna; James Cleaves Ii, H; Baddorf, Arthur P; Sumpter, Bobby G; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

2016-01-04

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N(9)-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

Atypical birdsong and artificial languages provide insights into how communication systems are shaped by learning, use, and transmission.

PubMed

Fehér, Olga

2017-02-01

In this article, I argue that a comparative approach focusing on the cognitive capacities and behavioral mechanisms that underlie vocal learning in songbirds and humans can provide valuable insights into the evolutionary origins of language. The experimental approaches I discuss use abnormal song and atypical linguistic input to study the processes of individual learning, social interaction, and cultural transmission. Atypical input places increased learning and communicative pressure on learners, so exploring how they respond to this type of input provides a particularly clear picture of the biases and constraints at work during learning and use. Furthermore, simulating the cultural transmission of these unnatural communication systems in the laboratory informs us about how learning and social biases influence the structure of communication systems in the long run. Findings based on these methods suggest fundamental similarities in the basic social-cognitive mechanisms underlying vocal learning in birds and humans, and continuing research promises insights into the uniquely human mechanisms and into how human cognition and social behavior interact, and ultimately impact on the evolution of language.

Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style

PubMed Central

Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

2014-01-01

Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase–polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma. PMID:24482532

Comparative genomics provide insights into evolution of trichoderma nutrition style.

PubMed

Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

2014-02-01

Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase-polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.

Expression profile of human tissue kallikrein 15 provides preliminary insights into its roles in the prostate and testis.

PubMed

Filippou, Panagiota S; Ren, Annie H; Soosaipillai, Antoninus; Papaioannou, Michail-Dimitrios; Korbakis, Dimitrios; Safar, Roaa; Diamandis, Eleftherios P; Conner, James

2018-06-26

Human tissue kallikrein 15 (KLK15) is the latest member of the kallikrein-related peptidase family. Little is known about the pathophysiological roles of KLK15. Previous studies implied a role of KLK15 in prostate cancer. In the present study, we examined KLK15 protein expression using a new immunoassay (ELISA) and immunohistochemistry (IHC). Highest KLK15 levels were detected in the testis and seminal fluid, whereas lower levels were observed in prostate and other tissues. Immunohistochemical analysis of testis suggests that KLK15 is strongly expressed in mature spermatids, but not in immature germ cells. KLK15 displayed predominantly nuclear localization in the basal cell layer of the prostatic epithelium. We also measured KLK15 in supernatants of various cell lines. Highest KLK15 levels were primarily detected in prostate cancer cell lines and KLK15 expression was hormone-independent, in contrast to KLK3. Collectively, our data provide insights into the localization and possible role of KLK15 in human physiology. Copyright © 2018. Published by Elsevier Inc.

Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout.

PubMed

Verrier, Eloi R; Genet, Carine; Laloë, Denis; Jaffrezic, Florence; Rau, Andrea; Esquerre, Diane; Dechamp, Nicolas; Ciobotaru, Céline; Hervet, Caroline; Krieg, Francine; Jouneau, Luc; Klopp, Christophe; Quillet, Edwige; Boudinot, Pierre

2018-06-19

The viral hemorrhagic septicemia virus (VHSV) is a major threat for salmonid farming and for wild fish populations worldwide. Previous studies have highlighted the importance of innate factors regulated by a major quantitative trait locus (QTL) for the natural resistance to waterborne VHSV infection in rainbow trout. The aim of this study was to analyze the early transcriptomic response to VHSV inoculation in cell lines derived from previously described resistant and susceptible homozygous isogenic lines of rainbow trout to obtain insights into the molecular mechanisms responsible for the resistance to the viral infection. We first confirmed the presence of the major QTL in a backcross involving a highly resistant fish isogenic line (B57) and a highly susceptible one (A22), and were able to define the confidence interval of the QTL and to identify its precise position. We extended the definition of the QTL since it controls not only resistance to waterborne infection but also the kinetics of mortality after intra-peritoneal injection. Deep sequencing of the transcriptome of B57 and A22 derived cell lines exposed to inactivated VHSV showed a stronger response to virus inoculation in the resistant background. In line with our previous observations, an early and strong induction of interferon and interferon-stimulated genes was correlated with the resistance to VHSV, highlighting the major role of innate immune factors in natural trout resistance to the virus. Interestingly, major factors of the antiviral innate immunity were much more expressed in naive B57 cells compared to naive A22 cells, which likely contributes to the ability of B57 to mount a fast antiviral response after viral infection. These observations were further extended by the identification of several innate immune-related genes localized close to the QTL area on the rainbow trout genome. Taken together, our results improve our knowledge in virus-host interactions in vertebrates and provide novel

Full-flow-regime storage-streamflow correlation patterns provide insights into hydrologic functioning over the continental US

NASA Astrophysics Data System (ADS)

Fang, Kuai; Shen, Chaopeng

2017-09-01

Interannual changes in low, median, and high regimes of streamflow have important implications for flood control, irrigation, and ecologic and human health. The Gravity Recovery and Climate Experiment (GRACE) satellites record global terrestrial water storage anomalies (TWSA), providing an opportunity to observe, interpret, and potentially utilize the complex relationships between storage and full-flow-regime streamflow. Here we show that utilizable storage-streamflow correlations exist throughout vastly different climates in the continental US (CONUS) across low- to high-flow regimes. A panoramic framework, the storage-streamflow correlation spectrum (SSCS), is proposed to examine macroscopic gradients in these relationships. SSCS helps form, corroborate or reject hypotheses about basin hydrologic behaviors. SSCS patterns vary greatly over CONUS with climate, land surface, and geologic conditions. Data mining analysis suggests that for catchments with hydrologic settings that favor storage over runoff, e.g., a large fraction of precipitation as snow, thick and highly-permeable permeable soil, SSCS values tend to be high. Based on our results, we form the hypotheses that groundwater flow dominates streamflows in Southeastern CONUS and Great Plains, while thin soils in a belt along the Appalachian Plateau impose alimit on water storage. SSCS also suggests shallow water table caused by high-bulk density soil and flat terrain induces rapid runoff in several regions. Our results highlight the importance of subsurface properties and groundwater flow in capturing flood and drought. We propose that SSCS can be used as a fundamental hydrologic signature to constrain models and to provide insights thatlead usto better understand hydrologic functioning.

The Sinocyclocheilus cavefish genome provides insights into cave adaptation.

PubMed

Yang, Junxing; Chen, Xiaoli; Bai, Jie; Fang, Dongming; Qiu, Ying; Jiang, Wansheng; Yuan, Hui; Bian, Chao; Lu, Jiang; He, Shiyang; Pan, Xiaofu; Zhang, Yaolei; Wang, Xiaoai; You, Xinxin; Wang, Yongsi; Sun, Ying; Mao, Danqing; Liu, Yong; Fan, Guangyi; Zhang, He; Chen, Xiaoyong; Zhang, Xinhui; Zheng, Lanping; Wang, Jintu; Cheng, Le; Chen, Jieming; Ruan, Zhiqiang; Li, Jia; Yu, Hui; Peng, Chao; Ma, Xingyu; Xu, Junmin; He, You; Xu, Zhengfeng; Xu, Pao; Wang, Jian; Yang, Huanming; Wang, Jun; Whitten, Tony; Xu, Xun; Shi, Qiong

2016-01-04

An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.

PubMed

Wang, Xia; Xu, Yuantao; Zhang, Siqi; Cao, Li; Huang, Yue; Cheng, Junfeng; Wu, Guizhi; Tian, Shilin; Chen, Chunli; Liu, Yan; Yu, Huiwen; Yang, Xiaoming; Lan, Hong; Wang, Nan; Wang, Lun; Xu, Jidi; Jiang, Xiaolin; Xie, Zongzhou; Tan, Meilian; Larkin, Robert M; Chen, Ling-Ling; Ma, Bin-Guang; Ruan, Yijun; Deng, Xiuxin; Xu, Qiang

2017-05-01

The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

Providers' response to child eating behaviors: A direct observation study.

PubMed

Tovar, Alison; Vaughn, Amber E; Fallon, Megan; Hennessy, Erin; Burney, Regan; Østbye, Truls; Ward, Dianne S

2016-10-01

Child care providers play an important role in feeding young children, yet little is known about children's influence on providers' feeding practices. This qualitative study examines provider and child (18 months -4 years) feeding interactions. Trained data collectors observed 200 eating occasions in 48 family child care homes and recorded providers' responses to children's meal and snack time behaviors. Child behaviors initiating provider feeding practices were identified and practices were coded according to higher order constructs identified in a recent feeding practices content map. Analysis examined the most common feeding practices providers used to respond to each child behavior. Providers were predominately female (100%), African-American (75%), and obese (77%) and a third of children were overweight/obese (33%). Commonly observed child behaviors were: verbal and non-verbal refusals, verbal and non-verbal acceptance, being "all done", attempts for praise/attention, and asking for seconds. Children's acceptance of food elicited more autonomy supportive practices vs. coercive controlling. Requests for seconds was the most common behavior, resulting in coercive controlling practices (e.g., insisting child eat certain food or clean plate). Future interventions should train providers on responding to children's behaviors and helping children become more aware of internal satiety and hunger cues. Copyright © 2016 Elsevier Ltd. All rights reserved.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

PubMed Central

Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B.; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng

2017-01-01

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. PMID:29023486

The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

PubMed

Zhang, Xiaojun; Sun, Lina; Yuan, Jianbo; Sun, Yamin; Gao, Yi; Zhang, Libin; Li, Shihao; Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng; Xiang, Jianhai

2017-10-01

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.

PubMed

Zhang, Guojie; Cowled, Christopher; Shi, Zhengli; Huang, Zhiyong; Bishop-Lilly, Kimberly A; Fang, Xiaodong; Wynne, James W; Xiong, Zhiqiang; Baker, Michelle L; Zhao, Wei; Tachedjian, Mary; Zhu, Yabing; Zhou, Peng; Jiang, Xuanting; Ng, Justin; Yang, Lan; Wu, Lijun; Xiao, Jin; Feng, Yue; Chen, Yuanxin; Sun, Xiaoqing; Zhang, Yong; Marsh, Glenn A; Crameri, Gary; Broder, Christopher C; Frey, Kenneth G; Wang, Lin-Fa; Wang, Jun

2013-01-25

Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor κB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

DOE PAGES

Wang, Jun; Bonnesen, Peter V; Rangel, E.; ...

2016-01-04

The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two ormore » more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.« less

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jun; Bonnesen, Peter V; Rangel, E.

The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two ormore » more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.« less

Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure.

PubMed

Hanson, Andrea J; Guho, Nicholas M; Paszczynski, Andrzej J; Coats, Erik R

2016-09-01

Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs.

Hyper-dry conditions provide new insights into the cause of extreme floods after wildfire

USGS Publications Warehouse

Moody, John A.; Ebel, Brian A.

2012-01-01

A catastrophic wildfire in the foothills of the Rocky Mountains near Boulder, Colorado provided a unique opportunity to investigate soil conditions immediately after a wildfire and before alteration by rainfall. Measurements of near-surface (θ; and matric suction, ψ), rainfall, and wind velocity were started 8 days after the wildfire began. These measurements established that hyper-dryconditions (θ 3 cm-3; ψ > ~ 3 x 105 cm) existed and provided an in-situ retention curve for these conditions. These conditions exacerbate the effects of water repellency (natural and fire-induced) and limit the effectiveness of capillarity and gravity driven infiltration into fire-affected soils. The important consequence is that given hyper-dryconditions, the critical rewetting process before the first rain is restricted to the diffusion–adsorption of water-vapor. This process typically has a time scale of days to weeks (especially when the hydrologic effects of the ash layer are included) that is longer than the typical time scale (minutes to hours) of some rainstorms, such that under hyper-dryconditions essentially no rain infiltrates. The existence of hyper-dryconditions provides insight into why, frequently during the first rain storm after a wildfire, nearly all rainfall becomes runoff causing extremefloods and debris flows.

Triploid Colubrid Snake Provides Insight into the Mechanism of Sex Determination in Advanced Snakes.

PubMed

Rovatsos, Michail; Augstenová, Barbora; Altmanová, Marie; Sloboda, Michal; Kodym, Petr; Kratochvíl, Lukáš

2018-06-19

The advanced snakes (Caenophidia), the important amniote lineage encompassing more than 3,000 living species, possess highly conserved female heterogamety across all families. However, we still lack any knowledge on the gene(s) and the molecular mechanism controlling sex determination. Triploid individuals spontaneously appear in populations of diploid species and can provide an important insight into the evolution of sex determination. Here, we report a case of spontaneous triploidy in a male of the twin-spotted ratsnake (Elaphe bimaculata) with ZZW sex chromosomes. We speculate that as both ZZ and ZZW individuals develop male gonads, the ratio between the number of Z chromosomes and autosomes, and not the presence of the W chromosome in the genome, drives sex determination in the advanced snakes. © 2018 S. Karger AG, Basel.

Genome-scale metabolic modeling to provide insight into the production of storage compounds during feast-famine cycles of activated sludge.

PubMed

Tajparast, Mohammad; Frigon, Dominic

2013-01-01

Studying storage metabolism during feast-famine cycles of activated sludge treatment systems provides profound insight in terms of both operational issues (e.g., foaming and bulking) and process optimization for the production of value added by-products (e.g., bioplastics). We examined the storage metabolism (including poly-β-hydroxybutyrate [PHB], glycogen, and triacylglycerols [TAGs]) during feast-famine cycles using two genome-scale metabolic models: Rhodococcus jostii RHA1 (iMT1174) and Escherichia coli K-12 (iAF1260) for growth on glucose, acetate, and succinate. The goal was to develop the proper objective function (OF) for the prediction of the main storage compound produced in activated sludge for given feast-famine cycle conditions. For the flux balance analysis, combinations of three OFs were tested. For all of them, the main OF was to maximize growth rates. Two additional sub-OFs were used: (1) minimization of biochemical fluxes, and (2) minimization of metabolic adjustments (MoMA) between the feast and famine periods. All (sub-)OFs predicted identical substrate-storage associations for the feast-famine growth of the above-mentioned metabolic models on a given substrate when glucose and acetate were set as sole carbon sources (i.e., glucose-glycogen and acetate-PHB), in agreement with experimental observations. However, in the case of succinate as substrate, the predictions depended on the network structure of the metabolic models such that the E. coli model predicted glycogen accumulation and the R. jostii model predicted PHB accumulation. While the accumulation of both PHB and glycogen was observed experimentally, PHB showed higher dynamics during an activated sludge feast-famine growth cycle with succinate as substrate. These results suggest that new modeling insights between metabolic predictions and population ecology will be necessary to properly predict metabolisms likely to emerge within the niches of activated sludge communities. Nonetheless

Fermi-LAT Gamma-Ray Bursts and Insights from Swift

NASA Technical Reports Server (NTRS)

Racusin, Judith L.

2010-01-01

A new revolution in Gamma-ray Burst (GRB) observations and theory has begun over the last two years since the launch of the Fermi Gamma-ray Space Telescope. The new window into high energy gamma-rays opened by the Fermi-Large Area Telescope (LAT) is providing insight into prompt emission mechanisms and possibly also afterglow physics. The LAT detected GRBs appear to be a new unique subset of extremely energetic and bright bursts compared to the large sample detected by Swift over the last 6 years. In this talk, I will discuss the context and recent discoveries from these LAT GRBs and the large database of broadband observations collected by the Swift X-ray Telescope (XRT) and UV/Optical Telescope (UVOT). Through comparisons between the GRBs detected by Swift-BAT, G8M, and LAT, we can learn about the unique characteristics, physical differences, and the relationships between each population. These population characteristics provide insight into the different physical parameters that contribute to the diversity of observational GRB properties.

Nature's Notebook Provides Phenology Observations for NASA Juniper Phenology and Pollen Transport Project

NASA Technical Reports Server (NTRS)

Luval, J. C.; Crimmins, T. M.; Sprigg, W. A.; Levetin, E.; Huete, A.; Nickovic, S.; Prasad, A.; Vukovic, A.; VandeWater, P. K.; Budge, A. M.;

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

PubMed

Mahajan, Anubha; Go, Min Jin; Zhang, Weihua; Below, Jennifer E; Gaulton, Kyle J; Ferreira, Teresa; Horikoshi, Momoko; Johnson, Andrew D; Ng, Maggie C Y; Prokopenko, Inga; Saleheen, Danish; Wang, Xu; Zeggini, Eleftheria; Abecasis, Goncalo R; Adair, Linda S; Almgren, Peter; Atalay, Mustafa; Aung, Tin; Baldassarre, Damiano; Balkau, Beverley; Bao, Yuqian; Barnett, Anthony H; Barroso, Ines; Basit, Abdul; Been, Latonya F; Beilby, John; Bell, Graeme I; Benediktsson, Rafn; Bergman, Richard N; Boehm, Bernhard O; Boerwinkle, Eric; Bonnycastle, Lori L; Burtt, Noël; Cai, Qiuyin; Campbell, Harry; Carey, Jason; Cauchi, Stephane; Caulfield, Mark; Chan, Juliana C N; Chang, Li-Ching; Chang, Tien-Jyun; Chang, Yi-Cheng; Charpentier, Guillaume; Chen, Chien-Hsiun; Chen, Han; Chen, Yuan-Tsong; Chia, Kee-Seng; Chidambaram, Manickam; Chines, Peter S; Cho, Nam H; Cho, Young Min; Chuang, Lee-Ming; Collins, Francis S; Cornelis, Marylin C; Couper, David J; Crenshaw, Andrew T; van Dam, Rob M; Danesh, John; Das, Debashish; de Faire, Ulf; Dedoussis, George; Deloukas, Panos; Dimas, Antigone S; Dina, Christian; Doney, Alex S; Donnelly, Peter J; Dorkhan, Mozhgan; van Duijn, Cornelia; Dupuis, Josée; Edkins, Sarah; Elliott, Paul; Emilsson, Valur; Erbel, Raimund; Eriksson, Johan G; Escobedo, Jorge; Esko, Tonu; Eury, Elodie; Florez, Jose C; Fontanillas, Pierre; Forouhi, Nita G; Forsen, Tom; Fox, Caroline; Fraser, Ross M; Frayling, Timothy M; Froguel, Philippe; Frossard, Philippe; Gao, Yutang; Gertow, Karl; Gieger, Christian; Gigante, Bruna; Grallert, Harald; Grant, George B; Grrop, Leif C; Groves, Chrisropher J; Grundberg, Elin; Guiducci, Candace; Hamsten, Anders; Han, Bok-Ghee; Hara, Kazuo; Hassanali, Neelam; Hattersley, Andrew T; Hayward, Caroline; Hedman, Asa K; Herder, Christian; Hofman, Albert; Holmen, Oddgeir L; Hovingh, Kees; Hreidarsson, Astradur B; Hu, Cheng; Hu, Frank B; Hui, Jennie; Humphries, Steve E; Hunt, Sarah E; Hunter, David J; Hveem, Kristian; Hydrie, Zafar I; Ikegami, Hiroshi; Illig, Thomas; Ingelsson, Erik; Islam, Muhammed; Isomaa, Bo; Jackson, Anne U; Jafar, Tazeen; James, Alan; Jia, Weiping; Jöckel, Karl-Heinz; Jonsson, Anna; Jowett, Jeremy B M; Kadowaki, Takashi; Kang, Hyun Min; Kanoni, Stavroula; Kao, Wen Hong L; Kathiresan, Sekar; Kato, Norihiro; Katulanda, Prasad; Keinanen-Kiukaanniemi, Kirkka M; Kelly, Ann M; Khan, Hassan; Khaw, Kay-Tee; Khor, Chiea-Chuen; Kim, Hyung-Lae; Kim, Sangsoo; Kim, Young Jin; Kinnunen, Leena; Klopp, Norman; Kong, Augustine; Korpi-Hyövälti, Eeva; Kowlessur, Sudhir; Kraft, Peter; Kravic, Jasmina; Kristensen, Malene M; Krithika, S; Kumar, Ashish; Kumate, Jesus; Kuusisto, Johanna; Kwak, Soo Heon; Laakso, Markku; Lagou, Vasiliki; Lakka, Timo A; Langenberg, Claudia; Langford, Cordelia; Lawrence, Robert; Leander, Karin; Lee, Jen-Mai; Lee, Nanette R; Li, Man; Li, Xinzhong; Li, Yun; Liang, Junbin; Liju, Samuel; Lim, Wei-Yen; Lind, Lars; Lindgren, Cecilia M; Lindholm, Eero; Liu, Ching-Ti; Liu, Jian Jun; Lobbens, Stéphane; Long, Jirong; Loos, Ruth J F; Lu, Wei; Luan, Jian'an; Lyssenko, Valeriya; Ma, Ronald C W; Maeda, Shiro; Mägi, Reedik; Männisto, Satu; Matthews, David R; Meigs, James B; Melander, Olle; Metspalu, Andres; Meyer, Julia; Mirza, Ghazala; Mihailov, Evelin; Moebus, Susanne; Mohan, Viswanathan; Mohlke, Karen L; Morris, Andrew D; Mühleisen, Thomas W; Müller-Nurasyid, Martina; Musk, Bill; Nakamura, Jiro; Nakashima, Eitaro; Navarro, Pau; Ng, Peng-Keat; Nica, Alexandra C; Nilsson, Peter M; Njølstad, Inger; Nöthen, Markus M; Ohnaka, Keizo; Ong, Twee Hee; Owen, Katharine R; Palmer, Colin N A; Pankow, James S; Park, Kyong Soo; Parkin, Melissa; Pechlivanis, Sonali; Pedersen, Nancy L; Peltonen, Leena; Perry, John R B; Peters, Annette; Pinidiyapathirage, Janini M; Platou, Carl G; Potter, Simon; Price, Jackie F; Qi, Lu; Radha, Venkatesan; Rallidis, Loukianos; Rasheed, Asif; Rathman, Wolfgang; Rauramaa, Rainer; Raychaudhuri, Soumya; Rayner, N William; Rees, Simon D; Rehnberg, Emil; Ripatti, Samuli; Robertson, Neil; Roden, Michael; Rossin, Elizabeth J; Rudan, Igor; Rybin, Denis; Saaristo, Timo E; Salomaa, Veikko; Saltevo, Juha; Samuel, Maria; Sanghera, Dharambir K; Saramies, Jouko; Scott, James; Scott, Laura J; Scott, Robert A; Segrè, Ayellet V; Sehmi, Joban; Sennblad, Bengt; Shah, Nabi; Shah, Sonia; Shera, A Samad; Shu, Xiao Ou; Shuldiner, Alan R; Sigurđsson, Gunnar; Sijbrands, Eric; Silveira, Angela; Sim, Xueling; Sivapalaratnam, Suthesh; Small, Kerrin S; So, Wing Yee; Stančáková, Alena; Stefansson, Kari; Steinbach, Gerald; Steinthorsdottir, Valgerdur; Stirrups, Kathleen; Strawbridge, Rona J; Stringham, Heather M; Sun, Qi; Suo, Chen; Syvänen, Ann-Christine; Takayanagi, Ryoichi; Takeuchi, Fumihiko; Tay, Wan Ting; Teslovich, Tanya M; Thorand, Barbara; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Tikkanen, Emmi; Trakalo, Joseph; Tremoli, Elena; Trip, Mieke D; Tsai, Fuu Jen; Tuomi, Tiinamaija; Tuomilehto, Jaakko; Uitterlinden, Andre G; Valladares-Salgado, Adan; Vedantam, Sailaja; Veglia, Fabrizio; Voight, Benjamin F; Wang, Congrong; Wareham, Nicholas J; Wennauer, Roman; Wickremasinghe, Ananda R; Wilsgaard, Tom; Wilson, James F; Wiltshire, Steven; Winckler, Wendy; Wong, Tien Yin; Wood, Andrew R; Wu, Jer-Yuarn; Wu, Ying; Yamamoto, Ken; Yamauchi, Toshimasa; Yang, Mingyu; Yengo, Loic; Yokota, Mitsuhiro; Young, Robin; Zabaneh, Delilah; Zhang, Fan; Zhang, Rong; Zheng, Wei; Zimmet, Paul Z; Altshuler, David; Bowden, Donald W; Cho, Yoon Shin; Cox, Nancy J; Cruz, Miguel; Hanis, Craig L; Kooner, Jaspal; Lee, Jong-Young; Seielstad, Mark; Teo, Yik Ying; Boehnke, Michael; Parra, Esteban J; Chambers, Jonh C; Tai, E Shyong; McCarthy, Mark I; Morris, Andrew P

2014-03-01

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

PubMed Central

2014-01-01

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry. PMID:24509480

Obsessive Compulsive Disorder Networks: Positron Emission Tomography and Neuropsychology Provide New Insights

PubMed Central

Millet, Bruno; Dondaine, Thibaut; Reymann, Jean-Michel; Bourguignon, Aurélie; Naudet, Florian; Jaafari, Nematollah; Drapier, Dominique; Turmel, Valérie; Mesbah, Habiba; Vérin, Marc; Le Jeune, Florence

2013-01-01

Background Deep brain stimulation has shed new light on the central role of the prefrontal cortex (PFC) in obsessive compulsive disorder (OCD). We explored this structure from a functional perspective, synchronizing neuroimaging and cognitive measures. Methods and Findings This case-control cross-sectional study compared 15 OCD patients without comorbidities and not currently on serotonin reuptake inhibitors or cognitive behavioural therapy with 15 healthy controls (matched for age, sex and education level) on resting-state 18FDG-PET scans and a neuropsychological battery assessing executive functions. We looked for correlations between metabolic modifications and impaired neuropsychological scores. Modifications in glucose metabolism were found in frontal regions (orbitofrontal cortex and dorsolateral cortices), the cingulate gyrus, insula and parietal gyrus. Neuropsychological differences between patients and controls, which were subtle, were correlated with the metabolism of the prefrontal, parietal, and temporal cortices. Conclusion As expected, we confirmed previous reports of a PFC dysfunction in OCD patients, and established a correlation with cognitive deficits. Other regions outside the prefrontal cortex, including the dorsoparietal cortex and the insula, also appeared to be implicated in the pathophysiology of OCD, providing fresh insights on the complexity of OCD syndromes. PMID:23326403

Transcriptome Analysis of Manganese-deficient Chlamydomonas reinhardtii Provides Insight on the Chlorophyll Biosynthesis Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lockhart, Ainsley; Zvenigorodsky, Natasha; Pedraza, Mary Ann

2011-08-11

The biosynthesis of chlorophyll and other tetrapyrroles is a vital but poorly understood process. Recent genomic advances with the unicellular green algae Chlamydomonas reinhardtii have created opportunity to more closely examine the mechanisms of the chlorophyll biosynthesis pathway via transcriptome analysis. Manganese is a nutrient of interest for complex reactions because of its multiple stable oxidation states and role in molecular oxygen coordination. C. reinhardtii was cultured in Manganese-deplete Tris-acetate-phosphate (TAP) media for 24 hours and used to create cDNA libraries for sequencing using Illumina TruSeq technology. Transcriptome analysis provided intriguing insight on possible regulatory mechanisms in the pathway. Evidencemore » supports similarities of GTR (Glutamyl-tRNA synthase) to its Chlorella vulgaris homolog in terms of Mn requirements. Data was also suggestive of Mn-related compensatory up-regulation for pathway proteins CHLH1 (Manganese Chelatase), GUN4 (Magnesium chelatase activating protein), and POR1 (Light-dependent protochlorophyllide reductase). Intriguingly, data suggests possible reciprocal expression of oxygen dependent CPX1 (coproporphyrinogen III oxidase) and oxygen independent CPX2. Further analysis using RT-PCR could provide compelling evidence for several novel regulatory mechanisms in the chlorophyll biosynthesis pathway.« less

PV Calibration Insights | NREL

Science.gov Websites

PV Calibration Insights PV Calibration Insights The Photovoltaic (PV) Calibration Insights blog will provide updates on the testing done by the NREL PV Device Performance group. This NREL research group measures the performance of any and all technologies and sizes of PV devices from around the world

InSight Encapsulation

NASA Image and Video Library

2018-04-16

In the Astrotech facility at Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is encapsulated in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

PubMed Central

Wilmes, Paul; Wexler, Margaret; Bond, Philip L.

2008-01-01

Background Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced biological phosphorus removal (EBPR). Methodology/Principal Findings A laboratory-scale sequencing batch reactor was successfully operated for different levels of EBPR, removing around 25, 40 and 55 mg/l P. The microbial communities were dominated by the uncultured polyphosphate-accumulating organism “Candidatus Accumulibacter phosphatis”. When EBPR failed, the sludge was dominated by tetrad-forming α-Proteobacteria. Representative and reproducible 2D gel protein separations were obtained for all sludge samples. 638 protein spots were matched across gels generated from the phosphate removing sludges. 111 of these were excised and 46 proteins were identified using recently available sludge metagenomic sequences. Many of these closely match proteins from “Candidatus Accumulibacter phosphatis” and could be directly linked to the EBPR process. They included enzymes involved in energy generation, polyhydroxyalkanoate synthesis, glycolysis, gluconeogenesis, glycogen synthesis, glyoxylate/TCA cycle, fatty acid β oxidation, fatty acid synthesis and phosphate transport. Several proteins involved in cellular stress response were detected. Conclusions/Significance Importantly, this study provides direct evidence linking the metabolic activities of “Accumulibacter” to the chemical transformations observed in EBPR. Finally, the results are discussed in relation to current EBPR metabolic models. PMID:18392150

76 FR 9551 - Proposed Information Collection; Comment Request; Northeast Region Observer Providers Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-18

... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration Proposed Information Collection; Comment Request; Northeast Region Observer Providers Requirements AGENCY: National Oceanic and...; formally request observer training by the Northeast Fisheries Observer Program (NEFOP); submit observer...

Anthropic Reasoning about Fine-Tuning, and Neoclassical Cosmology: Providence, Omnipresence, and Observation Selection Theory

NASA Astrophysics Data System (ADS)

Walker, Theodore, Jr.

2011-10-01

Anthropic reasoning about observation selection effects upon the appearance of cosmic providential fine-tuning (fine-tuning that provides for life) is often motivated by a desire to avoid theological implications (implications favoring the idea of a divine cosmic provider) without appealing to sheer lucky-for-us-cosmic-jackpot happenstance and coincidence. Cosmic coincidence can be rendered less incredible by appealing to a multiverse context. Cosmic providence can be rendered non-theological by appealing to an agent-less providential purpose, or by appealing to less-than-omnipresent/local providers, such as alien intelligences creating life- providing baby universes. Instead of choosing either cosmic coincidence or cosmic providence, as though they were mutually exclusive; it is better to accept both. Neoclassical thought accepts coincidence and providence, plus many local providers and one omnipresent provider. Moreover, fundamental observation selection theory should distinguish the many local observers of some events from the one omnipresent observer of all events. Accepting both coincidence and providence avoids classical theology (providence without coincidence) and classical atheism (coincidence without providence), but not neoclassical theology (providence with coincidence). Cosmology cannot avoid the idea of an all-inclusive omnipresent providential dice-throwing living-creative whole of reality, an idea essential to neoclassical theology, and to neoclassical cosmology.

InSight Encapsulation

NASA Image and Video Library

2018-04-16

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers encapsulate NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder.

PubMed

Takata, Atsushi; Miyake, Noriko; Tsurusaki, Yoshinori; Fukai, Ryoko; Miyatake, Satoko; Koshimizu, Eriko; Kushima, Itaru; Okada, Takashi; Morikawa, Mako; Uno, Yota; Ishizuka, Kanako; Nakamura, Kazuhiko; Tsujii, Masatsugu; Yoshikawa, Takeo; Toyota, Tomoko; Okamoto, Nobuhiko; Hiraki, Yoko; Hashimoto, Ryota; Yasuda, Yuka; Saitoh, Shinji; Ohashi, Kei; Sakai, Yasunari; Ohga, Shouichi; Hara, Toshiro; Kato, Mitsuhiro; Nakamura, Kazuyuki; Ito, Aiko; Seiwa, Chizuru; Shirahata, Emi; Osaka, Hitoshi; Matsumoto, Ayumi; Takeshita, Saoko; Tohyama, Jun; Saikusa, Tomoko; Matsuishi, Toyojiro; Nakamura, Takumi; Tsuboi, Takashi; Kato, Tadafumi; Suzuki, Toshifumi; Saitsu, Hirotomo; Nakashima, Mitsuko; Mizuguchi, Takeshi; Tanaka, Fumiaki; Mori, Norio; Ozaki, Norio; Matsumoto, Naomichi

2018-01-16

Recent studies have established important roles of de novo mutations (DNMs) in autism spectrum disorders (ASDs). Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the "de novo paradigm" of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244) and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

A new raptorial dinosaur with exceptionally long feathering provides insights into dromaeosaurid flight performance.

PubMed

Han, Gang; Chiappe, Luis M; Ji, Shu-An; Habib, Michael; Turner, Alan H; Chinsamy, Anusuya; Liu, Xueling; Han, Lizhuo

2014-07-15

Microraptorines are a group of predatory dromaeosaurid theropod dinosaurs with aerodynamic capacity. These close relatives of birds are essential for testing hypotheses explaining the origin and early evolution of avian flight. Here we describe a new 'four-winged' microraptorine, Changyuraptor yangi, from the Early Cretaceous Jehol Biota of China. With tail feathers that are nearly 30 cm long, roughly 30% the length of the skeleton, the new fossil possesses the longest known feathers for any non-avian dinosaur. Furthermore, it is the largest theropod with long, pennaceous feathers attached to the lower hind limbs (that is, 'hindwings'). The lengthy feathered tail of the new fossil provides insight into the flight performance of microraptorines and how they may have maintained aerial competency at larger body sizes. We demonstrate how the low-aspect-ratio tail of the new fossil would have acted as a pitch control structure reducing descent speed and thus playing a key role in landing.

Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France.

PubMed

Lecoq, H; Wipf-Scheibel, C; Nozeran, K; Millot, P; Desbiez, C

2014-06-24

Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape. Copyright © 2014 Elsevier B.V. All rights reserved.

A Parameterized Model of Amylopectin Synthesis Provides Key Insights into the Synthesis of Granular Starch

PubMed Central

Wu, Alex Chi; Morell, Matthew K.; Gilbert, Robert G.

2013-01-01

A core set of genes involved in starch synthesis has been defined by genetic studies, but the complexity of starch biosynthesis has frustrated attempts to elucidate the precise functional roles of the enzymes encoded. The chain-length distribution (CLD) of amylopectin in cereal endosperm is modeled here on the basis that the CLD is produced by concerted actions of three enzyme types: starch synthases, branching and debranching enzymes, including their respective isoforms. The model, together with fitting to experiment, provides four key insights. (1) To generate crystalline starch, defined restrictions on particular ratios of enzymatic activities apply. (2) An independent confirmation of the conclusion, previously reached solely from genetic studies, of the absolute requirement for debranching enzyme in crystalline amylopectin synthesis. (3) The model provides a mechanistic basis for understanding how successive arrays of crystalline lamellae are formed, based on the identification of two independent types of long amylopectin chains, one type remaining in the amorphous lamella, while the other propagates into, and is integral to the formation of, an adjacent crystalline lamella. (4) The model provides a means by which a small number of key parameters defining the core enzymatic activities can be derived from the amylopectin CLD, providing the basis for focusing studies on the enzymatic requirements for generating starches of a particular structure. The modeling approach provides both a new tool to accelerate efforts to understand granular starch biosynthesis and a basis for focusing efforts to manipulate starch structure and functionality using a series of testable predictions based on a robust mechanistic framework. PMID:23762422

New technologies provide insights into genetic basis of psychiatric disorders and explain their co-morbidity.

PubMed

Rudan, Igor

2010-06-01

The completion of Human Genome Project and the "HapMap" project was followed by translational activities from companies within the private sector. This led to the introduction of genome-wide scans based on hundreds of thousands of single nucleotide polymorphysms (SNP). These scans were based on common genetic variants in human populations. This new and powerful technology was then applied to the existing DNA-based datasets with information on psychiatric disorders. As a result, an unprecedented amount of novel scientific insights related to the underlying biology and genetics of psychiatric disorders was obtained. The dominant design of these studies, so called "genome-wide association studies" (GWAS), used statistical methods which minimized the risk of false positive reports and provided much greater power to detect genotype-phenotype associations. All findings were entirely data-driven rather than hypothesis-driven, which often made it difficult for researchers to understand or interpret the findings. Interestingly, this work in genetics is indicating how non-specific some genes are for psychiatric disorders, having associations in common for schizophrenia, bipolar disorder and autism. This suggests that the earlier stages of psychiatric disorders may be multi-valent and that early detection, coupled with a clearer understanding of the environmental factors, may allow prevention. At the present time, the rich "harvest" from GWAS still has very limited power to predict the variation in psychiatric disease status at individual level, typically explaining less than 5% of the total risk variance. The most recent studies of common genetic variation implicated the role of major histocompatibility complex in schizophrenia and other disorders. They also provided molecular evidence for a substantial polygenic component to the risk of psychiatric diseases, involving thousands of common alleles of very small effect. The studies of structural genetic variation, such as copy

Lessons Learned from Providing Internet Support for the Shoemaker-Levy 9 Observing Campaign

NASA Astrophysics Data System (ADS)

Raugh, A. C.

1994-12-01

In January of 1994, the comet/asteroid team of the University of Maryland Astronomy Department (including staff of the Small Bodies Node of the Planetary Data System) accepted the task of providing a central communications link for observers of the SL9 impact. To that end we established an email exploder, a log-in type bulletin board account, World Wide Web pages and an anonymous FTP server on an existing department node. It was obvious from the comments received from observers, however, that the nature of the impacts made reliable communication on the timescale of minutes to hours absolutely essential to extracting the best possible data from the concerted observations. To provide as stable a link as possible, we took several specific actions: we focused our efforts on providing well-defined services to the smaller community of observers, rather than attempting to provide complete service to the general public; we kept the solutions simple, both to implement and to maintain; and we developed contingency plans to be implemented immediately in the event of hardware failure, network failure or CPU overload.

Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development.

PubMed

Lee, Xin-Wei; Mat-Isa, Mohd-Noor; Mohd-Elias, Nur-Atiqah; Aizat-Juhari, Mohd Afiq; Goh, Hoe-Han; Dear, Paul H; Chow, Keng-See; Haji Adam, Jumaat; Mohamed, Rahmah; Firdaus-Raih, Mohd; Wan, Kiew-Lian

2016-01-01

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.

An Insight into Islamic Pedagogy at the University of University of al-Qarawiyyin

ERIC Educational Resources Information Center

Hardaker, Glenn; Sabki, A'ishah Ahmad

2012-01-01

Purpose: The purpose of this paper is to provide an insight into teaching practice of the University of al-Qarawiyyin, Morocco, with a particular focus on Islamic pedagogy. Design/methodology/approach: The authors conducted daily participant observations of "teaching circles" over a seven-month period. The participant observation was achieved from…

The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaohan; Hu, Rongbin; Yin, Hengfu

Crassulacean acid metabolism (CAM) is a specialized photosynthetic adaptation to arid environments, found predominantly in diverse eudicotyledonous (eudicot) and monocotyledonous (monocot) lineages that diverged approximately 135 million years ago. To test whether convergent evolution underpins the independent emergences of CAM, we present de novo genome assembly and gene expression data for Kalanchoë fedtschenkoi, an obligate CAM species that was shown by multigene phylogenetic analysis to represent one of the earliest-diverging lineages of core eudicots. Our combined analysis of K. fedtschenkoi and two monocot CAM species (Ananas comosus and Phalaenopsis equestris) identified signatures of convergence in protein sequence and in themore » diel re-scheduling of genes involved in metabolism and signaling. Lastly, our results provide significant insight into CAM evolution, facilitating CAM-into-C 3 engineering for enhancing drought tolerance in crops.« less

The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

DOE PAGES

Yang, Xiaohan; Hu, Rongbin; Yin, Hengfu; ...

2017-12-01

Crassulacean acid metabolism (CAM) is a specialized photosynthetic adaptation to arid environments, found predominantly in diverse eudicotyledonous (eudicot) and monocotyledonous (monocot) lineages that diverged approximately 135 million years ago. To test whether convergent evolution underpins the independent emergences of CAM, we present de novo genome assembly and gene expression data for Kalanchoë fedtschenkoi, an obligate CAM species that was shown by multigene phylogenetic analysis to represent one of the earliest-diverging lineages of core eudicots. Our combined analysis of K. fedtschenkoi and two monocot CAM species (Ananas comosus and Phalaenopsis equestris) identified signatures of convergence in protein sequence and in themore » diel re-scheduling of genes involved in metabolism and signaling. Lastly, our results provide significant insight into CAM evolution, facilitating CAM-into-C 3 engineering for enhancing drought tolerance in crops.« less

Development of Innovative Technology to Provide Low-Cost Surface Atmospheric Observations

NASA Astrophysics Data System (ADS)

Kucera, Paul; Steinson, Martin

2016-04-01

Accurate and reliable real-time monitoring and dissemination of observations of surface weather conditions is critical for a variety of societal applications. Applications that provide local and regional information about temperature, precipitation, moisture, and winds, for example, are important for agriculture, water resource monitoring, health, and monitoring of hazard weather conditions. In many regions in Africa (and other global locations), surface weather stations are sparsely located and/or of poor quality. Existing stations have often been sited incorrectly, not well-maintained, and have limited communications established at the site for real-time monitoring. The US National Weather Service (NWS) International Activities Office (IAO) in partnership with University Corporation for Atmospheric Research (UCAR)/National Center for Atmospheric Research (NCAR) and funded by the United States Agency for International Development (USAID) Office of Foreign Disaster Assistance (OFDA) has started an initiative to develop and deploy low-cost weather instrumentation in sparsely observed regions of the world. The goal is to provide observations for environmental monitoring, and early warning alert systems that can be deployed at weather services in developing countries. Instrumentation is being designed using innovative new technologies such as 3D printers, Raspberry Pi computing systems, and wireless communications. The initial effort is focused on designing a surface network using GIS-based tools, deploying an initial network in Zambia, and providing training to Zambia Meteorological Department (ZMD) staff. The presentation will provide an overview of the project concepts, design of the low cost instrumentation, and initial experiences deploying a surface network deployment in Zambia.

Vitiligo blood transcriptomics provides new insights into disease mechanisms and identifies potential novel therapeutic targets.

PubMed

Dey-Rao, Rama; Sinha, Animesh A

2017-01-28

Significant gaps remain regarding the pathomechanisms underlying the autoimmune response in vitiligo (VL), where the loss of self-tolerance leads to the targeted killing of melanocytes. Specifically, there is incomplete information regarding alterations in the systemic environment that are relevant to the disease state. We undertook a genome-wide profiling approach to examine gene expression in the peripheral blood of VL patients and healthy controls in the context of our previously published VL-skin gene expression profile. We used several in silico bioinformatics-based analyses to provide new insights into disease mechanisms and suggest novel targets for future therapy. Unsupervised clustering methods of the VL-blood dataset demonstrate a "disease-state"-specific set of co-expressed genes. Ontology enrichment analysis of 99 differentially expressed genes (DEGs) uncovers a down-regulated immune/inflammatory response, B-Cell antigen receptor (BCR) pathways, apoptosis and catabolic processes in VL-blood. There is evidence for both type I and II interferon (IFN) playing a role in VL pathogenesis. We used interactome analysis to identify several key blood associated transcriptional factors (TFs) from within (STAT1, STAT6 and NF-kB), as well as "hidden" (CREB1, MYC, IRF4, IRF1, and TP53) from the dataset that potentially affect disease pathogenesis. The TFs overlap with our reported lesional-skin transcriptional circuitry, underscoring their potential importance to the disease. We also identify a shared VL-blood and -skin transcriptional "hot spot" that maps to chromosome 6, and includes three VL-blood dysregulated genes (PSMB8, PSMB9 and TAP1) described as potential VL-associated genetic susceptibility loci. Finally, we provide bioinformatics-based support for prioritizing dysregulated genes in VL-blood or skin as potential therapeutic targets. We examined the VL-blood transcriptome in context with our (previously published) VL-skin transcriptional profile to address

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects

PubMed Central

Dugan, Jenifer E.; Hubbard, David M.; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S.

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects.

PubMed

Jaramillo, Eduardo; Dugan, Jenifer E; Hubbard, David M; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal

Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass.

PubMed

Chai, Kian Piaw; Othman, Noor Farhan Binti; Teh, Aik-Hong; Ho, Kok Lian; Chan, Kok-Gan; Shamsir, Mohd Shahir; Goh, Kian Mau; Ng, Chyan Leong

2016-03-15

A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca(2+) ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca(2+) ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.

Targeted gene panels and microbiota analysis provide insight into the effects of effects of alternative production diet formulations on channel catfish nutritional physiology

USDA-ARS?s Scientific Manuscript database

The present research evaluated targeted gene panels and microbiota analysis to provide greater insight into the effects of alternatively-sourced dietary ingredients on production indices, gut health, changes in the gut microbiota and genes involved in the regulation of appetite, growth, metabolism, ...

Observer Use of Standardized Observation Protocols in Consequential Observation Systems

ERIC Educational Resources Information Center

Bell, Courtney A.; Yi, Qi; Jones, Nathan D.; Lewis, Jennifer M.; McLeod, Monica; Liu, Shuangshuang

2014-01-01

Evidence from a handful of large-scale studies suggests that although observers can be trained to score reliably using observation protocols, there are concerns related to initial training and calibration activities designed to keep observers scoring accurately over time (e.g., Bell, et al, 2012; BMGF, 2012). Studies offer little insight into how…

High-frequency DOC and nitrate measurements provide new insights into their export and their relationships to rainfall-runoff processes

NASA Astrophysics Data System (ADS)

Schwab, Michael; Klaus, Julian; Pfister, Laurent; Weiler, Markus

2015-04-01

the Weierbach catchment are the delayed second peaks a few days after the rainfall event. Nitrate concentrations are following this second peak. We assume that this delayed response is going back to subsurface or upper groundwater flows, with nitrate enriched water. On an inter-event scale during low flow / base flow conditions, we observe interesting diurnal patterns of both DOC and nitrate concentrations. Overall, the long-term high-frequency measurements of DOC and nitrate provide us the opportunity to separate different rainfall-runoff processes and link the amount of DOC and nitrate export to them to quantify the overall relevance of the different processes.

Isothermal microcalorimetry provides new insights into biofilm variability and dynamics.

PubMed

Astasov-Frauenhoffer, Monika; Braissant, Olivier; Hauser-Gerspach, Irmgard; Daniels, Alma U; Weiger, Roland; Waltimo, Tuomas

2012-12-01

The purpose of this study was to investigate a three-species in vitro biofilm with peri-implantitis-related bacteria for its variability and metabolic activity. Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis were suspended in simulated body fluid containing 0.2% glucose to form biofilms on polished, protein-coated implant-grade titanium disks over 72 h using a flow chamber system. Thereafter, biofilm-coated disks were characterized by scanning electron microscopy and fluorescence in situ hybridization/confocal laser scanning microscopy. To assess metabolic activity within the biofilms, their heat flow was recorded for 480 h at 37 °C by IMC. The microscopic methods revealed that the total number of bacteria in the biofilms varied slightly among specimens (2.59 × 10(4)  ± 0.67 × 10(4)  cells mm(-2) ), whereas all three species were found constantly with unchanged proportions (S. sanguinis 41.3 ± 4.8%, F. nucleatum 17.7 ± 2.1%, and P. gingivalis 41.0 ± 4.9%). IMC revealed minor differences in time-to-peak heat flow (20.6 ± 4.5 h), a trend consistent with the small variation in bacterial species proportions as shown by microscopy. Peak heat flow (35.8 ± 42.6 μW), mean heat flow (13.1 ± 22.0 μW), and total heat over 480 h (23.5 ± 37.2 J) showed very high variation. These IMC results may be attributed to differences in the initial cell counts and relative proportions of the three species, their distribution and embedment in exopolysaccharide matrix on the test specimens. The present results provide new insights into variability and dynamics of biofilms on titanium disks, aspects that should be explored in future studies of dental surfaces. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

PubMed Central

Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

2015-01-01

Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

Year-round record of Dry Valley soil CO2 flux provides insights into Antarctic soil dynamics

NASA Astrophysics Data System (ADS)

Risk, D. A.; Lee, C.; Macintyre, C. M.; Cary, C.

2012-12-01

The McMurdo Dry Valleys of Antarctica host extreme soil microbial communities that have been extensively studied within the past decade. Activity of microbial communities is routinely measured via soil CO2 flux, and some useful Antarctic measurements have been made during short Austral summers. These studies are mostly spatial in nature, but temporal patterns are also valuable and may provide insights into critical thresholds and the interplay between various mechanisms that drive CO2 flux and its variation. New membrane-based Forced Diffusion (FD) soil efflux techniques offer promise for this application. The purpose of this study was to use a specially designed FD instrument in Hidden Valley of the Antarctic Dry Valleys to evaluate hardware performance in year-round deployments, and to identify features of interest with respect to soil CO2 flux variation. Overall, the deployment was successful. Small but sustained positive fluxes were present only twice during the year. The first such event was small but consistent and of long duration, occurring in the Austral winter. The second was more volatile and likely of microbial origin, and appeared for roughly a month at the end of the calendar year within the Austral summer. The observed patterns suggest that Hidden Valley soil CO2 fluxes are not solely biological in nature, but likely modulated by a combination of biological, geological, and physical processes, which will be discussed in this presentation. In future studies, additional measurement locations, and simultaneous subsurface and lower atmospheric gradient concentration measurements (power-permitting) would be extremely valuable for interpreting measured fluxes, to help identify advective depletion events, the depth source of fluxes, and changes in soil and atmospheric diffusivities.

Computational models and motor learning paradigms: Could they provide insights for neuroplasticity after stroke? An overview.

PubMed

Kiper, Pawel; Szczudlik, Andrzej; Venneri, Annalena; Stozek, Joanna; Luque-Moreno, Carlos; Opara, Jozef; Baba, Alfonc; Agostini, Michela; Turolla, Andrea

2016-10-15

Computational approaches for modelling the central nervous system (CNS) aim to develop theories on processes occurring in the brain that allow the transformation of all information needed for the execution of motor acts. Computational models have been proposed in several fields, to interpret not only the CNS functioning, but also its efferent behaviour. Computational model theories can provide insights into neuromuscular and brain function allowing us to reach a deeper understanding of neuroplasticity. Neuroplasticity is the process occurring in the CNS that is able to permanently change both structure and function due to interaction with the external environment. To understand such a complex process several paradigms related to motor learning and computational modeling have been put forward. These paradigms have been explained through several internal model concepts, and supported by neurophysiological and neuroimaging studies. Therefore, it has been possible to make theories about the basis of different learning paradigms according to known computational models. Here we review the computational models and motor learning paradigms used to describe the CNS and neuromuscular functions, as well as their role in the recovery process. These theories have the potential to provide a way to rigorously explain all the potential of CNS learning, providing a basis for future clinical studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative Hydraulic Models Of Early Land Plants Provide Insight Into Middle Paleozoic Terrestrial Paleoenvironmental Conditions

NASA Astrophysics Data System (ADS)

Wilson, J. P.; Fischer, W. W.

2010-12-01

Fossil plants provide useful proxies of Earth’s climate because plants are closely connected, through physiology and morphology, to the environments in which they lived. Recent advances in quantitative hydraulic models of plant water transport provide new insight into the history of climate by allowing fossils to speak directly to environmental conditions based on preserved internal anatomy. We report results of a quantitative hydraulic model applied to one of the earliest terrestrial plants preserved in three dimensions, the ~396 million-year-old vascular plant Asteroxylon mackei. This model combines equations describing the rate of fluid flow through plant tissues with detailed observations of plant anatomy; this allows quantitative estimates of two critical aspects of plant function. First and foremost, results from these models quantify the supply of water to evaporative surfaces; second, results describe the ability of plant vascular systems to resist tensile damage from extreme environmental events, such as drought or frost. This approach permits quantitative comparisons of functional aspects of Asteroxylon with other extinct and extant plants, informs the quality of plant-based environmental proxies, and provides concrete data that can be input into climate models. Results indicate that despite their small size, water transport cells in Asteroxylon could supply a large volume of water to the plant's leaves--even greater than cells from some later-evolved seed plants. The smallest Asteroxylon tracheids have conductivities exceeding 0.015 m^2 / MPa * s, whereas Paleozoic conifer tracheids do not reach this threshold until they are three times wider. However, this increase in conductivity came at the cost of little to no adaptations for transport safety, placing the plant’s vegetative organs in jeopardy during drought events. Analysis of the thickness-to-span ratio of Asteroxylon’s tracheids suggests that environmental conditions of reduced relative

Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass

PubMed Central

Chai, Kian Piaw; Othman, Noor Farhan Binti; Teh, Aik-Hong; Ho, Kok Lian; Chan, Kok-Gan; Shamsir, Mohd Shahir; Goh, Kian Mau; Ng, Chyan Leong

2016-01-01

A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite. PMID:26975884

Tissue regeneration in dentistry: Can salamanders provide insight?

PubMed

Sader, F; Denis, J-F; Roy, S

2018-05-01

The ability to regenerate damaged tissues would be of tremendous benefit for medicine and dentistry. Unfortunately, humans are unable to regenerate tissues such as teeth and fingers or to repair injured spinal cord. With an aging population, health problems are more prominent and dentistry is no exception as loss of bone tissue in the orofacial sphere from periodontal disease is on the rise. Humans can repair oral soft tissues exceptionally well; however, hard tissues, such as bone and teeth, are devoid of the ability to repair well or at all. Fortunately, Mother Nature has solved nearly every problem that we would like to solve for our own benefit and tissue regeneration is no exception. By studying animals that can regenerate, like Axolotls (Mexican salamander), we hope to find ways to stimulate regeneration in humans. We will discuss the role of the transforming growth factor beta cytokines as they are central to wound healing in humans and regeneration in Axolotls. We will also compare wound healing in humans (skin and oral mucosa) to Axolotl skin wound healing and limb regeneration. Finally, we will address the problem of bone regeneration and present results in salamanders which indicate that in order to regenerate bone you need to recruit non-bone cells. Fundamental research, such as the work being performed in animals that can regenerate, offers insight to help understand why some treatments are successful while others fail when it comes to specific tissues such as bones. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution

PubMed Central

Rutledge, Gavin G.; Böhme, Ulrike; Sanders, Mandy; Reid, Adam J.; Cotton, James A.; Maiga-Ascofare, Oumou; Djimdé, Abdoulaye A.; Apinjoh, Tobias O.; Amenga-Etego, Lucas; Manske, Magnus; Barnwell, John W.; Renaud, François; Ollomo, Benjamin; Prugnolle, Franck; Anstey, Nicholas M.; Auburn, Sarah; Price, Ric N.; McCarthy, James S.; Kwiatkowski, Dominic P.; Newbold, Chris I.; Berriman, Matthew; Otto, Thomas D.

2017-01-01

Elucidation of the evolutionary history and interrelatedness of Plasmodium species that infect humans has been hampered by a lack of genetic information for three human-infective species: P. malariae and two P. ovale species (P. o. curtisi and P. o. wallikeri)1. These species are prevalent across most regions in which malaria is endemic2,3 and are often undetectable by light microscopy4, rendering their study in human populations difficult5. The exact evolutionary relationship of these species to the other human-infective species has been contested6,7. Using a new reference genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to accurately place these species within the Plasmodium phylogeny. Sequencing of a P. malariae relative that infects chimpanzees reveals similar signatures of selection in the P. malariae lineage to another Plasmodium lineage shown to be capable of colonization of both human and chimpanzee hosts. Molecular dating suggests that these host adaptations occurred over similar evolutionary timescales. In addition to the core genome that is conserved between species, differences in gene content can be linked to their specific biology. The genome suggests that P. malariae expresses a family of heterodimeric proteins on its surface that have structural similarities to a protein crucial for invasion of red blood cells. The data presented here provide insight into the evolution of the Plasmodium genus as a whole. PMID:28117441

Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland.

PubMed

Martin, Alicia R; Karczewski, Konrad J; Kerminen, Sini; Kurki, Mitja I; Sarin, Antti-Pekka; Artomov, Mykyta; Eriksson, Johan G; Esko, Tõnu; Genovese, Giulio; Havulinna, Aki S; Kaprio, Jaakko; Konradi, Alexandra; Korányi, László; Kostareva, Anna; Männikkö, Minna; Metspalu, Andres; Perola, Markus; Prasad, Rashmi B; Raitakari, Olli; Rotar, Oxana; Salomaa, Veikko; Groop, Leif; Palotie, Aarno; Neale, Benjamin M; Ripatti, Samuli; Pirinen, Matti; Daly, Mark J

2018-05-03

Finland provides unique opportunities to investigate population and medical genomics because of its adoption of unified national electronic health records, detailed historical and birth records, and serial population bottlenecks. We assembled a comprehensive view of recent population history (≤100 generations), the timespan during which most rare-disease-causing alleles arose, by comparing pairwise haplotype sharing from 43,254 Finns to that of 16,060 Swedes, Estonians, Russians, and Hungarians from geographically and linguistically adjacent countries with different population histories. We find much more extensive sharing in Finns, with at least one ≥ 5 cM tract on average between pairs of unrelated individuals. By coupling haplotype sharing with fine-scale birth records from more than 25,000 individuals, we find that although haplotype sharing broadly decays with geographical distance, there are pockets of excess haplotype sharing; individuals from northeast Finland typically share several-fold more of their genome in identity-by-descent segments than individuals from southwest regions. We estimate recent effective population-size changes through time across regions of Finland, and we find that there was more continuous gene flow as Finns migrated from southwest to northeast between the early- and late-settlement regions than was dichotomously described previously. Lastly, we show that haplotype sharing is locally enriched by an order of magnitude among pairs of individuals sharing rare alleles and especially among pairs sharing rare disease-causing variants. Our work provides a general framework for using haplotype sharing to reconstruct an integrative view of recent population history and gain insight into the evolutionary origins of rare variants contributing to disease. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron

2013-04-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes showmore » activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.« less

Understanding how the shape and spatial distribution of ULVZs provides insight into their cause and to the nature of global-scale mantle convection

NASA Astrophysics Data System (ADS)

McNamara, Allen; Li, Mingming; Garnero, Ed; Marin, Nicole

2017-04-01

Seismic observations of the lower mantle infer multiple scales of compositional heterogeneity. The largest-scale heterogeneity, observed in seismic tomography models, is in the form of large, nearly antipodal regions referred to as the Large Low Shear Velocity Provinces (LLSVPs). In contrast, diffracted wave and core-reflection precursor seismic studies reveal small-scale Ultra Low Velocity Zones (ULVZs) at the base of the mantle that are almost two orders of magnitude smaller than the LLSVPs. We hypothesize that ULVZs provide insight into the nature of LLSVPs, and the LLSVPs, in turn, provide clues to the nature of global-scale mantle convection and compositional state. However, both LLSVPs and ULVZs are observations, and it remains unclear what is causing them. Here, we examine several related questions to aid in understanding their cause and the dynamical processes associated with them. Can we use seismic observations of ULVZ locations to differentiate whether they are caused by compositional heterogeneity or simply partial melting in otherwise normal mantle? Can we use the map-view shape of ULVZs to tell us about lowermost mantle flow directions and the temporal stability of these flow directions? Can the cross-sectional morphology of ULVZs tell us something about the viscosity difference between LLSVPs and background mantle? We performed geodynamical experiments to help answer these questions. We find that ULVZs caused by compositional heterogeneity preferentially form patch-like shapes along the margins of LLSVPs. Rounded patches indicate regions with long-lived stable mantle flow patterns, and linear patches indicate changing mantle flow patterns. Typically, these ULVZ patches have an asymmetrical cross-sectional shape; however, if LLSVPs have a larger grain-size than background mantle, their increased diffusion creep viscosity will act to make them more symmetrical. Alternatively, ULVZs caused simply by partial melting of normal mantle are preferentially

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers position NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

Encapsulated in its payload fairing NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is prepared for transport to Space Launch Complex 3 at Vandenberg Air Force Base in California. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Battery Installation

NASA Image and Video Library

2018-04-20

In the gantry at Space Launch Complex 3 at Vandenberg Air Force Base in California, a technician prepares batteries for installation in NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Battery Installation

NASA Image and Video Library

2018-04-20

In the gantry at Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers prepare batteries for installation in NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Media Day Preparation

NASA Image and Video Library

2018-04-05

NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, is in a clean room inside the Astrotech processing facility at Vandenberg Air Force Base in California. InSight is scheduled for liftoff on a United Launch Alliance Atlas V rocket May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Chandra Observations of Neutron Stars: An Overview

NASA Technical Reports Server (NTRS)

Weisskopf, Martin C.; Karovska, M.; Pavlov, G. G.; Zavlin, V. E.; Clarke, Tracy

2006-01-01

We present a brief review of Chandra X-ray Observatory observations of neutron stars. The outstanding spatial and spectral resolution of this great observatory have allowed for observations of unprecedented clarity and accuracy. Many of these observations have provided new insights into neutron star physics. We present an admittedly biased and overly brief overview of these observations, highlighting some new discoveries made possible by the Observatory's unique capabilities. We also include our analysis of recent multiwavelength observations of the putative pulsar and its pulsar-wind nebula in the IC 443 SNR.

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

PubMed Central

2011-01-01

Background Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

PubMed

Ragupathy, Raja; Rathinavelu, Rajkumar; Cloutier, Sylvie

2011-05-09

Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be

New Insights in Tropospheric Ozone and its Variability

NASA Technical Reports Server (NTRS)

Oman, Luke D.; Douglass, Anne R.; Ziemke, Jerry R.; Rodriquez, Jose M.

2011-01-01

We have produced time-slice simulations using the Goddard Earth Observing System Version 5 (GEOS-5) coupled to a comprehensive stratospheric and tropospheric chemical mechanism. These simulations are forced with observed sea surface temperatures over the past 25 years and use constant specified surface emissions, thereby providing a measure of the dynamically controlled ozone response. We examine the model performance in simulating tropospheric ozone and its variability. Here we show targeted comparisons results from our simulations with a multi-decadal tropical tropospheric column ozone dataset obtained from satellite observations of total column ozone. We use SHADOZ ozonesondes to gain insight into the observed vertical response and compare with the simulated vertical structure. This work includes but is not limited to ENSO related variability.

Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease*

PubMed Central

Packer, Nicolle H.; Schulz, Benjamin L.

2016-01-01

The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease. PMID:26929216

InSight Liftoff

NASA Image and Video Library

2018-05-05

A United Launch Alliance Atlas V rocket lifts off from Space Launch Complex 3 at Vandenberg Air Force Base, California, carrying NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. Liftoff was at 4:05 a.m. PDT (7:05 a.m. EDT). The spacecraft will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created.

Temperature-modulated DSC provides new insight about nickel-titanium wire transformations.

PubMed

Brantley, William A; Iijima, Masahiro; Grentzer, Thomas H

2003-10-01

Differential scanning calorimetry (DSC) is a well-known method for investigating phase transformations in nickel-titanium orthodontic wires; the microstructural phases and phase transformations in these wires have central importance for their clinical performance. The purpose of this study was to use the more recently developed technique of temperature-modulated DSC (TMDSC) to gain insight into transformations in 3 nickel-titanium orthodontic wires: Neo Sentalloy (GAC International, Islandia, NY), 35 degrees C Copper Ni-Ti (Ormco, Glendora, Calif) and Nitinol SE (3M Unitek, Monrovia, Calif). In the oral environment, the first 2 superelastic wires have shape memory, and the third wire has superelastic behavior but not shape memory. All wires had cross-section dimensions of 0.016 x 0.022 in. Archwires in the as-received condition and after bending 135 degrees were cut into 5 or 6 segments for test specimens. TMDSC analyses (Model 2910 DSC, TA Instruments, Wilmington, Del) were conducted between -125 degrees C and 100 degrees C, using a linear heating and cooling rate of 2 degrees C per min, an oscillation amplitude of 0.318 degrees C with a period of 60 seconds, and helium as the purge gas. For all 3 wire alloys, strong low-temperature martensitic transformations, resolved on the nonreversing heat-flow curves, were not present on the reversing heat-flow curves, and bending appeared to increase the enthalpy change for these peaks in some cases. For Neo Sentalloy, TMDSC showed that transformation between martensitic and austenitic nickel-titanium, suggested as occurring directly in the forward and reverse directions by conventional DSC, was instead a 2-step process involving the R-phase. Two-step transformations in the forward and reverse directions were also found for 35 degrees C Copper Ni-Ti and Nitinol SE. The TMDSC results show that structural transformations in these wires are complex. Some possible clinical implications of these observations are discussed.

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats

PubMed Central

Leggat, William; Bongaerts, Pim

2016-01-01

ABSTRACT For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts’ environment. PMID:27460792

On insight and psychosis: discussion paper.

PubMed Central

David, A S

1990-01-01

The concept of insight into psychosis has received scant attention in the psychiatric literature. Various types of insight are described after drawing on such sources as phenomenology, clinical observation and experimental psychology. It is proposed that insight is far from an all or none phenomenon but comprises three overlapping dimensions, namely, the recognition that one has a mental illness, compliance with treatment and the ability to re-label unusual mental events (delusions and hallucinations) as pathological. PMID:2199672

Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs.

PubMed

Tanaka, Kohei; Zelenitsky, Darla K; Therrien, François

2015-01-01

Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests

Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs

PubMed Central

2015-01-01

Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests

High Resolution Insights into Snow Distribution Provided by Drone Photogrammetry

NASA Astrophysics Data System (ADS)

Redpath, T.; Sirguey, P. J.; Cullen, N. J.; Fitzsimons, S.

2017-12-01

accumulation and ablation, snow depth maps provide geostatistically robust insights into seasonal snow processes, with unprecedented detail. Such data may enhance understanding of physical processes controlling spatial and temporal distribution of seasonal snow, and their relative importance at varying spatial and temporal scales.

Social network analysis provides insights into African swine fever epidemiology.

PubMed

Lichoti, Jacqueline Kasiiti; Davies, Jocelyn; Kitala, Philip M; Githigia, Samuel M; Okoth, Edward; Maru, Yiheyis; Bukachi, Salome A; Bishop, Richard P

2016-04-01

Pig movements play a significant role in the spread of economically important infectious diseases such as the African swine fever. Characterization of movement networks between pig farms and through other types of farm and household enterprises that are involved in pig value chains can provide useful information on the role that different participants in the networks play in pathogen transmission. Analysis of social networks that underpin these pig movements can reveal pathways that are important in the transmission of disease, trade in commodities, the dissemination of information and the influence of behavioural norms. We assessed pig movements among pig keeping households within West Kenya and East Uganda and across the shared Kenya-Uganda border in the study region, to gain insight into within-country and trans-boundary pig movements. Villages were sampled using a randomized cluster design. Data were collected through interviews in 2012 and 2013 from 683 smallholder pig-keeping households in 34 villages. NodeXL software was used to describe pig movement networks at village level. The pig movement and trade networks were localized and based on close social networks involving family ties, friendships and relationships with neighbours. Pig movement network modularity ranged from 0.2 to 0.5 and exhibited good community structure within the network implying an easy flow of knowledge and adoption of new attitudes and beliefs, but also promoting an enhanced rate of disease transmission. The average path length of 5 defined using NodeXL, indicated that disease could easily reach every node in a cluster. Cross-border boar service between Uganda and Kenya was also recorded. Unmonitored trade in both directions was prevalent. While most pig transactions in the absence of disease, were at a small scale (<5km) and characterized by regular agistment, most pig sales during ASF outbreaks were to traders or other farmers from outside the sellers' village at a range of >10km

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, a crane is used to lift NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander for mating atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Media Day Preparation

NASA Image and Video Library

2018-04-05

NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, is in a clean room inside the Astrotech processing facility at Vandenberg Air Force Base in California. The spacecraft's protective heat shield is in view at right. InSight is scheduled for liftoff on a United Launch Alliance Atlas V rocket May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Media Day Preparation

NASA Image and Video Library

2018-04-05

NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, at right, is in a clean room inside the Astrotech processing facility at Vandenberg Air Force Base in California. The spacecraft's protective heat shield is in view at left. InSight is scheduled for liftoff on a United Launch Alliance Atlas V rocket May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Media Day Preparation

NASA Image and Video Library

2018-04-05

NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, is in a clean room inside the Astrotech processing facility at Vandenberg Air Force Base in California. The spacecraft's protective heat shield is in view at left. InSight is scheduled for liftoff on a United Launch Alliance Atlas V rocket May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology.

PubMed

Yuan, Zhaohe; Fang, Yanming; Zhang, Taikui; Fei, Zhangjun; Han, Fengming; Liu, Cuiyu; Liu, Min; Xiao, Wei; Zhang, Wenjing; Wu, Shan; Zhang, Mengwei; Ju, Youhui; Xu, Huili; Dai, He; Liu, Yujun; Chen, Yanhui; Wang, Lili; Zhou, Jianqing; Guan, Dian; Yan, Ming; Xia, Yanhua; Huang, Xianbin; Liu, Dongyuan; Wei, Hongmin; Zheng, Hongkun

2017-12-22

Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Modeling fMRI signals can provide insights into neural processing in the cerebral cortex.

PubMed

Vanni, Simo; Sharifian, Fariba; Heikkinen, Hanna; Vigário, Ricardo

2015-08-01

Every stimulus or task activates multiple areas in the mammalian cortex. These distributed activations can be measured with functional magnetic resonance imaging (fMRI), which has the best spatial resolution among the noninvasive brain imaging methods. Unfortunately, the relationship between the fMRI activations and distributed cortical processing has remained unclear, both because the coupling between neural and fMRI activations has remained poorly understood and because fMRI voxels are too large to directly sense the local neural events. To get an idea of the local processing given the macroscopic data, we need models to simulate the neural activity and to provide output that can be compared with fMRI data. Such models can describe neural mechanisms as mathematical functions between input and output in a specific system, with little correspondence to physiological mechanisms. Alternatively, models can be biomimetic, including biological details with straightforward correspondence to experimental data. After careful balancing between complexity, computational efficiency, and realism, a biomimetic simulation should be able to provide insight into how biological structures or functions contribute to actual data processing as well as to promote theory-driven neuroscience experiments. This review analyzes the requirements for validating system-level computational models with fMRI. In particular, we study mesoscopic biomimetic models, which include a limited set of details from real-life networks and enable system-level simulations of neural mass action. In addition, we discuss how recent developments in neurophysiology and biophysics may significantly advance the modelling of fMRI signals. Copyright © 2015 the American Physiological Society.

Modeling fMRI signals can provide insights into neural processing in the cerebral cortex

PubMed Central

Sharifian, Fariba; Heikkinen, Hanna; Vigário, Ricardo

2015-01-01

Every stimulus or task activates multiple areas in the mammalian cortex. These distributed activations can be measured with functional magnetic resonance imaging (fMRI), which has the best spatial resolution among the noninvasive brain imaging methods. Unfortunately, the relationship between the fMRI activations and distributed cortical processing has remained unclear, both because the coupling between neural and fMRI activations has remained poorly understood and because fMRI voxels are too large to directly sense the local neural events. To get an idea of the local processing given the macroscopic data, we need models to simulate the neural activity and to provide output that can be compared with fMRI data. Such models can describe neural mechanisms as mathematical functions between input and output in a specific system, with little correspondence to physiological mechanisms. Alternatively, models can be biomimetic, including biological details with straightforward correspondence to experimental data. After careful balancing between complexity, computational efficiency, and realism, a biomimetic simulation should be able to provide insight into how biological structures or functions contribute to actual data processing as well as to promote theory-driven neuroscience experiments. This review analyzes the requirements for validating system-level computational models with fMRI. In particular, we study mesoscopic biomimetic models, which include a limited set of details from real-life networks and enable system-level simulations of neural mass action. In addition, we discuss how recent developments in neurophysiology and biophysics may significantly advance the modelling of fMRI signals. PMID:25972586

Simulations of VLBI observations of a geodetic satellite providing co-location in space

NASA Astrophysics Data System (ADS)

Anderson, James M.; Beyerle, Georg; Glaser, Susanne; Liu, Li; Männel, Benjamin; Nilsson, Tobias; Heinkelmann, Robert; Schuh, Harald

2018-02-01

We performed Monte Carlo simulations of very-long-baseline interferometry (VLBI) observations of Earth-orbiting satellites incorporating co-located space-geodetic instruments in order to study how well the VLBI frame and the spacecraft frame can be tied using such measurements. We simulated observations of spacecraft by VLBI observations, time-of-flight (TOF) measurements using a time-encoded signal in the spacecraft transmission, similar in concept to precise point positioning, and differential VLBI (D-VLBI) observations using angularly nearby quasar calibrators to compare their relative performance. We used the proposed European Geodetic Reference Antenna in Space (E-GRASP) mission as an initial test case for our software. We found that the standard VLBI technique is limited, in part, by the present lack of knowledge of the absolute offset of VLBI time to Coordinated Universal Time at the level of microseconds. TOF measurements are better able to overcome this problem and provide frame ties with uncertainties in translation and scale nearly a factor of three smaller than those yielded from VLBI measurements. If the absolute time offset issue can be resolved by external means, the VLBI results can be significantly improved and can come close to providing 1 mm accuracy in the frame tie parameters. D-VLBI observations with optimum performance assumptions provide roughly a factor of two higher uncertainties for the E-GRASP orbit. We additionally simulated how station and spacecraft position offsets affect the frame tie performance.

Soil chemical insights provided through vibrational spectroscopy

USDA-ARS?s Scientific Manuscript database

Vibrational spectroscopy techniques provide a powerful approach to study environmental materials and processes. These multifunctional analysis tools can be used to probe molecular vibrations of solid, liquid, and gaseous samples for characterizing materials, elucidating reaction mechanisms, and exam...

InSight Liftoff

NASA Image and Video Library

2018-05-05

A United Launch Alliance Atlas V rocket lifts off from Space Launch Complex 3 at Vandenberg Air Force Base, California, carrying NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. Liftoff was at 4:05 a.m. PDT (7:05 a.m. EDT). The spacecraft will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created.

The genome of Laccaria bicolor provides insights into

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, F; Aerts, A.; Ahren, D

Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assemblymore » contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

PubMed

Wallberg, Andreas; Han, Fan; Wellhagen, Gustaf; Dahle, Bjørn; Kawata, Masakado; Haddad, Nizar; Simões, Zilá Luz Paulino; Allsopp, Mike H; Kandemir, Irfan; De la Rúa, Pilar; Pirk, Christian W; Webster, Matthew T

2014-10-01

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system- and sperm motility-related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.

Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights

PubMed Central

Heinrich, Stephanie; Derrer, Carina Patrizia; Lari, Azra; Weis, Karsten; Montpetit, Ben

2017-01-01

The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression. PMID:28052353

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

Encapsulated in its payload fairing NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander arrives at Space Launch Complex 3 at Vandenberg Air Force Base in California. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

PubMed Central

2011-01-01

Background We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. PMID:21854559

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

PubMed

Renfree, Marilyn B; Papenfuss, Anthony T; Deakin, Janine E; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, Paul D; Pharo, Elizabeth A; Shaw, Geoff; Wong, Emily S W; Lefèvre, Christophe M; Nicholas, Kevin R; Kuroki, Yoko; Wakefield, Matthew J; Zenger, Kyall R; Wang, Chenwei; Ferguson-Smith, Malcolm; Nicholas, Frank W; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R; Siddle, Hannah V; Frankenberg, Stephen R; Chew, Keng Yih; Menzies, Brandon R; Stringer, Jessica M; Suzuki, Shunsuke; Hore, Timothy A; Delbridge, Margaret L; Patel, Hardip R; Mohammadi, Amir; Schneider, Nanette Y; Hu, Yanqiu; O'Hara, William; Al Nadaf, Shafagh; Wu, Chen; Feng, Zhi-Ping; Cocks, Benjamin G; Wang, Jianghui; Flicek, Paul; Searle, Stephen M J; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M; Suzuki, Yutaka; Sugano, Sumio; Toyoda, Atsushi; Sakaki, Yoshiyuki; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; McColl, Kaighin A; Lansdell, Benjamin; Weinstock, George; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, Artem; Hazar-Rethinam, Mehlika; Hall, Allison; Davis, John; Wood, David; Williams, Sarah; Sundaravadanam, Yogi; Muzny, Donna M; Jhangiani, Shalini N; Lewis, Lora R; Morgan, Margaret B; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Nazareth, Lynne; Cree, Andrew; Fowler, Gerald; Kovar, Christie L; Dinh, Huyen H; Joshi, Vandita; Jing, Chyn; Lara, Fremiet; Thornton, Rebecca; Chen, Lei; Deng, Jixin; Liu, Yue; Shen, Joshua Y; Song, Xing-Zhi; Edson, Janette; Troon, Carmen; Thomas, Daniel; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, Richard A; Cooper, Desmond W; Speed, Terence P; Fujiyama, Asao; Graves, Jennifer A M; O'Neill, Rachel J; Pask, Andrew J; Forrest, Susan M; Worley, Kim C

2011-08-29

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Initial Insights into Phoneme Awareness Intervention for Children with Complex Communication Needs

ERIC Educational Resources Information Center

Clendon, Sally; Gillon, Gail; Yoder, David

2005-01-01

This study provides insights into the benefits of phoneme awareness intervention for children with complex communication needs (CCN). The specific aims of the study were: (1) to determine whether phoneme awareness skills can be successfully trained in children with CCN; and (2) to observe any transfer effects to phoneme awareness tasks not…

Learning by observation: insights from Williams syndrome.

PubMed

Foti, Francesca; Menghini, Deny; Mandolesi, Laura; Federico, Francesca; Vicari, Stefano; Petrosini, Laura

2013-01-01

Observing another person performing a complex action accelerates the observer's acquisition of the same action and limits the time-consuming process of learning by trial and error. Observational learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by observation or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they reproduced the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became accurate and speedy. Participants with Williams syndrome beneficiated of observational training (in which they observed an actor detecting the visuo-motor sequence) in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by observation, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, observational experience was advantageous for acquiring competencies

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism

PubMed Central

Fernandes, Carlos A. H.; Pazin, Wallance M.; Dreyer, Thiago R.; Bicev, Renata N.; Cavalcante, Walter L. G.; Fortes-Dias, Consuelo L.; Ito, Amando S.; Oliveira, Cristiano L. P.; Fernandez, Roberto Morato; Fontes, Marcos R. M.

2017-01-01

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation. PMID:28256632

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism.

PubMed

Fernandes, Carlos A H; Pazin, Wallance M; Dreyer, Thiago R; Bicev, Renata N; Cavalcante, Walter L G; Fortes-Dias, Consuelo L; Ito, Amando S; Oliveira, Cristiano L P; Fernandez, Roberto Morato; Fontes, Marcos R M

2017-03-03

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A 2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation.

Human Performance on Insight Problem Solving: A Review

ERIC Educational Resources Information Center

Chu, Yun; MacGregor, James N.

2011-01-01

The article provides a review of recent research on insight problem-solving performance. We discuss what insight problems are, the different types of classic and newer insight problems, and how we can classify them. We also explain some of the other aspects that affect insight performance, such as hints, analogs, training, thinking aloud, and…

Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness.

PubMed

Willems, Sara M; Wright, Daniel J; Day, Felix R; Trajanoska, Katerina; Joshi, Peter K; Morris, John A; Matteini, Amy M; Garton, Fleur C; Grarup, Niels; Oskolkov, Nikolay; Thalamuthu, Anbupalam; Mangino, Massimo; Liu, Jun; Demirkan, Ayse; Lek, Monkol; Xu, Liwen; Wang, Guan; Oldmeadow, Christopher; Gaulton, Kyle J; Lotta, Luca A; Miyamoto-Mikami, Eri; Rivas, Manuel A; White, Tom; Loh, Po-Ru; Aadahl, Mette; Amin, Najaf; Attia, John R; Austin, Krista; Benyamin, Beben; Brage, Søren; Cheng, Yu-Ching; Cięszczyk, Paweł; Derave, Wim; Eriksson, Karl-Fredrik; Eynon, Nir; Linneberg, Allan; Lucia, Alejandro; Massidda, Myosotis; Mitchell, Braxton D; Miyachi, Motohiko; Murakami, Haruka; Padmanabhan, Sandosh; Pandey, Ashutosh; Papadimitriou, Ioannis; Rajpal, Deepak K; Sale, Craig; Schnurr, Theresia M; Sessa, Francesco; Shrine, Nick; Tobin, Martin D; Varley, Ian; Wain, Louise V; Wray, Naomi R; Lindgren, Cecilia M; MacArthur, Daniel G; Waterworth, Dawn M; McCarthy, Mark I; Pedersen, Oluf; Khaw, Kay-Tee; Kiel, Douglas P; Pitsiladis, Yannis; Fuku, Noriyuki; Franks, Paul W; North, Kathryn N; van Duijn, Cornelia M; Mather, Karen A; Hansen, Torben; Hansson, Ola; Spector, Tim; Murabito, Joanne M; Richards, J Brent; Rivadeneira, Fernando; Langenberg, Claudia; Perry, John R B; Wareham, Nick J; Scott, Robert A

2017-07-12

Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10 -8 ) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.

Genome-wide investigation of transcription factors provides insights into transcriptional regulation in Plutella xylostella.

PubMed

Zhao, Qian; Ma, Dongna; Huang, Yuping; He, Weiyi; Li, Yiying; Vasseur, Liette; You, Minsheng

2018-04-01

Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P. xylostella or Lepidoptera. RNA-seq analysis showed that some of the TF families, such as zinc fingers, homeobox, bZIP, bHLH, and MADF_DNA_bdg genes, were highly expressed in certain tissues including midgut, salivary glands, fat body, and hemocytes, with an obvious sex-biased expression pattern. In addition, a number of TFs showed significant differences in expression between insecticide susceptible and resistant strains, suggesting that these TFs play a role in regulating genes related to insecticide resistance. Finally, we identified an expansion of the HOX cluster in Lepidoptera, which might be related to Lepidoptera-specific evolution. Knockout of this cluster using CRISPR/Cas9 showed that the egg cannot hatch, indicating that this cluster may be related to egg development and maturation. This is the first comprehensive study on identifying and characterizing TFs in P. xylostella. Our results suggest that some TF families are expanded in the P. xylostella genome, and these TFs may have important biological roles in growth, development, sexual dimorphism, and resistance to insecticides. The present work provides a solid foundation for understanding regulation via TFs in P. xylostella and insights into the evolution of the P. xylostella genome.

Military Medics Insight into Providing Womens Health Services

DTIC Science & Technology

2015-12-22

determining a patient’s preference in a provider rather than gender (Buck & Littleton, 2014). Medics, particularly male medics, were keenly aware of...KS, Littleton HL. (2014). Stereotyped beliefs about male and female OB-GYNS: relationship to provider choice and patient satisfaction. Journal of...health care resource during deployment. Male and female IDCs felt obligated to educate women about how to conduct themselves on ship. In a

The Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation

PubMed Central

Huang, Zhuo; Zhang, Hong-Mei; Liu, Wei; Liu, Le; Ma, Junping; Xia, Zhilan; Chen, Yuxin; Chen, Yuewen; Wang, Depeng; Ni, Peixiang; Guo, An-Yuan; Xiong, Xingyao

2012-01-01

Background Ganoderma lucidum (Reishi or Ling Zhi) is one of the most famous Traditional Chinese Medicines and has been widely used in the treatment of various human diseases in Asia countries. It is also a fungus with strong wood degradation ability with potential in bioenergy production. However, genes, pathways and mechanisms of these functions are still unknown. Methodology/Principal Findings The genome of G. lucidum was sequenced and assembled into a 39.9 megabases (Mb) draft genome, which encoded 12,080 protein-coding genes and ∼83% of them were similar to public sequences. We performed comprehensive annotation for G. lucidum genes and made comparisons with genes in other fungi genomes. Genes in the biosynthesis of the main G. lucidum active ingredients, ganoderic acids (GAs), were characterized. Among the GAs synthases, we identified a fusion gene, the N and C terminal of which are homologous to two different enzymes. Moreover, the fusion gene was only found in basidiomycetes. As a white rot fungus with wood degradation ability, abundant carbohydrate-active enzymes and ligninolytic enzymes were identified in the G. lucidum genome and were compared with other fungi. Conclusions/Significance The genome sequence and well annotation of G. lucidum will provide new insights in function analyses including its medicinal mechanism. The characterization of genes in the triterpene biosynthesis and wood degradation will facilitate bio-engineering research in the production of its active ingredients and bioenergy. PMID:22567134

Comparative genome analysis of two Streptococcus phocae subspecies provides novel insights into pathogenicity.

PubMed

Bethke, J; Avendaño-Herrera, R

2017-02-01

Streptococcus phocae is a beta-hemolytic, Gram-positive bacterium that was first isolated in Norway from clinical specimens of harbor seal (Phoca vitulina) affected by pneumonia or respiratory infection, and in 2005, this bacterium was identified from disease outbreaks at an Atlantic salmon farm. A recent comparative polyphasic study reclassified Streptococcus phocae as subsp. phocae and subsp. salmonis, and there are currently two S. phocae NCBI sequencing projects for the type strains ATCC 51973 T and C-4 T . The present study compared these genome sequences to determine shared properties between the pathogenic mammalian and fish S. phocae subspecies. Both subspecies presented genomic islands, prophages, CRISPRs, and multiple gene activator and RofA regulator regions that could play key roles in the pathogenesis of streptococcal species. Likewise, proteins possibly influencing immune system evasion and virulence strategies were identified in both genomes, including Streptokinases, Streptolysin S, IgG endopeptidase, Fibronectin binding proteins, Daunorubicin, and Penicillin resistance proteins. Comparative differences in phage, non-phage, and genomic island sequences may form the genetic basis for the virulence, pathogenicity, and ability of S. phocae subsp. salmonis to infect and cause disease in Atlantic salmon, in contrast to S. phocae subsp. phocae. This comparative genomic study between two S. phocae subsp. provides novel insights into virulence factors and pathogenicity, offering important information that will facilitate the development of preventive and treatment measures against this pathogen. Copyright © 2016 Elsevier B.V. All rights reserved.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is positioned atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

Encapsulated in its payload fairing, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is transported to Space Launch Complex 3 at Vandenberg Air Force Base in California. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers position NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

Encapsulated in its payload fairing NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is transported to Space Launch Complex 3 at Vandenberg Air Force Base in California. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander has been mated atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Atlas V Tower Roll

NASA Image and Video Library

2018-03-22

At Space Launch Complex 3 at Vandenberg Air Force Base in California, the gantry is rolled back on the United Launch Alliance (ULA) Atlas V to a Centaur upper stage aft stub adapter (ASA) and interstage adapter (ISA) for NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. The next step will be arrival of InSight encapsulated in its payload faring for mating atop the rocket. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments.

PubMed

Petruk, Ariel A; Defelipe, Lucas A; Rodríguez Limardo, Ramiro G; Bucci, Hernán; Marti, Marcelo A; Turjanski, Adrian G

2013-01-08

It is now clear that proteins are flexible entities that in solution switch between conformations to achieve their function. Hydrogen/Deuterium Exchange Mass Spectrometry (HX/MS) is an invaluable tool to understand dynamic changes in proteins modulated by cofactor binding, post-transductional modifications, or protein-protein interactions. ERK2MAPK, a protein involved in highly conserved signal transduction pathways of paramount importance for normal cellular function, has been extensively studied by HX/MS. Experiments of the ERK2MAPK in the inactive and active states (in the presence or absence of bound ATP) have provided valuable information on the plasticity of the MAPK domain. However, interpretation of the HX/MS data is difficult, and changes are mostly explained in relation to available X-ray structures, precluding a complete atomic picture of protein dynamics. In the present work, we have used all atom Molecular Dynamics simulations (MD) to provide a theoretical framework for the interpretation of HX/MS data. Our results show that detailed analysis of protein-solvent interaction along the MD simulations allows (i) prediction of the number of protons exchanged for each peptide in the HX/MS experiments, (ii) rationalization of the experimentally observed changes in exchange rates in different protein conditions at the residue level, and (iii) that at least for ERK2MAPK, most of the functionally observed differences in protein dynamics are related to what can be considered the native state conformational ensemble. In summary, the combination of HX/MS experiments with all atom MD simulations emerges as a powerful approach to study protein native state dynamics with atomic resolution.

Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization.

PubMed

Shen, Yanyue; Zhang, Yu; Zou, Jun; Meng, Jinling; Wang, Jianbo

2015-01-01

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. Although genomic and transcriptomic changes have been observed in polyploids, the effects of polyploidization on proteomic divergence are poorly understood. In this study, we reported quantitative analysis of proteomic changes in leaves of Brassica hexaploid and its parents using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. A total of 2044 reproducible proteins were quantified by at least two unique peptides. We detected 452 proteins differentially expressed between Brassica hexaploid and its parents, and 100 proteins were non-additively expressed in Brassica hexaploid, which suggested a trend of non-additive protein regulation following genomic merger and doubling. Functional categories of cellular component biogenesis, immune system process, and response to stimulus, were significantly enriched in non-additive proteins, probably providing a driving force for variation and adaptation in allopolyploids. In particular, majority of the total 452 differentially expressed proteins showed expression level dominance of one parental expression, and there was an expression level dominance bias toward the tetraploid progenitor. In addition, the percentage of differentially expressed proteins that matched previously reported differentially genes were relatively low. This study aimed to get new insights into the effects of polyploidization on proteomic divergence. Using iTRAQ LC-MS/MS technology, we identified 452 differentially expressed proteins between allopolyploid and its parents which involved in response to stimulus, multi-organism process, and immune system process, much more than previous studies using 2-DE coupled with mass spectrometry technology. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in allopolyploid and its parents, which will lead to a better understanding of

Isostasy, Stress and Gravitational Potential Energy in the Southern Atlantic - Insights from Satellite Gravity Observations

NASA Astrophysics Data System (ADS)

Goetze, H. J.; Klinge, L.; Scheck-Wenderoth, M.; Dressel, I.; Sippel, J.

2015-12-01

New satellite gravity fields e.g. EGM2008, GoCo3S and very recently EIGEN-6C4 (Förste et al., 2014) provide high-accuracy and globally uniform information of the Earth's gravity field and partly of its gradients. The main goal of this study is to investigate the impact of this new gravity field and its processed anomalies (Bouguer, Free-air and Vening-Meinesz residual fields) on lithospheric modelling of passive plate margins in the area of the Southern Atlantic. In an area fixed by the latitudes 20° N - 50° S and longitudes 70° W - 20° E we calculated station-complete Bouguer anomalies (bathymetry/topography corrected) both on- and offshore and compared them with the gravity effect of a velocity model which bases on S - waves tomography (Schaeffer and Lebedev, 2013). The corresponding maps provide more insight in the abnormal mass distribution of oceanic lithosphere and the ocean-continent transition zones on both sides of the Atlantic Ocean than Free-air anomalies which are masked by bathymetry. In a next step we calculated isostatic residual fields (Vening-Meinesz isostasy with regard to different lithospheric rigidities) to remove global components (long wavelengths) from the satellite gravity. The Isostatic residual field will be compared with the GPE (gravitational potential energy). GPE variations in the Southern Atlantic, relative to the reference state, were calculated as ΔGPE. Often the oceanic lithosphere is characterized by negative ΔGPE values indicating that the ocean basin is in compression. Differences from this observation will be compared with the state of stress in the area of the passive margins of South America and South Africa and the oceanic lithosphere in between. Schaeffer, A. J. and S. Lebedev, Global shear-speed structure of the upper mantle and transition zone. Geophys. J. Int., 194 (1), 417-449, 2013. doi:10.1093/gji/ggt095

Insight and psychopathology in never-treated schizophrenia.

PubMed

Tirupati, Srinivasan; Padmavati, Raman; Thara, Rangaswamy; McCreadie, Robin G

2007-01-01

Insight is a feature of schizophrenia related to psychopathology, which could be modified by treatment. The real relationship will be more evident in the never-treated state. This study compared insight and its relationship to psychopathology in 143 never-treated patients with chronic schizophrenia with 183 treated patients. The treated patients had not received any structured intervention for improvement of insight. The item on insight and judgment from the Positive and Negative Syndrome Scale for schizophrenia was used as a measure of insight. Never-treated patients were more ill and poorer in insight than the TT group. Sex, age, duration of illness, negative symptoms related to insight only in the TT group. Positive symptoms score correlated with insight in both the groups, but negative symptoms correlated with insight only among the treated patients. Delusions, uncooperativeness, and poor attention predicted 27% of variation in the level of insight in the never-treated, whereas age; duration of illness; and symptoms of emotional withdrawal, difficulty in abstract thinking, and uncooperativeness predicted 30.3% of variation in insight of the TT group. The observed differences between the never-treated and treated subjects were due to influence of treatment on the association between insight and psychopathology. A subgroup of patients with a treatment-resistant trait of negative symptoms associated with poor insight was hypothesized.

Liftoff of InSight

NASA Image and Video Library

2018-05-05

A United Launch Alliance Atlas V rocket lifts off at 4:05 a.m. PDT (7:05 a.m. EDT) from Space Launch Complex 3 at Vandenberg Air Force Base in California carrying NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

At Space l Launch Complex 3 at Vandenberg Air Force Base in California, a crane is used to lift NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander for mating atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Rollout to Pad

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, a crane is used to lift NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander for mating atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration

PubMed Central

2011-01-01

Background Most agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by mechanical impact (bruising). Tuber susceptibility to bruising is a complex trait of the cultivated potato (Solanum tuberosum) that is crucial for crop quality. As phenotypic evaluation of bruising is cumbersome, the application of diagnostic molecular markers would empower the selection of low bruising potato varieties. The genetic factors and molecular networks underlying enzymatic tissue discoloration are sparsely known. Hitherto there is no association study dealing with tuber bruising and diagnostic markers for enzymatic discoloration are rare. Results The natural genetic diversity for bruising susceptibility was evaluated in elite middle European potato germplasm in order to elucidate its molecular basis. Association genetics using a candidate gene approach identified allelic variants in genes that function in tuber bruising and enzymatic browning. Two hundred and five tetraploid potato varieties and breeding clones related by descent were evaluated for two years in six environments for tuber bruising susceptibility, specific gravity, yield, shape and plant maturity. Correlations were found between different traits. In total 362 polymorphic DNA fragments, derived from 33 candidate genes and 29 SSR loci, were scored in the population and tested for association with the traits using a mixed model approach, which takes into account population structure and kinship. Twenty one highly significant (p < 0.001) and robust marker-trait associations were identified. Conclusions The observed trait correlations and associated marker fragments provide new insight in the molecular basis of bruising susceptibility and its natural variation. The markers diagnostic for increased or decreased bruising susceptibility will facilitate the combination of superior

Insights into the dynamics of Etna volcano from 20-year time span microgravity and GPS observations

NASA Astrophysics Data System (ADS)

Bonforte, Alessandro; Fanizza, Giovanni; Greco, Filippo; Matera, Alfredo; Sulpizio, Roberto

2016-04-01

A common ground deformation and microgravity array of benchmarks lies on the southern slope of Mt. Etna volcano and is routinely measured by GPS and relative gravimetry methods. The array was installed for monitoring the ground motion and underground mass changes along the southern rift of the volcano and data are usually processed and interpreted independently. The benchmarks have been installed mainly along a main road crossing the southern side of the volcano with an E-W direction and reaching 2000 m of altitude. The gravity array covers the entire path of the road, while the ground deformation one only the upper one, due to the woods at lower altitude preventing good GPS measurements. Furthermore, microgravity surveys are usually carried out more frequently with respect to the GPS ones. In this work, an integrated analysis of microgravity and ground deformation is performed over a 20-year time span (1994-2014). Gravity variations have been first corrected for the free-air effect using the GPS observed vertical deformation and the theoretical vertical gravity gradient (-308.6 μGal/m). The free-air corrected gravity changes were then reduced from the high frequency variations (noise) and the seasonal fluctuations, mainly due to water-table fluctuations. This long-term dataset constitutes a unique opportunity to examine the behavior of Etna in a period in which the volcano exhibited different styles of activity characterized by recharging phases, flank eruptions and fountaining episodes. The gravity and deformation data allow investigating the response of the volcano in a wider perspective providing insights into the definition of its dynamic behavior and posing the basis to track the unrest evolution and to forecast the style of the eruption. The joint analysis highlights common periods, in which the signals underwent contemporaneous changes occurring mainly in the central and eastern stations. On the other hand, no significant changes in the behavior of

Observations-based GPP estimates

NASA Astrophysics Data System (ADS)

Joiner, J.; Yoshida, Y.; Jung, M.; Tucker, C. J.; Pinzon, J. E.

2017-12-01

We have developed global estimates of gross primary production based on a relatively simple satellite observations-based approach using reflectance data from the MODIS instruments in the form of vegetation indices that provide information about photosynthetic capacity at both high temporal and spatial resolution and combined with information from chlorophyll solar-induced fluorescence from the Global Ozone Monitoring Experiment-2 instrument that is noisier and available only at lower temporal and spatial scales. We compare our gross primary production estimates with those from eddy covariance flux towers and show that they are competitive with more complicated extrapolated machine learning gross primary production products. Our results provide insight into the amount of variance in gross primary production that can be explained with satellite observations data and also show how processing of the satellite reflectance data is key to using it for accurate GPP estimates.

Characterization of hairless (Hr) and FGF5 genes provides insights into the molecular basis of hair loss in cetaceans

PubMed Central

2013-01-01

Background Hair is one of the main distinguishing characteristics of mammals and it has many important biological functions. Cetaceans originated from terrestrial mammals and they have evolved a series of adaptations to aquatic environments, which are of evolutionary significance. However, the molecular mechanisms underlying their aquatic adaptations have not been well explored. This study provided insights into the evolution of hair loss during the transition from land to water by investigating and comparing two essential regulators of hair follicle development and hair follicle cycling, i.e., the Hairless (Hr) and FGF5 genes, in representative cetaceans and their terrestrial relatives. Results The full open reading frame sequences of the Hr and FGF5 genes were characterized in seven cetaceans. The sequence characteristics and evolutionary analyses suggested the functional loss of the Hr gene in cetaceans, which supports the loss of hair during their full adaptation to aquatic habitats. By contrast, positive selection for the FGF5 gene was found in cetaceans where a series of positively selected amino acid residues were identified. Conclusions This is the first study to investigate the molecular basis of the hair loss in cetaceans. Our investigation of Hr and FGF5, two indispensable regulators of the hair cycle, provide some new insights into the molecular basis of hair loss in cetaceans. The results suggest that positive selection for the FGF5 gene might have promoted the termination of hair growth and early entry into the catagen stage of hair follicle cycling. Consequently, the hair follicle cycle was disrupted and the hair was lost completely due to the loss of the Hr gene function in cetaceans. This suggests that cetaceans have evolved an effective and complex mechanism for hair loss. PMID:23394579

Comparative transcriptome analysis provides new insights into erect and prostrate growth in bermudagrass (Cynodon dactylon L.).

PubMed

Zhang, Bing; Xiao, Xiaolin; Zong, Junqin; Chen, Jingbo; Li, Jianjian; Guo, Hailin; Liu, Jianxiu

2017-12-01

Bermudagrass (Cynodon dactylon L.) is a prominent warm-season turf and forage grass species with multiple applications. In most C. dactylon cultivars and accessions, erect-growing stems (shoot) and prostrate-growing stems (stolon) often coexist. These two types of stems are both formed through tillering but grow in two directions with different tiller angles. Elucidating the mechanism of tiller angle regulation in bermudagrass could provide important clues to breed cultivars with different plant architectural features for diverse usage. In this study, we compared the stem internode transcriptome of two bermudagrass wild accessions with extremely different tiller angles and stem growth directions. A total of 2088 and 12,141 unigenes were preferentially expressed in prostrate-growing wild accession C792 and erect-growing wild accession C793, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology-based Annotation System (KOBAS) analyses further indicated that light- and gravity-responsive genes were enriched in accession C792, whereas lignin synthesis-related genes were enriched in accession C793, which well explains the difference in lignification of vascular bundles and mechanical tissues in the two accessions. These results not only expand our understanding of the genetic control of tiller angle and stem growth direction in bermudagrass but also provide insight for future molecular breeding of C. dactylon and other turfgrass species with different plant architectures. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Plumes Provide New Insight Into the Physis of Mars' Atmosphere.

NASA Astrophysics Data System (ADS)

Andersson, L.; Ergun, R.; Malaspina, D.; Thayer, F.; Yelle, R. V.; Merkel, A. W.; Stevens, M.; Mitchell, D. L.; McFadden, J. P.; Horanyi, M.; Jakosky, B. M.; Fowler, C. M.; Pilinski, M.

2017-12-01

Low-resolution time series data measured by the Langmuir Probe and Waves (LPW) instrument on the Mars Atmosphere and Volatile EvolutioN spacecraft suggest the existence of a low-density dayside `dust' cloud stretching into the night side. At the poles, along the sunlit-shadow line, plumes of high concentration (1 #/m3) `dust particles' are observed. During one periapsis, the LPW instrument operated in a high-resolution dust mode to verify that the observed plumes in the low-resolution data are indeed created by dust particles impacting the spacecraft. This presentation will describe the observations and propose the cause of the plumes. These observations suggest that we do not yet fully understand the dust environment of Mars' atmosphere.

Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans

PubMed Central

Wang, Zhengfei; Xu, Shixia; Du, Kexing; Huang, Fang; Chen, Zhuo; Zhou, Kaiya; Ren, Wenhua; Yang, Guang

2016-01-01

Although cetaceans (whales, porpoises, and dolphins) have multi-chambered stomachs, feeding habits of modern cetaceans have dramatically changed from herbivorous to carnivorous. However, the genetic basis underlying this dietary switch remains unexplored. Here, we present the first systematic investigation of 10 digestive enzymes genes (i.e., CYP7A1, CTRC, LIPC, LIPF, PNLIP, PGC, PRSS1, SI, SLC5A1, and TMPRSS15) of representative cetaceans, and the evolutionary trajectory of RNASE1 in cetartiodactylans. Positive selections were detected with proteinases (i.e., CTRC, PRSS1, and TMPRSS15) and lipases (i.e., CYP7A1, LIPF, and PNLIP) suggesting that cetaceans have evolved an enhanced digestion capacity for proteins and lipids, the major nutritional components of their prey (fishes and invertebrates). In addition, it was found that RNASE1 gene duplicated after the cetartiodactylan speciation and two independent gene duplication events took place in Camelidae and Ruminantia. Positive selection was detected with RNASE1 of Camelidae and Bovidae, suggesting enhanced digestive efficiency in the ruminants. Remarkably, even though the ancestors of cetaceans were terrestrial artiodactyls that are herbivorous, modern cetaceans lost the pancreatic RNASE1 copy with digestive function, which is in accordance with the dietary change from herbivorous to carnivorous. In sum, this is the first study that provides new insights into the evolutionary mechanism of dietary switch in cetaceans. PMID:27651393

Observational Insights into N2O5 Heterogeneous Chemistry: Influencing Factors and Contribution to Wintertime Air Pollution

NASA Astrophysics Data System (ADS)

McDuffie, E. E.; Fibiger, D. L.; Womack, C.; Dube, W. P.; Lopez-Hilfiker, F.; Goldberger, L.; Thornton, J. A.; Shah, V.; Jaegle, L.; Guo, H.; Weber, R. J.; Schroder, J. C.; Campuzano Jost, P.; Jimenez, J. L.; Franchin, A.; Middlebrook, A. M.; Baasandorj, M.; Brown, S. S.

2017-12-01

Chemical mechanisms that underlie wintertime air pollution, including tropospheric ozone and aerosol nitrate, are poorly characterized. Due to colder temperatures and fewer hours of solar radiation, nocturnal heterogeneous uptake of N2O5 plays a relatively larger role during wintertime in controlling the oxidation of NOx (=NO+NO2) and its influence on ozone and soluble nitrate. After uptake to aerosol, N2O5 can act as both a nocturnal NOx reservoir and sink depending on the partitioning between its nitric acid and photo labile, ClNO2 reaction products. In addition, N2O5 itself can act as a NOx reservoir if the aerosol uptake coefficient is small. As a result, the nocturnal fate of N2O5 dictates the amount of NOx in an air parcel and the subsequent formation of aerosol nitrate and following-day ozone. Models of winter air pollution therefore require accurate parameterization of the N2O5 uptake coefficient, as well as factors that control its magnitude and N2O5 product partitioning. There are currently only a small number of ambient N2O5 and ClNO2 observations during the winter season concurrent with measurements of relevant variables such as aerosol size distributions and composition. The Wintertime INvestigation of Transport, Emissions, and Reactivity (WINTER) campaign conducted 10 nighttime research flights with the NCAR C-130 over the eastern U.S. during February and March, 2015. The more recent Utah Wintertime Fine Particulate Study (UWFPS) conducted over 20 research flights with the NOAA twin otter aircraft during January-February 2017 in three mountain basins near and including Salt Lake City, Utah. The two campaigns were similarly instrumented and have provided the first aircraft observations of N2O5, ClNO2, and aerosol composition in the wintertime boundary layer in these urban-influenced regions. Analysis of heterogeneous chemistry under a wide range of real environmental conditions provides insight into the factors controlling the N2O5 uptake coefficient

An integrated Biophysical CGE model to provide Sustainable Development Goal insights

NASA Astrophysics Data System (ADS)

Sanchez, Marko; Cicowiez, Martin; Howells, Mark; Zepeda, Eduardo

2016-04-01

Future projected changes in the energy system will inevitably result in changes to the level of appropriation of environmental resources, particularly land and water, and this will have wider implications for environmental sustainability, and may affect other sectors of the economy. An integrated climate, land, energy and water (CLEW) system will provide useful insights, particularly with regard to the environmental sustainability. However, it will require adequate integration with other tools to detect economic impacts and broaden the scope for policy analysis. A computable general equilibrium (CGE) model is a well suited tool to channel impacts, as detected in a CLEW analysis, onto all sectors of the economy, and evaluate trade-offs and synergies, including those of possible policy responses. This paper will show an application of such integration in a single-country CGE model with the following key characteristics. Climate is partly exogenous (as proxied by temperature and rainfall) and partly endogenous (as proxied by emissions generated by different sectors) and has an impact on endogenous variables such as land productivity and labor productivity. Land is a factor of production used in agricultural and forestry activities which can be of various types if land use alternatives (e.g., deforestation) are to be considered. Energy is an input to the production process of all economic sectors and a consumption good for households. Because it is possible to allow for substitution among different energy sources (e.g. renewable vs non-renewable) in the generation of electricity, the production process of energy products can consider the use of natural resources such as oil and water. Water, data permitting, can be considered as an input into the production process of agricultural sectors, which is particularly relevant in case of irrigation. It can also be considered as a determinant of total factor productivity in hydro-power generation. The integration of a CLEW

InSight MARCO Installation Cubesats

NASA Image and Video Library

2018-03-17

At Vandenberg Air Force Base in California, twin communications-relay CubeSats, called Mars Cube One (MarCO) are installed on an Atlas V rocket. MarCO constitutes a technology demonstration being built by NASA's Jet Propulsion Laboratory, Pasadena in California. They will launch in on the same United Launch Alliance Atlas V rocket as NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. CubeSats are a class of spacecraft based on a standardized small size and modular use of off-the-shelf technologies. Many have been made by university students, and dozens have been launched into Earth orbit using extra payload mass available on launches of larger spacecraft. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity.

PubMed

Kwon, Sunghark; Nishitani, Yuichi; Hirao, Yoshinori; Kanai, Tamotsu; Atomi, Haruyuki; Miki, Kunio

2018-04-15

The immature large subunit of [NiFe] hydrogenases undergoes C-terminal cleavage by a specific protease in the final step of the post-translational process before assembly with other subunits. It has been reported that the [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis (TkHycI) has the catalytic ability to target the membrane-bound hydrogenase large subunit MbhL from T. kodakarensis. However, the detailed mechanism of its substrate recognition remains elusive. We determined the crystal structure of TkHycI at 1.59 Å resolution to clarify how TkHycI recognizes its own substrate MbhL. Although the overall structure of TkHycI is similar to that of its homologous protease TkHybD, TkHycI adopts a larger loop than TkHybD, thereby creating a broad and deep cleft. We analyzed the structural properties of the TkHycI cleft probably involved in its substrate recognition. Our findings provide novel and profound insights into the substrate selectivity of TkHycI. Copyright © 2018 Elsevier Inc. All rights reserved.

InSight Rollout for Launch

NASA Image and Video Library

2018-05-04

At Vandenberg Air Force Base in California, the gantry rolls back at Space Launch Complex 3 in preparation for the liftoff of NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. The United Launch Alliance Atlas V rocket now is poised to boost the spacecraft with liftoff scheduled for 4:05 a.m. PDT (7:05 a.m. EDT). InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created.

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals.

PubMed

Yum, Lauren K; Baumgarten, Sebastian; Röthig, Till; Roder, Cornelia; Roik, Anna; Michell, Craig; Voolstra, Christian R

2017-07-25

Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.

Measuring the development of insight by dental health professionals in training using workplace-based assessment.

PubMed

Prescott-Clements, L E; van der Vleuten, C P M; Schuwirth, L; Gibb, E; Hurst, Y; Rennie, J S

2011-08-01

For health professionals, the development of insight into their performance is vital for safe practice, professional development and self-regulation. This study investigates whether the development of dental trainees' insight, when provided with external feedback on performance, can be assessed using a single criterion on a simple global ratings form such as the Longitudinal Evaluation of Performance or Mini Clinical Evaluation Exercise. Postgraduate dental trainees (N = 139) were assessed using this tool on a weekly basis for 6 months. Regression analysis of the data was carried out using SPSS, and a short trainer questionnaire was implemented to investigate feasibility. Ratings for insight were shown to increase with time in a similar manner to the growth observed in other essential skills. The gradient of the slope for growth of insight was slightly less than that of the other observed skills. Trainers were mostly positive about the new criterion assessing trainees' insight, although the importance of training for trainers in this process was highlighted. Our data suggest that practitioners' insight into their performance can be developed with experience and regular feedback. However, this is most likely a complex skill dependent on a number of intrinsic and external factors. The development of trainees' insight into their performance can be assessed using a single criterion on a simple global ratings form. The process involves no additional burden on evaluators in terms of their time or cost, and promotes best practice in the provision of feedback for trainees. © 2011 John Wiley & Sons A/S.

Vegetation effects on event water dynamics - Insights from in-situ stable isotope observations and dye patterns

NASA Astrophysics Data System (ADS)

Volkmann, Till; Haberer, Kristine; Gessler, Arthur; Weiler, Markus

2014-05-01

The predicted changes of climate and land-use could have drastic effects on the water balance of ecosystems, particularly under frequent drought and subsequent rewetting conditions. Yet, inference of these effects and related consequences for the structure and functioning of ecosystems, groundwater recharge, leaching of nutrients and pollutants, drinking water availability, and the water cycle is currently impeded by gaps in our understanding of the manifold interactions between vegetation and soil water dynamics. While plants require water and nutrients, they also exert, for instance, important below-ground controls on the distribution and movement of water and chemicals in the rooted soil horizons via uptake and redistribution of water, modification of soil hydraulic properties, and formation of conduits for rapid preferential water flow. This work aims to contribute to fill existing gaps by assessing the effects of different plant types and their rooting systems on the soil water dynamics. Therefore, we conducted artificial drought and subsequent rewetting experiments using isotopically and dye (Brilliant Blue FCF) labeled water on plots of various surface cover (bare soil, grass, beech, oak, vine) established on relatively homogeneous luvisol on loess in southwestern Germany. Detailed insight into the short-term dynamics of event water infiltration and root uptake during the field experiments was facilitated by the application of novel techniques for high-frequency in-situ monitoring of stable isotope signatures in pore and transpiration water using commercial laser-based spectrometers, augmenting conventional observations of soil physicochemical states (soil water content, matric potential, electrical conductivity). The temporal point information is complemented by dye staining profiles, providing a detailed picture of spatial infiltration patterns, and by root density observations. The results of the experiments allow for a comprehensive spatiotemporal

Whole-genome sequencing provides new insights into the clonal architecture of Barrett’s esophagus and esophageal adenocarcinoma

PubMed Central

Warren, Andrew; Cheetham, R. Keira; Northen, Helen; O’Donovan, Maria; Malhotra, Shalini; di Pietro, Massimiliano; Ivakhno, Sergii; He, Miao; Weaver, Jamie M.J.; Lynch, Andy G.; Kingsbury, Zoya; Ross, Mark; Humphray, Sean; Bentley, David; Fitzgerald, Rebecca C.

2015-01-01

The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its precursor lesion, Barrett’s esophagus, is poorly understood. Using whole-genome sequencing on 23 paired Barrett’s esophagus and EAC samples, together with one in-depth Barrett’s esophagus case-study sampled over time and space, we have provided new insights on the following aspects: i) Barrett’s esophagus is polyclonal and highly mutated even in the absence of dysplasia; ii) when cancer develops, copy number increases and heterogeneity persists such that the spectrum of mutations often shows surprisingly little overlap between EAC and adjacent Barrett’s esophagus; and iii) despite differences in specific coding mutations the mutational context suggests a common causative insult underlying these two conditions. From a clinical perspective, the histopathological assessment of dysplasia appears to be a poor reflection of the molecular disarray within the Barrett’s epithelium and a molecular Cytosponge™ technique overcomes sampling bias and has capacity to reflect the entire clonal architecture. PMID:26192915

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.

PubMed

Ghadie, Mohamed Ali; Lambourne, Luke; Vidal, Marc; Xia, Yu

2017-08-01

Alternative splicing is known to remodel protein-protein interaction networks ("interactomes"), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing.

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing

PubMed Central

Lambourne, Luke; Vidal, Marc

2017-01-01

Alternative splicing is known to remodel protein-protein interaction networks (“interactomes”), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experimentally-determined interactions between reference proteins. Then, we construct the isoform interactome by predicting that an isoform loses an interaction if it loses the domain mediating the interaction. Our prediction framework is of high-quality when assessed by experimental data. The predicted human isoform interactome reveals extensive network remodeling by alternative splicing. Protein pairs interacting with different isoforms of the same gene tend to be more divergent in biological function, tissue expression, and disease phenotype than protein pairs interacting with the same isoforms. Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing. PMID:28846689

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats.

PubMed

Hernandez-Agreda, Alejandra; Leggat, William; Bongaerts, Pim; Ainsworth, Tracy D

2016-07-26

For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts' environment. Corals have been proposed as the most diverse microbial biosphere. The high variability of microbial communities has hampered the identification of bacteria playing key functional roles that contribute to coral

Athena: Providing Insight into the History of the Universe

NASA Technical Reports Server (NTRS)

Murphy, Gloria A.

2010-01-01

The American Institute for Aeronautics and Astronautics has provided a Request for Proposal which calls for a manned mission to a Near-Earth Object. It is the goal of Team COLBERT to respond to their request by providing a reusable system that can be implemented as a solid stepping stone for future manned trips to Mars and beyond. Despite Team COLBERT consisting of only students in Aerospace Engineering, in order to achieve this feat, the team must employ the use of Systems Engineering. Tools and processes from Systems Engineering will provide quantitative and semi-quantitative tools for making design decisions and evaluating items such as budgets and schedules. This paper will provide an in-depth look at some of the Systems Engineering processes employed and will step through the design process of a Human Asteroid Exploration System.

Assessing stability in mild and moderate Parkinson's disease: Can clinical measures provide insight?

PubMed

Hubble, Ryan P; Silburn, Peter A; Naughton, Geraldine A; Cole, Michael H

2016-09-01

This cross-sectional study aimed to investigate the relationship between accelerometer-derived measures of movement rhythmicity and clinical measures of mobility, balance confidence and gait difficulty in people with Parkinson's disease (PD). Twenty-nine independently-living PD patients (Hoehn & Yahr Stages 1-3) with no history of significant injury or orthopaedic/deep brain stimulation surgery were recruited from a database of patients who had expressed an interest to participate in research. Participants completed clinical assessments of mobility, postural stability, balance confidence and symptom severity, while head and trunk rhythmicity was evaluated during gait using accelerometers. Following data collection, patients were stratified based on disease stage into either a Mild (Hoehn & Yahr Stage 1) or Moderate (Hoehn & Yahr Stages 2-3) PD group. The results highlighted that the Moderate PD group had poorer quality of life, reduced balance confidence and increased gait and falls difficulty. Furthermore, for these patients, gait disability and the number of previous falls were both negatively correlated with multiple components of head and trunk rhythmicity. For the Mild PD group, six-meter walk time was positively correlated with ML head rhythmicity and linear regression highlighted a significant predictive relationship between these outcomes. For the Mild and Moderate PD groups, balance confidence respectively predicted anterior-posterior trunk rhythmicity and vertical head rhythmicity. While these findings demonstrate that falls history and the Gait and Falls questionnaire provide moderate insight into head and trunk rhythmicity in Moderate PD patients, objective and clinically-feasible measures of postural instability would assist with the management of these symptoms. Copyright © 2016 Elsevier B.V. All rights reserved.

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization

PubMed Central

Fan, Guangyi; Jiao, Yu; Zhang, He; Huang, Ronglian; Zheng, Zhe; Bian, Chao; Deng, Yuewen; Wang, Qingheng; Wang, Zhongduo; Liang, Xinming; Liang, Haiying; Shi, Chengcheng; Zhao, Xiaoxia; Sun, Fengming; Hao, Ruijuan; Bai, Jie; Liu, Jialiang; Chen, Wenbin; Liang, Jinlian; Liu, Weiqing; Xu, Zhe; Shi, Qiong; Xu, Xun

2017-01-01

Abstract Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many aspects of the biomineralization process and its evolutionary origin remain unknown. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms that underlie its production of shells and pearls are not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins, chondroitin sulfotransferases, and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre suggests that elements of chitin- and collagen-based matrices have deep roots and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems. PMID:28873964

Identifying and Interpreting Stratification in Sedimentary Rocks on Mars: Insight from Rover and Orbital Observations and Terrestrial Field Analogs

NASA Astrophysics Data System (ADS)

Edgar, Lauren A.

Sedimentary rocks on Mars provide insight into past aqueous and atmospheric processes, climate regimes, and potential habitability. The stratigraphic architecture of sedimentary rocks on Mars is similar to that of Earth, indicating that the processes that govern deposition and erosion on Mars can be reasonably inferred through reference to analogous terrestrial systems. This dissertation aims to understand Martian surface processes through the use of (1) ground-based observations from the Mars Exploration Rovers, (2) orbital data from the High Resolution Imaging Science Experiment onboard the Mars Reconnaissance Orbiter, and (3) the use of terrestrial field analogs to understand bedforms and sediment transport on Mars. Chapters 1 and 2 trace the history of aqueous activity at Meridiani Planum, through the reconstruction of eolian bedforms at Victoria crater, and the identification of a potential mudstone facies at Santa Maria crater. Chapter 3 uses Terrestrial Laser Scanning to study cross-bedding in pyroclastic surge deposits on Earth in order to understand sediment transport in these events and to establish criteria for their identification on Mars. The final chapter analyzes stratal geometries in the Martian North Polar Layered Deposits using tools for sequence stratigraphic analysis, to better constrain past surface processes and past climate conditions on Mars.

InSight Atlas V ISA-ASA Transport

NASA Image and Video Library

2018-03-05

At Vandenberg Air Force Base in California, the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V rocket is prepared for transport from Building 7525 to Space Launch Complex 3. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Atlas V ISA-ASA Transport

NASA Image and Video Library

2018-03-05

At Vandenberg Air Force Base in California, the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V arrive at Space Launch Complex 3. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Atlas V ISA-ASA Transport

NASA Image and Video Library

2018-03-05

At Space Launch Complex 3 at Vandenberg Air Force Base in California, the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V are lifted by crane for mating atop a Centaur upper stage. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Atlas V ISA-ASA Transport

NASA Image and Video Library

2018-03-05

At Vandenberg Air Force Base in California, the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V rocket are transported to Space Launch Complex 3. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Insights into the Nature of Mercury's Exosphere: Early Results from the MESSENGER Orbital Mission Phase

NASA Technical Reports Server (NTRS)

McClintock, William E.; Burger, Matthew H.; Killen, Rosemary M.; Merkel, Aimee W.; Sarantos, Menelaos; Sprague, Ann L.; Solomon, Sean C.; Vervack, Ronald J., Jr.

2011-01-01

The Ultraviolet and Visible Spectrometer aboard the MESSENGER spacecraft has been making routine observations of Mercury's exosphere since March 29, 2011. Correlations of the spatial distributions of Ca, Mg, and Na with MESSENGER magnetic field and energetic particle distribution data provide insight into the processes that populate the neutral exosphere

Complementary transcriptome and proteome profiling in cabbage buds of a recessive male sterile mutant provides new insights into male reproductive development.

PubMed

Ji, Jialei; Yang, Limei; Fang, Zhiyuan; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao; Liu, Yumei; Li, Zhansheng

2018-05-15

Plant male reproductive development is a very complex biological process that involves multiple metabolic pathways. To reveal novel insights into male reproductive development, we conducted an integrated profiling of gene activity in the developing buds of a cabbage recessive genetic male sterile mutant. Using RNA-Seq and label-free quantitative proteomics, 2881 transcripts and 1245 protein species were identified with significant differential abundance between the male sterile line 83121A and its isogenic maintainer line 83121B. Analyses of function annotations and correlations between transcriptome and proteome and protein interaction networks were also conducted, which suggested that the male sterility involves a complex regulatory pattern. Moreover, several key biological processes, such as fatty acid metabolism, tapetosome biosynthesis, amino acid metabolism and protein synthesis and degradation were identified as being of relevance to male reproductive development. A large number of protein species involved in sporopollenin synthesis, amino acid synthesis, ribosome assembly, protein processing in endoplasmic reticulum and lipid transfer were observed to be significantly down-accumulated in 83121A buds, indicating their potential roles in the regulation of cabbage microspore abortion. In summary, the conjoint analysis of the transcriptome and proteome provided a global picture regarding the molecular dynamics in male sterile buds of 83121A. Male sterile mutants are excellent materials for the study of plant male reproductive development. This study revealed the molecular dynamics of recessive male sterility in cabbage at the transcriptome and proteome levels, which deepens our understanding of the metabolic pathways involved in male development. Moreover, the male sterility-related genes identified in this study could provide a reference for the artificial regulation of cabbage fertility by using genetic engineering technology, which may result in potential

The Atlantic salmon genome provides insights into rediploidization

USDA-ARS?s Scientific Manuscript database

The common ancestor of salmonids underwent an autotetraploid whole genome duplication event (Ss4R) approximately eighty million years ago, which provides unique opportunities to study the early evolutionary fate of a duplicated vertebrate genome in different extant lineages. Here, we present a high ...

The ISI Classroom Observation System: Examining the Literacy Instruction Provided to Individual Students

ERIC Educational Resources Information Center

Connor, Carol McDonald; Morrison, Frederick J.; Fishman, Barry J.; Ponitz, Claire Cameron; Glasney, Stephanie; Underwood, Phyllis S.; Piasta, Shayne B.; Crowe, Elizabeth Coyne; Schatschneider, Christopher

2009-01-01

The Individualizing Student Instruction (ISI) classroom observation and coding system is designed to provide a detailed picture of the classroom environment at the level of the individual student. Using a multidimensional conceptualization of the classroom environment, foundational elements (teacher warmth and responsiveness to students, classroom…

Global-scale Observations of the Limb and Disk (GOLD) Mission - Observing Forcing of the Thermosphere-Ionosphere System from Above and Below

NASA Astrophysics Data System (ADS)

Eastes, Richard; McClintock, William; Burns, Alan

2015-04-01

The GOLD mission will provide unprecedented imaging of the Earth’s space environment and its response to forcing from the Sun and the lower atmosphere. The mission will fly a far ultraviolet imaging spectrograph and is scheduled for launch into geostationary (GEO) orbit in October 2017 as a hosted payload on a commercial communications satellite flying over eastern South America. From this vantage point GOLD will repeatedly image the American hemisphere at a thirty-minute cadence. Fundamental parameters that will be derived from these measurements include composition (O/N2) and temperature of the neutral atmosphere on the dayside disk. Imaging of atmospheric composition, at only a daily cadence, has already provided many new insights into the behavior of the Thermosphere-Ionosphere (T-I) system. Combining composition with simultaneous temperature images will provide revolutionary insights into the behavior of the T-I system and its response to external forcing. Since GOLD will repeatedly observe the same geographic locations, it can distinguish between spatial and temporal variations in the TI system caused by geomagnetic storms, variations in solar EUV, and forcing from the lower atmosphere. GOLD’s measurements and observing approach will give the scientific community a new understanding of the T-I system.

Pleiotropic phenotypes of the sticky peel mutant provide new insight into the role of CUTIN DEFICIENT2 in epidermal cell function in tomato.

PubMed

Nadakuduti, Satya Swathi; Pollard, Mike; Kosma, Dylan K; Allen, Charles; Ohlrogge, John B; Barry, Cornelius S

2012-07-01

Plant epidermal cells have evolved specialist functions associated with adaptation to stress. These include the synthesis and deposition of specialized metabolites such as waxes and cutin together with flavonoids and anthocyanins, which have important roles in providing a barrier to water loss and protection against UV radiation, respectively. Characterization of the sticky peel (pe) mutant of tomato (Solanum lycopersicum) revealed several phenotypes indicative of a defect in epidermal cell function, including reduced anthocyanin accumulation, a lower density of glandular trichomes, and an associated reduction in trichome-derived terpenes. In addition, pe mutant fruit are glossy and peels have increased elasticity due to a severe reduction in cutin biosynthesis and altered wax deposition. Leaves of the pe mutant are also cutin deficient and the epicuticular waxes contain a lower proportion of long-chain alkanes. Direct measurements of transpiration, together with chlorophyll-leaching assays, indicate increased cuticular permeability of pe leaves. Genetic mapping revealed that the pe locus represents a new allele of CUTIN DEFICIENT2 (CD2), a member of the class IV homeodomain-leucine zipper gene family, previously only associated with cutin deficiency in tomato fruit. CD2 is preferentially expressed in epidermal cells of tomato stems and is a homolog of Arabidopsis (Arabidopsis thaliana) ANTHOCYANINLESS2 (ANL2). Analysis of cuticle composition in leaves of anl2 revealed that cutin accumulates to approximately 60% of the levels observed in wild-type Arabidopsis. Together, these data provide new insight into the role of CD2 and ANL2 in regulating diverse metabolic pathways and in particular, those associated with epidermal cells.

Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis.

PubMed

Liu, Yan; Xu, Cui; Tang, Xuebing; Pei, Surui; Jin, Di; Guo, Minghao; Yang, Meng; Zhang, Yaowei

2018-07-30

Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage. Copyright © 2018 Elsevier B.V. All rights reserved.

The Mirror Neuron System and Observational Learning: Implications for the Effectiveness of Dynamic Visualizations

ERIC Educational Resources Information Center

van Gog, Tamara; Paas, Fred; Marcus, Nadine; Ayres, Paul; Sweller, John

2009-01-01

Learning by observing and imitating others has long been recognized as constituting a powerful learning strategy for humans. Recent findings from neuroscience research, more specifically on the mirror neuron system, begin to provide insight into the neural bases of learning by observation and imitation. These findings are discussed here, along…

Hindsight Bias and Outcome-Consistent Thoughts when Observing and Making Service Provider Decisions

ERIC Educational Resources Information Center

Louie, Therese A.

2005-01-01

Two studies examined the relationship between hindsight bias and corresponding open-ended thoughts for decisions in a service provider setting. Perspectives of those observing and making decisions were examined. In study 1, business students who learned the results of a financial advisor's stock purchase showed the traditional hindsight effect…

Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum.

PubMed

de Jonge, Ronnie; Ebert, Malaika K; Huitt-Roehl, Callie R; Pal, Paramita; Suttle, Jeffrey C; Spanner, Rebecca E; Neubauer, Jonathan D; Jurick, Wayne M; Stott, Karina A; Secor, Gary A; Thomma, Bart P H J; Van de Peer, Yves; Townsend, Craig A; Bolton, Melvin D

2018-06-12

Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis ( CTB ) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae , the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide. Copyright © 2018 the Author(s). Published by PNAS.

Dystrophin-deficient pigs provide new insights into the hierarchy of physiological derangements of dystrophic muscle.

PubMed

Klymiuk, Nikolai; Blutke, Andreas; Graf, Alexander; Krause, Sabine; Burkhardt, Katinka; Wuensch, Annegret; Krebs, Stefan; Kessler, Barbara; Zakhartchenko, Valeri; Kurome, Mayuko; Kemter, Elisabeth; Nagashima, Hiroshi; Schoser, Benedikt; Herbach, Nadja; Blum, Helmut; Wanke, Rüdiger; Aartsma-Rus, Annemieke; Thirion, Christian; Lochmüller, Hanns; Walter, Maggie C; Wolf, Eckhard

2013-11-01

Duchenne muscular dystrophy (DMD) is caused by mutations in the X-linked dystrophin (DMD) gene. The absence of dystrophin protein leads to progressive muscle weakness and wasting, disability and death. To establish a tailored large animal model of DMD, we deleted DMD exon 52 in male pig cells by gene targeting and generated offspring by nuclear transfer. DMD pigs exhibit absence of dystrophin in skeletal muscles, increased serum creatine kinase levels, progressive dystrophic changes of skeletal muscles, impaired mobility, muscle weakness and a maximum life span of 3 months due to respiratory impairment. Unlike human DMD patients, some DMD pigs die shortly after birth. To address the accelerated development of muscular dystrophy in DMD pigs when compared with human patients, we performed a genome-wide transcriptome study of biceps femoris muscle specimens from 2-day-old and 3-month-old DMD and age-matched wild-type pigs. The transcriptome changes in 3-month-old DMD pigs were in good concordance with gene expression profiles in human DMD, reflecting the processes of degeneration, regeneration, inflammation, fibrosis and impaired metabolic activity. In contrast, the transcriptome profile of 2-day-old DMD pigs showed similarities with transcriptome changes induced by acute exercise muscle injury. Our studies provide new insights into early changes associated with dystrophin deficiency in a clinically severe animal model of DMD.

Sleep does not facilitate insight in older adults.

PubMed

Debarnot, Ursula; Rossi, Marta; Faraguna, Ugo; Schwartz, Sophie; Sebastiani, Laura

2017-04-01

Sleep has been shown to foster the process of insight generation in young adults during problem solving activities. Aging is characterized by substantial changes in sleep architecture altering memory consolidation. Whether sleep might promote the occurrence of insight in older adults as well has not yet been tested experimentally. To address this issue, we tested healthy young and old volunteers on an insight problem solving task, involving both explicit and implicit features, before and after a night of sleep or a comparable wakefulness period. Data showed that insight emerged significantly less frequently after a night of sleep in older adults compared to young. Moreover, there was no difference in the magnitude of insight occurrence following sleep and daytime -consolidation in aged participants. We further found that acquisition of implicit knowledge in the task before sleep potentiated the gain of insight in young participants, but this effect was not observed in aged participants. Overall, present findings demonstrate that a period of sleep does not significantly promote insight in problem solving in older adults. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic correlates of insight in schizophrenia.

PubMed

Xavier, Rose Mary; Vorderstrasse, Allison; Keefe, Richard S E; Dungan, Jennifer R

2018-05-01

Insight in schizophrenia is clinically important as it is associated with several adverse outcomes. Genetic contributions to insight are unknown. We examined genetic contributions to insight by investigating if polygenic risk scores (PRS) and candidate regions were associated with insight. Schizophrenia case-only analysis of the Clinical Antipsychotics Trials of Intervention Effectiveness trial. Schizophrenia PRS was constructed using Psychiatric Genomics Consortium (PGC) leave-one out GWAS as discovery data set. For candidate regions, we selected 105 schizophrenia-associated autosomal loci and 11 schizophrenia-related oligodendrocyte genes. We used regressions to examine PRS associations and set-based testing for candidate analysis. We examined data from 730 subjects. Best-fit PRS at p-threshold of 1e-07 was associated with total insight (R 2 =0.005, P=0.05, empirical P=0.054) and treatment insight (R 2 =0.005, P=0.048, empirical P=0.048). For models that controlled for neurocognition, PRS significantly predicted treatment insight but at higher p-thresholds (0.1 to 0.5) but did not survive correction. Patients with highest polygenic burden had 5.9 times increased risk for poor insight compared to patients with lowest burden. PRS explained 3.2% (P=0.002, empirical P=0.011) of variance in poor insight. Set-based analyses identified two variants associated with poor insight- rs320703, an intergenic variant (within-set P=6e-04, FDR P=0.046) and rs1479165 in SOX2-OT (within-set P=9e-04, FDR P=0.046). To the best of our knowledge, this is the first study examining genetic basis of insight. We provide evidence for genetic contributions to impaired insight. Relevance of findings and necessity for replication are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments

PubMed Central

Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

2016-01-01

Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. PMID:27401233

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation

PubMed Central

Mueller-Dieckmann, Christoph; Kernstock, Stefan; Lisurek, Michael; von Kries, Jens Peter; Haag, Friedrich; Weiss, Manfred S.; Koch-Nolte, Friedrich

2006-01-01

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-α-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors. PMID:17015823

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

PubMed Central

Bian, Chao; Hu, Yinchang; Ravi, Vydianathan; Kuznetsova, Inna S.; Shen, Xueyan; Mu, Xidong; Sun, Ying; You, Xinxin; Li, Jia; Li, Xiaofeng; Qiu, Ying; Tay, Boon-Hui; Thevasagayam, Natascha May; Komissarov, Aleksey S.; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Luo, Jianren; Liu, Yi; Song, Hongmei; Liu, Chao; Wang, Xuejie; Gu, Dangen; Yang, Yexin; Li, Wujiao; Polgar, Gianluca; Fan, Guangyi; Zeng, Peng; Zhang, He; Xiong, Zijun; Tang, Zhujing; Peng, Chao; Ruan, Zhiqiang; Yu, Hui; Chen, Jieming; Fan, Mingjun; Huang, Yu; Wang, Min; Zhao, Xiaomeng; Hu, Guojun; Yang, Huanming; Wang, Jian; Wang, Jun; Xu, Xun; Song, Linsheng; Xu, Gangchun; Xu, Pao; Xu, Junmin; O’Brien, Stephen J.; Orbán, László; Venkatesh, Byrappa; Shi, Qiong

2016-01-01

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas. PMID:27089831

The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.

PubMed

Huang, Jian; Zhang, Chunmei; Zhao, Xing; Fei, Zhangjun; Wan, KangKang; Zhang, Zhong; Pang, Xiaoming; Yin, Xiao; Bai, Yang; Sun, Xiaoqing; Gao, Lizhi; Li, Ruiqiang; Zhang, Jinbo; Li, Xingang

2016-12-01

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

New insights about cloud vertical structure from CloudSat and CALIPSO observations

NASA Astrophysics Data System (ADS)

Oreopoulos, Lazaros; Cho, Nayeong; Lee, Dongmin

2017-09-01

Active cloud observations from A-Train's CloudSat and CALIPSO satellites offer new opportunities to examine the vertical structure of hydrometeor layers. We use the 2B-CLDCLASS-LIDAR merged CloudSat-CALIPSO product to examine global aspects of hydrometeor vertical stratification. We group the data into major cloud vertical structure (CVS) classes based on our interpretation of how clouds in three standard atmospheric layers overlap and provide their global frequency of occurrence. The two most frequent CVS classes are single-layer (per our definition) low and high clouds that represent 53% of cloudy skies, followed by high clouds overlying low clouds, and vertically extensive clouds that occupy near-contiguously a large portion of the troposphere. The prevalence of these configurations changes seasonally and geographically, between daytime and nighttime, and between continents and oceans. The radiative effects of the CVS classes reveal the major radiative warmers and coolers from the perspective of the planet as a whole, the surface, and the atmosphere. Single-layer low clouds dominate planetary and atmospheric cooling and thermal infrared surface warming. We also investigate the consistency between passive and active views of clouds by providing the CVS breakdowns of Moderate Resolution Imaging Spectroradiometer cloud regimes for spatiotemporally coincident MODIS-Aqua (also on the A-Train) and CloudSat-CALIPSO daytime observations. When the analysis is expanded for a more in-depth look at the most heterogeneous of the MODIS cloud regimes, it ultimately confirms previous interpretations of their makeup that did not have the benefit of collocated active observations.

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

PubMed Central

Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. PMID:26560065

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

PubMed Central

2011-01-01

Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a

The role of insight in exploratory psychodynamic psychotherapy.

PubMed

Høglend, P; Engelstad, V; Sørbye, O; Heyerdahl, O; Amlo, S

1994-12-01

Psychoanalytic theory holds that dynamic insight is used for self-observation and self-analysis during and after explorative therapy. Such self-analysis is held to lead to stable dynamic change. Within a sample of 43 moderately disturbed out-patients, pre-treatment level of insight was associated with treatment length, with not being an early or late drop-out, and with receiving additional psychotherapy during a four-year follow-up period. Pre-treatment level of insight turned out to be not directly correlated with outcome two and four years after therapy. However, level of insight was significantly correlated with outcome in interaction with treatment length. Gain of insight measured at two-year follow-up was the strongest predictor of overall dynamic change four years after therapy, compared with all the other outcome assessments made at two-year follow-up.

Spider genomes provide insight into composition and evolution of venom and silk

PubMed Central

Sanggaard, Kristian W.; Bechsgaard, Jesper S.; Fang, Xiaodong; Duan, Jinjie; Dyrlund, Thomas F.; Gupta, Vikas; Jiang, Xuanting; Cheng, Ling; Fan, Dingding; Feng, Yue; Han, Lijuan; Huang, Zhiyong; Wu, Zongze; Liao, Li; Settepani, Virginia; Thøgersen, Ida B.; Vanthournout, Bram; Wang, Tobias; Zhu, Yabing; Funch, Peter; Enghild, Jan J.; Schauser, Leif; Andersen, Stig U.; Villesen, Palle; Schierup, Mikkel H; Bilde, Trine; Wang, Jun

2014-01-01

Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk. PMID:24801114

The politics of insight

PubMed Central

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs. PMID:26810954

The politics of insight.

PubMed

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.

Fermi-LAT Gamma-ray Bursts and Insight from Swift

NASA Technical Reports Server (NTRS)

Racusin, Judith L.

2011-01-01

A new revolution in GRB observation and theory has begun over the last 3 years since the launch of the Fermi gamma-ray space telescope. The new window into high energy gamma-rays opened by the Fermi-LAT is providing insight into prompt emission mechanisms and possibly also afterglow physics. The LAT detected GRBs appear to be a new unique subset of extremely energetic and bright bursts. In this talk I will discuss the context and recent discoveries from these LAT GRBs and the large database of broadband observations collected by Swift over the last 7 years and how through comparisons between the Swift, GBM, and LAT GRB samples, we can learn about the unique characteristics and relationships between each population.

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes.

PubMed

Chauhan, Pallavi; Hansson, Bengt; Kraaijeveld, Ken; de Knijff, Peter; Svensson, Erik I; Wellenreuther, Maren

2014-09-22

considerable ecological and evolutionary interest for this and other insect orders. Our work presents a comprehensive transcriptome resource for the ancient insect order Odonata and provides insight into their biology and physiology. The transcriptomic resource can provide a foundation for future investigations into this diverse group, including the evolution of colour, vision, olfaction and thermal adaptation.

InSight Final Flight Installation of Heatshield

NASA Image and Video Library

2018-04-12

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers place the heatshield on NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander prior to encapsulation in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

A comparison of the seasonal movements of tiger sharks and green turtles provides insight into their predator-prey relationship.

PubMed

Fitzpatrick, Richard; Thums, Michele; Bell, Ian; Meekan, Mark G; Stevens, John D; Barnett, Adam

2012-01-01

During the reproductive season, sea turtles use a restricted area in the vicinity of their nesting beaches, making them vulnerable to predation. At Raine Island (Australia), the highest density green turtle Chelonia mydas rookery in the world, tiger sharks Galeocerdo cuvier have been observed to feed on green turtles, and it has been suggested that they may specialise on such air-breathing prey. However there is little information with which to examine this hypothesis. We compared the spatial and temporal components of movement behaviour of these two potentially interacting species in order to provide insight into the predator-prey relationship. Specifically, we tested the hypothesis that tiger shark movements are more concentrated at Raine Island during the green turtle nesting season than outside the turtle nesting season when turtles are not concentrated at Raine Island. Turtles showed area-restricted search behaviour around Raine Island for ∼3-4 months during the nesting period (November-February). This was followed by direct movement (transit) to putative foraging grounds mostly in the Torres Straight where they switched to area-restricted search mode again, and remained resident for the remainder of the deployment (53-304 days). In contrast, tiger sharks displayed high spatial and temporal variation in movement behaviour which was not closely linked to the movement behaviour of green turtles or recognised turtle foraging grounds. On average, tiger sharks were concentrated around Raine Island throughout the year. While information on diet is required to determine whether tiger sharks are turtle specialists our results support the hypothesis that they target this predictable and plentiful prey during turtle nesting season, but they might not focus on this less predictable food source outside the nesting season.

A Comparison of the Seasonal Movements of Tiger Sharks and Green Turtles Provides Insight into Their Predator-Prey Relationship

PubMed Central

Fitzpatrick, Richard; Thums, Michele; Bell, Ian; Meekan, Mark G.; Stevens, John D.; Barnett, Adam

2012-01-01

During the reproductive season, sea turtles use a restricted area in the vicinity of their nesting beaches, making them vulnerable to predation. At Raine Island (Australia), the highest density green turtle Chelonia mydas rookery in the world, tiger sharks Galeocerdo cuvier have been observed to feed on green turtles, and it has been suggested that they may specialise on such air-breathing prey. However there is little information with which to examine this hypothesis. We compared the spatial and temporal components of movement behaviour of these two potentially interacting species in order to provide insight into the predator-prey relationship. Specifically, we tested the hypothesis that tiger shark movements are more concentrated at Raine Island during the green turtle nesting season than outside the turtle nesting season when turtles are not concentrated at Raine Island. Turtles showed area-restricted search behaviour around Raine Island for ∼3–4 months during the nesting period (November–February). This was followed by direct movement (transit) to putative foraging grounds mostly in the Torres Straight where they switched to area-restricted search mode again, and remained resident for the remainder of the deployment (53–304 days). In contrast, tiger sharks displayed high spatial and temporal variation in movement behaviour which was not closely linked to the movement behaviour of green turtles or recognised turtle foraging grounds. On average, tiger sharks were concentrated around Raine Island throughout the year. While information on diet is required to determine whether tiger sharks are turtle specialists our results support the hypothesis that they target this predictable and plentiful prey during turtle nesting season, but they might not focus on this less predictable food source outside the nesting season. PMID:23284819

A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria.

PubMed

Yang, Yunpeng; Zhang, Lu; Huang, He; Yang, Chen; Yang, Sheng; Gu, Yang; Jiang, Weihong

2017-01-24

Catabolite control protein A (CcpA) is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR) and carbon catabolite activation (CCA), two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt) consensus site that is called a catabolite response element (cre) within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named cre var , has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA). It was found that the length of the intervening spacer of cre var can affect CcpA binding affinity, and moreover, the core palindromic sequence of cre var is the key structure for regulation. Such a variable architecture of cre var shows potential importance for CcpA's diverse and fine regulation. A total of 103 potential cre var sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs), and 30 sites were confirmed to be bound by CcpA. These 30 cre var sites are associated with 27 genes involved in many important pathways. Also of significance, the cre var sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria. In Gram-positive bacteria, the global regulator CcpA controls a large number of important physiological and metabolic processes. Although a typical consensus CcpA-binding site, cre, has been identified, it remains

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

PubMed Central

Yu, Xiaozhen; Sigler, Sara C.; Hossain, Delwar; Wierdl, Monika; Gwaltney, Steven R.; Potter, Philip M.; Wadkins, Randy M.

2013-01-01

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member. PMID:22127613

New insights into insight: Neurophysiological correlates of the difference between the intrinsic "aha" and the extrinsic "oh yes" moment.

PubMed

Rothmaler, Katrin; Nigbur, Roland; Ivanova, Galina

2017-01-27

Insight refers to a situation in which a problem solver immediately changes his understanding of a problem situation. This representational change can either be triggered by external stimuli, like a hint or the solution itself, or by internal solution attempts. In the present paper, the differences and similarities between these two phenomena, namely "extrinsic" and "intrinsic" insight, are examined. To this end, electroencephalogram (EEG) is recorded while subjects either recognize or generate solutions to German verbal compound remote associate problems (CRA). Based on previous studies, we compare the alpha power prior to insightful solution recognition with the alpha power prior to insightful solution generation. Results show that intrinsic insights are preceded by an increase in alpha power at right parietal electrodes, while extrinsic insights are preceded by a respective decrease. These results can be interpreted in two ways. In consistency with other studies, the increase in alpha power before intrinsic insights can be interpreted as an increased internal focus of attention. Accordingly, the decrease in alpha power before extrinsic insights may be associated with a more externally oriented focus of attention. Alternatively, the increase in alpha power prior to intrinsic insights can be interpreted as an active inhibition of solution-related information, while the alpha power decrease prior to extrinsic insights may reflect its activation. Regardless of the interpretation, the results provide strong evidence that extrinsic and intrinsic insight differ on the behavioral as well as the neurophysiological level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction.

PubMed

Martinson, Ellen O; Hackett, Jeremiah D; Machado, Carlos A; Arnold, A Elizabeth

2015-01-01

A striking property of the mutualism between figs and their pollinating wasps is that wasps consistently oviposit in the inner flowers of the fig syconium, which develop into galls that house developing larvae. Wasps typically do not use the outer ring of flowers, which develop into seeds. To better understand differences between gall and seed flowers, we used a metatranscriptomic approach to analyze eukaryotic gene expression within fig flowers at the time of oviposition choice and early gall development. Consistent with the unbeatable seed hypothesis, we found significant differences in gene expression between gall- and seed flowers in receptive syconia prior to oviposition. In particular, transcripts assigned to flavonoids and carbohydrate metabolism were significantly up-regulated in gall flowers relative to seed flowers. In response to oviposition, gall flowers significantly up-regulated the expression of chalcone synthase, which previously has been connected to gall formation in other plants. We propose several genes encoding proteins with signal peptides or associations with venom of other Hymenoptera as candidate genes for gall initiation or growth. This study simultaneously evaluates the gene expression profile of both mutualistic partners in a plant-insect mutualism and provides insight into a possible stability mechanism in the ancient fig-fig wasp association.

Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction

PubMed Central

Martinson, Ellen O.; Hackett, Jeremiah D.; Machado, Carlos A.; Arnold, A. Elizabeth

2015-01-01

A striking property of the mutualism between figs and their pollinating wasps is that wasps consistently oviposit in the inner flowers of the fig syconium, which develop into galls that house developing larvae. Wasps typically do not use the outer ring of flowers, which develop into seeds. To better understand differences between gall and seed flowers, we used a metatranscriptomic approach to analyze eukaryotic gene expression within fig flowers at the time of oviposition choice and early gall development. Consistent with the unbeatable seed hypothesis, we found significant differences in gene expression between gall- and seed flowers in receptive syconia prior to oviposition. In particular, transcripts assigned to flavonoids and carbohydrate metabolism were significantly up-regulated in gall flowers relative to seed flowers. In response to oviposition, gall flowers significantly up-regulated the expression of chalcone synthase, which previously has been connected to gall formation in other plants. We propose several genes encoding proteins with signal peptides or associations with venom of other Hymenoptera as candidate genes for gall initiation or growth. This study simultaneously evaluates the gene expression profile of both mutualistic partners in a plant-insect mutualism and provides insight into a possible stability mechanism in the ancient fig-fig wasp association. PMID:26090817

Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes

PubMed Central

Li, Yongchao; Wang, Yang; Jiang, Haobo; Deng, Junpeng

2009-01-01

Arthropod phenoloxidase (PO) generates quinones and other toxic compounds to sequester and kill pathogens during innate immune responses. It is also involved in wound healing and other physiological processes. Insect PO is activated from its inactive precursor, prophenoloxidase (PPO), by specific proteolysis via a serine protease cascade. Here, we report the crystal structure of PPO from a lepidopteran insect at a resolution of 1.97 Å, which is the initial structure for a PPO from the type 3 copper protein family. Manduca sexta PPO is a heterodimer consisting of 2 homologous polypeptide chains, PPO1 and PPO2. The active site of each subunit contains a canonical type 3 di-nuclear copper center, with each copper ion coordinated with 3 structurally conserved histidines. The acidic residue Glu-395 located at the active site of PPO2 may serve as a general base for deprotonation of monophenolic substrates, which is key to the ortho-hydroxylase activity of PO. The structure provides unique insights into the mechanism by which type 3 copper proteins differ in their enzymatic activities, albeit sharing a common active center. A drastic change in electrostatic surface induced on cleavage at Arg-51 allows us to propose a model for localized PPO activation in insects. PMID:19805072

Systematic characterization of the peroxidase gene family provides new insights into fungal pathogenicity in Magnaporthe oryzae

PubMed Central

Mir, Albely Afifa; Park, Sook-Young; Sadat, Md. Abu; Kim, Seongbeom; Choi, Jaeyoung; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a part of host innate immunity. Recent studies proposed peroxidases as components of antioxidant defense system. However, the role of fungal peroxidases during interaction with host plants has not been explored at the genomic level. Here, we systematically identified peroxidase genes and analyzed their impact on fungal pathogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. Phylogeny reconstruction placed 27 putative peroxidase genes into 15 clades. Expression profiles showed that majority of them are responsive to in planta condition and in vitro H2O2. Our analysis of individual deletion mutants for seven selected genes including MoPRX1 revealed that these genes contribute to fungal development and/or pathogenesis. We identified significant and positive correlations among sensitivity to H2O2, peroxidase activity and fungal pathogenicity. In-depth analysis of MoPRX1 demonstrated that it is a functional ortholog of thioredoxin peroxidase in Saccharomyces cerevisiae and is required for detoxification of the oxidative burst within host cells. Transcriptional profiling of other peroxidases in ΔMoprx1 suggested interwoven nature of the peroxidase-mediated antioxidant defense system. The results from this study provide insight into the infection strategy built on evolutionarily conserved peroxidases in the rice blast fungus. PMID:26134974

Profiling and Quantifying Differential Gene Transcription Provide Insights into Ganoderic Acid Biosynthesis in Ganoderma lucidum in Response to Methyl Jasmonate

PubMed Central

Shi, Liang; Mu, Da-Shuai; Jiang, Ai-Liang; Han, Qin; Zhao, Ming-Wen

2013-01-01

Ganoderma lucidum is a mushroom with traditional medicinal properties that has been widely used in China and other countries in Eastern Asia. Ganoderic acids (GA) produced by G. lucidum exhibit important pharmacological activities. Previous studies have demonstrated that methyl jasmonate (MeJA) is a potent inducer of GA biosynthesis and the expression of genes involved in the GA biosynthesis pathway in G. lucidum. To further explore the mechanism of GA biosynthesis, cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) was used to identify genes that are differentially expressed in response to MeJA. Using 64 primer combinations, over 3910 transcriptionally derived fragments (TDFs) were obtained. Reliable sequence data were obtained for 390 of 458 selected TDFs. Ninety of these TDFs were annotated with known functions through BLASTX searching the GenBank database, and 12 annotated TDFs were assigned into secondary metabolic pathways by searching the KEGGPATHWAY database. Twenty-five TDFs were selected for qRT-PCR analysis to confirm the expression patterns observed with cDNA-AFLP. The qRT-PCR results were consistent with the altered patterns of gene expression revealed by the cDNA-AFLP technique. Additionally, the transcript levels of 10 genes were measured at the mycelium, primordia, and fruiting body developmental stages of G. lucidum. The greatest expression levels were reached during primordia for all of the genes except cytochrome b2 reached its highest expression level in the mycelium stage. This study not only identifies new candidate genes involved in the regulation of GA biosynthesis but also provides further insight into MeJA-induced gene expression and secondary metabolic response in G. lucidum. PMID:23762280

Video observation in HIT development: lessons learned on benefits and challenges.

PubMed

Høstgaard, Anna Marie; Bertelsen, Pernille

2012-08-22

Experience shows that the precondition for the development of successful health information technologies is a thorough insight into clinical work practice. In contemporary clinical work practice, clinical work and health information technology are integrated, and part of the practice is tacit. When work practice becomes routine, it slips to the background of the conscious awareness and becomes difficult to recognize without the context to support recall. This means that it is difficult to capture with traditional ethnographic research methods or in usability laboratories or clinical set ups. Observation by the use of the video technique within healthcare settings has proven to be capable of providing a thorough insight into the complex clinical work practice and its context - including parts of the tacit practice. The objective of this paper is 1) to argue for the video observation technique to inform and improve health-information-technology development and 2) to share insights and lessons learned on benefits and challenges when using the video observation technique within healthcare settings. A multiple case study including nine case studies conducted by DaCHI researchers 2004-2011 using audio-visual, non-participant video observation for data collection within different healthcare settings. In HIT development, video observation is beneficial for 1) informing and improving system design 2) studying changes in work practice 3) identifying new potentials and 4) documenting current work practices. The video observation technique used within healthcare settings is superior to other ethnographic research methods when it comes to disclosing the complexity in clinical work practice. The insights gained are far more realistic compared to traditional ethnographic studies or usability studies and studies in clinical set ups. Besides, the data generated through video recordings provide a solid basis for dialog between the health care professionals involved. The most

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

PubMed

Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

2016-10-01

Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

PubMed Central

Sorokin, Dimitry Y.; Makarova, Kira S.; Abbas, Ben; Ferrer, Manuel; Golyshin, Peter N.; Galinski, Erwin A.; Ciordia, Sergio; Mena, María Carmen; Merkel, Alexander Y.; Wolf, Yuri I.; van Loosdrecht, Mark C.M.; Koonin, Eugene V.

2017-01-01

Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes, and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage “Methanonatronarchaeia” that is most closely related to the class Halobacteria. Similar to the Halobacteria, “Methanonatronarchaeia” are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that “Methanonatronarchaeia” employ the “salt-in” osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that utilize C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterosulfide reductase and cytochromes. These features differentiates “Methanonatronarchaeia” from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway. PMID:28555626

Elephant Transcriptome Provides Insights into the Evolution of Eutherian Placentation

PubMed Central

Hou, Zhuo-Cheng; Sterner, Kirstin N.; Romero, Roberto; Than, Nandor Gabor; Gonzalez, Juan M.; Weckle, Amy; Xing, Jun; Benirschke, Kurt; Goodman, Morris; Wildman, Derek E.

2012-01-01

The chorioallantoic placenta connects mother and fetus in eutherian pregnancies. In order to understand the evolution of the placenta and provide further understanding of placenta biology, we sequenced the transcriptome of a term placenta of an African elephant (Loxodonta africana) and compared these data with RNA sequence and microarray data from other eutherian placentas including human, mouse, and cow. We characterized the composition of 55,910 expressed sequence tag (i.e., cDNA) contigs using our custom annotation pipeline. A Markov algorithm was used to cluster orthologs of human, mouse, cow, and elephant placenta transcripts. We found 2,963 genes are commonly expressed in the placentas of these eutherian mammals. Gene ontology categories previously suggested to be important for placenta function (e.g., estrogen receptor signaling pathway, cell motion and migration, and adherens junctions) were significantly enriched in these eutherian placenta–expressed genes. Genes duplicated in different lineages and also specifically expressed in the placenta contribute to the great diversity observed in mammalian placenta anatomy. We identified 1,365 human lineage–specific, 1,235 mouse lineage–specific, 436 cow lineage–specific, and 904 elephant-specific placenta-expressed (PE) genes. The most enriched clusters of human-specific PE genes are signal/glycoprotein and immunoglobulin, and humans possess a deeply invasive human hemochorial placenta that comes into direct contact with maternal immune cells. Inference of phylogenetically conserved and derived transcripts demonstrates the power of comparative transcriptomics to trace placenta evolution and variation across mammals and identified candidate genes that may be important in the normal function of the human placenta, and their dysfunction may be related to human pregnancy complications. PMID:22546564

The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees

PubMed Central

Wan, KangKang; Zhang, Zhong; Pang, Xiaoming; Yin, Xiao; Bai, Yang; Sun, Xiaoqing; Gao, Lizhi; Li, Ruiqiang; Zhang, Jinbo

2016-01-01

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar ‘Junzao’ and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of ‘Dongzao’, a fresh jujube, was ~86.5 Mb larger than that of the ‘Junzao’, partially due to the recent insertions of transposable elements in the ‘Dongzao’ genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication. PMID:28005948

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Providing guidance for genomics-based cancer treatment decisions: insights from stakeholder engagement for post-prostatectomy radiation therapy.

PubMed

Abe, James; Lobo, Jennifer M; Trifiletti, Daniel M; Showalter, Timothy N

2017-08-24

Despite the emergence of genomics-based risk prediction tools in oncology, there is not yet an established framework for communication of test results to cancer patients to support shared decision-making. We report findings from a stakeholder engagement program that aimed to develop a framework for using Markov models with individualized model inputs, including genomics-based estimates of cancer recurrence probability, to generate personalized decision aids for prostate cancer patients faced with radiation therapy treatment decisions after prostatectomy. We engaged a total of 22 stakeholders, including: prostate cancer patients, urological surgeons, radiation oncologists, genomic testing industry representatives, and biomedical informatics faculty. Slides were at each meeting to provide background information regarding the analytical framework. Participants were invited to provide feedback during the meeting, including revising the overall project aims. Stakeholder meeting content was reviewed and summarized by stakeholder group and by theme. The majority of stakeholder suggestions focused on aspects of decision aid design and formatting. Stakeholders were enthusiastic about the potential value of using decision analysis modeling with personalized model inputs for cancer recurrence risk, as well as competing risks from age and comorbidities, to generate a patient-centered tool to assist decision-making. Stakeholders did not view privacy considerations as a major barrier to the proposed decision aid program. A common theme was that decision aids should be portable across multiple platforms (electronic and paper), should allow for interaction by the user to adjust model inputs iteratively, and available to patients both before and during consult appointments. Emphasis was placed on the challenge of explaining the model's composite result of quality-adjusted life years. A range of stakeholders provided valuable insights regarding the design of a personalized decision

Fluid mechanics in dentinal microtubules provides mechanistic insights into the difference between hot and cold dental pain.

PubMed

Lin, Min; Luo, Zheng Yuan; Bai, Bo Feng; Xu, Feng; Lu, Tian Jian

2011-03-23

Dental thermal pain is a significant health problem in daily life and dentistry. There is a long-standing question regarding the phenomenon that cold stimulation evokes sharper and more shooting pain sensations than hot stimulation. This phenomenon, however, outlives the well-known hydrodynamic theory used to explain dental thermal pain mechanism. Here, we present a mathematical model based on the hypothesis that hot or cold stimulation-induced different directions of dentinal fluid flow and the corresponding odontoblast movements in dentinal microtubules contribute to different dental pain responses. We coupled a computational fluid dynamics model, describing the fluid mechanics in dentinal microtubules, with a modified Hodgkin-Huxley model, describing the discharge behavior of intradental neuron. The simulated results agreed well with existing experimental measurements. We thence demonstrated theoretically that intradental mechano-sensitive nociceptors are not "equally sensitive" to inward (into the pulp) and outward (away from the pulp) fluid flows, providing mechanistic insights into the difference between hot and cold dental pain. The model developed here could enable better diagnosis in endodontics which requires an understanding of pulpal histology, neurology and physiology, as well as their dynamic response to the thermal stimulation used in dental practices.

Fluid Mechanics in Dentinal Microtubules Provides Mechanistic Insights into the Difference between Hot and Cold Dental Pain

PubMed Central

Lin, Min; Luo, Zheng Yuan; Bai, Bo Feng; Xu, Feng; Lu, Tian Jian

2011-01-01

Dental thermal pain is a significant health problem in daily life and dentistry. There is a long-standing question regarding the phenomenon that cold stimulation evokes sharper and more shooting pain sensations than hot stimulation. This phenomenon, however, outlives the well-known hydrodynamic theory used to explain dental thermal pain mechanism. Here, we present a mathematical model based on the hypothesis that hot or cold stimulation-induced different directions of dentinal fluid flow and the corresponding odontoblast movements in dentinal microtubules contribute to different dental pain responses. We coupled a computational fluid dynamics model, describing the fluid mechanics in dentinal microtubules, with a modified Hodgkin-Huxley model, describing the discharge behavior of intradental neuron. The simulated results agreed well with existing experimental measurements. We thence demonstrated theoretically that intradental mechano-sensitive nociceptors are not “equally sensitive” to inward (into the pulp) and outward (away from the pulp) fluid flows, providing mechanistic insights into the difference between hot and cold dental pain. The model developed here could enable better diagnosis in endodontics which requires an understanding of pulpal histology, neurology and physiology, as well as their dynamic response to the thermal stimulation used in dental practices. PMID:21448459

Synchrotron imaging of dentition provides insights into the biology of Hesperornis and Ichthyornis, the "last" toothed birds.

PubMed

Dumont, Maïtena; Tafforeau, Paul; Bertin, Thomas; Bhullar, Bhart-Anjan; Field, Daniel; Schulp, Anne; Strilisky, Brandon; Thivichon-Prince, Béatrice; Viriot, Laurent; Louchart, Antoine

2016-09-23

The dentitions of extinct organisms can provide pivotal information regarding their phylogenetic position, as well as paleobiology, diet, development, and growth. Extant birds are edentulous (toothless), but their closest relatives among stem birds, the Cretaceous Hesperornithiformes and Ichthyornithiformes, retained teeth. Despite their significant phylogenetic position immediately outside the avian crown group, the dentitions of these taxa have never been studied in detail. To obtain new insight into the biology of these 'last' toothed birds, we use cutting-edge visualisation techniques to describe their dentitions at unprecedented levels of detail, in particular propagation phase contrast x-ray synchrotron microtomography at high-resolution. Among other characteristics of tooth shape, growth, attachment, implantation, replacement, and dental tissue microstructures, revealed by these analyses, we find that tooth morphology and ornamentation differ greatly between the Hesperornithiformes and Ichthyornithiformes. We also highlight the first Old World, and youngest record of the major Mesozoic clade Ichthyornithiformes. Both taxa exhibit extremely thin and simple enamel. The extension rate of Hesperornis tooth dentine appears relatively high compared to non-avian dinosaurs. Root attachment is found for the first time to be fully thecodont via gomphosis in both taxa, but in Hesperornis secondary evolution led to teeth implantation in a groove, at least locally without a periodontal ligament. Dental replacement is shown to be lingual via a resorption pit in the root, in both taxa. Our results allow comparison with other archosaurs and also mammals, with implications regarding dental character evolution across amniotes. Some dental features of the 'last' toothed birds can be interpreted as functional adaptations related to diet and mode of predation, while others appear to be products of their peculiar phylogenetic heritage. The autapomorphic Hesperornis groove might

Light-cone observables and gauge-invariance in the geodesic light-cone formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scaccabarozzi, Fulvio; Yoo, Jaiyul, E-mail: fulvio@physik.uzh.ch, E-mail: jyoo@physik.uzh.ch

The remarkable properties of the geodesic light-cone (GLC) coordinates allow analytic expressions for the light-cone observables, providing a new non-perturbative way for calculating the effects of inhomogeneities in our Universe. However, the gauge-invariance of these expressions in the GLC formalism has not been shown explicitly. Here we provide this missing part of the GLC formalism by proving the gauge-invariance of the GLC expressions for the light-cone observables, such as the observed redshift, the luminosity distance, and the physical area and volume of the observed sources. Our study provides a new insight on the properties of the GLC coordinates and itmore » complements the previous work by the GLC collaboration, leading to a comprehensive description of light propagation in the GLC representation.« less

Methodological tools for the collection and analysis of participant observation data using grounded theory.

PubMed

Laitinen, Heleena; Kaunonen, Marja; Astedt-Kurki, Päivi

2014-11-01

To give clarity to the analysis of participant observation in nursing when implementing the grounded theory method. Participant observation (PO) is a method of collecting data that reveals the reality of daily life in a specific context. In grounded theory, interviews are the primary method of collecting data but PO gives a distinctive insight, revealing what people are really doing, instead of what they say they are doing. However, more focus is needed on the analysis of PO. An observational study carried out to gain awareness of nursing care and its electronic documentation in four acute care wards in hospitals in Finland. Discussion of using the grounded theory method and PO as a data collection tool. The following methodological tools are discussed: an observational protocol, jotting of notes, microanalysis, the use of questioning, constant comparison, and writing and illustrating. Each tool has specific significance in collecting and analysing data, working in constant interaction. Grounded theory and participant observation supplied rich data and revealed the complexity of the daily reality of acute care. In this study, the methodological tools provided a base for the study at the research sites and outside. The process as a whole was challenging. It was time-consuming and it required rigorous and simultaneous data collection and analysis, including reflective writing. Using these methodological tools helped the researcher stay focused from data collection and analysis to building theory. Using PO as a data collection method in qualitative nursing research provides insights. It is not commonly discussed in nursing research and therefore this study can provide insight, which cannot be seen or revealed by using other data collection methods. Therefore, this paper can produce a useful tool for those who intend to use PO and grounded theory in their nursing research.

Neural Activity When People Solve Verbal Problems with Insight

PubMed Central

Bowden, Edward M; Haberman, Jason; Frymiare, Jennifer L; Arambel-Liu, Stella; Greenblatt, Richard; Reber, Paul J

2004-01-01

People sometimes solve problems with a unique process called insight, accompanied by an “Aha!” experience. It has long been unclear whether different cognitive and neural processes lead to insight versus noninsight solutions, or if solutions differ only in subsequent subjective feeling. Recent behavioral studies indicate distinct patterns of performance and suggest differential hemispheric involvement for insight and noninsight solutions. Subjects solved verbal problems, and after each correct solution indicated whether they solved with or without insight. We observed two objective neural correlates of insight. Functional magnetic resonance imaging (Experiment 1) revealed increased activity in the right hemisphere anterior superior temporal gyrus for insight relative to noninsight solutions. The same region was active during initial solving efforts. Scalp electroencephalogram recordings (Experiment 2) revealed a sudden burst of high-frequency (gamma-band) neural activity in the same area beginning 0.3 s prior to insight solutions. This right anterior temporal area is associated with making connections across distantly related information during comprehension. Although all problem solving relies on a largely shared cortical network, the sudden flash of insight occurs when solvers engage distinct neural and cognitive processes that allow them to see connections that previously eluded them. PMID:15094802

Plantation forestry under global warming: hybrid poplars with improved thermotolerance provide new insights on the in vivo function of small heat shock protein chaperones.

PubMed

Merino, Irene; Contreras, Angela; Jing, Zhong-Ping; Gallardo, Fernando; Cánovas, Francisco M; Gómez, Luis

2014-02-01

Climate-driven heat stress is a key factor affecting forest plantation yields. While its effects are expected to worsen during this century, breeding more tolerant genotypes has proven elusive. We report here a substantial and durable increase in the thermotolerance of hybrid poplar (Populus tremula×Populus alba) through overexpression of a major small heat shock protein (sHSP) with convenient features. Experimental evidence was obtained linking protective effects in the transgenic events with the unique chaperone activity of sHSPs. In addition, significant positive correlations were observed between phenotype strength and heterologous sHSP accumulation. The remarkable baseline levels of transgene product (up to 1.8% of total leaf protein) have not been reported in analogous studies with herbaceous species. As judged by protein analyses, such an accumulation is not matched either by endogenous sHSPs in both heat-stressed poplar plants and field-grown adult trees. Quantitative real time-polymerase chain reaction analyses supported these observations and allowed us to identify the poplar members most responsive to heat stress. Interestingly, sHSP overaccumulation was not associated with pleiotropic effects that might decrease yields. The poplar lines developed here also outperformed controls under in vitro and ex vitro culture conditions (callus biomass, shoot production, and ex vitro survival), even in the absence of thermal stress. These results reinforce the feasibility of improving valuable genotypes for plantation forestry, a field where in vitro recalcitrance, long breeding cycles, and other practical factors constrain conventional genetic approaches. They also provide new insights into the biological functions of the least understood family of heat shock protein chaperones.

Comparative lesion sequencing provides insights into tumor evolution.

PubMed

Jones, Siân; Chen, Wei-Dong; Parmigiani, Giovanni; Diehl, Frank; Beerenwinkel, Niko; Antal, Tibor; Traulsen, Arne; Nowak, Martin A; Siegel, Christopher; Velculescu, Victor E; Kinzler, Kenneth W; Vogelstein, Bert; Willis, Joseph; Markowitz, Sanford D

2008-03-18

We show that the times separating the birth of benign, invasive, and metastatic tumor cells can be determined by analysis of the mutations they have in common. When combined with prior clinical observations, these analyses suggest the following general conclusions about colorectal tumorigenesis: (i) It takes approximately 17 years for a large benign tumor to evolve into an advanced cancer but <2 years for cells within that cancer to acquire the ability to metastasize; (ii) it requires few, if any, selective events to transform a highly invasive cancer cell into one with the capacity to metastasize; (iii) the process of cell culture ex vivo does not introduce new clonal mutations into colorectal tumor cell populations; and (iv) the rates at which point mutations develop in advanced cancers are similar to those of normal cells. These results have important implications for understanding human tumor pathogenesis, particularly those associated with metastasis.

Prediction, scenarios and insight: The uses of an end-to-end model

NASA Astrophysics Data System (ADS)

Steele, John H.

2012-09-01

A major function of ecosystem models is to provide extrapolations from observed data in terms of predictions or scenarios or insight. These models can be at various levels of taxonomic resolution such as total community production, abundance of functional groups, or species composition, depending on the data input as drivers. A 40-year dynamic simulation of end-to-end processes in the Georges Bank food web is used to illustrate the input/output relations and the insights gained at the three levels of food web aggregation. The focus is on the intermediate level and the longer term changes in three functional fish guilds - planktivores, benthivores and piscivores - in terms of three ecosystem-based metrics - nutrient input, relative productivity of plankton and benthos, and food intake by juvenile fish. These simulations can describe the long term constraints imposed on guild structure and productivity by energy fluxes over the 40 years but cannot explain concurrent switches in abundance of individual species within guilds. Comparing time series data for individual species with model output provides insights; but including the data in the model would confer only limited extra information. The advantages and limitations of the three levels of resolution of models in relation to ecosystem-based management are: The correlations between primary production and total yield of fish imply a “bottom-up” constraint on end-to-end energy flow through the food web that can provide predictions of such yields. Functionally defined metrics such as nutrient input, relative productivity of plankton and benthos and food intake by juvenile fish, represent bottom-up, mid-level and top-down forcing of the food web. Model scenarios using these metrics can demonstrate constraints on the productivity of these functionally defined guilds within the limits set by (1). Comparisons of guild simulations with time series of fish species provide insight into the switches in species dominance

Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus.

PubMed

Li, Yinjia; Zuo, Sheng; Zhang, Zhiliang; Li, Zhanjie; Han, Jinlei; Chu, Zhaoqing; Hasterok, Robert; Wang, Kai

2018-03-01

Brachypodium distachyon is a well-established model monocot plant, and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as Avena sativa (oats), Hordeum vulgare (barley) and Triticum aestivum (wheat). Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. As the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus. In this study, we isolated the centromeric DNA of the B. distachyon reference line Bd21 and characterized its composition via the chromatin immunoprecipitation of the nucleosomes that contain the centromere-specific histone CENH3. We revealed that the centromeres of Bd21 have the features of typical multicellular eukaryotic centromeres. Strikingly, these centromeres contain relatively few centromeric satellite DNAs; in particular, the centromere of chromosome 5 (Bd5) consists of only ~40 kb. Moreover, the centromeric retrotransposons in B. distachyon (CRBds) are evolutionarily young. These transposable elements are located both within and adjacent to the CENH3 binding domains, and have similar compositions. Moreover, based on the presence of CRBds in the centromeres, the species in this study can be grouped into two distinct lineages. This may provide new evidence regarding the phylogenetic relationships within the Brachypodium genus. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

InSight Atlas V MARCO Cubesats Installation

NASA Image and Video Library

2018-03-17

At Vandenberg Air Force Base in California, twin communications-relay CubeSats, called Mars Cube One (MarCO) are prepared for installation on an Atlas V rocket. MarCO constitutes a technology demonstration being built by NASA's Jet Propulsion Laboratory, Pasadena in California. They will launch in on the same United Launch Alliance Atlas V rocket as NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. CubeSats are a class of spacecraft based on a standardized small size and modular use of off-the-shelf technologies. Many have been made by university students, and dozens have been launched into Earth orbit using extra payload mass available on launches of larger spacecraft. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for

InSight Atlas V MARCO Cubesats Installation

NASA Image and Video Library

2018-03-17

At Vandenberg Air Force Base in California, twin communications-relay CubeSats, called Mars Cube One (MarCO) are installed on an Atlas V rocket. MarCO constitutes a technology demonstration being built by NASA's Jet Propulsion Laboratory, Pasadena in California. They will launch in on the same United Launch Alliance Atlas V rocket as NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. CubeSats are a class of spacecraft based on a standardized small size and modular use of off-the-shelf technologies. Many have been made by university students, and dozens have been launched into Earth orbit using extra payload mass available on launches of larger spacecraft. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Insight and search in Katona's five-square problem.

PubMed

Ollinger, Michael; Jones, Gary; Knoblich, Günther

2014-01-01

Insights are often productive outcomes of human thinking. We provide a cognitive model that explains insight problem solving by the interplay of problem space search and representational change, whereby the problem space is constrained or relaxed based on the problem representation. By introducing different experimental conditions that either constrained the initial search space or helped solvers to initiate a representational change, we investigated the interplay of problem space search and representational change in Katona's five-square problem. Testing 168 participants, we demonstrated that independent hints relating to the initial search space and to representational change had little effect on solution rates. However, providing both hints caused a significant increase in solution rates. Our results show the interplay between problem space search and representational change in insight problem solving: The initial problem space can be so large that people fail to encounter impasse, but even when representational change is achieved the resulting problem space can still provide a major obstacle to finding the solution.

Simulations of CYP51A from Aspergillus fumigatus in a model bilayer provide insights into triazole drug resistance.

PubMed

Nash, Anthony; Rhodes, Johanna

2018-04-01

Azole antifungal drugs target CYP51A in Aspergillus fumigatus by binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole antifungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, predominantly conferring resistance to itraconazole, although cross-resistance has been reported in conjunction with other mutations. In this study, we create a homology model of CYP51A using a recently published crystal structure of the paralog protein CYP51B. The derived structures, wild type, and L98H mutant are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighboring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set of dynamics of the A. fumigatus Lanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance.

Simulations of CYP51A from Aspergillus fumigatus in a model bilayer provide insights into triazole drug resistance

PubMed Central

Nash, Anthony; Rhodes, Johanna

2018-01-01

Abstract Azole antifungal drugs target CYP51A in Aspergillus fumigatus by binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole antifungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, predominantly conferring resistance to itraconazole, although cross-resistance has been reported in conjunction with other mutations. In this study, we create a homology model of CYP51A using a recently published crystal structure of the paralog protein CYP51B. The derived structures, wild type, and L98H mutant are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighboring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set of dynamics of the A. fumigatus Lanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance. PMID:28992260

Genome analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of the etiologic agent of tuberculosis

PubMed Central

Supply, Philip; Marceau, Michael; Mangenot, Sophie; Roche, David; Rouanet, Carine; Khanna, Varun; Majlessi, Laleh; Criscuolo, Alexis; Tap, Julien; Pawlik, Alexandre; Fiette, Laurence; Orgeur, Mickael; Fabre, Michel; Parmentier, Cécile; Frigui, Wafa; Simeone, Roxane; Boritsch, Eva C.; Debrie, Anne-Sophie; Willery, Eve; Walker, Danielle; Quail, Michael A.; Ma, Laurence; Bouchier, Christiane; Salvignol, Grégory; Sayes, Fadel; Cascioferro, Alessandro; Seemann, Torsten; Barbe, Valérie; Locht, Camille; Gutierrez, Maria-Cristina; Leclerc, Claude; Bentley, Stephen; Stinear, Timothy P.; Brisse, Sylvain; Médigue, Claudine; Parkhill, Julian; Cruveiller, Stéphane; Brosch, Roland

2013-01-01

Global spread and genetic monomorphism are hallmarks of Mycobacterium tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii, and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology, are restricted to East-Africa. Here, we sequenced and analyzed the genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5x coverage), 454/Roche (13-18x coverage) and/or Illumina DNA sequencing (45-105x coverage). We show that STB are highly recombinogenic and evolutionary early-branching, with larger genome sizes, 25-fold more SNPs, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse-infection experiments revealed that STB are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral, STB-like pool of mycobacteria by gain of persistence and virulence mechanisms and we provide genome-wide insights into the molecular events involved. PMID:23291586

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, F.; Aerts, A.; Ahren, D.

Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants 1, 2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabasemore » genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles

Effects of antipsychotic drugs on insight in schizophrenia.

PubMed

Bianchini, Oriana; Porcelli, Stefano; Nespeca, Claudia; Cannavò, Dario; Trappoli, Angela; Aguglia, Eugenio; De Ronchi, Diana; Serretti, Alessandro

2014-08-15

Lack of insight is predominant in schizophrenia though the causes are still unclear. The present study was carried on to investigate the effect of three Second Generation Antipsychotics (SGAs) and Haloperidol on insight and the associations among different clusters of symptoms and insight. Fifty-five patients have been recruited at the moment of pharmacological switch needed for psychotic exacerbation, from other antipsychotic drugs to Olanzapine, Aripiprazole, Ziprasidone and Haloperidol. Patients have been followed for 6 months and evaluated at baseline, after 3 months and after 6 months. Regarding the insight improvement, all SGAs resulted more effective than Haloperidol, while no difference was detected among different SGAs. Concerning psychopathology, all SGAs showed a better efficacy than Haloperidol, positive symptoms apart. All SGAs showed a similar efficacy on all domains, except for negative symptoms which resulted less responsive to ziprasidone and haloperidol. An association between improvement of insight and psychopathology was detected. Furthermore, insight appears to be related to psychopathology severity, particularly to negative symptoms. However, the observed different effectiveness of Ziprasidone on negative symptoms and insight suggests that these psychopathological features may be not strictly related and, thus, they may be sustained by different psychopathological processes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Comparative proteomic analysis provides insight into 10-hydroxy-2-decenoic acid biosynthesis in honey bee workers.

PubMed

Yang, Xiao-Hui; Yang, Shi-Fa; Wang, Rui-Ming

2017-07-01

10-Hydroxy-2-decenoic acid (10-HDA) is the major compound produced from the mandibular glands (MGs) of honey bee workers. However, little information is available on the molecular mechanisms of 10-HDA biosynthesis. In our study, based on investigating the 10-HDA secretion pattern and the morphological characteristics of MGs from honey bee workers of different ages, a comparative proteomic analysis was performed in the MGs of workers with different 10-HDA production. In total, 59 up-regulated protein species representing 45 unique proteins were identified in high 10-HDA-producing workers by 2-DE-MALDI-TOF/TOF MS. These proteins were involved in carbohydrate/energy metabolism, fatty acid metabolism, protein metabolism and folding, antioxidation, cytoskeleton, development and cell signaling. Proteins related to fatty acid metabolism, including fatty acid synthase and β-oxidation enzymes, are potentially crucial proteins involved in 10-HDA biosynthesis pathway. And RNA interference (RNAi) results demonstrated that knockdown of electron transfer flavoprotein subunit beta (ETF-β), one of the protein related to fatty acid metabolism, decreased 10-HDA production of worker bees, suggesting that ETF-β was necessary for 10-HDA biosynthesis. This study reveals the characteristics of MGs of worker bees at different developmental stages and proteins associated with 10-HDA biosynthesis, which provides the first insight into the molecular mechanism of 10-HDA biosynthesis.

Information and Complexity Measures Applied to Observed and Simulated Soil Moisture Time Series

USDA-ARS?s Scientific Manuscript database

Time series of soil moisture-related parameters provides important insights in functioning of soil water systems. Analysis of patterns within these time series has been used in several studies. The objective of this work was to compare patterns in observed and simulated soil moisture contents to u...

Stellar Abundance Observations and Heavy Element Formation

NASA Astrophysics Data System (ADS)

Cowan, J. J.

2005-05-01

Abundance observations indicate the presence of rapid-neutron capture (i.e., r-process) elements in old Galactic halo and globular cluster stars. These observations provide insight into the nature of the earliest generations of stars in the Galaxy -- the progenitors of the halo stars -- responsible for neutron-capture synthesis of the heavy elements. Abundance comparisons among the r-process-rich halo stars show that the heaviest neutron-capture elements (i.e., Ba and above) are consistent with a scaled solar system r-process abundance distribution, while the lighter neutron-capture elements do not conform to the solar pattern. These comparisons suggest the possibility of two r-process sites in stars. The large star-to-star scatter observed in the abundances of neutron-capture element/iron ratios at low metallicities -- which disappears with increasing metallicity or [Fe/H] -- suggests the formation of these heavy elements (presumably from certain types of supernovae) was rare in the early Galaxy. The stellar abundances also indicate a change from the r-process to the slow neutron capture (i.e., s-) process at higher metallicities in the Galaxy and provide insight into Galactic chemical evolution. Finally, the detection of thorium and uranium in halo and globular cluster stars offers an independent age-dating technique that can put lower limits on the age of the Galaxy, and hence the Universe. This work has been supported in part by NSF grant AST 03-07279 (J.J.C.) and by STScI grants GO-8111, GO-8342 and GO-9359.

InSight Atlas V ISA-ASA Lift and Mate

NASA Image and Video Library

2018-03-05

At Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers mate the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V to a Centaur upper stage. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Atlas V ISA-ASA Lift and Mate

NASA Image and Video Library

2018-03-05

At Vandenberg Air Force Base in California, the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V arrives at Space Launch Complex 3. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

Providing Opportunities to Learn in Home-Based Child Care Settings: Observations of Learning Contexts and Behavior

ERIC Educational Resources Information Center

Rusby, Julie C.; Crowley, Ryann; Jones, Laura B.; Smolkowski, Keith

2017-01-01

Research Findings: This observation study investigated the prevalence and correlates of learning contexts provided to preschool-age children in 133 registered child care homes in below-average-income neighborhoods in the U.S. Pacific Northwest. On average, 30% of the observed proportion of time was spent in structured teacher-led activities, 51%…

Animal Toxins Providing Insights into TRPV1 Activation Mechanism

PubMed Central

Geron, Matan; Hazan, Adina

2017-01-01

Beyond providing evolutionary advantages, venoms offer unique research tools, as they were developed to target functionally important proteins and pathways. As a key pain receptor in the nociceptive pathway, transient receptor potential vanilloid 1 (TRPV1) of the TRP superfamily has been shown to be a target for several toxins, as a way of producing pain to deter predators. Importantly, TRPV1 is involved in thermoregulation, inflammation, and acute nociception. As such, toxins provide tools to understand TRPV1 activation and modulation, a critical step in advancing pain research and the development of novel analgesics. Indeed, the phytotoxin capsaicin, which is the spicy chemical in chili peppers, was invaluable in the original cloning and characterization of TRPV1. The unique properties of each subsequently characterized toxin have continued to advance our understanding of functional, structural, and biophysical characteristics of TRPV1. By building on previous reviews, this work aims to provide a comprehensive summary of the advancements made in TRPV1 research in recent years by employing animal toxins, in particular DkTx, RhTx, BmP01, Echis coloratus toxins, APHCs and HCRG21. We examine each toxin’s functional aspects, behavioral effects, and structural features, all of which have contributed to our current knowledge of TRPV1. We additionally discuss the key features of TRPV1’s outer pore domain, which proves to be the target of the currently discussed toxins. PMID:29035314

Directly observed daily mouth care provided to care home residents in one area of Kent, UK.

PubMed

Zander, A; Boniface, D

2017-03-01

To gather accurate data on the daily mouth care provided in care homes including tooth brushing, oral health assessment, and recording of care provided. Direct observation and notes review. Both nursing and 'regular' care homes. 365 Residents living in 16 care homes and their carers underwent observation, notes review or data collection in some form. Provision of mouth morning care. Of 161 residents observed, most (93, 58%) did not have their teeth/dentures brushed. If performed, brushing was often carried out by the resident themselves (36 cases, 53%), rather than by a carer (32 cases, 44%). Carers used a toothbrush to clean inside a resident's mouth in just 7 cases (4.3% of all personal care routines observed). Smaller care homes were no more likely to brush residents teeth than larger care homes, and nursing homes were no more likely to brush teeth than other care homes. Of the 309 sets of notes available for review, 41 (13%) contained a dedicated oral health needs assessment, and 109 (35%) contained a daily oral care chart in some form. Mouth care was often recorded inaccurately (15% of cases). This is the first observational study in the UK to assess oral care actually provided to residents by carers in care homes. The findings reveal a substantially different picture of daily mouth care than was previously understood and suggest that many of the nation's care home residents may not be receiving adequate, or any, oral health care. Copyright© 2017 Dennis Barber Ltd

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales.

PubMed

Garland, Ellen C; Rendell, Luke; Lamoni, Luca; Poole, M Michael; Noad, Michael J

2017-07-24

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: ( i ) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or ( ii ) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained "similar sounds arranged in a similar pattern." Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture.

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales

PubMed Central

Garland, Ellen C.; Rendell, Luke; Lamoni, Luca; Poole, M. Michael; Noad, Michael J.

2017-01-01

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: (i) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or (ii) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained “similar sounds arranged in a similar pattern.” Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture. PMID:28739940

Archiving InSight Lander Science Data Using PDS4 Standards

NASA Astrophysics Data System (ADS)

Stein, T.; Guinness, E. A.; Slavney, S.

2017-12-01

The InSight Mars Lander is scheduled for launch in 2018, and science data from the mission will be archived in the NASA Planetary Data System (PDS) using the new PDS4 standards. InSight is a geophysical lander with a science payload that includes a seismometer, a probe to measure subsurface temperatures and heat flow, a suite of meteorology instruments, a magnetometer, an experiment using radio tracking, and a robotic arm that will provide soil physical property information based on interactions with the surface. InSight is not the first science mission to archive its data using PDS4. However, PDS4 archives do not currently contain examples of the kinds of data that several of the InSight instruments will produce. Whereas the existing common PDS4 standards were sufficient for most of archiving requirements of InSight, the data generated by a few instruments required development of several extensions to the PDS4 information model. For example, the seismometer will deliver a version of its data in SEED format, which is standard for the terrestrial seismology community. This format required the design of a new product type in the PDS4 information model. A local data dictionary has also been developed for InSight that contains attributes that are not part of the common PDS4 dictionary. The local dictionary provides metadata relevant to all InSight data sets, and attributes specific to several of the instruments. Additional classes and attributes were designed for the existing PDS4 geometry dictionary that will capture metadata for the lander position and orientation, along with camera models for stereo image processing. Much of the InSight archive planning and design work has been done by a Data Archiving Working Group (DAWG), which has members from the InSight project and the PDS. The group coordinates archive design, schedules and peer review of the archive documentation and test products. The InSight DAWG archiving effort for PDS is being led by the PDS Geosciences

Transcriptome and Metabolome Analyses Provide Insights into the Occurrence of Peel Roughing Disorder on Satsuma Mandarin (Citrus unshiu Marc.) Fruit

PubMed Central

Lu, Xiao-Peng; Li, Fei-Fei; Xiong, Jiang; Cao, Xiong-Jun; Ma, Xiao-Chuan; Zhang, Zi-Mu; Cao, Shang-Yin; Xie, Shen-Xi

2017-01-01

Roughing disorder (RD) is a significant quality barrier in citrus fruit, prevalent on easy-peeling mandarins. As RD is not yet well-understood, this study aimed to examine the changes and synergic molecular processes involved in peel RD. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing, and targeted and untargeted metabolic analyses were conducted. The results showed that the primary metabolites of sugars, organic acids and amino acids are dramatically changed in RD peel. The RD peel was always characterized by higher magnesium content during development. Comparative transcriptome profiling was performed for CK and RD peels at 30, 80, and 170 days after full bloom (DAFB) which represented fruit at cell division stage, cell enlargement stage and fruit maturity stage, respectively. Physiological and molecular biological evidence suggested that the month after full bloom is a crucial stage for RD initiation. A total of 4,855 differentially expressed genes (DEGs) in RD peel, relative to CK peel were detected at cell division stage, about 2 to 4-fold more than other stages had. Among the differentially expressed transcription factors, the bHLH family were affected most by RD, and six bHLH transcription factors functionally involved in GA metabolism were assessed to associate with RD occurrence. Gene set enrichment analysis suggested that RD significantly altered starch and GA metabolism in peel. Higher starch content and hydrolysed chain status were found in RD peel at cell division stage. RD occurrence on the peel was influenced significantly by GA, especially abundant GA before July. These changes may mean a significant alteration in sink strength of RD peel. The findings of this study provide insights into the emergence, development and molecular mechanisms of RD. PMID:29163622

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

DOE PAGES

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy; ...

2016-05-11

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Taurus II Stage Test Simulations: Using Large-Scale CFD Simulations to Provide Critical Insight into Plume Induced Environments During Design

NASA Technical Reports Server (NTRS)

Struzenberg, L. L.; West, J. S.

2011-01-01

This paper describes the use of targeted Loci/CHEM CFD simulations to evaluate the effects of a dual-engine first-stage hot-fire test on an evolving integrated launch pad/test article design. This effort was undertaken as a part of the NESC Independent Assessment of the Taurus II Stage Test Series. The underlying conceptual model included development of a series of computational models and simulations to analyze the plume induced environments on the pad, facility structures and test article. A pathfinder simulation was first developed, capable of providing quick-turn around evaluation of plume impingement pressures on the flame deflector. Results from this simulation were available in time to provide data for an ongoing structural assessment of the deflector. The resulting recommendation was available in a timely manner and was incorporated into construction schedule for the new launch stand under construction at Wallops Flight Facility. A series of Reynolds-Averaged Navier-Stokes (RANS) quasi-steady simulations representative of various key elements of the test profile was performed to identify potential concerns with the test configuration and test profile. As required, unsteady Hybrid-RANS/LES simulations were performed, to provide additional insight into critical aspects of the test sequence. Modifications to the test-specific hardware and facility structures thermal protection as well as modifications to the planned hot-fire test profile were implemented based on these simulation results.

Insight and psychosis: Functional and anatomical brain connectivity and self-reflection in Schizophrenia.

PubMed

Ćurčić-Blake, Branislava; van der Meer, Lisette; Pijnenborg, Gerdina H M; David, Anthony S; Aleman, André

2015-12-01

Impaired insight into illness, associated with worse treatment outcome, is common in schizophrenia. Insight has been related to the self-reflective processing, centred on the medial frontal cortex. We hypothesized that anatomical and functional routes to and from the ventromedial prefrontal cortex (vmPFC) would differ in patients according to their degree of impaired insight. Forty-five schizophrenia patients and 19 healthy subjects performed a self-reflection task during fMRI, and underwent diffusion tensor imaging. Using dynamic causal modelling we observed increased effective connectivity from the posterior cingulate cortex (PCC), inferior parietal lobule (IPL), and dorsal mPFC (dmPFC) towards the vmPFC with poorer insight and decrease from vmPFC to the IPL. Stronger connectivity from the PCC to vmPFC during judgment of traits related to self was associated with poorer insight. We found small-scale significant changes in white matter integrity associated with clinical insight. Self-reflection may be influenced by synaptic changes that lead to the observed alterations in functional connectivity accompanied by the small-scale but measurable alterations in anatomical connections. Our findings may point to a neural compensatory response to an impairment of connectivity between self-processing regions. Similarly, the observed hyper-connectivity might be a primary deficit linked to inefficiency in the component cognitive processes that lead to impaired insight. We suggest that the stronger cognitive demands placed on patients with poor insight is reflected in increased effective connectivity during the task in this study. © 2015 Wiley Periodicals, Inc.

ALMA observations of Titan's atmospheric chemistry and seasonal variation

NASA Astrophysics Data System (ADS)

Cordiner, Martin

2017-04-01

Titan is the largest moon of Saturn, with a thick (1.45 bar) atmosphere composed primarily of molecular nitrogen and methane. Photochemistry in Titan's upper atmosphere results in the production of a wide range of organic molecules, including hydrocarbons, nitriles and aromatics, some of which could be of pre-biotic relevance. Thus, we obtain insights into the possible molecular inventories of primitive (reducing) planetary atmospheres. Titan's atmosphere also provides a unique laboratory for testing our understanding of fundamental processes involving the chemistry and spectroscopy of complex organic molecules. In this talk, results will be presented from our studies using the Atacama Large Millimeter/submillimeter Array (ALMA) during the period 2012-2015, focussing in particular on the detection and mapping of emission from various nitrile species. By combining data from multiple ALMA observations, our spectra have reached an unprecedented sensitivity level, enabling the first spectroscopic detection and mapping of C2H3CN (vinyl cyanide) on Titan. Liquid-phase simulations of Titan's seas indicate that vinyl cyanide molecules could combine to form vesicle membranes (similar to the cells of terrestrial biology), and the astrobiological implications of this discovery will be discussed. Furthermore, ALMA observations provide instantaneous snapshot mapping of Titan's entire Earth-facing hemisphere, for gases inaccessible to previous instruments. Combined with complementary data obtained from the Cassini Saturn orbiter, as well as theoretical models and laboratory studies, our observed, seasonally variable, spatially resolved abundance patterns are capable of providing new insights into photochemical production and transport in primitive planetary atmospheres in the Solar System and beyond.

Overutilization and underutilization of operating rooms - insights from behavioral health care operations management.

PubMed

Fügener, Andreas; Schiffels, Sebastian; Kolisch, Rainer

2017-03-01

The planning of surgery durations is crucial for efficient usage of operating theaters. Both planning too long and too short durations for surgeries lead to undesirable consequences, e.g. idle time, overtime, or rescheduling of surgeries. We define these consequences as operating room inefficiency. The overall objective of planning surgery durations is to minimize expected operating room inefficiency, since surgery durations are stochastic. While most health care studies assume economically rational behavior of decision makers, experimental studies have shown that decision makers often do not act according to economic incentives. Based on insights from health care operations management, medical decision making, behavioral operations management, as well as empirical observations, we derive hypotheses that surgeons' behavior deviates from economically rational behavior. To investigate this, we undertake an experimental study where experienced surgeons are asked to plan surgeries with uncertain durations. We discover systematic deviations from optimal decision making and offer behavioral explanations for the observed biases. Our research provides new insights to tackle a major problem in hospitals, i.e. low operating room utilization going along with staff overtime.

Parental insightfulness and parenting behavior: a two-dimensional analysis of parent contributions to child cognitive outcomes.

PubMed

Gomez, Jessie A; Carter, Alice S; Forbes, Danielle; Gray, Sarah A O

2018-06-01

Utilizing a two-dimensional model of parenting emphasizing both (1) proximity seeking and (2) exploration, consistent with a conceptual framework rooted in attachment theory, the relations between parental insightfulness, observed parenting, and child cognitive outcomes were investigated in a low-income sample of 64 of caregivers and their young 3-5-year-old children. Specifically, observed parental sensitivity (proximity seeking) and intrusiveness (exploration) and parental insightfulness assessed dimensionally to capture Positive Insight and Focus on Child were examined in relation to child cognitive outcomes. Parental intrusiveness was negatively correlated with cognitive performance; however, parental sensitivity was not associated with child cognitive outcomes. Parents' capacity to remain child-focused during the Insightfulness Assessment was negatively correlated with observed intrusiveness and was associated with child cognitive performance. These results suggest unique contributions of dimensions of parental insightfulness and parenting behaviors to child cognitive outcomes - specifically, parents' capacity to remain focused on children's experience during the Insightfulness Assessment and nonintrusive parenting behavior, which may reflect strategies to support children's exploration.

Insights from Human/Mouse genome comparisons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pennacchio, Len A.

2003-03-30

Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestrymore » of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.« less

The mystery of the "Kite" radio source in Abell 2626: Insights from new Chandra observations

NASA Astrophysics Data System (ADS)

Ignesti, A.; Gitti, M.; Brunetti, G.; O'Sullivan, E.; Sarazin, C.; Wong, K.

2018-03-01

Context. We present the results of a new Chandra study of the galaxy cluster Abell 2626. The radio emission of the cluster shows a complex system of four symmetric arcs without known correlations with the thermal X-ray emission. The mirror symmetry of the radio arcs toward the center and the presence of two optical cores in the central galaxy suggested that they may be created by pairs of precessing radio jets powered by dual active galactic nuclei (AGNs) inside the core dominant galaxy. However, previous observations failed to observe the second jetted AGN and the spectral trend due to radiative age along the radio arcs, thus challenging this interpretation. Aim. The new Chandra observation had several scientific objectives, including the search for the second AGN that would support the jet precession model. We focus here on the detailed study of the local properties of the thermal and non-thermal emission in the proximity of the radio arcs, in order to obtain further insights into their origin. Methods: We performed a standard data reduction of the Chandra dataset deriving the radial profiles of temperature, density, pressure and cooling time of the intra-cluster medium. We further analyzed the two-dimensional (2D) distribution of the gas temperature, discovering that the south-western junction of the radio arcs surrounds the cool core of the cluster. Results: We studied the X-ray surface brightness and spectral profiles across the junction, finding a cold front spatially coincident with the radio arcs. This may suggest a connection between the sloshing of the thermal gas and the nature of the radio filaments, raising new scenarios for their origin. A tantalizing possibility is that the radio arcs trace the projection of a complex surface connecting the sites where electrons are most efficiently reaccelerated by the turbulence that is generated by the gas sloshing. In this case, diffuse emission embedded by the arcs and with extremely steep spectrum should be

Observational insights into aerosol formation from isoprene.

PubMed

Worton, David R; Surratt, Jason D; Lafranchi, Brian W; Chan, Arthur W H; Zhao, Yunliang; Weber, Robin J; Park, Jeong-Hoo; Gilman, Jessica B; de Gouw, Joost; Park, Changhyoun; Schade, Gunnar; Beaver, Melinda; Clair, Jason M St; Crounse, John; Wennberg, Paul; Wolfe, Glenn M; Harrold, Sara; Thornton, Joel A; Farmer, Delphine K; Docherty, Kenneth S; Cubison, Michael J; Jimenez, Jose-Luis; Frossard, Amanda A; Russell, Lynn M; Kristensen, Kasper; Glasius, Marianne; Mao, Jingqiu; Ren, Xinrong; Brune, William; Browne, Eleanor C; Pusede, Sally E; Cohen, Ronald C; Seinfeld, John H; Goldstein, Allen H

2013-10-15

Atmospheric photooxidation of isoprene is an important source of secondary organic aerosol (SOA) and there is increasing evidence that anthropogenic oxidant emissions can enhance this SOA formation. In this work, we use ambient observations of organosulfates formed from isoprene epoxydiols (IEPOX) and methacrylic acid epoxide (MAE) and a broad suite of chemical measurements to investigate the relative importance of nitrogen oxide (NO/NO2) and hydroperoxyl (HO2) SOA formation pathways from isoprene at a forested site in California. In contrast to IEPOX, the calculated production rate of MAE was observed to be independent of temperature. This is the result of the very fast thermolysis of MPAN at high temperatures that affects the distribution of the MPAN reservoir (MPAN / MPA radical) reducing the fraction that can react with OH to form MAE and subsequently SOA (F(MAE formation)). The strong temperature dependence of F(MAE formation) helps to explain our observations of similar concentrations of IEPOX-derived organosulfates (IEPOX-OS; ~1 ng m(-3)) and MAE-derived organosulfates (MAE-OS; ~1 ng m(-3)) under cooler conditions (lower isoprene concentrations) and much higher IEPOX-OS (~20 ng m(-3)) relative to MAE-OS (<0.0005 ng m(-3)) at higher temperatures (higher isoprene concentrations). A kinetic model of IEPOX and MAE loss showed that MAE forms 10-100 times more ring-opening products than IEPOX and that both are strongly dependent on aerosol water content when aerosol pH is constant. However, the higher fraction of MAE ring opening products does not compensate for the lower MAE production under warmer conditions (higher isoprene concentrations) resulting in lower formation of MAE-derived products relative to IEPOX at the surface. In regions of high NOx, high isoprene emissions and strong vertical mixing the slower MPAN thermolysis rate aloft could increase the fraction of MPAN that forms MAE resulting in a vertically varying isoprene SOA source.

The VBB SEIS experiment of InSight

NASA Astrophysics Data System (ADS)

De Raucourt, Sebastien; Gabsi, Taoufik; Tanguy, Nebut; Mimoun, David; Lognonne, Philippe; Gagnepain-Beyneix, Jeannine; Banerdt, William; Tillier, Sylvain; Hurst, Kenneth

2012-07-01

SEIS is the core payload of InSight, one of the three missions selected for competitive phase A in the frame of the 2010 Discovery AO. It aims at providing unique observation of the interior structure of Mars and to monitor seismic activity of Mars. SEIS will provide the first seismic model from another planet than Earth. SEIS is an hybrid seismometer composed of 3 SPs and 3 VBBs axes providing ground motion measurement from Dc to 50Hz. A leveling system will ensure the coupling between the ground and the sensors as well as the horizontality of the VBB sphere. This assembly will be deployed on the ground of Mars and will be shielded by a strong thermal insulation and a wind shield. The 24 bits low noise acquisition electronics will remain in the warm electronic box of the lander with the sensors feedback and leveling system electronics. The VBB sphere enclosed three single axis sensors. Those sensors are based on an inverted leaf spring pendulum, which convert ground acceleration into mobile mass displacement. A capacitive displacement sensor monitors this mass displacement to provide a measurement. A force feedback allows transfer function and sensitivity tuning. The VBB sensor has a very strong heritage from previous project and benefits from recent work to improve its performances. Both the mechanical design and the displacement sensors have optimized to improve performances while reducing technological risk and keeping a high TRL. From those development a self-noise well below 10 ^{-9} m.s ^{-2}/sqrt Hz is expected. Environmental sensitivity of SEIS has been minimized by the design of a very efficient wind and thermal shield. Remaining noise is expected to be very close to the VBB self-noise. Associated sources and budget will be discussed. If InSight is selected to fly in 2016, this experiment will provide very high quality seismic signal measurement with a wider bandwidth, higher sensitivity and lower noise than previous Mars seismometer (Viking and Optimism

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication.

PubMed

Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

International Observe the Moon Night: Providing Opportunities for the Public to Engage in Lunar Observation

NASA Astrophysics Data System (ADS)

Hsu, B. C.; Bleacher, L.; Day, B. H.; Daou, D.; Jones, A. P.; Mitchell, B.; Shaner, A. J.; Shipp, S. S.

2010-12-01

International Observe the Moon Night (InOMN) is designed to engage lunar science and education communities, our partner networks, amateur astronomers, space enthusiasts, and the general public in annual lunar observation campaigns that share the excitement of lunar science and exploration. InOMN enables the public to maintain its curiosity about the Moon and gain a better understanding of the Moon's formation, its evolution, and its place in the sky. For 2010, members of the public were encouraged to host their own InOMN events. InOMN hosts such as astronomy clubs, museums, schools, or other groups could find helpful resources and share information about InOMN events they organized on the InOMN website (http://observethemoonnight.org). Images, feedback, and lessons learned from the 2010 InOMN event will be shared in order to encourage increased planning and hosting of InOMN events in 2011. From various interpretations of the lunar “face,” early pictograms of the Moon’s phases, or to the use of the lunar cycle for festivals or harvests, the Moon has an undeniable influence on human civilization. We have chosen the 2011 InOMN theme to provide an opportunity for individuals to share their personal or cultural connections to the Moon. For 2011, the InOMN website will include a ‘lunar bulletin board’ where InOMN participants can post pictures and share stories of what the Moon means to them. The 2011 InOMN contest will encourage people to submit their works of art, poems, short stories, or music about the Moon all centered around the theme “What does the Moon mean to you?” As with the winners of previous contests, winning entries will be incorporated into the following year’s InOMN advertisements and events.

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.

PubMed

Wille, Lukas; Messmer, Monika M; Studer, Bruno; Hohmann, Pierre

2018-04-12

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extend plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarises (i) the current knowledge of resistance against soil-borne pathogens in grain legumes, (ii) evidence for genetic variation for rhizosphere-related traits, (iii) the role of root exudation in microbe-mediated disease resistance and elaborates (iv) how these traits can be incorporated in resistance breeding programmes. This article is protected by copyright. All rights reserved.

Neuroanatomy of the Vestimentiferan Tubeworm Lamellibrachia satsuma Provides Insights into the Evolution of the Polychaete Nervous System

PubMed Central

Miyamoto, Norio; Shinozaki, Ayuta; Fujiwara, Yoshihiro

2013-01-01

Vestimentiferan tubeworms are marine invertebrates that inhabit chemosynthetic environments, and although recent molecular phylogenetic analyses have suggested that vestimentiferan tubeworms are derived from polychaete annelids, they show some morphological features that are different from other polychaetes. For example, vestimentiferans lack a digestive tract and have less body segments and comparative neuroanatomy can provide essential insight into the vestimentiferan body plan and its evolution. In the present study, we investigated the adult nervous system in the vestimentiferan Lamellibrachia satsuma using antibodies against synapsin, serotonin, FMRMamide and acetylated α-tubulin. We also examined the expressions of neural marker genes, elav and synaptotagmin to reveal the distribution of neuronal cell bodies. Brain anatomy shows simple organization in Lamellibrachia compared to other polychaetes. This simplification is probably due to the loss of the digestive tract, passing through the body between the brain and the subesophageal ganglion. In contrast, the ventral nerve cord shows a repeated organizational structure as in the other polychaetes, despite the absence of the multiple segmentation of the trunk. These results suggest that the brain anatomy is variable depending on the function and the condition of surrounding tissues, and that the formation of the rope ladder-like nervous system of the ventral nerve cord is independent from segmentation in polychaetes. PMID:23372830

Adaptive evolution of osmoregulatory-related genes provides insight into salinity adaptation in Chinese mitten crab, Eriocheir sinensis.

PubMed

Wang, Zhengfei; Bai, Yuze; Zhang, Daizhen; Tang, Boping

2018-06-01

Osmoregulation is an important mechanism by which euryhaline crustaceans regulate osmotic and ionic concentrations. The Chinese mitten crab (Eriocheir sinensis) is a strong osmoregulating animal model among crustacean species, as it can maintain its hemolymph composition and survives well in either seawater or freshwater. Osmoregulation by E. sinensis during physiological adaptation has been studied extensively. However, the genetic basis of osmoregulation in E. sinensis for acclimating to changing salinities remains unclear. The current study investigated five genes involved in E. sinensis osmoregulation and compared them with a representative marine crab Portunus trituberculatus to test whether adaptive evolution has occurred changing salinity conditions. The results showed that carbonic anhydrase (CA), cytochrome P450 4C (CYP4C), glutamate dehydrogenase (GDH), and the Na + /H + exchanger (NHE) have undergone positive selection (i.e., directional selection) in E. sinensis. Thus, the positive selection in CA and NHE suggests that E. sinensis has enhanced capacity for maintaining systemic acid-base balance and ion regulation. GDH and CYP4C also demonstrated positive selection in E. sinensis, suggesting that E. sinensis might have acquired an enhanced capacity to metabolize glutamate and synthesize ecdysteroids in response to a change in osmotic concentration. The present study provides new insight into the molecular genetic basis of salinity adaption in E. sinensis.

InSight Atlas V ISA-ASA Lift and Mate

NASA Image and Video Library

2018-03-05

At Space Launch Complex 3 at Vandenberg Air Force Base in California, a technician assists as the aft stub adapter (ASA) and interstage adapter (ISA) for a United Launch Alliance (ULA) Atlas V is lifted by crane for mating atop a Centaur upper stage. The launch vehicle will send NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. InSight is scheduled for liftoff May 5, 2018. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. NASA’s Jet Propulsion Laboratory in Pasadena, California, manages the InSight mission for the agency’s Science Mission Directorate. InSight is part of NASA's Discovery Program, managed by its Marshall Space Flight Center in Huntsville, Alabama. The spacecraft, including cruise stage and lander, was built and tested by Lockheed Martin Space in Denver. Several European partners, including France's space agency, the Centre National d'Étude Spatiales, and the German Aerospace Center, are supporting the mission. United Launch Alliance of Centennial, Colorado, is providing the Atlas V launch service. NASA’s Launch Services Program, based at its Kennedy Space Center in Florida, is responsible for launch management.

InSight Planetary Protection Status

NASA Astrophysics Data System (ADS)

Benardini, James; La Duc, Myron; Willis, Jason

The NASA Discovery Program’s next mission, Interior Exploration using Seismic Investigations, Geodesy and Heat Transport (InSIght), consists of a single spacecraft that will be launched aboard an Atlas V 401 rocket from Vandenberg Air Force Base (Space Launch Complex 3E) during the March 2016 timeframe. The overarching mission goal is to illuminate the fundamentals of formation and evolution of terrestrial planets by investigating the interior structure and processes of Mars. The flight system consists of a heritage cruise stage, aeroshell (heatshield and backshell), and Lander from the 2008 Phoenix mission. Included in the lander payload are various cameras, a seismometer, an auxiliary sensor suite to measure wind, temperature, and pressure, and a mole to penetrate the regolith (<5 meters) and assess the subsurface geothermal gradient of Mars. Being a Mars lander mission without life detection instruments, InSight has been designated a PP Category Iva mission. As such, planetary protection bioburden requirements apply which require microbial reduction procedures and biological burden reporting. The InSight project is current with required PP documentation, having completed an approved Planetary Protection Plan, Subsidiary PP Plans, and a PP Implementation Plan. The InSight mission’s early planetary protection campaign has commenced, coinciding with the fabrication and assembly of payload and flight system hardware and the baseline analysis of existing flight spares. A report on the status of InSight PP activities will be provided.

ASTER satellite observations for international disaster management

USGS Publications Warehouse

Duda, K.A.; Abrams, M.

2012-01-01

When lives are threatened or lost due to catastrophic disasters, and when massive financial impacts are experienced, international emergency response teams rapidly mobilize to provide urgently required support. Satellite observations of affected areas often provide essential insight into the magnitude and details of the impacts. The large cost and high complexity of developing and operating satellite flight and ground systems encourages international collaboration in acquiring imagery for such significant global events in order to speed delivery of critical information to help those affected, and optimize spectral, spatial, and temporal coverage of the areas of interest. The International Charter-Space and Major Disasters was established to enable such collaboration in sensor tasking during times of crisis and is often activated in response to calls for assistance from authorized users. Insight is provided from a U.S. perspective into sensor support for Charter activations and other disaster events through a description of the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), which has been used to support emergency situations for over a decade through its expedited tasking and near real-time data delivery capabilities. Examples of successes achieved and challenges encountered in international collaboration to develop related systems and fulfill tasking requests suggest operational considerations for new missions as well as areas for future enhancements.

Observational Signatures of Magnetic Reconnection in the Extended Corona

NASA Technical Reports Server (NTRS)

Savage, Sabrina; West, Matthew J.; Seaton, Daniel B.; Kobelski, Adam

2016-01-01

Observational signatures of reconnection have been studied extensively in the lower corona for decades, successfully providing insight into energy release mechanisms in the region above post-flare arcade loops and below 1.5 solar radii. During large eruptive events, however, energy release continues to occur well beyond the presence of reconnection signatures at these low heights. Supra-Arcade Downflows (SADs) and Supra-Arcade Downflowing Loops (SADLs) are particularly useful measures of continual reconnection in the corona as they may indicate the presence and path of retracting post-reconnection loops. SADs and SADLs have been faintly observed up to 18 hours beyond the passage of coronas mass ejections through the SOHO/LASCO field of view, but a recent event from 2014 October 14 associated with giant arches provides very clear observations of these downflows for days after the initial eruption. We report on this unique event and compare these findings with observational signatures of magnetic reconnection in the extended corona for more typical eruptions.

Observational Signatures of Magnetic Reconnection in the Extended Corona

NASA Technical Reports Server (NTRS)

Savage, Sabrina; West, Matthew J.; Seaton, Danial B.; Kobelski, Adam

2016-01-01

Observational signatures of reconnection have been studied extensively in the lower corona for decades, successfully providing insight into energy release mechanisms in the region above post-flare arcade loops and below 1.5 solar radii. During large eruptive events, however, energy release continues to occur well beyond the presence of reconnection signatures at these low heights. Supra-Arcade Downflows (SADs) and Supra-Arcade Downflowing Loops (SADLs) are particularly useful measures of continual reconnection in the corona as they may indicate the presence and path of retracting post-reconnection loops. SADs and SADLs have been faintly observed up to 18 hours beyond the passage of corona mass ejections through the SOHO/LASCO field of view, but a recent event from 2014 October 14 associated with giant arches provides very clear observations of these downflows for days after the initial eruption. We report on this unique event and compare these findings with observational signatures of magnetic reconnection in the extended corona for more typical eruptions.

Observational Signatures of Magnetic Reconnection in the Extended Corona

NASA Technical Reports Server (NTRS)

Savage, Sabrina; West, Matthew J.; Seaton, Daniel B.; Kobelski, Adam

2017-01-01

Observational signatures of reconnection have been studied extensively in the lower corona for decades, successfully providing insight into energy release mechanisms in the region above post-flare arcade loops and below 1.5 solar radii. During large eruptive events, however, energy release continues to occur well beyond the presence of reconnection signatures at these low heights. Supra-Arcade Downflows (SADs) and Supra-Arcade Downflowing Loops (SADLs) are particularly useful measures of continual reconnection in the corona as they may indicate the presence and path of retracting post-reconnection loops. SADs and SADLs have been faintly observed up to 18 hours beyond the passage of corona mass ejections through the SOHO/LASCO field of view, but a recent event from 2014 October 14 associated with giant arches provides very clear observations of these downflows for days after the initial eruption. We report on this unique event and compare these findings with observational signatures of magnetic reconnection in the extended corona for more typical eruptions.

Refining the classification of left ventricular hypertrophy to provide new insights into the progression from hypertension to heart failure.

PubMed

Garg, Sonia; Drazner, Mark H

2016-07-01

Left ventricular hypertrophy (LVH), an important consequence of hypertension, is traditionally classified as either concentric or eccentric based on the presence or absence of increased relative wall thickness. In 2010, we proposed a novel four-tiered classification that accounted for LV dilatation in addition to LV wall thickness. The purpose of this review is to discuss the rationale for this revised classification and highlight subsequent studies that have assessed its utility. A series of recent observational studies have tested whether the four-tiered classification identifies subphenotypes of LVH with differential risk of adverse outcomes, including incident heart failure. The majority have confirmed that eccentric hypertrophy can be subdivided into a high-risk and a low-risk group based on whether LV dilatation is present. Additional studies have shown that LV dilatation is an independent risk factor for the development of heart failure. Incorporation of LV dilatation into the assessment of LVH identifies important subphenotypes within the standard two-tiered classification that have differential risk. Such refinements in the classification of LVH may yield new insights into how LVH progresses to heart failure, help identify risk factors for this transition, and improve therapeutic efforts to prevent its occurrence.

Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.).

PubMed

Sun, Chengming; Wang, Benqi; Yan, Lei; Hu, Kaining; Liu, Sheng; Zhou, Yongming; Guan, Chunyun; Zhang, Zhenqian; Li, Jiana; Zhang, Jiefu; Chen, Song; Wen, Jing; Ma, Chaozhi; Tu, Jinxing; Shen, Jinxiong; Fu, Tingdong; Yi, Bin

2016-01-01

Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

PubMed

Tavanti, Michele; Porter, Joanne L; Levy, Colin W; Gómez Castellanos, J Rubén; Flitsch, Sabine L; Turner, Nicholas J

2018-07-02

The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes. Copyright © 2018 Elsevier Inc. All rights reserved.

Analysis of Regolith Properties Using Seismic Signals Generated by InSight's HP3 Penetrator

NASA Astrophysics Data System (ADS)

Kedar, Sharon; Andrade, Jose; Banerdt, Bruce; Delage, Pierre; Golombek, Matt; Grott, Matthias; Hudson, Troy; Kiely, Aaron; Knapmeyer, Martin; Knapmeyer-Endrun, Brigitte; Krause, Christian; Kawamura, Taichi; Lognonne, Philippe; Pike, Tom; Ruan, Youyi; Spohn, Tilman; Teanby, Nick; Tromp, Jeroen; Wookey, James

2017-10-01

InSight's Seismic Experiment for Interior Structure (SEIS) provides a unique and unprecedented opportunity to conduct the first geotechnical survey of the Martian soil by taking advantage of the repeated seismic signals that will be generated by the mole of the Heat Flow and Physical Properties Package (HP3). Knowledge of the elastic properties of the Martian regolith have implications to material strength and can constrain models of water content, and provide context to geological processes and history that have acted on the landing site in western Elysium Planitia. Moreover, it will help to reduce travel-time errors introduced into the analysis of seismic data due to poor knowledge of the shallow subsurface. The challenge faced by the InSight team is to overcome the limited temporal resolution of the sharp hammer signals, which have significantly higher frequency content than the SEIS 100 Hz sampling rate. Fortunately, since the mole propagates at a rate of ˜1 mm per stroke down to 5 m depth, we anticipate thousands of seismic signals, which will vary very gradually as the mole travels. Using a combination of field measurements and modeling we simulate a seismic data set that mimics the InSight HP3-SEIS scenario, and the resolution of the InSight seismometer data. We demonstrate that the direct signal, and more importantly an anticipated reflected signal from the interface between the bottom of the regolith layer and an underlying lava flow, are likely to be observed both by Insight's Very Broad Band (VBB) seismometer and Short Period (SP) seismometer. We have outlined several strategies to increase the signal temporal resolution using the multitude of hammer stroke and internal timing information to stack and interpolate multiple signals, and demonstrated that in spite of the low resolution, the key parameters—seismic velocities and regolith depth—can be retrieved with a high degree of confidence.

Impact of interpersonal factors on insight in schizophrenia.

PubMed

Hélène, Tastet; Hélène, Verdoux; Jean, Bouisson; Jean-Marc, Destaillats; Antoinette, Prouteau

2014-11-01

Whereas clinical insight in schizophrenia has been consistently associated with personal factors (i.e. sociodemographic characteristics, symptoms or cognition), little is known about its relationships with interpersonal factors (i.e. close environment and personal characteristics involved in social interactions). Most of the few studies available have focused on one particular interpersonal factor, such as social cognition, contact frequencies or therapeutic alliance. To date, no study has explored the specificity of associations between clinical insight and different levels of interpersonal factors, neither if these associations are independent of personal factors. Associations between insight and interpersonal factors were explored through multiple regression in a sample of 80 outpatients with schizophrenia spectrum disorders. Lower insight was associated with lower interpersonal functioning, independently from personal factors such as age, gender, age at first hospitalization, executive functioning and symptoms. Our findings replicate previous studies with regard to the associations between clinician-rated insight and social cognition or social contact frequencies. They also provide new information about specific associations between clinician-rated insight and perceived social support as well as between patient-rated insight and therapeutic alliance. Finally, models of insight based on personal factors were significantly improved by the inclusion of interpersonal factors. These results strongly support the crucial role of interpersonal factors in insight, both from the clinician's and the patient's point of view. These exploratory data require further replication. Copyright © 2014 Elsevier B.V. All rights reserved.

Is creative insight task-specific? A coordinate-based meta-analysis of neuroimaging studies on insightful problem solving.

PubMed

Shen, Wangbing; Yuan, Yuan; Liu, Chang; Zhang, Xiaojiang; Luo, Jing; Gong, Zhe

2016-12-01

The question of whether creative insight varies across problem types has recently come to the forefront of studies of creative cognition. In the present study, to address the nature of creative insight, the coordinate-based activation likelihood estimation (ALE) technique was utilized to individually conduct three quantitative meta-analyses of neuroimaging experiments that used the compound remote associate (CRA) task, the prototype heuristic (PH) task and the Chinese character chunk decomposition (CCD) task. These tasks were chosen because they are frequently used to uncover the neurocognitive correlates of insight. Our results demonstrated that creative insight reliably activates largely non-overlapping brain regions across task types, with the exception of some shared regions: the CRA task mainly relied on the right parahippocampal gyrus, the superior frontal gyrus and the inferior frontal gyrus; the PH task primarily depended on the right middle occipital gyrus (MOG), the bilateral superior parietal lobule/precuneus, the left inferior parietal lobule, the left lingual gyrus and the left middle frontal gyrus; and the CCD task activated a broad cerebral network consisting of most dorsolateral and medial prefrontal regions, frontoparietal regions and the right MOG. These results provide the first neural evidence of the task dependence of creative insight. The implications of these findings for resolving conflict surrounding the different theories of creative cognition and for defining insight as a set of heterogeneous processes are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Perspectives on Social Network Analysis for Observational Scientific Data

NASA Astrophysics Data System (ADS)

Singh, Lisa; Bienenstock, Elisa Jayne; Mann, Janet

This chapter is a conceptual look at data quality issues that arise during scientific observations and their impact on social network analysis. We provide examples of the many types of incompleteness, bias and uncertainty that impact the quality of social network data. Our approach is to leverage the insights and experience of observational behavioral scientists familiar with the challenges of making inference when data are not complete, and suggest avenues for extending these to relational data questions. The focus of our discussion is on network data collection using observational methods because they contain high dimensionality, incomplete data, varying degrees of observational certainty, and potential observer bias. However, the problems and recommendations identified here exist in many other domains, including online social networks, cell phone networks, covert networks, and disease transmission networks.

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma.

PubMed

Tremblay, Marie-Pier; Armero, Victoria E S; Allaire, Andréa; Boudreault, Simon; Martenon-Brodeur, Camille; Durand, Mathieu; Lapointe, Elvy; Thibault, Philippe; Tremblay-Létourneau, Maude; Perreault, Jean-Pierre; Scott, Michelle S; Bisaillon, Martin

2016-08-26

Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data. Our study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control. This study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC.

Pleiotropic Phenotypes of the sticky peel Mutant Provide New Insight into the Role of CUTIN DEFICIENT2 in Epidermal Cell Function in Tomato1[W][OA

PubMed Central

Nadakuduti, Satya Swathi; Pollard, Mike; Kosma, Dylan K.; Allen, Charles; Ohlrogge, John B.; Barry, Cornelius S.

2012-01-01

Plant epidermal cells have evolved specialist functions associated with adaptation to stress. These include the synthesis and deposition of specialized metabolites such as waxes and cutin together with flavonoids and anthocyanins, which have important roles in providing a barrier to water loss and protection against UV radiation, respectively. Characterization of the sticky peel (pe) mutant of tomato (Solanum lycopersicum) revealed several phenotypes indicative of a defect in epidermal cell function, including reduced anthocyanin accumulation, a lower density of glandular trichomes, and an associated reduction in trichome-derived terpenes. In addition, pe mutant fruit are glossy and peels have increased elasticity due to a severe reduction in cutin biosynthesis and altered wax deposition. Leaves of the pe mutant are also cutin deficient and the epicuticular waxes contain a lower proportion of long-chain alkanes. Direct measurements of transpiration, together with chlorophyll-leaching assays, indicate increased cuticular permeability of pe leaves. Genetic mapping revealed that the pe locus represents a new allele of CUTIN DEFICIENT2 (CD2), a member of the class IV homeodomain-leucine zipper gene family, previously only associated with cutin deficiency in tomato fruit. CD2 is preferentially expressed in epidermal cells of tomato stems and is a homolog of Arabidopsis (Arabidopsis thaliana) ANTHOCYANINLESS2 (ANL2). Analysis of cuticle composition in leaves of anl2 revealed that cutin accumulates to approximately 60% of the levels observed in wild-type Arabidopsis. Together, these data provide new insight into the role of CD2 and ANL2 in regulating diverse metabolic pathways and in particular, those associated with epidermal cells. PMID:22623518

The complete mitochondrial genome of the scab mite Psoroptes cuniculi (Arthropoda: Arachnida) provides insights into Acari phylogeny

PubMed Central

2014-01-01

Background Limited available sequence information has greatly impeded population genetics, phylogenetics and systematics studies in the subclass Acari (mites and ticks). Mitochondrial (mt) DNA is well known to provide genetic markers for investigations in these areas, but complete mt genomic data have been lacking for many Acari species. Herein, we present the complete mt genome of the scab mite Psoroptes cuniculi. Methods P. cuniculi was collected from a naturally infected New Zealand white rabbit from China and identified by morphological criteria. The complete mt genome of P. cuniculi was amplified by PCR and then sequenced. The relationships of this scab mite with selected members of the Acari were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP). Results This mt genome (14,247 bp) is circular and consists of 37 genes, including 13 genes for proteins, 22 genes for tRNA, 2 genes for rRNA. The gene arrangement in mt genome of P. cuniculi is the same as those of Dermatophagoides farinae (Pyroglyphidae) and Aleuroglyphus ovatus (Acaridae), but distinct from those of Steganacarus magnus (Steganacaridae) and Panonychus citri (Tetranychidae). Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (BI, ML and MP), showed the division of subclass Acari into two superorders, supported the monophylies of the both superorders Parasitiformes and Acariformes; and the three orders Ixodida and Mesostigmata and Astigmata, but rejected the monophyly of the order Prostigmata. Conclusions The mt genome of P. cuniculi represents the first mt genome of any member of the family Psoroptidae. Analysis of mt genome sequences in the present study has provided new insights into the phylogenetic relationships among several major lineages of Acari species. PMID:25052180

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

PubMed Central

Maiga, Mamoudou; Abeel, Thomas; Shea, Terrance; Desjardins, Christopher A.; Diarra, Bassirou; Baya, Bocar; Sanogo, Moumine; Diallo, Souleymane; Earl, Ashlee M.; Bishai, William R.

2016-01-01

Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system. Methodology/Principal Findings We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes. Conclusions This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity. PMID:26751217

Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data

USGS Publications Warehouse

Lester L. Yuan,; Amina I. Pollard,; Carlisle, Daren M.

2009-01-01

Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure.

Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data

USGS Publications Warehouse

Yuan, L.L.; Pollard, A.I.; Carlisle, D.M.

2009-01-01

Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure. ?? 2009 SETAC.

Fluorescent Protein Aided Insights on Plastids and their Extensions: A Critical Appraisal

PubMed Central

Delfosse, Kathleen; Wozny, Michael R.; Jaipargas, Erica-Ashley; Barton, Kiah A.; Anderson, Cole; Mathur, Jaideep

2016-01-01

Multi-colored fluorescent proteins targeted to plastids have provided new insights on the dynamic behavior of these organelles and their interactions with other cytoplasmic components and compartments. Sub-plastidic components such as thylakoids, stroma, the inner and outer membranes of the plastid envelope, nucleoids, plastoglobuli, and starch grains have been efficiently highlighted in living plant cells. In addition, stroma filled membrane extensions called stromules have drawn attention to the dynamic nature of the plastid and its interactions with the rest of the cell. Use of dual and triple fluorescent protein combinations has begun to reveal plastid interactions with mitochondria, the nucleus, the endoplasmic reticulum and F-actin and suggests integral roles of plastids in retrograde signaling, cell to cell communication as well as plant-pathogen interactions. While the rapid advances and insights achieved through fluorescent protein based research on plastids are commendable it is necessary to endorse meaningful observations but subject others to closer scrutiny. Here, in order to develop a better and more comprehensive understanding of plastids and their extensions we provide a critical appraisal of recent information that has been acquired using targeted fluorescent protein probes. PMID:26834765

Transform Faults and Lithospheric Structure: Insights from Numerical Models and Shipboard and Geodetic Observations

NASA Astrophysics Data System (ADS)

Takeuchi, Christopher S.

In this dissertation, I study the influence of transform faults on the structure and deformation of the lithosphere, using shipboard and geodetic observations as well as numerical experiments. I use marine topography, gravity, and magnetics to examine the effects of the large age-offset Andrew Bain transform fault on accretionary processes within two adjacent segments of the Southwest Indian Ridge. I infer from morphology, high gravity, and low magnetization that the extremely cold and thick lithosphere associated with the Andrew Bain strongly suppresses melt production and crustal emplacement to the west of the transform fault. These effects are counteracted by enhanced temperature and melt production near the Marion Hotspot, east of the transform fault. I use numerical models to study the development of lithospheric shear zones underneath continental transform faults (e.g. the San Andreas Fault in California), with a particular focus on thermomechanical coupling and shear heating produced by long-term fault slip. I find that these processes may give rise to long-lived localized shear zones, and that such shear zones may in part control the magnitude of stress in the lithosphere. Localized ductile shear participates in both interseismic loading and postseismic relaxation, and predictions of models including shear zones are within observational constraints provided by geodetic and surface heat flow data. I numerically investigate the effects of shear zones on three-dimensional postseismic deformation. I conclude that the presence of a thermally-activated shear zone minimally impacts postseismic deformation, and that thermomechanical coupling alone is unable to generate sufficient localization for postseismic relaxation within a ductile shear zone to kinematically resemble that by aseismic fault creep (afterslip). I find that the current record geodetic observations of postseismic deformation do not provide robust discriminating power between candidate linear and

The Association of DRD2 with Insight Problem Solving.

PubMed

Zhang, Shun; Zhang, Jinghuan

2016-01-01

Although the insight phenomenon has attracted great attention from psychologists, it is still largely unknown whether its variation in well-functioning human adults has a genetic basis. Several lines of evidence suggest that genes involved in dopamine (DA) transmission might be potential candidates. The present study explored for the first time the association of dopamine D2 receptor gene ( DRD2 ) with insight problem solving. Fifteen single-nucleotide polymorphisms (SNPs) covering DRD2 were genotyped in 425 unrelated healthy Chinese undergraduates, and were further tested for association with insight problem solving. Both single SNP and haplotype analysis revealed several associations of DRD2 SNPs and haplotypes with insight problem solving. In conclusion, the present study provides the first evidence for the involvement of DRD2 in insight problem solving, future studies are necessary to validate these findings.

The Association of DRD2 with Insight Problem Solving

PubMed Central

Zhang, Shun; Zhang, Jinghuan

2016-01-01

Although the insight phenomenon has attracted great attention from psychologists, it is still largely unknown whether its variation in well-functioning human adults has a genetic basis. Several lines of evidence suggest that genes involved in dopamine (DA) transmission might be potential candidates. The present study explored for the first time the association of dopamine D2 receptor gene (DRD2) with insight problem solving. Fifteen single-nucleotide polymorphisms (SNPs) covering DRD2 were genotyped in 425 unrelated healthy Chinese undergraduates, and were further tested for association with insight problem solving. Both single SNP and haplotype analysis revealed several associations of DRD2 SNPs and haplotypes with insight problem solving. In conclusion, the present study provides the first evidence for the involvement of DRD2 in insight problem solving, future studies are necessary to validate these findings. PMID:27933030

Astrophysical observations: lensing and eclipsing Einstein's theories.

PubMed

Bennett, Charles L

2005-02-11

Albert Einstein postulated the equivalence of energy and mass, developed the theory of special relativity, explained the photoelectric effect, and described Brownian motion in five papers, all published in 1905, 100 years ago. With these papers, Einstein provided the framework for understanding modern astrophysical phenomena. Conversely, astrophysical observations provide one of the most effective means for testing Einstein's theories. Here, I review astrophysical advances precipitated by Einstein's insights, including gravitational redshifts, gravitational lensing, gravitational waves, the Lense-Thirring effect, and modern cosmology. A complete understanding of cosmology, from the earliest moments to the ultimate fate of the universe, will require developments in physics beyond Einstein, to a unified theory of gravity and quantum physics.

Cruise Stage of NASA's InSight Spacecraft

NASA Image and Video Library

2017-08-28

Lockheed Martin spacecraft specialists check the cruise stage of NASA's InSight spacecraft in this photo taken June 22, 2017, in a Lockheed Martin clean room facility in Littleton, Colorado. The cruise stage will provide vital functions during the flight from Earth to Mars, and then will be jettisoned before the InSight lander, enclosed in its aeroshell, enters Mars' atmosphere. The InSight mission (for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) is scheduled to launch in May 2018 and land on Mars Nov. 26, 2018. It will investigate processes that formed and shaped Mars and will help scientists better understand the evolution of our inner solar system's rocky planets, including Earth. https://photojournal.jpl.nasa.gov/catalog/PIA21845

Development of Innovative Technology to Provide Low-Cost Surface Atmospheric Observations in Data Sparse Regions

NASA Astrophysics Data System (ADS)

Kucera, Paul; Steinson, Martin

2017-04-01

Accurate and reliable real-time monitoring and dissemination of observations of surface weather conditions is critical for a variety of societal applications. Applications that provide local and regional information about temperature, precipitation, moisture, and winds, for example, are important for agriculture, water resource monitoring, health, and monitoring of hazard weather conditions. In many regions of the World, surface weather stations are sparsely located and/or of poor quality. Existing stations have often been sited incorrectly, not well-maintained, and have limited communications established at the site for real-time monitoring. The University Corporation for Atmospheric Research (UCAR)/National Center for Atmospheric Research (NCAR), with support from USAID, has started an initiative to develop and deploy low-cost weather instrumentation in sparsely observed regions of the world. The project is focused on improving weather observations for environmental monitoring and early warning alert systems on a regional to global scale. Instrumentation that has been developed use innovative new technologies such as 3D printers, Raspberry Pi computing systems, and wireless communications. The goal of the project is to make the weather station designs, software, and processing tools an open community resource. The weather stations can be built locally by agencies, through educational institutions, and residential communities as a citizen effort to augment existing networks to improve detection of natural hazards for disaster risk reduction. The presentation will provide an overview of the open source weather station technology and evaluation of sensor observations for the initial networks that have been deployed in Africa.

Observation and modelling of the Fe XXI line profile observed by IRIS during the impulsive phase of flares

NASA Astrophysics Data System (ADS)

Polito, V.; Testa, P.; De Pontieu, B.; Allred, J. C.

2017-12-01

The observation of the high temperature (above 10 MK) Fe XXI 1354.1 A line with the Interface Region Imaging Spectrograph (IRIS) has provided significant insights into the chromospheric evaporation process in flares. In particular, the line is often observed to be completely blueshifted, in contrast to previous observations at lower spatial and spectral resolution, and in agreement with predictions from theoretical models. Interestingly, the line is also observed to be mostly symmetric and with a large excess above the thermal width. One popular interpretation for the excess broadening is given by assuming a superposition of flows from different loop strands. In this work, we perform a statistical analysis of Fe XXI line profiles observed by IRIS during the impulsive phase of flares and compare our results with hydrodynamic simulations of multi-thread flare loops performed with the 1D RADYN code. Our results indicate that the multi-thread models cannot easily reproduce the symmetry of the line and that some other physical process might need to be invoked in order to explain the observed profiles.

Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box.

PubMed

Reid, Thomas; Chaganti, Subba Rao; Droppo, Ian G; Weisener, Christopher G

2018-06-01

Baseline biogeochemical surveys of natural environments is an often overlooked field of environmental studies. Too often research begins once contamination has occurred, with a knowledge gap as to how the affected area behaved prior to outside (often anthropogenic) influences. These baseline characterizations can provide insight into proposed bioremediation strategies crucial in cleaning up chemical spill sites or heavily mined regions. Hence, this study was conducted to survey the in-situ microbial activity within freshwater hydrocarbon-rich environments cutting through the McMurray formation - the geologic strata constituting the oil sands. We are the first to report in-situ functional variations among these freshwater microbial ecosystems using metatranscriptomics, providing insight into the in-situ gene expression within these naturally hydrocarbon-rich sites. Key genes involved in energy metabolism (nitrogen, sulfur and methane) and hydrocarbon degradation, including transcripts relating to the observed expression of methane oxidation are reported. This information provides better linkages between hydrocarbon impacted environments, closing knowledge gaps for optimizing not only oil sands mine reclamation but also enhancing microbial reclamation strategies in various freshwater environments. These finding can also be applied to existing contaminated environments, in need of efficient reclamation efforts. Copyright © 2018 Elsevier Ltd. All rights reserved.

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis

PubMed Central

Guarnieri, Michael T.; Chou, Yat-Chen; Salvachúa, Davinia; Mohagheghi, Ali; St. John, Peter C.; Peterson, Darren J.; Bomble, Yannick J.

2017-01-01

ABSTRACT Actinobacillus succinogenes, a Gram-negative facultative anaerobe, exhibits the native capacity to convert pentose and hexose sugars to succinic acid (SA) with high yield as a tricarboxylic acid (TCA) cycle intermediate. In addition, A. succinogenes is capnophilic, incorporating CO2 into SA, making this organism an ideal candidate host for conversion of lignocellulosic sugars and CO2 to an emerging commodity bioproduct sourced from renewable feedstocks. In this work, we report the development of facile metabolic engineering capabilities in A. succinogenes, enabling examination of SA flux determinants via knockout of the primary competing pathways—namely, acetate and formate production—and overexpression of the key enzymes in the reductive branch of the TCA cycle leading to SA. Batch fermentation experiments with the wild-type and engineered strains using pentose-rich sugar streams demonstrate that the overexpression of the SA biosynthetic machinery (in particular, the enzyme malate dehydrogenase) enhances flux to SA. Additionally, removal of competitive carbon pathways leads to higher-purity SA but also triggers the generation of by-products not previously described from this organism (e.g., lactic acid). The resultant engineered strains also lend insight into energetic and redox balance and elucidate mechanisms governing organic acid biosynthesis in this important natural SA-producing microbe. IMPORTANCE Succinic acid production from lignocellulosic residues is a potential route for enhancing the economic feasibility of modern biorefineries. Here, we employ facile genetic tools to systematically manipulate competing acid production pathways and overexpress the succinic acid-producing machinery in Actinobacillus succinogenes. Furthermore, the resulting strains are evaluated via fermentation on relevant pentose-rich sugar streams representative of those from corn stover. Overall, this work demonstrates genetic modifications that can lead to succinic

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis.

PubMed

Guarnieri, Michael T; Chou, Yat-Chen; Salvachúa, Davinia; Mohagheghi, Ali; St John, Peter C; Peterson, Darren J; Bomble, Yannick J; Beckham, Gregg T

2017-09-01

Actinobacillus succinogenes , a Gram-negative facultative anaerobe, exhibits the native capacity to convert pentose and hexose sugars to succinic acid (SA) with high yield as a tricarboxylic acid (TCA) cycle intermediate. In addition, A. succinogenes is capnophilic, incorporating CO 2 into SA, making this organism an ideal candidate host for conversion of lignocellulosic sugars and CO 2 to an emerging commodity bioproduct sourced from renewable feedstocks. In this work, we report the development of facile metabolic engineering capabilities in A. succinogenes , enabling examination of SA flux determinants via knockout of the primary competing pathways-namely, acetate and formate production-and overexpression of the key enzymes in the reductive branch of the TCA cycle leading to SA. Batch fermentation experiments with the wild-type and engineered strains using pentose-rich sugar streams demonstrate that the overexpression of the SA biosynthetic machinery (in particular, the enzyme malate dehydrogenase) enhances flux to SA. Additionally, removal of competitive carbon pathways leads to higher-purity SA but also triggers the generation of by-products not previously described from this organism (e.g., lactic acid). The resultant engineered strains also lend insight into energetic and redox balance and elucidate mechanisms governing organic acid biosynthesis in this important natural SA-producing microbe. IMPORTANCE Succinic acid production from lignocellulosic residues is a potential route for enhancing the economic feasibility of modern biorefineries. Here, we employ facile genetic tools to systematically manipulate competing acid production pathways and overexpress the succinic acid-producing machinery in Actinobacillus succinogenes Furthermore, the resulting strains are evaluated via fermentation on relevant pentose-rich sugar streams representative of those from corn stover. Overall, this work demonstrates genetic modifications that can lead to succinic acid

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guarnieri, Michael T.; Chou, Yat -Chen; Salvachua, Davinia Rodriquez

Actinobacillus succinogenes, a Gram-negative facultative anaerobe, exhibits the native capacity to convert pentose and hexose sugars to succinic acid (SA) with high yield as a tricarboxylic acid (TCA) cycle intermediate. In addition, A. succinogenes is capnophilic, incorporating CO 2 into SA, making this organism an ideal candidate host for conversion of lignocellulosic sugars and CO 2 to an emerging commodity bioproduct sourced from renewable feedstocks. In this work, we report the development of facile metabolic engineering capabilities in A. succinogenes, enabling examination of SA flux determinants via knockout of the primary competing pathways—namely, acetate and formate production—and overexpression of themore » key enzymes in the reductive branch of the TCA cycle leading to SA. Batch fermentation experiments with the wild-type and engineered strains using pentose-rich sugar streams demonstrate that the overexpression of the SA biosynthetic machinery (in particular, the enzyme malate dehydrogenase) enhances flux to SA. Additionally, removal of competitive carbon pathways leads to higher-purity SA but also triggers the generation of by-products not previously described from this organism (e.g., lactic acid). The resultant engineered strains also lend insight into energetic and redox balance and elucidate mechanisms governing organic acid biosynthesis in this important natural SA-producing microbe. IMPORTANCE Succinic acid production from lignocellulosic residues is a potential route for enhancing the economic feasibility of modern biorefineries. Here, we employ facile genetic tools to systematically manipulate competing acid production pathways and overexpress the succinic acid-producing machinery in Actinobacillus succinogenes. Furthermore, the resulting strains are evaluated via fermentation on relevant pentose-rich sugar streams representative of those from corn stover. Altogether, this work demonstrates genetic modifications that can lead to succinic

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis

DOE PAGES

Guarnieri, Michael T.; Chou, Yat -Chen; Salvachua, Davinia Rodriquez; ...

2017-06-16

Actinobacillus succinogenes, a Gram-negative facultative anaerobe, exhibits the native capacity to convert pentose and hexose sugars to succinic acid (SA) with high yield as a tricarboxylic acid (TCA) cycle intermediate. In addition, A. succinogenes is capnophilic, incorporating CO 2 into SA, making this organism an ideal candidate host for conversion of lignocellulosic sugars and CO 2 to an emerging commodity bioproduct sourced from renewable feedstocks. In this work, we report the development of facile metabolic engineering capabilities in A. succinogenes, enabling examination of SA flux determinants via knockout of the primary competing pathways—namely, acetate and formate production—and overexpression of themore » key enzymes in the reductive branch of the TCA cycle leading to SA. Batch fermentation experiments with the wild-type and engineered strains using pentose-rich sugar streams demonstrate that the overexpression of the SA biosynthetic machinery (in particular, the enzyme malate dehydrogenase) enhances flux to SA. Additionally, removal of competitive carbon pathways leads to higher-purity SA but also triggers the generation of by-products not previously described from this organism (e.g., lactic acid). The resultant engineered strains also lend insight into energetic and redox balance and elucidate mechanisms governing organic acid biosynthesis in this important natural SA-producing microbe. IMPORTANCE Succinic acid production from lignocellulosic residues is a potential route for enhancing the economic feasibility of modern biorefineries. Here, we employ facile genetic tools to systematically manipulate competing acid production pathways and overexpress the succinic acid-producing machinery in Actinobacillus succinogenes. Furthermore, the resulting strains are evaluated via fermentation on relevant pentose-rich sugar streams representative of those from corn stover. Altogether, this work demonstrates genetic modifications that can lead to succinic

Association between insight, cognitive insight, positive symptoms and violence in patients with schizophrenia.

PubMed

Ekinci, Okan; Ekinci, Asli

2013-04-01

Violence is a significant clinical and public concern and is a frequent occurrence in patients with schizophrenia. The relationship between insight and violence remains controversial. In addition, there is a lack of research on insight, cognitive insight, demographic and psychopathologic variables in violent versus nonviolent schizophrenia patients. We aimed to compare insight, cognitive insight, psychopathological and demographic variables in violent and nonviolent subjects suffering from schizophrenia. In addition, we aimed to determine the demographic and clinical predictors of violent behaviour in patients with schizophrenia. We recruited 133 schizophrenic patients without concomitant substance abuse or axis II disorder. Diagnoses were based on the SCID-I and SCID-II. Violent behaviours were assessed using the Overt Aggression Scale. Insight and cognitive insight were assessed with the Scale to Assess Unawareness of Mental Disorder and the Beck Cognitive Insight Scale, respectively. We compared 47 patients with violent schizophrenia with 86 nonviolent patients. Non-violent patients had more severe depression, lower scores on positive symptoms, better clinical insight, more self-reflectivity and higher R-C index scores than did violent patients. In addition, history of violence, lower self-reflectiveness, worse clinical insight and delusion severity were significant predictors of violence in schizophrenia. The present study suggests that the inclusion of insight and cognitive insight may increase the prediction of violence in this population. In addition, clinicians should consider using non-pharmacological techniques that are based on cognitive behaviour therapy and enhance insight, particularly cognitive insight, among patients with schizophrenia who exhibit violent behaviour.

Exploring How Gender Figures the Identity Trajectories of Two Doctoral Students in Observational Astrophysics

ERIC Educational Resources Information Center

Gonsalves, Allison J.

2018-01-01

[This paper is part of the Focused Collection on Astronomy Education Research.] This paper presents the cases of two doctoral students in observational astrophysics whose circumstances and experiences led them on a career trajectory out of academic research. In this article, I employ a sociocultural lens that provides insight into the dynamics of…

The InSight Mission's Martian Atmospheric Science Goals, Capabilities and Instrumentation

NASA Astrophysics Data System (ADS)

Smrekar, S. E.; Banfield, D. J.

2015-12-01

The InSight Mission to Mars will launch in March 2016 and land in September 2016, beginning at least 1 Mars year of observations from the surface of Mars. The primary scientific goal of the InSight mission is to characterize the interior of Mars (both deep and near-surface), but it is also equipped with very capable meteorological instrumentation, and consequently has atmospheric science goals as well. The instrumentation InSight carries includes a very sensitive and fast response pressure sensor, as well as a pair of wind and temperature sensors that are similar to those flown on MSL and will be on Mars2020. These sensors will operate essentially continuously at Mars, a first; enabling the production of a complete sampling of the Martian environment, including short-lived transients. InSight also carries cameras that can be used to survey not only the ground in the near environment, but also sky conditions. The pressure sensor responds to signals below 10Hz (~10X its predecessors) and has a noise level of about 10 mPa (better than 1/10 its predecessors). The pair of wind and temperature sensors have been carefully placed opposite one another on the deck to minimize lander interference as much as possible, leaving one sensor on the windward side of the lander at any time. These capabilities, combined with their continuous sampling enable us to pursue new atmospheric science questions at Mars, including quantifying thresholds for aeolian change, detailed dust devil characterization, bolide infrasonic detection and characterization, and quantifying secular trends in pressure. This is in addition to characterizing the normal meteorology at the InSight landing site, which while not completely new, will provide incremental and important constraints for Martian Atmospheric models. We also expect there to be unexpected discoveries, as well as more synergistic approaches to coordination among all the instruments on InSight that may result even more novel capabilities.

The Evolution of a Long-Lived Mesoscale Convective System Observed by GLM

NASA Astrophysics Data System (ADS)

Peterson, M. J.; Rudlosky, S. D.; Antunes, L.

2017-12-01

Continuous Geostationary Lightning Mapper (GLM) observations are used to document total lightning activity over the life cycle of a long-lived Mesoscale Convective System (MCS). MCS's may be few in number, but they are important for the Global Electric Circuit (GEC) because they sustain high lightning flash rates and quasi steady state conduction currents (Wilson currents) over longer time periods than ordinary isolated convection. The optical characteristics of the flashes produced by MCS's change over time, providing additional insights into the precipitation structure, convective mode, and evolution of the storm system. These insights are particularly useful in areas void of radar observations. Intercalibrated passive microwave radiometer data from the Global Precipitation Measurement (GPM) constellation also are used to estimate changes in Wilson current generation as the system evolves. These results highlight the role of MCS's in the GEC, and showcase how optical flash descriptors relate to thunderstorm organization, maturity, and structure.

International Collaboration in Satellite Observations for Disaster Management

NASA Technical Reports Server (NTRS)

Duda, Kenneth A.; Abrams, Michael

2012-01-01

When lives are threatened or lost due to catastrophic disasters, and when massive financial impacts are experienced, international emergency response teams rapidly mobilize to provide urgently required support. Satellite observations of affected areas often provide essential insight into the magnitude and details of the impacts. The large cost and high complexity of developing and operating satellite flight and ground systems encourages international collaboration in acquiring imagery for such significant global events in order to speed delivery of critical information to help those affected, and optimize spectral, spatial, and temporal coverage of the areas of interest. The International Charter-Space and Major Disasters was established to enable such collaboration in sensor tasking during times of crisis and is often activated in response to calls for assistance from authorized users. Insight is provided from a U.S. perspective into sensor support for Charter activations and other disaster events through a description of the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), which has been used to support emergency situations for over a decade through its expedited tasking and near real-time data delivery capabilities. Examples of successes achieved and challenges encountered in international collaboration to develop related systems and fulfill tasking requests suggest operational considerations for new missions as well as areas for future enhancements.

A picture's worth a thousand words: a food-selection observational method.

PubMed

Carins, Julia E; Rundle-Thiele, Sharyn R; Parkinson, Joy E

2016-05-04

Issue addressed: Methods are needed to accurately measure and describe behaviour so that social marketers and other behaviour change researchers can gain consumer insights before designing behaviour change strategies and so, in time, they can measure the impact of strategies or interventions when implemented. This paper describes a photographic method developed to meet these needs. Methods: Direct observation and photographic methods were developed and used to capture food-selection behaviour and examine those selections according to their healthfulness. Four meals (two lunches and two dinners) were observed at a workplace buffet-style cafeteria over a 1-week period. The healthfulness of individual meals was assessed using a classification scheme developed for the present study and based on the Australian Dietary Guidelines. Results: Approximately 27% of meals (n = 168) were photographed. Agreement was high between raters classifying dishes using the scheme, as well as between researchers when coding photographs. The subset of photographs was representative of patterns observed in the entire dining room. Diners chose main dishes in line with the proportions presented, but in opposition to the proportions presented for side dishes. Conclusions: The present study developed a rigorous observational method to investigate food choice behaviour. The comprehensive food classification scheme produced consistent classifications of foods. The photographic data collection method was found to be robust and accurate. Combining the two observation methods allows researchers and/or practitioners to accurately measure and interpret food selections. Consumer insights gained suggest that, in this setting, increasing the availability of green (healthful) offerings for main dishes would assist in improving healthfulness, whereas other strategies (e.g. promotion) may be needed for side dishes. So what?: Visual observation methods that accurately measure and interpret food

Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression

PubMed Central

Giorgio, Elisa; Rolyan, Harshvardhan; Kropp, Laura; Chakka, Anish Baswanth; Yatsenko, Svetlana; Gregorio, Eleonora Di; Lacerenza, Daniela; Vaula, Giovanna; Talarico, Flavia; Mandich, Paola; Toro, Camilo; Pierre, Eleonore Eymard; Labauge, Pierre; Capellari, Sabina; Cortelli, Pietro; Vairo, Filippo Pinto; Miguel, Diego; Stubbolo, Danielle; Marques, Lourenco Charles; Gahl, William; Boespflug-Tanguy, Odile; Melberg, Atle; Hassin-Baer, Sharon; Cohen, Oren S; Pjontek, Rastislav; Grau, Armin; Klopstock, Thomas; Fogel, Brent; Meijer, Inge; Rouleau, Guy; Bouchard, Jean-Pierre L; Ganapathiraju, Madhavi; Vanderver, Adeline; Dahl, Niklas; Hobson, Grace; Brusco, Alfredo; Brussino, Alessandro; Padiath, Quasar Saleem

2013-01-01

ABSTRACT Autosomal dominant leukodystrophy (ADLD) is an adult onset demyelinating disorder that is caused by duplications of the lamin B1 (LMNB1) gene. However, as only a few cases have been analyzed in detail, the mechanisms underlying LMNB1 duplications are unclear. We report the detailed molecular analysis of the largest collection of ADLD families studied, to date. We have identified the minimal duplicated region necessary for the disease, defined all the duplication junctions at the nucleotide level and identified the first inverted LMNB1 duplication. We have demonstrated that the duplications are not recurrent; patients with identical duplications share the same haplotype, likely inherited from a common founder and that the duplications originated from intrachromosomal events. The duplication junction sequences indicated that nonhomologous end joining or replication-based mechanisms such fork stalling and template switching or microhomology-mediated break induced repair are likely to be involved. LMNB1 expression was increased in patients’ fibroblasts both at mRNA and protein levels and the three LMNB1 alleles in ADLD patients show equal expression, suggesting that regulatory regions are maintained within the rearranged segment. These results have allowed us to elucidate duplication mechanisms and provide insights into allele-specific LMNB1 expression levels. PMID:23649844

Whole-Genome Sequencing of Theileria parva Strains Provides Insight into Parasite Migration and Diversification in the African Continent

PubMed Central

Hayashida, Kyoko; Abe, Takashi; Weir, William; Nakao, Ryo; Ito, Kimihito; Kajino, Kiichi; Suzuki, Yutaka; Jongejan, Frans; Geysen, Dirk; Sugimoto, Chihiro

2013-01-01

The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa. We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains (Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains. Comparison with the reference Muguga genome sequence revealed 34 814–121 545 single nucleotide polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic trees were constructed with selected informative SNPs that allowed the investigation of possible complex recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (non-synonymous substitutions per non-synonymous site divided by synonymous substitutions per synonymous site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates. This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with prediction of possible past recombination events, providing insight into the migration, diversification, and evolution of this parasite species in the African continent. PMID:23404454

Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent.

PubMed

Hayashida, Kyoko; Abe, Takashi; Weir, William; Nakao, Ryo; Ito, Kimihito; Kajino, Kiichi; Suzuki, Yutaka; Jongejan, Frans; Geysen, Dirk; Sugimoto, Chihiro

2013-06-01

The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa. We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains (Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains. Comparison with the reference Muguga genome sequence revealed 34 814-121 545 single nucleotide polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic trees were constructed with selected informative SNPs that allowed the investigation of possible complex recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (non-synonymous substitutions per non-synonymous site divided by synonymous substitutions per synonymous site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates. This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with prediction of possible past recombination events, providing insight into the migration, diversification, and evolution of this parasite species in the African continent.

Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1*

PubMed Central

Chenge, Jude T.; Duyet, Le Van; Swami, Shalini; McLean, Kirsty J.; Kavanagh, Madeline E.; Coyne, Anthony G.; Rigby, Stephen E. J.; Cheesman, Myles R.; Girvan, Hazel M.; Levy, Colin W.; Rupp, Bernd; von Kries, Jens P.; Abell, Chris; Leys, David; Munro, Andrew W.

2017-01-01

The Mycobacterium tuberculosis H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many M. tuberculosis P450s remain uncharacterized, suggesting that their further analysis may provide new insights into M. tuberculosis metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands. A survey of azole antifungal drugs showed that CYP126A1 is inhibited strongly by azoles containing an imidazole ring but not by those tested containing a triazole ring. To further explore the molecular preferences of CYP126A1 and search for probes of enzyme function, we conducted a high throughput screen. Compounds containing three or more ring structures dominated the screening hits, including nitroaromatic compounds that induce substrate-like shifts in the heme spectrum of CYP126A1. Spectroelectrochemical measurements revealed a 155-mV increase in heme iron potential when bound to one of the newly identified nitroaromatic drugs. CYP126A1 dimers were observed in crystal structures of ligand-free CYP126A1 and for CYP126A1 bound to compounds discovered in the screen. However, ketoconazole binds in an orientation that disrupts the BC-loop regions at the P450 dimer interface and results in a CYP126A1 monomeric crystal form. Structural data also reveal that nitroaromatic ligands “moonlight” as substrates by displacing the CYP126A1 distal water but inhibit enzyme activity. The relatively polar active site of CYP126A1 distinguishes it from its most closely related sterol-binding P450s in M. tuberculosis, suggesting that further investigations will reveal its diverse substrate selectivity. PMID:27932461

The Genome of Laccaria Bi color Provides Insights into Mycorrhizal Symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, F; Aerts, A.; Ahren, D

Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assemblymore » contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles

Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation

PubMed Central

Koppstein, David; Ashour, Joseph; Bartel, David P.

2015-01-01

The influenza polymerase cleaves host RNAs ∼10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand this process of cap snatching, we used high-throughput sequencing to determine the 5′ ends of A/WSN/33 (H1N1) influenza mRNAs. The sequences provided clear evidence for nascent-chain realignment during transcription initiation and revealed a strong influence of the viral template on the frequency of realignment. After accounting for the extra nucleotides inserted through realignment, analysis of the capped fragments indicated that the different viral mRNAs were each prepended with a common set of sequences and that the polymerase often cleaved host RNAs after a purine and often primed transcription on a single base pair to either the terminal or penultimate residue of the viral template. We also developed a bioinformatic approach to identify the targeted host transcripts despite limited information content within snatched fragments and found that small nuclear RNAs and small nucleolar RNAs contributed the most abundant capped leaders. These results provide insight into the mechanism of viral transcription initiation and reveal the diversity of the cap-snatched repertoire, showing that noncoding transcripts as well as mRNAs are used to make influenza mRNAs. PMID:25901029

Reading skills, creativity, and insight: exploring the connections.

PubMed

Mourgues, Catalina V; Preiss, David D; Grigorenko, Elena L

2014-08-04

Studies of the relationship between creativity and specific reading disabilities have produced inconclusive results. We explored their relationship in a sample of 259 college students (age range: 17 to 38 years-old) from three Chilean universities. The students were tested on their verbal ability, creativity, and insight. A simple linear regression was performed on the complete sample, and on high- and low-achievement groups that were formed based on reading test scores. We observed a significant correlation in the total sample between outcomes on the verbal ability tasks, and on the creativity and insight tasks (range r =. 152 to r =. 356, ps <.001). Scores on the reading comprehension and phonological awareness tasks were the best predictors of performance on creativity and insight tasks (range β = .315 to β = .155, ps <.05). A comparison of the low- and high-scoring groups on verbal ability tasks yielded results to the same effect. These findings do not support the hypothesis that specific reading disability is associated with better performance on creative tasks. Instead, higher verbal ability was found to be associated with higher creativity and insight.

New Insights on the Morphology of Adult Mouse Penis1

PubMed Central

Rodriguez, Esequiel; Weiss, Dana A.; Yang, Jennifer H.; Menshenina, Julia; Ferretti, Max; Cunha, Tristan J.; Barcellos, Dale; Chan, Lok Yun; Risbridger, Gail; Cunha, Gerald R.; Baskin, Laurence S.

2011-01-01

ABSTRACT The adult mouse penis represents the end point of masculine sex differentiation of the embryonic genital tubercle and contains bone, cartilage, the urethra, erectile bodies, several types of epithelium, and many individual cell types arrayed into specific anatomical structures. Using contemporary high-resolution imaging techniques, we sought to provide new insights to the current description of adult mouse penile morphology to enable understanding of penile abnormalities, including hypospadias. Examination of serial transverse and longitudinal sections, scanning electron microscopy, and three-dimensional (3D) reconstruction provided a new appreciation of the individual structures in the adult mouse penis and their 3D interrelationships. In so doing, we discovered novel paired erectile bodies, the male urogenital mating protuberance (MUMP), and more accurately described the urethral meatus. These morphological observations were quantified by morphometric analysis and now provide accurate morphological end points of sex differentiation of mouse penis that will be the foundation of future studies to identify normal and abnormal penile development. PMID:21918128

Kohler's Insight Revisited.

ERIC Educational Resources Information Center

Windholtz, George

1985-01-01

Psychology textbooks frequently present Wolfgang Kohler's two-stick experiment with chimpanzees as having demonstrated insight in learning. Studies that replicated Kohler's work support his findings but not his interpretation in terms of insightful solution. The uncritical inclusion of Kohler's insight interpretation in texts is not warranted in…

Adding tetrahydrofuran to dilute acid pretreatment provides new insights into substrate changes that greatly enhance biomass deconstruction by Clostridium thermocellum and fungal enzymes

DOE PAGES

Thomas, Vanessa A.; Donohoe, Bryon S.; Li, Mi; ...

2017-11-30

Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using fungal enzymes for biological conversion of lignocellulosic biomass. However, limited research has integrated CBP with real pretreated biomass, and understanding how pretreatment impacts subsequent deconstruction by CBP vs. fungal enzymes can provide valuable insights into CBP and suggest other novel biomass deconstruction strategies. This study focused on determining the effect of pretreatment by dilute sulfuric acid alone (DA) and with tetrahydrofuran (THF) addition via co-solvent-enhanced lignocellulosic fractionation (CELF) on deconstruction of corn stover and Populusmore » with much different recalcitrance by C. thermocellum vs. fungal enzymes and changes in pretreated biomass related to these differences.« less

Adding tetrahydrofuran to dilute acid pretreatment provides new insights into substrate changes that greatly enhance biomass deconstruction by Clostridium thermocellum and fungal enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, Vanessa A.; Donohoe, Bryon S.; Li, Mi

Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using fungal enzymes for biological conversion of lignocellulosic biomass. However, limited research has integrated CBP with real pretreated biomass, and understanding how pretreatment impacts subsequent deconstruction by CBP vs. fungal enzymes can provide valuable insights into CBP and suggest other novel biomass deconstruction strategies. This study focused on determining the effect of pretreatment by dilute sulfuric acid alone (DA) and with tetrahydrofuran (THF) addition via co-solvent-enhanced lignocellulosic fractionation (CELF) on deconstruction of corn stover and Populusmore » with much different recalcitrance by C. thermocellum vs. fungal enzymes and changes in pretreated biomass related to these differences.« less

Functionally different α-synuclein inclusions yield insight into Parkinson’s disease pathology

PubMed Central

Raiss, Christian C.; Braun, Theresa S.; Konings, Irene B. M.; Grabmayr, Heinrich; Hassink, Gerco C.; Sidhu, Arshdeep; le Feber, Joost; Bausch, Andreas R.; Jansen, Casper; Subramaniam, Vinod; Claessens, Mireille M. A. E.

2016-01-01

The formation of α-synuclein (α-S) amyloid aggregates, called Lewy bodies (LBs), is a hallmark of Parkinson’s disease (PD). The function of LBs in the disease process is however still unclear; they have been associated with both neuroprotection and toxicity. To obtain insight into this contradiction, we induced the formation of α-S inclusions, using three different induction methods in SH-SY5Y cells and rat-derived primary neuronal cells. Using confocal and STED microscopy we observed induction-dependent differences in α-S inclusion morphology, location and function. The aggregation of α-S in functionally different compartments correlates with the toxicity of the induction method measured in viability assays. The most cytotoxic treatment largely correlates with the formation of proteasome-associated, juxta-nuclear inclusions. With less toxic methods cytosolic deposits that are not associated with the proteasome are more prevalent. The distribution of α-S over at least two different types of inclusions is not limited to cell models, but is also observed in primary neuronal cells and in human mesencephalon. The existence of functionally different LBs, in vivo and in vitro, gives important insights in the impact of Lewy Body formation on neuronal functioning and may thereby provide a platform for discovering therapeutics. PMID:26984067

Earth Sciences data user community feedbacks to PARSE.Insight

NASA Astrophysics Data System (ADS)

Giaretta, David; Guidetti, Veronica

2010-05-01

The presentation in point reports on the topic of long term availability of environmental data as perceived by the Earth Science data user community. In the context of the European strategy for preserving Earth Observation (EO) data and as partner of the EU FP7 PARSE.Insight project (http://www.parse-insight.eu/), the European Space Agency (ESA) issued a public consultation on-line targeting its EO data user base. The timely and active participation confirmed the high interest in the addressed topic. Primary target of such an action is to provide ESA teams dedicated to environmental data access, archiving and re-processing with the first insight from the Earth Science community on the preservation of space data in the long-term. As a significant example, ESA's Climate Change Initiative requires activities like long-term preservation, recalibration and re-processing of data records. The time-span of EO data archives extends from a few years to decades and their value as scientific time-series increases considerably regarding the topic of global change. Future research in the field of Earth Sciences is of invaluable importance: to carry it on researchers worldwide must be enabled to find and access data of interest quickly. At present several thousands of scientists, principal investigators and operators, access EO missions' metadata, data and derived information daily. Main objectives may be to study the global climate change, to check the status of the instrument and the quality of EO data. There is a huge worldwide scientific community calling for the need to keep EO data accessible without time constrains, easily and quickly. The scientific community's standpoint is given over the stewardship of environmental data and the appropriateness of current EO data access systems as enabling digital preservation and offering HPC capabilities. This insight in the Earth Sciences community provides a comprehensive illustration of the users' responses over topics like use

Airborne observations of cloud properties on HALO during NARVAL

NASA Astrophysics Data System (ADS)

Konow, Heike; Hansen, Akio; Ament, Felix

2016-04-01

The representation of cloud and precipitation processes is one of the largest sources of uncertainty in climate and weather predictions. To validate model predictions of convective processes over the Atlantic ocean, usually satellite data are used. However, satellite products provide just a coarse view with poor temporal resolution of convective maritime clouds. Aircraft-based observations offer a more detailed insight due to lower altitude and high sampling rates. The research aircraft HALO (High Altitude Long Range Research Aircraft) is operated by the German Aerospace Center (DLR). With a ceiling of 15 km, and a range of 10,000 km and more than 10 hours it is able to reach remote regions and operate from higher altitudes than most other research aircraft. Thus, it provides the unique opportunity to exploit regions of the atmosphere that cannot be easily accessed otherwise. Measurements conducted on HALO provide more detailed insights than achievable from satellite data. Therefore, this measurement platform bridges the gap between previous airborne measurements and satellites. The payload used for this study consists of, amongst others, a suite of passive microwave radiometers, a cloud radar, and a water vapor DIAL. To investigate cloud and precipitation properties of convective maritime clouds, the NARVAL (Next-generation Aircraft Remote-Sensing for Validation Studies) campaign was conducted in winter 2013/2014 out of Barbados and Keflavik (Iceland). This campaign was one of the first that took place on the HALO aircraft. During the experiment's two parts 15 research flights were conducted (8 flights during NARVAL-South out of Barbados to investigate trade-wind cumuli and 7 flights out of Keflavik with focus on mid-latitude cyclonic systems). Flight durations were between five and nine hours, amounting to roughly 118 flight hours overall. 121 dropsondes were deployed. In fall 2016 two additional aircraft campaigns with the same payload will take place: The

Novel insights into mitotic chromosome condensation

PubMed Central

Piskadlo, Ewa; Oliveira, Raquel A.

2016-01-01

The fidelity of mitosis is essential for life, and successful completion of this process relies on drastic changes in chromosome organization at the onset of nuclear division. The mechanisms that govern chromosome compaction at every cell division cycle are still far from full comprehension, yet recent studies provide novel insights into this problem, challenging classical views on mitotic chromosome assembly. Here, we briefly introduce various models for chromosome assembly and known factors involved in the condensation process (e.g. condensin complexes and topoisomerase II). We will then focus on a few selected studies that have recently brought novel insights into the mysterious way chromosomes are condensed during nuclear division. PMID:27508072

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

PubMed Central

Rasigade, Jean-Philippe; Barbier, Maxime; Dumitrescu, Oana; Pichat, Catherine; Carret, Gérard; Ronnaux-Baron, Anne-Sophie; Blasquez, Ghislaine; Godin-Benhaim, Christine; Boisset, Sandrine; Carricajo, Anne; Jacomo, Véronique; Fredenucci, Isabelle; Pérouse de Montclos, Michèle; Flandrois, Jean-Pierre; Ader, Florence; Supply, Philip; Lina, Gérard; Wirth, Thierry

2017-01-01

The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P < 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data. PMID:28349973

Caregiver Insightfulness and Young Children’s Violence Exposure: Testing a Relational Model of Risk and Resilience

PubMed Central

Gray, Sarah A. O.; Forbes, Danielle; Briggs-Gowan, Margaret; Carter, Alice S.

2016-01-01

This study employed a relational post-traumatic stress frame to explore the co-contribution of young children’s exposure to violence and caregiver insightfulness on child behavioral outcomes in a high-risk, non-referred sample of caregivers and preschoolers (n = 64; mean age 3.83 years, SD = .77). Caregiver insightfulness did not have a main effect on child outcomes but did moderate the relation between violence exposure and child behavior across all observed outcomes. Violence-exposed children with non-insightful caregivers demonstrated higher caregiver-rated internalizing and externalizing behaviors and observer-rated negative affect than all other groups. Among children not exposed to violence, insightfulness was not related to children’s behavior problems or negative affect, suggesting violence-specific processes. Though cross-sectional, results suggest that the effects of violence and caregiver insightfulness on child outcomes are contingent on one another and that caregiver insightfulness may play a protective role in contexts of violence. PMID:26503175

New insights on stromules: stroma filled tubules extended by independent plastids.

PubMed

Schattat, Martin H; Klösgen, Ralf Bernd; Mathur, Jaideep

2012-09-01

The recognition of stromules as sporadically extended stroma filled tubules from all kinds of plastids constitutes one of the major insights that resulted from the direct application of green fluorescent protein aided imaging of living plant cells. Observations of dynamic green fluorescent stromules strongly suggested that plastids frequently interact with each other while photo-bleaching of interconnected plastids indicated that proteins can move within the stroma filled tubules. These observations readily fit into the prevailing concept of the endosymbiogenic origins of plastids and provided stromules the status of conduits for inter-plastid communication and macromolecule transfer. However, experimental evidence obtained recently through the use of photoconvertible protein labeled stromules strongly supports plastid independence rather than their interconnectivity. Additional information on stress conditions inducing stromules and observations on their alignment with other organelles suggests that the major role of stromules is to increase the interactive surface of a plastid with the rest of the cytoplasm.

A multidisciplinary approach providing new insight into fruit flesh browning physiology in apple (Malus x domestica Borkh.).

PubMed

Di Guardo, Mario; Tadiello, Alice; Farneti, Brian; Lorenz, Giorgia; Masuero, Domenico; Vrhovsek, Urska; Costa, Guglielmo; Velasco, Riccardo; Costa, Fabrizio

2013-01-01

In terms of the quality of minimally processed fruit, flesh browning is fundamentally important in the development of an aesthetically unpleasant appearance, with consequent off-flavours. The development of browning depends on the enzymatic action of the polyphenol oxidase (PPO). In the 'Golden Delicious' apple genome ten PPO genes were initially identified and located on three main chromosomes (2, 5 and 10). Of these genes, one element in particular, here called Md-PPO, located on chromosome 10, was further investigated and genetically mapped in two apple progenies ('Fuji x Pink Lady' and 'Golden Delicious x Braeburn'). Both linkage maps, made up of 481 and 608 markers respectively, were then employed to find QTL regions associated with fruit flesh browning, allowing the detection of 25 QTLs related to several browning parameters. These were distributed over six linkage groups with LOD values spanning from 3.08 to 4.99 and showed a rate of phenotypic variance from 26.1 to 38.6%. Anchoring of these intervals to the apple genome led to the identification of several genes involved in polyphenol synthesis and cell wall metabolism. Finally, the expression profile of two specific candidate genes, up and downstream of the polyphenolic pathway, namely phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), provided insight into flesh browning physiology. Md-PPO was further analyzed and two haplotypes were characterised and associated with fruit flesh browning in apple.

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

PubMed Central

Farneti, Brian; Lorenz, Giorgia; Masuero, Domenico; Vrhovsek, Urska; Costa, Guglielmo; Velasco, Riccardo; Costa, Fabrizio

2013-01-01

In terms of the quality of minimally processed fruit, flesh browning is fundamentally important in the development of an aesthetically unpleasant appearance, with consequent off-flavours. The development of browning depends on the enzymatic action of the polyphenol oxidase (PPO). In the ‘Golden Delicious’ apple genome ten PPO genes were initially identified and located on three main chromosomes (2, 5 and 10). Of these genes, one element in particular, here called Md-PPO, located on chromosome 10, was further investigated and genetically mapped in two apple progenies (‘Fuji x Pink Lady’ and ‘Golden Delicious x Braeburn’). Both linkage maps, made up of 481 and 608 markers respectively, were then employed to find QTL regions associated with fruit flesh browning, allowing the detection of 25 QTLs related to several browning parameters. These were distributed over six linkage groups with LOD values spanning from 3.08 to 4.99 and showed a rate of phenotypic variance from 26.1 to 38.6%. Anchoring of these intervals to the apple genome led to the identification of several genes involved in polyphenol synthesis and cell wall metabolism. Finally, the expression profile of two specific candidate genes, up and downstream of the polyphenolic pathway, namely phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), provided insight into flesh browning physiology. Md-PPO was further analyzed and two haplotypes were characterised and associated with fruit flesh browning in apple. PMID:24205065

Great New Insights from Failed Experiments, Unanticipated Results and Embracing Controversial Observations

NASA Technical Reports Server (NTRS)

Nuth, Joseph A., III; Johnson, Natasha M.; Ferguson, Frank T.; Rietmeijer, Frans J. M.; Hill, Hugh G. M.

2015-01-01

Experimental data and observations, whether telescopic or analytical, are never wrong, though data derived from such sources can be misinterpreted or applied inappropriately to derive conclusions that are incorrect. Given that nature always behaves according to the laws of physics and chemistry, rather than according to currently popular models and theories, experimental results should always be considered correct even when the results are far from those that one might initially expect. We discuss a number of cases where the results of experiments, even one carried out as a simple calibration measure, produced wildly different results that generally required many years of effort or contemplation to understand. On the positive side, exploration of the circumstances that produced the errant results often led to new and interesting insights concerning processes that might occur in natural environments and that were well worth the effort involved. Specifically, we show how an experiment that "failed" due to a broken conductor led to experiments that made the first refractory oxide solids containing mass independently fractionated oxygen isotopes and to 1998 predictions of the oxygen isotopic composition of the sun that were confirmed by the analysis of Genesis samples in 2011. We describe a calibration experiment that unexpectedly produced single magnetic domain iron particles. We discuss how tracking down a persistent source of "contamination" in experiments intended to produce amorphous iron and magnesium silicate smokes led to a series of studies on the synthesis of carbonaceous grain coatings that turn out to be very efficient Fischer-Tropsch catalysts and have great potential for trapping the planetary noble gases found in meteorites. We describe how models predicting the instability of silicate grains in circumstellar environments spurred new measurements of the vapor pressure of SiO partially based on previous experiments showing unexpected but systematic non

Psychology of Sport. Issues & Insights.

ERIC Educational Resources Information Center

Fisher, A. Craig, Ed.

This book is designed to provide instructors and students in sport psychology courses with a learning instrument that combines the continuity of a textbook with the range of opinion, in-depth treatment of selected issues, and insight into research methods of a book of readings. The subject is divided into four topical categories. Under the heading…

Insights into Industry and Technology. Curriculum Guide.

ERIC Educational Resources Information Center

North Dakota State Board for Vocational Education, Bismarck.

One of a set of six guides for an industrial arts curriculum at the junior high school level, this guide provides the basic foundation to develop a one-semester course based on the following cluster concept: insights into industry and technology. An overview of industry and technology is provided to serve as an integrator or unifier of industry…

New insight on petroleum system modeling of Ghadames basin, Libya

NASA Astrophysics Data System (ADS)

Bora, Deepender; Dubey, Siddharth

2015-12-01

Underdown and Redfern (2008) performed a detailed petroleum system modeling of the Ghadames basin along an E-W section. However, hydrocarbon generation, migration and accumulation changes significantly across the basin due to complex geological history. Therefore, a single section can't be considered representative for the whole basin. This study aims at bridging this gap by performing petroleum system modeling along a N-S section and provides new insights on source rock maturation, generation and migration of the hydrocarbons using 2D basin modeling. This study in conjunction with earlier work provides a 3D context of petroleum system modeling in the Ghadames basin. Hydrocarbon generation from the lower Silurian Tanezzuft formation and the Upper Devonian Aouinet Ouenine started during the late Carboniferous. However, high subsidence rate during middle to late Cretaceous and elevated heat flow in Cenozoic had maximum impact on source rock transformation and hydrocarbon generation whereas large-scale uplift and erosion during Alpine orogeny has significant impact on migration and accumulation. Visible migration observed along faults, which reactivated during Austrian unconformity. Peak hydrocarbon expulsion reached during Oligocene for both the Tanezzuft and the Aouinet Ouenine source rocks. Based on modeling results, capillary entry pressure driven downward expulsion of hydrocarbons from the lower Silurian Tanezzuft formation to the underlying Bir Tlacsin formation observed during middle Cretaceous. Kinetic modeling has helped to model hydrocarbon composition and distribution of generated hydrocarbons from both the source rocks. Application of source to reservoir tracking technology suggest some accumulations at shallow stratigraphic level has received hydrocarbons from both the Tanezzuft and Aouinet Ouenine source rocks, implying charge mixing. Five petroleum systems identified based on source to reservoir correlation technology in Petromod*. This Study builds

InSight Spacecraft Lift to Spin Table & Pre-Spin Processing

NASA Image and Video Library

2018-03-28

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers inspect NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft after it was placed on a spin table during preflight processing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Lift/Mate to PLA with SC to GTV

NASA Image and Video Library

2018-04-11

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers monitor progress as NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is prepared for encapsulation in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Unraveling the insight paradox: One-year longitudinal study on the relationships between insight, self-stigma, and life satisfaction among people with schizophrenia spectrum disorders.

PubMed

Chio, Floria H N; Mak, Winnie W S; Chan, Randolph C H; Tong, Alan C Y

2018-01-30

The promotion of insight among people with schizophrenia spectrum disorders has posed a dilemma to service providers as higher insight has been linked to positive clinical outcomes but negative psychological outcomes. The negative meaning that people attached to the illness (self-stigma content) and the recurrence of such stigmatizing thoughts (self-stigma process) may explain why increased insight is associated with negative outcomes. The present study examined how the presence of high self-stigma content and self-stigma process may contribute to the negative association between insight and life satisfaction. A total of 181 people with schizophrenia spectrum disorders were assessed at baseline. 130 and 110 participants were retained and completed questionnaire at 6-month and 1-year follow-up, respectively. Results showed that baseline insight was associated with lower life satisfaction at 6-month when self-stigma process or self-stigma content was high. Furthermore, baseline insight was predictive of better life satisfaction at 1-year follow-up when self-stigma process was low. Findings suggested that the detrimental effects of insight can be a result from both the presence of cognitive content and habitual process of self-stigma. Future insight promotion interventions should also address self-stigma content and process among people with schizophrenia spectrum disorders so as to maximize the beneficial effects of insight. Copyright © 2018 Elsevier B.V. All rights reserved.

Personal Perspectives on Providing Services to Foster Youth

ERIC Educational Resources Information Center

Whitman, Kenyon L.

2018-01-01

Utilizing an academic capital framework and student perspectives, this chapter provides insight into the ways that programs and services can help students develop the skills needed to succeed in college.

Some strategies to address the challenges of collecting observational data in a busy clinical environment.

PubMed

Jackson, Debra; McDonald, Glenda; Luck, Lauretta; Waine, Melissa; Wilkes, Lesley

2016-01-01

Studies drawing on observational methods can provide vital data to enhance healthcare. However, collecting observational data in clinical settings is replete with challenges, particularly where multiple data-collecting observers are used. Observers collecting data require shared understanding and training to ensure data quality, and particularly, to confirm accurate and consistent identification, discrimination and recording of data. The aim of this paper is to describe strategies for preparing and supporting multiple researchers tasked with collecting observational data in a busy, and often unpredictable, hospital environment. We hope our insights might assist future researchers undertaking research in similar settings.

Proteomic analysis of FUS interacting proteins provides insights into FUS function and its role in ALS.

PubMed

Kamelgarn, Marisa; Chen, Jing; Kuang, Lisha; Arenas, Alexandra; Zhai, Jianjun; Zhu, Haining; Gal, Jozsef

2016-10-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Mutations in the Fused in Sarcoma/Translocated in Liposarcoma (FUS/TLS) gene cause a subset of familial ALS cases and are also implicated in sporadic ALS. FUS is typically localized to the nucleus. The ALS-related FUS mutations cause cytoplasmic mis-localization and the formation of stress granule-like structures. Abnormal cytoplasmic FUS localization was also found in a subset of frontotemporal dementia (FTLD) cases without FUS mutations. To better understand the function of FUS, we performed wild-type and mutant FUS pull-downs followed by proteomic identification of the interacting proteins. The FUS interacting partners we identified are involved in multiple pathways, including chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. FUS interacted with hnRNPA1 and Matrin-3, RNA binding proteins whose mutations were also reported to cause familial ALS, suggesting that hnRNPA1 and Matrin-3 may play common pathogenic roles with FUS. The FUS interactions displayed varied RNA dependence. Numerous FUS interacting partners that we identified are components of exosomes. We found that FUS itself was present in exosomes, suggesting that the secretion of FUS might contribute to the cell-to-cell spreading of FUS pathology. FUS interacting proteins were sequestered into the cytoplasmic mutant FUS inclusions that could lead to their mis-regulation or loss of function, contributing to ALS pathogenesis. Our results provide insights into the physiological functions of FUS as well as important pathways where mutant FUS can interfere with cellular processes and potentially contribute to the pathogenesis of ALS. Copyright © 2016 Elsevier B.V. All rights reserved.

Online Patient-Provider E-cigarette Consultations: Perceptions of Safety and Harm.

PubMed

Brown-Johnson, Cati G; Burbank, Andrea; Daza, Eric J; Wassmann, Arianna; Chieng, Amy; Rutledge, Geoffrey W; Prochaska, Judith J

2016-12-01

E-cigarettes are popular and unregulated. Patient-provider communications concerning e-cigarettes were characterized to identify patient concerns, provider advice and attitudes, and research needs. An observational study of online patient-provider communications was conducted January 2011-June 2015 from a network providing free medical advice, and analyzed July 2014-May 2016. Patient and provider themes, and provider attitudes toward e-cigarettes (positive, negative, or neutral) were coded qualitatively. Provider attitudes were analyzed with cumulative logit modeling to account for clustering. Patient satisfaction with provider responses was expressed via a Thank function. An increase in e-cigarette-related questions was observed over time. Patient questions (N=512) primarily concerned specific side effects and harms (34%); general safety (27%); e-cigarettes as quit aids (19%); comparison of e-cigarette harms relative to combusted tobacco (18%); use with pre-existing medical conditions (18%); and nicotine-free e-cigarettes (14%). Half of provider responses discussed e-cigarettes as a harm reduction option (48%); 26% discussed them as quit aids. Overall, 47% of providers' responses represented a negative attitude toward e-cigarettes; 33% were neutral (contradictory or non-committal); and 20% were positive. Attitudes did not differ statistically by medical specialty; provider responses positive toward e-cigarettes received significantly more Thanks. Examination of online patient-provider communications provides insight into consumer health experience with emerging alternative tobacco products. Patient concerns largely related to harms and safety, and patients preferred provider responses positively inclined toward e-cigarettes. Lacking conclusive evidence of e-cigarette safety or efficacy, healthcare providers encouraged smoking cessation and recommended first-line cessation treatment approaches. Copyright © 2016 American Journal of Preventive Medicine. Published by

"Sniffing" Jupiter's moon Europa through ground-based IR observations

NASA Astrophysics Data System (ADS)

Paganini, Lucas; Mumma, Michael J.; Hurford, Terry; Roth, Lorenz; Villanueva, Geronimo Luis

2016-10-01

The ability to sample possible plumes from the subsurface ocean in Europa represents a major step in our search for extraterrestrial life. If plumes exist, sampling the effluent material would provide insights into their chemistry and relevant information about the prospect that life could exist, or now exists, within the ocean. Most of the difficulties in detecting plumes come from the less frequent observational coverage of Europa, which contrasts strongly with the frequent Cassini flybys of Enceladus (Spencer & Nimmo 2013). Recent observations have been taken with HST/STIS in 2014/2015, but results have shown no evident confirmation of the 2012 plume detection (Roth et al. 2014, 2015). Future in situ observations (Europa Mission) will provide definitive insights, but not before the spacecraft's arrival in ~2025, thus an interim approach is needed to inform such space mission planning and to complement existing observations at other wavelengths.In 2015, we initiated a strong campaign to build a comprehensive survey of possible plumes on Europa through high-resolution IR spectroscopy with Keck/NIRSPEC. We were awarded 10 nights out of 15 total nights available for Key Strategic Mission Support projects for the 2016A, 2016B, 2017A, and 2017B semesters under NASA time with the Keck Observatory. In 2016A, we observed Europa during 10 half-nights and will continue to do so for another 10 half-nights in 2017A. We target a serendipitous search of gaseous activity from Europa to confirm and constrain the chemical composition of possible Europan plumes that can aid the investigation of physical processes underlying (or on) its surface. Ultimately, we seek to: (1) provide information that can inform planning for NASA's Europa mission, (2) further our current understanding of Europa's gas environment, and (3) complement studies that are currently underway with other facilities (like the Hubble Space Telescope). In this presentation, we will discuss preliminary results

Transcriptome Response to Embolism Formation in Stems of Populus trichocarpa Provides Insight into Signaling and the Biology of Refilling1[W][OA

PubMed Central

Secchi, Francesca; Gilbert, Matthew E.; Zwieniecki, Maciej A.

2011-01-01

The mechanism of embolism repair in transpiring plants is still not understood, despite significant scientific effort. The refilling process is crucial to maintaining stem transport capacity and ensuring survival for plants experiencing dynamic changes in water stress. Refilling air-filled xylem vessels requires an energy and water source that can only be provided by adjacent living parenchyma cells. Here, we report an analysis of the transcriptome response of xylem parenchyma cells after embolism formation in Populus trichocarpa trees. Genes encoding aquaporins, ion transporters, and carbohydrate metabolic pathways were up-regulated, and there was a significant reduction in the expression of genes responding to oxidative stress. Thus, a novel view of the plant response to embolism emerges that suggests a role for oxygen in embolized vessels as a signal triggering xylem refilling and for the activity of cation transport as having a significant role in the generation of the energy gradient necessary to heal embolized vessels. These findings redefine current hypotheses surrounding the refilling phenomenon and provide insight into the complexity of the biological response to the seemingly simple physical event of xylem embolism formation. PMID:21951466

How to Detect Insight Moments in Problem Solving Experiments.

PubMed

Laukkonen, Ruben E; Tangen, Jason M

2018-01-01

Arguably, it is not possible to study insight moments during problem solving without being able to accurately detect when they occur (Bowden and Jung-Beeman, 2007). Despite over a century of research on the insight moment, there is surprisingly little consensus on the best way to measure them in real-time experiments. There have also been no attempts to evaluate whether the different ways of measuring insight converge. Indeed, if it turns out that the popular measures of insight diverge , then this may indicate that researchers who have used one method may have been measuring a different phenomenon to those who have used another method. We compare the strengths and weaknesses of the two most commonly cited ways of measuring insight: The feelings-of-warmth measure adapted from Metcalfe and Wiebe (1987), and the self-report measure adapted from Bowden and Jung-Beeman (2007). We find little empirical agreement between the two measures, and conclude that the self-report measure of Aha! is superior both methodologically and theoretically, and provides a better representation of what is commonly regarded as insight. We go on to describe and recommend a novel visceral measure of insight using a dynamometer as described in Creswell et al. (2016).

How to Detect Insight Moments in Problem Solving Experiments

PubMed Central

Laukkonen, Ruben E.; Tangen, Jason M.

2018-01-01

Arguably, it is not possible to study insight moments during problem solving without being able to accurately detect when they occur (Bowden and Jung-Beeman, 2007). Despite over a century of research on the insight moment, there is surprisingly little consensus on the best way to measure them in real-time experiments. There have also been no attempts to evaluate whether the different ways of measuring insight converge. Indeed, if it turns out that the popular measures of insight diverge, then this may indicate that researchers who have used one method may have been measuring a different phenomenon to those who have used another method. We compare the strengths and weaknesses of the two most commonly cited ways of measuring insight: The feelings-of-warmth measure adapted from Metcalfe and Wiebe (1987), and the self-report measure adapted from Bowden and Jung-Beeman (2007). We find little empirical agreement between the two measures, and conclude that the self-report measure of Aha! is superior both methodologically and theoretically, and provides a better representation of what is commonly regarded as insight. We go on to describe and recommend a novel visceral measure of insight using a dynamometer as described in Creswell et al. (2016). PMID:29593598

Objectively Optimized Observation Direction System Providing Situational Awareness for a Sensor Web

NASA Astrophysics Data System (ADS)

Aulov, O.; Lary, D. J.

2010-12-01

There is great utility in having a flexible and automated objective observation direction system for the decadal survey missions and beyond. Such a system allows us to optimize the observations made by suite of sensors to address specific goals from long term monitoring to rapid response. We have developed such a prototype using a network of communicating software elements to control a heterogeneous network of sensor systems, which can have multiple modes and flexible viewing geometries. Our system makes sensor systems intelligent and situationally aware. Together they form a sensor web of multiple sensors working together and capable of automated target selection, i.e. the sensors “know” where they are, what they are able to observe, what targets and with what priorities they should observe. This system is implemented in three components. The first component is a Sensor Web simulator. The Sensor Web simulator describes the capabilities and locations of each sensor as a function of time, whether they are orbital, sub-orbital, or ground based. The simulator has been implemented using AGIs Satellite Tool Kit (STK). STK makes it easy to analyze and visualize optimal solutions for complex space scenarios, and perform complex analysis of land, sea, air, space assets, and shares results in one integrated solution. The second component is target scheduler that was implemented with STK Scheduler. STK Scheduler is powered by a scheduling engine that finds better solutions in a shorter amount of time than traditional heuristic algorithms. The global search algorithm within this engine is based on neural network technology that is capable of finding solutions to larger and more complex problems and maximizing the value of limited resources. The third component is a modeling and data assimilation system. It provides situational awareness by supplying the time evolution of uncertainty and information content metrics that are used to tell us what we need to observe and the

A novel methodology providing insights into removal of biofilm-mimicking hydrogel from lateral morphological features of the root canal during irrigation procedures.

PubMed

Macedo, R G; Robinson, J P; Verhaagen, B; Walmsley, A D; Versluis, M; Cooper, P R; van der Sluis, L W M

2014-11-01

To introduce and characterize a reproducible hydrogel as a suitable biofilm mimic in endodontic research. To monitor and visualize the removal of hydrogel from a simulated lateral canal and isthmus for the following: I) Ultrasonic-Activated Irrigation (UAI) with water, ii) UAI with NaOCl and iii) NaOCl without UAI. A rheometer was used to characterize the viscoelastic properties and cohesive strength of the hydrogel for suitability as a biofilm mimic. The removal rate of the hydrogel from a simulated lateral canal or isthmus was measured by high-speed imaging operating at frame rates from 50 to 30,000 fps. The hydrogel demonstrated viscoelastic behaviour with mechanical properties comparable to real biofilms. UAI enhanced the cleaning effect of NaOCl in isthmi (P < 0.001) and both NaOCl and water in lateral canals (P < 0.001). A greater depth of cleaning was achieved from an isthmus (P = 0.009) than from a lateral canal with UAI and also at a faster rate for the first 20 s. NaOCl without UAI resulted in a greater depth of hydrogel removal from a lateral canal than an isthmus (P < 0.001). The effect of UAI was reduced when stable bubbles were formed and trapped in the lateral canal. Different removal characteristics were observed in the isthmus and the lateral canal, with initial highly unstable behaviour followed by slower viscous removal inside the isthmus. The biofilm-mimicking hydrogel is reproducible, homogenous and can be easily applied and modified. Visualization of its removal from lateral canal anatomy provides insights into the cleaning mechanisms of UAI for a biofilm-like material. Initial results showed that UAI improves hydrogel removal from the accessory canal anatomy, but the creation of stable bubbles on the hydrogel-liquid interface may reduce the cleaning rate. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Theory of mind correlates with clinical insight but not cognitive insight in patients with schizophrenia.

PubMed

Zhang, Qi; Li, Xu; Parker, Giverny J; Hong, Xiao-Hong; Wang, Yi; Lui, Simon S Y; Neumann, David L; Cheung, Eric F C; Shum, David H K; Chan, Raymond C K

2016-03-30

Research on the relationship between insight and social cognition, in particular Theory of Mind (ToM), in schizophrenia has yielded mixed findings to date. Very few studies, however, have assessed both clinical insight and cognitive insight when examining their relationships with ToM in schizophrenia. The current study thus investigated the relationship between clinical insight, cognitive insight, and ToM in a sample of 56 patients with schizophrenia and 30 healthy controls. Twenty-seven patients were classified as low in clinical insight according to their scores on the 'insight' item (G12) of the Positive and Negative Syndrome Scale (PANSS). Moreover, cognitive insight and ToM were assessed with the Beck Cognitive Insight Scale (BCIS) and the Yoni task, respectively. The results indicated that patients with poor clinical insight performed worse on tasks of second-order cognitive and affective ToM, while the ToM performance of patients with high clinical insight was equivalent to that of healthy controls. Furthermore, while clinical insight was correlated with ToM and clinical symptoms, cognitive insight did not correlate with clinical insight, ToM, or clinical symptoms. Clinical insight thus appears to be an important factor related to ToM in schizophrenia. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Creutzfeldt-Jakob disease with mixed transcortical aphasia: insights into echolalia.

PubMed

McPherson, S E; Kuratani, J D; Cummings, J L; Shih, J; Mischel, P S; Vinters, H V

1994-01-01

Aphasia is a common manifestation of Creutzfeldt-Jakob disease (CJD), and investigation of the linguistic disorders of CJD patients may provide insights into the neurobiological mechanisms of language and aphasia. We report an autopsy-confirmed case of CJD in which the presenting symptom was change in language abilities. The patient ultimately evidenced mixed transcortical aphasia (MTA) with echolalia. Disruption of frontal-subcortical circuits with environmental dependency accounts for the symptoms in MTA, including intact repetition and echolalia. Observation in this patient and a review of the literature suggest that frontal-subcortical circuit dysfunction may contribute to the syndrome of echolalia. This hypothesis offers an alternative explanation to "isolation" of the speech area as the cause of MTA.

Comparative transcriptome analysis provides insights into molecular mechanisms for parthenocarpic fruit development in eggplant (Solanum melongena L.).

PubMed

Chen, Xia; Zhang, Min; Tan, Jie; Huang, Shuping; Wang, Chunli; Zhang, Hongyuan; Tan, Taiming

2017-01-01

Genetic control of parthenocarpy, a desirable trait in edible fruit with hard seeds, has been extensively studied. However, the molecular mechanism of parthenocarpic fruit development in eggplant (Solanum melongena L.) is still unclear. To provide insights into eggplant parthenocarpy, the transcriptomic profiles of a natural parthenocarpic (PP05) and two non-parthenocarpic (PnP05 and GnP05) eggplant lines were analyzed using RNA-sequencing (RNA-seq) technology. These sequences were assembled into 38925 unigenes, of which 22683 had an annotated function and 3419 were predicted as novel genes or from alternative splicing. 4864 and 1592 unigenes that were identified as DEGs between comparison groups PP05 vs PnP05 and PP05 vs GnP05, respectively. 506 common DEGs were found contained in both comparison groups, including 258 up-regulated and 248 down-regulated genes. Functional enrichment analyses identified many common or specific biological processes and gene set potentially associated with plant development. The most pronounced findings are that differentially regulated genes potentially-related with auxin signaling between parthenocarpic and non-parthenocarpic eggplants, e.g. calcium-binding protein PBP1 and transcription factor E2FB, which mediate the auxin distribution and auxin-dependent cell division, respectively, are up-regulated in the PP05; whereas homologs of GH3.1 and AUX/IAA, which are involved in inactivation of IAA and interference of auxin signaling, respectively, are down-regulated in PP05. Furthermore, gibberellin and cytokinin signaling genes and genes related to flower development were found differentially regulated between these eggplant lines. The present study provides comprehensive transcriptomic profiles of eggplants with or without parthenocarpic capacity. The information will deepen our understanding of the molecular mechanisms of eggplant parthenocarpy. The DEGs, especially these filtered from PP05 vs PnP05 + GnP05, will be valuable for

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Networked high-speed auroral observations combined with radar measurements for multi-scale insights

NASA Astrophysics Data System (ADS)

Hirsch, M.; Semeter, J. L.

2015-12-01

Networks of ground-based instruments to study terrestrial aurora for the purpose of analyzing particle precipitation characteristics driving the aurora have been established. Additional funding is pouring into future ground-based auroral observation networks consisting of combinations of tossable, portable, and fixed installation ground-based legacy equipment. Our approach to this problem using the High Speed Tomography (HiST) system combines tightly-synchronized filtered auroral optical observations capturing temporal features of order 10 ms with supporting measurements from incoherent scatter radar (ISR). ISR provides a broader spatial context up to order 100 km laterally on one minute time scales, while our camera field of view (FOV) is chosen to be order 10 km at auroral altitudes in order to capture 100 m scale lateral auroral features. The dual-scale observations of ISR and HiST fine-scale optical observations may be coupled through a physical model using linear basis functions to estimate important ionospheric quantities such as electron number density in 3-D (time, perpendicular and parallel to the geomagnetic field).Field measurements and analysis using HiST and PFISR are presented from experiments conducted at the Poker Flat Research Range in central Alaska. Other multiscale configuration candidates include supplementing networks of all-sky cameras such as THEMIS with co-locations of HiST-like instruments to fuse wide FOV measurements with the fine-scale HiST precipitation characteristic estimates. Candidate models for this coupling include GLOW and TRANSCAR. Future extensions of this work may include incorporating line of sight total electron count estimates from ground-based networks of GPS receivers in a sensor fusion problem.

Ozone process insights from field experiments - part I: overview

NASA Astrophysics Data System (ADS)

Hidy, G. M.

This paper gives an overview of selected approaches recently adopted to analyze observations from field experiments that characterize the tropospheric physics and chemistry of ozone and related oxidation products. Analysis of ambient oxidant and precursor concentration measurements, combined with meteorological observations, has provided important information about tropospheric processes. Projection of the response of tropospheric ozone concentrations to changes in precursor emissions is achieved through emissions based air quality models (AQMs). These models integrate several "process" elements from source emissions to meteorological and chemical phenomena. Through field campaigns, new knowledge has become available which has enabled workers to better understand the strengths and weaknesses of AQMs and their components. Examples of insightful results include: (a) reconciliation of ambient concentrations of speciated volatile organic compounds (VOCs) with estimates from emissions models, and inventories, (b) verification of chemical mechanisms for ozone formation from its precursors using approximations applicable in different chemical regimes, (c) inference of regimes of sensitivity in ozone concentration to changes in VOC and NO x precursors from ozone management practices, (d) conceptualization of important air mass transport and mixing processes on different spatial and temporal scales that affect ozone and precursor concentrations distributions, and (e) application of the analysis of spatial and temporal variance to infer the origins of chemical product transport, and precursor distributions. Studies from the first category have been used to improve emissions models substantially over previous forms. The remainder of the analyses has yielded valuable insight into the chemical and meteorological mechanisms at work on different spatial and temporal scales. The methods have provided an observationally based framework for effective choices to improve ozone

The North American light rail experience : insights for Hamilton.

DOT National Transportation Integrated Search

2012-04-01

This report provides a high level overview of the North American Light Rail Experience with the goal of : providing insights for Hamilton, Ontario. Light rail transit (LRT) is a term that emerged at the : Transportation Research Boards first confe...

Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification

PubMed Central

Caetano-Anollés, Gustavo

2013-01-01

Reconstructing the evolutionary history of modern species is a difficult problem complicated by the conceptual and technical limitations of phylogenetic tree building methods. Here, we propose a comparative proteomic and functionomic inferential framework for genome evolution that allows resolving the tripartite division of cells and sketching their history. Evolutionary inferences were derived from the spread of conserved molecular features, such as molecular structures and functions, in the proteomes and functionomes of contemporary organisms. Patterns of use and reuse of these traits yielded significant insights into the origins of cellular diversification. Results uncovered an unprecedented strong evolutionary association between Bacteria and Eukarya while revealing marked evolutionary reductive tendencies in the archaeal genomic repertoires. The effects of nonvertical evolutionary processes (e.g., HGT, convergent evolution) were found to be limited while reductive evolution and molecular innovation appeared to be prevalent during the evolution of cells. Our study revealed a strong vertical trace in the history of proteins and associated molecular functions, which was reliably recovered using the comparative genomics approach. The trace supported the existence of a stem line of descent and the very early appearance of Archaea as a diversified superkingdom, but failed to uncover a hidden canonical pattern in which Bacteria was the first superkingdom to deploy superkingdom-specific structures and functions. PMID:24492748

Dynamic morphology of gas hydrate on a methane bubble in water: Observations and new insights for hydrate film models

NASA Astrophysics Data System (ADS)

Warzinski, Robert P.; Lynn, Ronald; Haljasmaa, Igor; Leifer, Ira; Shaffer, Frank; Anderson, Brian J.; Levine, Jonathan S.

2014-10-01

Predicting the fate of subsea hydrocarbon gases escaping into seawater is complicated by potential formation of hydrate on rising bubbles that can enhance their survival in the water column, allowing gas to reach shallower depths and the atmosphere. The precise nature and influence of hydrate coatings on bubble hydrodynamics and dissolution is largely unknown. Here we present high-definition, experimental observations of complex surficial mechanisms governing methane bubble hydrate formation and dissociation during transit of a simulated oceanic water column that reveal a temporal progression of deep-sea controlling mechanisms. Synergistic feedbacks between bubble hydrodynamics, hydrate morphology, and coverage characteristics were discovered. Morphological changes on the bubble surface appear analogous to macroscale, sea ice processes, presenting new mechanistic insights. An inverse linear relationship between hydrate coverage and bubble dissolution rate is indicated. Understanding and incorporating these phenomena into bubble and bubble plume models will be necessary to accurately predict global greenhouse gas budgets for warming ocean scenarios and hydrocarbon transport from anthropogenic or natural deep-sea eruptions.

Observer Comments Provided at the Peer Consultation Workshop (Appendix E)

EPA Pesticide Factsheets

The peer consultation workshop included three observer comment periods, one on the first day of the workshop and two on the second day of the workshop. This appendix includes verbatim transcripts (to the extent that specific remarks were audible from recordings) of the observer comments, in the order the comments were given.

Insight in first-episode psychosis.

PubMed

McEvoy, Joseph P; Johnson, Jackie; Perkins, Diana; Lieberman, Jeffrey A; Hamer, Robert M; Keefe, Richard S E; Tohen, Mauricio; Glick, Ira D; Sharma, Tonmoy

2006-10-01

We report here a study examining the relationships between insight and psychopathology, cognitive performance, brain volume and co-morbid depression in 251 patients experiencing a first episode of psychosis, who were then randomly assigned to 2 years of double-blind treatment with either olanzapine or haloperidol. Repeated measures of insight were obtained at baseline and 12, 24, 52 and 104 weeks by the Insight and Treatment Attitudes Questionnaire (ITAQ). Older age, female gender and white ethnicity were associated with more insight. Higher total, positive, negative and general psychopathology scores on the Positive and Negative Syndromes Scale (PANSS) were associated with less insight. Higher depression scores were associated with more insight. Better neurocognitive function and large brain volumes were associated with more insight. More insight throughout the study was associated with longer time to medication non-adherence. However, baseline insight was not significantly related to the probability of discontinuing the study before 2 years. Insight improved significantly over the course of the study, but the improvement in insight was not significantly different between the two antipsychotic treatment groups. Multiple factors contribute to insight. Patients experiencing a first episode of psychosis who have little insight are at increased risk of discontinuing their medication.

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

DOE PAGES

Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko; ...

2014-12-04

Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on freshcut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genesmore » involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.« less

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

PubMed Central

Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Suzuki, Hitoshi; Master, Emma; Ferreira, Patricia; Ruiz-Dueñas, Francisco J.; Held, Benjamin; Canessa, Paulo; Larrondo, Luis F.; Schmoll, Monika; Druzhinina, Irina S.; Kubicek, Christian P.; Gaskell, Jill A.; Kersten, Phil; St. John, Franz; Glasner, Jeremy; Sabat, Grzegorz; Splinter BonDurant, Sandra; Syed, Khajamohiddin; Yadav, Jagjit; Mgbeahuruike, Anthony C.; Kovalchuk, Andriy; Asiegbu, Fred O.; Lackner, Gerald; Hoffmeister, Dirk; Rencoret, Jorge; Gutiérrez, Ana; Sun, Hui; Lindquist, Erika; Barry, Kerrie; Riley, Robert; Grigoriev, Igor V.; Henrissat, Bernard; Kües, Ursula; Berka, Randy M.; Martínez, Angel T.; Covert, Sarah F.; Blanchette, Robert A.; Cullen, Daniel

2014-01-01

Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes. PMID:25474575

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko

Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on freshcut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genesmore » involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.« less

General College: Provider of Social Services.

ERIC Educational Resources Information Center

Hixson, Bruce, Ed.

1981-01-01

Three programs in the General College of the University of Minnesota that provide direct social services as well as education to special populations are described: The INSIGHT Program available at Stillwater State Prison; and the Upward Bound and University Day Community programs both offered on the Minneapolis campus. According to Daniel F.…

Comparisons of aerosol optical depth provided by seviri satellite observations and CAMx air quality modelling

NASA Astrophysics Data System (ADS)

Fernandes, A.; Riffler, M.; Ferreira, J.; Wunderle, S.; Borrego, C.; Tchepel, O.

2015-04-01

Satellite data provide high spatial coverage and characterization of atmospheric components for vertical column. Additionally, the use of air pollution modelling in combination with satellite data opens the challenging perspective to analyse the contribution of different pollution sources and transport processes. The main objective of this work is to study the AOD over Portugal using satellite observations in combination with air pollution modelling. For this purpose, satellite data provided by Spinning Enhanced Visible and Infra-Red Imager (SEVIRI) on-board the geostationary Meteosat-9 satellite on AOD at 550 nm and modelling results from the Chemical Transport Model (CAMx - Comprehensive Air quality Model) were analysed. The study period was May 2011 and the aim was to analyse the spatial variations of AOD over Portugal. In this study, a multi-temporal technique to retrieve AOD over land from SEVIRI was used. The proposed method takes advantage of SEVIRI's high temporal resolution of 15 minutes and high spatial resolution. CAMx provides the size distribution of each aerosol constituent among a number of fixed size sections. For post processing, CAMx output species per size bin have been grouped into total particulate sulphate (PSO4), total primary and secondary organic aerosols (POA + SOA), total primary elemental carbon (PEC) and primary inert material per size bin (CRST1 to CRST_4) to be used in AOD quantification. The AOD was calculated by integration of aerosol extinction coefficient (Qext) on the vertical column. The results were analysed in terms of temporal and spatial variations. The analysis points out that the implemented methodology provides a good spatial agreement between modelling results and satellite observation for dust outbreak studied (10th -17th of May 2011). A correlation coefficient of r=0.79 was found between the two datasets. This work provides relevant background to start the integration of these two different types of the data in order

Interferometric observations of large biologically interesting interstellar and cometary molecules

PubMed Central

Snyder, Lewis E.

2006-01-01

Interferometric observations of high-mass regions in interstellar molecular clouds have revealed hot molecular cores that have substantial column densities of large, partly hydrogen-saturated molecules. Many of these molecules are of interest to biology and thus are labeled “biomolecules.” Because the clouds containing these molecules provide the material for star formation, they may provide insight into presolar nebular chemistry, and the biomolecules may provide information about the potential of the associated interstellar chemistry for seeding newly formed planets with prebiotic organic chemistry. In this overview, events are outlined that led to the current interferometric array observations. Clues that connect this interstellar hot core chemistry to the solar system can be found in the cometary detection of methyl formate and the interferometric maps of cometary methanol. Major obstacles to understanding hot core chemistry remain because chemical models are not well developed and interferometric observations have not been very sensitive. Differentiation in the molecular isomers glycolaldehdye, methyl formate, and acetic acid has been observed, but not explained. The extended source structure for certain sugars, aldehydes, and alcohols may require nonthermal formation mechanisms such as shock heating of grains. Major advances in understanding the formation chemistry of hot core species can come from observations with the next generation of sensitive, high-resolution arrays. PMID:16894168

Insight Is Not in the Problem: Investigating Insight in Problem Solving across Task Types.

PubMed

Webb, Margaret E; Little, Daniel R; Cropper, Simon J

2016-01-01

The feeling of insight in problem solving is typically associated with the sudden realization of a solution that appears obviously correct (Kounios et al., 2006). Salvi et al. (2016) found that a solution accompanied with sudden insight is more likely to be correct than a problem solved through conscious and incremental steps. However, Metcalfe (1986) indicated that participants would often present an inelegant but plausible (wrong) answer as correct with a high feeling of warmth (a subjective measure of closeness to solution). This discrepancy may be due to the use of different tasks or due to different methods in the measurement of insight (i.e., using a binary vs. continuous scale). In three experiments, we investigated both findings, using many different problem tasks (e.g., Compound Remote Associates, so-called classic insight problems, and non-insight problems). Participants rated insight-related affect (feelings of Aha-experience, confidence, surprise, impasse, and pleasure) on continuous scales. As expected we found that, for problems designed to elicit insight, correct solutions elicited higher proportions of reported insight in the solution compared to non-insight solutions; further, correct solutions elicited stronger feelings of insight compared to incorrect solutions.

Insight Is Not in the Problem: Investigating Insight in Problem Solving across Task Types

PubMed Central

Webb, Margaret E.; Little, Daniel R.; Cropper, Simon J.

2016-01-01

The feeling of insight in problem solving is typically associated with the sudden realization of a solution that appears obviously correct (Kounios et al., 2006). Salvi et al. (2016) found that a solution accompanied with sudden insight is more likely to be correct than a problem solved through conscious and incremental steps. However, Metcalfe (1986) indicated that participants would often present an inelegant but plausible (wrong) answer as correct with a high feeling of warmth (a subjective measure of closeness to solution). This discrepancy may be due to the use of different tasks or due to different methods in the measurement of insight (i.e., using a binary vs. continuous scale). In three experiments, we investigated both findings, using many different problem tasks (e.g., Compound Remote Associates, so-called classic insight problems, and non-insight problems). Participants rated insight-related affect (feelings of Aha-experience, confidence, surprise, impasse, and pleasure) on continuous scales. As expected we found that, for problems designed to elicit insight, correct solutions elicited higher proportions of reported insight in the solution compared to non-insight solutions; further, correct solutions elicited stronger feelings of insight compared to incorrect solutions. PMID:27725805

Combined Radio and Space-Based Solar Observations: From Techniques to New Results - Preface

NASA Astrophysics Data System (ADS)

Kontar, Eduard P.; Nindos, Alexander

2018-06-01

The phenomena observed at the Sun have a variety of unique radio signatures that can be used to diagnose the processes in the solar atmosphere. The insights provided by radio observations are further enhanced when they are combined with observations from space-based telescopes. This Topical collection demonstrates the power of combination methodology at work and provides new results on i) type I solar radio bursts and thermal emission to study active regions; ii) type II and IV bursts to better understand the structure of coronal mass ejections; and iii) non-thermal gyro-synchrotron and/or type III bursts to improve the characterisation of particle acceleration in solar flares. The ongoing improvements in time, frequency, and spatial resolutions of ground-based telescopes reveal new levels in the complexity of solar phenomena and pose new questions.

Affording shared responsibility for universal coverage: insights from California.

PubMed

Curtis, Rick; Neuschler, Ed

2009-01-01

This paper presents key insights from California's recent experience in developing a plan for universal health coverage with "shared responsibility" among individuals, employers, and governments. A major challenge was finding an acceptable balance among the goals of affordability, equity, and cost to the state. Although reform did not pass, the state's approach-particularly differences from Massachusetts regarding modest-income workers and related employer and public roles-provides important insights for federal reform.

Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases.

PubMed

Chiti, Fabrizio; Calamai, Martino; Taddei, Niccolo; Stefani, Massimo; Ramponi, Giampietro; Dobson, Christopher M

2002-12-10

Protein aggregation and the formation of highly insoluble amyloid structures is associated with a range of debilitating human conditions, which include Alzheimer's disease, Parkinson's disease, and the Creutzfeldt-Jakob disease. Muscle acylphosphatase (AcP) has already provided significant insights into mutational changes that modulate amyloid formation. In the present paper, we have used this system to investigate the effects of mutations that modify the charge state of a protein without affecting significantly the hydrophobicity or secondary structural propensities of the polypeptide chain. A highly significant inverse correlation was found to exist between the rates of aggregation of the protein variants under denaturing conditions and their overall net charge. This result indicates that aggregation is generally favored by mutations that bring the net charge of the protein closer to neutrality. In light of this finding, we have analyzed natural mutations associated with familial forms of amyloid diseases that involve alteration of the net charge of the proteins or protein fragments associated with the diseases. Sixteen mutations have been identified for which the mechanism of action that causes the pathological condition is not yet known or fully understood. Remarkably, 14 of these 16 mutations cause the net charge of the corresponding peptide or protein that converts into amyloid deposits to be reduced. This result suggests that charge has been a key parameter in molecular evolution to ensure the avoidance of protein aggregation and identifies reduction of the net charge as an important determinant in at least some forms of protein deposition diseases.

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

PubMed Central

Vital, Marius; Chai, Benli; Østman, Bjørn; Cole, James; Konstantinidis, Konstantinos T; Tiedje, James M

2015-01-01

Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species. PMID:25343512

Growth plate expression profiling: Large and small breed dogs provide new insights in endochondral bone formation.

PubMed

Teunissen, Michelle; Riemers, Frank M; van Leenen, Dik; Groot Koerkamp, Marian J A; Meij, Björn P; Alblas, Jacqueline; Penning, Louis C; Miranda-Bedate, Alberto; Tryfonidou, Marianna A

2018-01-01

The difference in the adult height of mammals, and hence in endochondral bone formation, is not yet fully understood and may serve to identify targets for bone and cartilage regeneration. In line with this hypothesis, the intra-species disparity between the adult height of Great Danes and Miniature Poodles was investigated at a transcriptional level. Microarray analysis of the growth plate of five Great Danes and five Miniature Poodles revealed 2,981 unique genes that were differentially expressed, including many genes with an unknown role in skeletal development. A signaling pathway impact analysis indicated activation of the cell cycle, extracellular matrix receptor interaction and the tight junction pathway, and inhibition of pathways associated with inflammation and the complement cascade. In additional validation steps, the gene expression profile of the separate growth plate zones for both dog breeds were determined. Given that the BMP signaling is known for its crucial role in skeletal development and fracture healing, and BMP-2 is used in orthopaedic and spine procedures for bone augmentation, further investigations concentrated on the BMP pathway.The canonical BMP-2 and BMP-6 signaling pathway was activated in the Great Danes compared to Miniature Poodles. In conclusion, investigating the differential expression of genes involved in endochondral bone formation in small and large breed dogs, could be a game changing strategy to provide new insights in growth plate development and identify new targets for bone and cartilage regeneration. © 2017 The Authors. Journal of Orthopaedic Research® published by Wiley Periodicals, Inc. on behalf of the Orthopaedic Research Society. J Orthop Res 36:138-148, 2018. © 2017 The Authors. Journal of Orthopaedic Research® Published by Wiley Periodicals Inc. on behalf of the Orthopaedic Research Society.

Learning-by-Doing in Transnational Operations Networks: Insights from Economic Geography

ERIC Educational Resources Information Center

Spring, Martin

2006-01-01

Purpose: The purpose of this paper is to explore how insights from economic geography, which are typically explanatory or directed at policy prescription, might be utilized to provide managerial insight at firm level into the processes of and conditions for tacit knowledge transfer. Design/methodology/approach: This is a theoretical paper. The…

Cognitive insight in schizophrenia patients and their biological parents: a pilot study.

PubMed

Raffard, Stéphane; Bortolon, Catherine; Macgregor, Alexandra; Norton, Joanna; Boulenger, Jean-Philippe; El Haj, Mohamad; Capdevielle, Delphine

2014-11-01

Clinical insight in schizophrenia patients is partly associated with familial environment but has been poorly studied to date. We aimed to explore (1) the relationship between parents' cognitive insight and their offspring's; (2) the relationship between parents' cognitive insight and their clinical insight into the disease of their offspring; and (3) the clinical and cognitive determinants of cognitive insight in parents. Cognitive insight was assessed in 37 patient-biological parent pairs/dyads with the Beck Cognitive Insight Scale (BCIS). Other measures included the Scale to assess Unawareness of Mental Disorder and cognitive assessments. We found no significant association between parents' cognitive insight and their offspring's. Conversely, a positive association between parents' cognitive insight and parents' insight into their offspring's symptoms was found. Better awareness of their offspring's specific symptoms was associated with lower levels of overconfidence in one's beliefs and with BCIS total score. BCIS Self-Certainty and BCIS total score were associated with better executive functioning and verbal comprehension. Better insight into their offspring's symptoms is associated with cognitive insight in biological parents of schizophrenia patients. Our results support the integration of cognitive intervention targeting parents' cognitive flexibility in family psychoeducational programs and provide an important first step towards developing a more refined understanding of the factors involved in insight into symptoms of illness in parents of schizophrenia patients. Copyright © 2014 Elsevier B.V. All rights reserved.

Regional Homogeneity Predicts Creative Insight: A Resting-State fMRI Study.

PubMed

Lin, Jiabao; Cui, Xuan; Dai, Xiaoying; Mo, Lei

2018-01-01

Creative insight plays an important role in our daily life. Previous studies have investigated the neural correlates of creative insight by functional magnetic resonance imaging (fMRI), however, the intrinsic resting-state brain activity associated with creative insight is still unclear. In the present study, we used regional homogeneity (ReHo) as an index in resting-state fMRI (rs-fMRI) to identify brain regions involved in individual differences in creative insight, which was compued by the response time (RT) of creative Chinese character chunk decomposition. The findings indicated that ReHo in the anterior cingulate cortex (ACC)/caudate nucleus (CN) and angular gyrus (AG)/superior temporal gyrus (STG)/inferior parietal lobe (IPL) negatively predicted creative insight. Furthermore, these findings suggested that spontaneous brain activity in multiple regions related to breaking and establishing mental sets, goal-directed solutions exploring, shifting attention, forming new associations and emotion experience contributes to creative insight. In conclusion, the present study provides new evidence to further understand the cognitive processing and neural correlates of creative insight.

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function.

PubMed

Gupta, Payal; Dash, Prasanta K

2017-09-11

Secretory phospholipase A 2 (sPLA 2 ) are low molecular weight proteins (12-18 kDa) involved in a suite of plant cellular processes imparting growth and development. With myriad roles in physiological and biochemical processes in plants, detailed analysis of sPLA 2 in flax/linseed is meagre. The present work, first in flax, embodies cloning, expression, purification and molecular characterisation of two distinct sPLA 2 s (I and II) from flax. PLA 2 activity of the cloned sPLA 2 s were biochemically assayed authenticating them as bona fide phospholipase A 2 . Physiochemical properties of both the sPLA 2 s revealed they are thermostable proteins requiring di-valent cations for optimum activity.While, structural analysis of both the proteins revealed deviations in the amino acid sequence at C- & N-terminal regions; hydropathic study revealed LusPLA 2 I as a hydrophobic protein and LusPLA 2 II as a hydrophilic protein. Structural analysis of flax sPLA 2 s revealed that secondary structure of both the proteins are dominated by α-helix followed by random coils. Modular superimposition of LusPLA 2 isoforms with rice sPLA 2 confirmed monomeric structural preservation among plant phospholipase A 2 and provided insight into structure of folded flax sPLA 2 s.

The effects of gender and self-insight on early semantic processing.

PubMed

Xu, Xu; Kang, Chunyan; Guo, Taomei

2014-01-01

This event-related potential (ERP) study explored individual differences associated with gender and level of self-insight in early semantic processing. Forty-eight Chinese native speakers completed a semantic judgment task with three different categories of words: abstract neutral words (e.g., logic, effect), concrete neutral words (e.g., teapot, table), and emotion words (e.g., despair, guilt). They then assessed their levels of self-insight. Results showed that women engaged in greater processing than did men. Gender differences also manifested in the relationship between level of self-insight and word processing. For women, level of self-insight was associated with level of semantic activation for emotion words and abstract neutral words, but not for concrete neutral words. For men, level of self-insight was related to processing speed, particularly in response to abstract and concrete neutral words. These findings provide electrophysiological evidence for the effects of gender and self-insight on semantic processing and highlight the need to take into consideration subject variables in related research.

Pediatric Provider Insight Into Newborn Screening for Glucose-6-Phosphate Dehydrogenase Deficiency.

PubMed

Bernardo, Janine; Nock, Mary

2015-06-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a major contributor to neonatal hyperbilirubinemia, yet newborn screening for this disorder in the United States is not standard practice. We surveyed pediatric providers regarding a novel newborn G6PD screening program successfully implemented in 2007 at a US urban women's hospital newborn nursery. An electronic survey was distributed to 472 pediatric providers addressing extent to which they were influenced by the screening program. Ninety-two (20%) providers responded, of whom 74 (80%) had taken care of G6PD-deficient patients diagnosed by the screening program. A majority found the diagnosis helpful for patient management and influential in their management. Most common changes in management included more counseling on jaundice and follow-up and avoidance of hemolytic crisis triggers. General pediatric providers support newborn G6PD screening and appreciate the current program. Knowing the G6PD deficiency status of newborns informed and influenced pediatric providers' care. © The Author(s) 2014.

Theoretical Insight into Shocked Gases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leiding, Jeffery Allen

2016-09-29

I present the results of statistical mechanical calculations on shocked molecular gases. This work provides insight into the general behavior of shock Hugoniots of gas phase molecular targets with varying initial pressures. The dissociation behavior of the molecules is emphasized. Impedance matching calculations are performed to determine the maximum degree of dissociation accessible for a given flyer velocity as a function of initial gas pressure.

Bolide Airbursts as a Seismic Source for the 2018 Mars InSight Mission

NASA Astrophysics Data System (ADS)

Stevanović, J.; Teanby, N. A.; Wookey, J.; Selby, N.; Daubar, I. J.; Vaubaillon, J.; Garcia, R.

2017-10-01

In 2018, NASA will launch InSight, a single-station suite of geophysical instruments, designed to characterise the martian interior. We investigate the seismo-acoustic signal generated by a bolide entering the martian atmosphere and exploding in a terminal airburst, and assess this phenomenon as a potential observable for the SEIS seismic payload. Terrestrial analogue data from four recent events are used to identify diagnostic airburst characteristics in both the time and frequency domain. In order to estimate a potential number of detectable events for InSight, we first model the impactor source population from observations made on the Earth, scaled for planetary radius, entry velocity and source density. We go on to calculate a range of potential airbursts from the larger incident impactor population. We estimate there to be {˜} 1000 events of this nature per year on Mars. To then derive a detectable number of airbursts for InSight, we scale this number according to atmospheric attenuation, air-to-ground coupling inefficiencies and by instrument capability for SEIS. We predict between 10-200 detectable events per year for InSight.

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Stu Spath, InSight program manager, Lockheed Martin Space, left, and Tom Hoffman, InSight project manager, NASA JPL, discuss NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Insight and illness perception in Mexican patients with psychosis.

PubMed

Gómez-de-Regil, Lizzette

2015-03-01

Insight and illness perception are two concepts of interest in the study of factors related to clinical outcome in patients with psychosis. Insight implies a risk of emotional distress for the patient. Illness perceptions, regardless of their accuracy, might be favorable or not to illness. Literature provides evidence of significant correlates of these factors with clinical outcome, but they are rarely included in a single study. 1) assessing insight and illness perception in a sample of Mexican patients who have experienced psychosis and, 2) analyzing how insight and illness perception relate to each other and how they relate to clinical status (i.e., positive, negative, and general psychopathology, depression, and anxiety). Sixty-one participants (55.7% females) were recruited from a public psychiatric hospital; insight and illness perceptions were assessed with the SUMD and the Brief-IPQ, respectively. Clinical status was assessed with the PANSS, CDS and BAI scales. Participants showed good insight, favorable illness perceptions for the cognitive and comprehension dimensions, but unfavorable for the emotional dimension. Clinical status of sample was characterized by mild symptoms. Poor insight related to positive symptoms and general psychopathology. Cognitive and emotional perceptions of illness were significantly associated to most clinical status parameters, whereas comprehension showed no significant results. The study not only replicates the significant association on insight and illness perception with clinical outcome, but shows how their patterns of interactions are different, reinforcing the idea that they are two distinct factors worthy of being habitually acknowledged in research and clinical practice.

Insight Problem Solving: A Critical Examination of the Possibility of Formal Theory

ERIC Educational Resources Information Center

Batchelder, William H.; Alexander, Gregory E.

2012-01-01

This paper provides a critical examination of the current state and future possibility of formal cognitive theory for insight problem solving and its associated "aha!" experience. Insight problems are contrasted with move problems, which have been formally defined and studied extensively by cognitive psychologists since the pioneering…

Stellar Rotation: New Insight from CoRoT

NASA Astrophysics Data System (ADS)

Catala, C.; Goupil, M. J.; Michel, E.; Baglin, A.; de Medeiros, J. Renan; Gondoin, Ph.

2009-02-01

We present an overview of the new insight provided by the CoRoT satellite on stellar rotation. Thanks to its ultra-high precision, high duty cycle, long photometric monitoring of thousands of stars, CoRoT gives us a powerful tool to study stellar rotational modulation, and therefore to measure stellar rotational periods and to study active structures at the surface of stars. This paper presents preliminary results concerning this type of study. CoRoT will also provide us with an insight of internal stellar rotation via the measurement and exploitation of rotational splittings of oscillation modes. This approach to stellar rotation with CoRoT will require a careful analysis of the oscillation power spectra, which is in progress, but prospects for such measurements are presented.

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

PubMed

Moazzzam Jazi, Maryam; Seyedi, Seyed Mahdi; Ebrahimie, Esmaeil; Ebrahimi, Mansour; De Moro, Gianluca; Botanga, Christopher

2017-08-17

of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.

Animal NLRs provide structural insights into plant NLR function.

PubMed

Bentham, Adam; Burdett, Hayden; Anderson, Peter A; Williams, Simon J; Kobe, Bostjan

2017-03-01

The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa. This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation. Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and

Developmental Social Cognitive Neuroscience: Insights from Deafness

ERIC Educational Resources Information Center

Corina, David; Singleton, Jenny

2009-01-01

The condition of deafness presents a developmental context that provides insight into the biological, cultural, and linguistic factors underlying the development of neural systems that impact social cognition. Studies of visual attention, behavioral regulation, language development, and face and human action perception are discussed. Visually…

Metabolomic Analysis Provides Insights on Paraquat-Induced Parkinson-Like Symptoms in Drosophila melanogaster.

PubMed

Shukla, Arvind Kumar; Ratnasekhar, Ch; Pragya, Prakash; Chaouhan, Hitesh Singh; Patel, Devendra Kumar; Chowdhuri, Debapratim Kar; Mudiam, Mohana Krishna Reddy

2016-01-01

Paraquat (PQ) exposure causes degeneration of the dopaminergic neurons in an exposed organism while altered metabolism has a role in various neurodegenerative disorders. Therefore, the study presented here was conceived to depict the role of altered metabolism in PQ-induced Parkinson-like symptoms and to explore Drosophila as a potential model organism for such studies. Metabolic profile was generated in control and in flies that were fed PQ (5, 10, and 20 mM) in the diet for 12 and 24 h concurrent with assessment of indices of oxidative stress, dopaminergic neurodegeneration, and behavioral alteration. PQ was found to significantly alter 24 metabolites belonging to different biological pathways along with significant alterations in the above indices. In addition, PQ attenuated brain dopamine content in the exposed organism. The study demonstrates that PQ-induced alteration in the metabolites leads to oxidative stress and neurodegeneration in the exposed organism along with movement disorder, a phenotype typical of Parkinson-like symptoms. The study is relevant in the context of Drosophila and humans because similar alteration in the metabolic pathways has been observed in both PQ-exposed Drosophila and in postmortem samples of patients with Parkinsonism. Furthermore, this study provides advocacy towards the applicability of Drosophila as an alternate model organism for pre-screening of environmental chemicals for their neurodegenerative potential with altered metabolism.

Understanding ecosystem services provided by rice fields

USDA-ARS?s Scientific Manuscript database

While the concept of ecosystem services is not new, there is revived interest in how these services should be measured, monitored, and valued. Focused research over the last four years has provided insight into the mitigation capabilities of rice fields in the lower Mississippi River Valley of the ...

Quality of pharmaceutical care at the pharmacy counter: patients' experiences versus video observation.

PubMed

Koster, Ellen S; Blom, Lyda; Overbeeke, Marloes R; Philbert, Daphne; Vervloet, Marcia; Koopman, Laura; van Dijk, Liset

2016-01-01

Consumer Quality Index questionnaires are used to assess quality of care from patients' experiences. To provide insight into the agreement about quality of pharmaceutical care, measured both by a patient questionnaire and video observations. Pharmaceutical encounters in four pharmacies were video-recorded. Patients completed a questionnaire based upon the Consumer Quality Index Pharmaceutical Care after the encounter containing questions about patients' experiences regarding information provision, medication counseling, and pharmacy staff's communication style. An observation protocol was used to code the recorded encounters. Agreement between video observation and patients' experiences was calculated. In total, 109 encounters were included for analysis. For the domains "medication counseling" and "communication style", agreement between patients' experiences and observations was very high (>90%). Less agreement (45%) was found for "information provision", which was rated more positive by patients compared to the observations, especially for the topic, encouragement of patients' questioning behavior. A questionnaire is useful to assess the quality of medication counseling and pharmacy staff's communication style, but might be less suitable to evaluate information provision and pharmacy staff's encouragement of patients' questioning behavior. Although patients may believe that they have received all necessary information to use their new medicine, some information on specific instructions was not addressed during the encounter. When using questionnaires to get insight into information provision, observations of encounters are very informative to validate the patient questionnaires and make necessary adjustments.

Promoting compliance: the patient-provider partnership.

PubMed

Wilson, B M

1995-07-01

Compliance has been defined traditionally in terms of how well a patient follows through with the recommendations of a health care provider. Patient education has often consisted of a one-way communication of provider to patient. This article advocates a multifaceted approach to compliance issues in which patients and health care providers set mutually agreed upon treatment goals. These goals must be consistent with patients' priorities and lifestyles. Patient compliance issues are examined in the context of three theoretical frameworks: (1) the Health-Belief Model, (2) Locus of Control Theory, and (3) Piaget's Theory of Cognitive Development. The insights gained from these models are then used to provide practical suggestions for enhancing compliance.

Experimental Observation and Theoretical Description of Multisoliton Fission in Shallow Water

NASA Astrophysics Data System (ADS)

Trillo, S.; Deng, G.; Biondini, G.; Klein, M.; Clauss, G. F.; Chabchoub, A.; Onorato, M.

2016-09-01

We observe the dispersive breaking of cosine-type long waves [Phys. Rev. Lett. 15, 240 (1965)] in shallow water, characterizing the highly nonlinear "multisoliton" fission over variable conditions. We provide new insight into the interpretation of the results by analyzing the data in terms of the periodic inverse scattering transform for the Korteweg-de Vries equation. In a wide range of dispersion and nonlinearity, the data compare favorably with our analytical estimate, based on a rigorous WKB approach, of the number of emerging solitons. We are also able to observe experimentally the universal Fermi-Pasta-Ulam recurrence in the regime of moderately weak dispersion.

Genomics and Comparative Genomic Analyses Provide Insight into the Taxonomy and Pathogenic Potential of Novel Emmonsia Pathogens.

PubMed

Yang, Ying; Ye, Qiang; Li, Kang; Li, Zongwei; Bo, Xiaochen; Li, Zhen; Xu, Yingchun; Wang, Shengqi; Wang, Peng; Chen, Huipeng; Wang, Junzhi

2017-01-01

physiological adaptations of new Emmonsia , but this question warrants further investigation. Overall, our analyses provide a framework from which to further study the evolutionary dynamics of Emmonsia strains and identity the underlying molecular mechanisms that determine the infectious and pathogenic potency of these fungal pathogens, and also provide insight into potential targets for therapeutic intervention of emmonsiosis and further research.

50 CFR 679.52 - Observer provider permitting and responsibilities.

Code of Federal Regulations, 2014 CFR

2014-10-01

... samples from the observer's deployment by the completion of the electronic vessel and/or processor survey(s); (ii) Complete NMFS electronic vessel and/or processor surveys before performing other jobs or... or experimental fishing as defined in § 600.10 of this chapter. (2) Must not have a direct financial...

50 CFR 679.52 - Observer provider permitting and responsibilities.

Code of Federal Regulations, 2013 CFR

2013-10-01

... samples from the observer's deployment by the completion of the electronic vessel and/or processor survey(s); (ii) Complete NMFS electronic vessel and/or processor surveys before performing other jobs or... or experimental fishing as defined in § 600.10 of this chapter. (2) Must not have a direct financial...

Insights into Modern Human Prehistory Using Ancient Genomes.

PubMed

Yang, Melinda A; Fu, Qiaomei

2018-03-01

The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

Leveraging Human Insights by Combining Multi-Objective Optimization with Interactive Evolution

DTIC Science & Technology

2015-03-26

application, a program that used human selections to guide the evolution of insect -like images. He was able to demonstrate that humans provide key insights...LEVERAGING HUMAN INSIGHTS BY COMBINING MULTI-OBJECTIVE OPTIMIZATION WITH INTERACTIVE EVOLUTION THESIS Joshua R. Christman, Second Lieutenant, USAF...COMBINING MULTI-OBJECTIVE OPTIMIZATION WITH INTERACTIVE EVOLUTION THESIS Presented to the Faculty Department of Electrical and Computer Engineering

[Lack of insight in schizophrenia: a review].

PubMed

Raffard, S; Bayard, S; Capdevielle, D; Garcia, F; Boulenger, J-P; Gely-Nargeot, M-C

2008-10-01

appear related to the severity of symptomatology or to the emotional state of the patients argue against this hypothesis. Conversely, a considerable body of literature emphasized how unawareness may result from cognitive deficits. Research in neuropsychology and cognitive psychology has provided consistent results concerning the link between deficit in executive functions, frontal lobe dysfunction and poor insight. Recent studies on bias in cognitive information treatment and social cognition theories currently open new prospects.

Population genomics provide insights into the evolution and adaptation of the eastern honey bee (Apis cerana).

PubMed

Chen, Chao; Wang, Huihua; Liu, Zhiguang; Chen, Xiao; Tang, Jiao; Meng, Fanming; Shi, Wei

2018-06-20

The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we re-sequenced the genome of 180 A. cerana individuals from eighteen populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A. cerana. Patterns of genetic differentiation indicate high divergence at the subspecies level, and physical barriers rather than distance are the driving force for population divergence. Estimations of divergence time suggested that the main branches diverged between 300 and 500 ka. Analyses of the population history revealed a substantial influence of the Earth's climate on the effective population size of A. cerana, as increased population sizes were observed during warmer periods. Further analyses identified candidate genes under natural selection that are potentially related to honey bee cognition, temperature adaptation, and olfactory. Based on our results, A. cerana may have great potential in response to climate change. Our study provides fundamental knowledge of the evolution and adaptation of A. cerana.

Ancient duplications and functional divergence in the interferon regulatory factors of vertebrates provide insights into the evolution of vertebrate immune systems.

PubMed

Du, Kang; Zhong, Zaixuan; Fang, Chengchi; Dai, Wei; Shen, Yanjun; Gan, Xiaoni; He, Shunping

2018-04-01

Interferon regulatory factors (IRFs) were first discovered as transcription factors that regulate the transcription of human interferon (IFN)-β. Increasing evidence shows that they might be important players involved in Adaptive immune system (AIS) evolution. Although numbers of IRFs have been identified in chordates, the evolutionary history and functional diversity of this gene family during the early evolution of vertebrates have remained obscure. Using IRF HMM profile and HMMER searches, we identified 148 IRFs in 11 vertebrates and 4 protochordates. For them, we reconstructed the phylogenetic relationships, determined the synteny conservation, investigated the profile of natural selection, and analyzed the expression patterns in four "living fossil" vertebrates: lamprey, elephant shark, coelacanth and bichir. The results from phylogeny and synteny analysis imply that vertebrate IRFs evolved from three predecessors, instead of four as suggested in a previous study, as results from an ancient duplication followed by special expansions and lost during the vertebrate evolution. The profile of natural selection and expression reveals functional dynamics during the process. Together, they suggest that the 2nd whole-genome duplication (2WGD) provided raw materials for innovation in the IRF family, and that the birth of type-I IFN might be an important factor inducing the establishment of IRF-mediated immune networks. As a member involved in the AIS evolution, IRF provide insights into the process and mechanism involved in the complexity and novelties of vertebrate immune systems. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Multiwavelength Observations of Volatiles in Comets

NASA Technical Reports Server (NTRS)

Milam, Stefanie N.; Charnley, Steven B.; Kuan, Yi-Jehng; Chuang, Yo-Ling; DiSanti, Michael A.; Bonev, Boncho P.; Remijan, Anthony J.

2011-01-01

Recently, there have been complimentary observations from multiple facilities to try to unravel the chemical complexity of comets. Incorporating results from various techniques, including: single-dish millimeter wavelength observations, interferometers, and/or IR spectroscopy, one can gain further insight into the abundances, production rates, distributions, and formation mechanisms of molecules in these objects [I]. Such studies have provided great detail towards molecules with a-typical chemistries, such as H2CO [2]. We report spectral observations of C/2006 M4 (SWAN), C/2007 N3 (Lulin), and C/2009 RI (McNaught) with the Arizona Radio Observatory's SMT and 12-m telescopes, as well as the NRAO Greenbank telescope and IRTFCSHELL. Multiple parent volatiles (HCN, CH3OH, CO, CH4, C2H6, and H2O) plus two photodissociation products (CS and OH) have been detected in these objects. We will present a comparison of molecular abundances in these comets to those observed in others, supporting a long-term effort of building a comet taxonomy based on composition. Previous work has revealed a range of abundances of parent species (from "organics-poor" to "organics-rich") with respect to water among comets [3,4,5], however the statistics are stiII poorly constrained and interpretations of the observed compositional diversity are uncertain.

Impaired insight into illness and cognitive insight in schizophrenia spectrum disorders: Resting state functional connectivity

PubMed Central

Gerretsen, Philip; Menon, Mahesh; Mamo, David C.; Fervaha, Gagan; Remington, Gary; Pollock, Bruce G.; Graff-Guerrero, Ariel

2015-01-01

Background Impaired insight into illness (clinical insight) in schizophrenia has negative effects on treatment adherence and clinical outcomes. Schizophrenia is described as a disorder of disrupted brain connectivity. In line with this concept, resting state networks (RSNs) appear differentially affected in persons with schizophrenia. Therefore, impaired clinical, or the related construct of cognitive insight (which posits that impaired clinical insight is a function of metacognitive deficits), may reflect alterations in RSN functional connectivity (fc). Based on our previous research, which showed that impaired insight into illness was associated with increased left hemisphere volume relative to right, we hypothesized that impaired clinical insight would be associated with increased connectivity in the DMN with specific left hemisphere brain regions. Methods Resting state MRI scans were acquired for participants with schizophrenia or schizoaffective disorder (n = 20). Seed-to-voxel and ROI-to-ROI fc analyses were performed using the CONN-fMRI fc toolbox v13 for established RSNs. Clinical and cognitive insight were measured with the Schedule for the Assessment of Insight—Expanded Version and Beck Cognitive Insight Scale, respectively, and included as the regressors in fc analyses. Results As hypothesized, impaired clinical insight was associated with increased connectivity in the default mode network (DMN) with the left angular gyrus, and also in the self-referential network (SRN) with the left insula. Cognitive insight was associated with increased connectivity in the dorsal attention network (DAN) with the right inferior frontal cortex (IFC) and left anterior cingulate cortex (ACC). Conclusion Increased connectivity in DMN and SRN with the left angular gyrus and insula, respectively, may represent neural correlates of impaired clinical insight in schizophrenia spectrum disorders, and is consistent with the literature attributing impaired insight to left

The African coelacanth genome provides insights into tetrapod evolution.

PubMed

Amemiya, Chris T; Alföldi, Jessica; Lee, Alison P; Fan, Shaohua; Philippe, Hervé; Maccallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor; Rohner, Nicolas; Organ, Chris; Chalopin, Domitille; Smith, Jeramiah J; Robinson, Mark; Dorrington, Rosemary A; Gerdol, Marco; Aken, Bronwen; Biscotti, Maria Assunta; Barucca, Marco; Baurain, Denis; Berlin, Aaron M; Blatch, Gregory L; Buonocore, Francesco; Burmester, Thorsten; Campbell, Michael S; Canapa, Adriana; Cannon, John P; Christoffels, Alan; De Moro, Gianluca; Edkins, Adrienne L; Fan, Lin; Fausto, Anna Maria; Feiner, Nathalie; Forconi, Mariko; Gamieldien, Junaid; Gnerre, Sante; Gnirke, Andreas; Goldstone, Jared V; Haerty, Wilfried; Hahn, Mark E; Hesse, Uljana; Hoffmann, Steve; Johnson, Jeremy; Karchner, Sibel I; Kuraku, Shigehiro; Lara, Marcia; Levin, Joshua Z; Litman, Gary W; Mauceli, Evan; Miyake, Tsutomu; Mueller, M Gail; Nelson, David R; Nitsche, Anne; Olmo, Ettore; Ota, Tatsuya; Pallavicini, Alberto; Panji, Sumir; Picone, Barbara; Ponting, Chris P; Prohaska, Sonja J; Przybylski, Dariusz; Saha, Nil Ratan; Ravi, Vydianathan; Ribeiro, Filipe J; Sauka-Spengler, Tatjana; Scapigliati, Giuseppe; Searle, Stephen M J; Sharpe, Ted; Simakov, Oleg; Stadler, Peter F; Stegeman, John J; Sumiyama, Kenta; Tabbaa, Diana; Tafer, Hakim; Turner-Maier, Jason; van Heusden, Peter; White, Simon; Williams, Louise; Yandell, Mark; Brinkmann, Henner; Volff, Jean-Nicolas; Tabin, Clifford J; Shubin, Neil; Schartl, Manfred; Jaffe, David B; Postlethwait, John H; Venkatesh, Byrappa; Di Palma, Federica; Lander, Eric S; Meyer, Axel; Lindblad-Toh, Kerstin

2013-04-18

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

A Representation for Gaining Insight into Clinical Decision Models

PubMed Central

Jimison, Holly B.

1988-01-01

For many medical domains uncertainty and patient preferences are important components of decision making. Decision theory is useful as a representation for such medical models in computer decision aids, but the methodology has typically had poor performance in the areas of explanation and user interface. The additional representation of probabilities and utilities as random variables serves to provide a framework for graphical and text insight into complicated decision models. The approach allows for efficient customization of a generic model that describes the general patient population of interest to a patient- specific model. Monte Carlo simulation is used to calculate the expected value of information and sensitivity for each model variable, thus providing a metric for deciding what to emphasize in the graphics and text summary. The computer-generated explanation includes variables that are sensitive with respect to the decision or that deviate significantly from what is typically observed. These techniques serve to keep the assessment and explanation of the patient's decision model concise, allowing the user to focus on the most important aspects for that patient.

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis.

PubMed

Wang, Zi; Ramsey, Benjamin J; Wang, Dali; Wong, Kwai; Li, Husheng; Wang, Eric; Bao, Zhirong

2016-01-01

With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

Technological aspects of hospital communication challenges: an observational study.

PubMed

Popovici, Ilinca; Morita, Plinio P; Doran, Diane; Lapinsky, Stephen; Morra, Dante; Shier, Ashleigh; Wu, Robert; Cafazzo, Joseph A

2015-06-01

To gain insights into how technological communication tools impact effective communication among clinicians, which is critical for patient safety. This multi-site observational study analyzes inter-clinician communication and interaction with information technology, with a focus on the critical process of patient transfer from the Emergency Department to General Internal Medicine. Mount Sinai Hospital, Sunnybrook Health Sciences Centre and Toronto General Hospital. At least five ED and general internal medicine nurses and physicians directly involved in patient transfers were observed on separate occasions at each institution. N/A. N/A. The study provides insight into clinician workflow, evaluates current hospital communication systems and identifies key issues affecting communication: interruptions, issues with numeric pagers, lack of integrated communication tools, lack of awareness of consultation status, inefficiencies related to the paper chart, unintuitive user interfaces, mixed use of electronic and paper systems and lack of up-to-date contact information. It also identifies design trade-offs to be negotiated: synchronous communication vs. reducing interruptions, notification of patient status vs. reducing interruptions and speed vs. quality of handovers. The issues listed should be considered in the design of new technology for hospital communications. © The Author 2015. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

Implementation of Insight Responsibilities in Process Engineering

NASA Technical Reports Server (NTRS)

Osborne, Deborah M.

1997-01-01

This report describes an approach for evaluating flight readiness (COFR) and contractor performance evaluation (award fee) as part of the insight role of NASA Process Engineering at Kennedy Space Center. Several evaluation methods are presented, including systems engineering evaluations and use of systems performance data. The transition from an oversight function to the insight function is described. The types of analytical tools appropriate for achieving the flight readiness and contractor performance evaluation goals are described and examples are provided. Special emphasis is placed upon short and small run statistical quality control techniques. Training requirements for system engineers are delineated. The approach described herein would be equally appropriate in other directorates at Kennedy Space Center.

Proofs that Develop Insight

ERIC Educational Resources Information Center

Weber, Keith

2010-01-01

Many mathematics educators have noted that mathematicians do not only read proofs to gain conviction but also to obtain insight. The goal of this article is to discuss what this insight is from mathematicians' perspective. Based on interviews with nine research-active mathematicians, two sources of insight are discussed. The first is reading a…

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.

PubMed

Tisserant, Emilie; Malbreil, Mathilde; Kuo, Alan; Kohler, Annegret; Symeonidi, Aikaterini; Balestrini, Raffaella; Charron, Philippe; Duensing, Nina; Frei dit Frey, Nicolas; Gianinazzi-Pearson, Vivienne; Gilbert, Luz B; Handa, Yoshihiro; Herr, Joshua R; Hijri, Mohamed; Koul, Raman; Kawaguchi, Masayoshi; Krajinski, Franziska; Lammers, Peter J; Masclaux, Frederic G; Murat, Claude; Morin, Emmanuelle; Ndikumana, Steve; Pagni, Marco; Petitpierre, Denis; Requena, Natalia; Rosikiewicz, Pawel; Riley, Rohan; Saito, Katsuharu; San Clemente, Hélène; Shapiro, Harris; van Tuinen, Diederik; Bécard, Guillaume; Bonfante, Paola; Paszkowski, Uta; Shachar-Hill, Yair Y; Tuskan, Gerald A; Young, J Peter W; Young, Peter W; Sanders, Ian R; Henrissat, Bernard; Rensing, Stefan A; Grigoriev, Igor V; Corradi, Nicolas; Roux, Christophe; Martin, Francis

2013-12-10

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

PubMed Central

Tisserant, Emilie; Malbreil, Mathilde; Kuo, Alan; Kohler, Annegret; Symeonidi, Aikaterini; Balestrini, Raffaella; Charron, Philippe; Duensing, Nina; Frei dit Frey, Nicolas; Gianinazzi-Pearson, Vivienne; Gilbert, Luz B.; Handa, Yoshihiro; Herr, Joshua R.; Hijri, Mohamed; Koul, Raman; Kawaguchi, Masayoshi; Krajinski, Franziska; Lammers, Peter J.; Masclaux, Frederic G.; Murat, Claude; Morin, Emmanuelle; Ndikumana, Steve; Pagni, Marco; Petitpierre, Denis; Requena, Natalia; Rosikiewicz, Pawel; Riley, Rohan; Saito, Katsuharu; San Clemente, Hélène; Shapiro, Harris; van Tuinen, Diederik; Bécard, Guillaume; Bonfante, Paola; Paszkowski, Uta; Shachar-Hill, Yair Y.; Tuskan, Gerald A.; Young, J. Peter W.; Sanders, Ian R.; Henrissat, Bernard; Rensing, Stefan A.; Grigoriev, Igor V.; Corradi, Nicolas; Roux, Christophe; Martin, Francis

2013-01-01

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota. PMID:24277808

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.

PubMed

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Ying; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tom Tang, Y; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lu, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhongjian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

2014-12-02

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

PubMed Central

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Ying; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tom Tang, Y.; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lu, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhongjian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L.; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

2014-01-01

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates. PMID:25463417

INSIGHT (interaction of low-orbiting satellites with the surrounding ionosphere and thermosphere)

NASA Astrophysics Data System (ADS)

Schlicht, Anja; Reussner, Elisabeth; Lühr, Hermann; Stolle, Claudia; Xiong, Chao; Schmidt, Michael; Blossfeld, Mathis; Erdogan, Eren; Pancetta, Francesca; Flury, Jakob

2016-04-01

In the framework of the DFG special program "Dynamic Earth" the project INSIGHT, started in September 2015, is studying the interactions between the ionosphere and thermosphere as well as the role of the satellites and their instruments in observing the space environment. Accelerometers on low-Earth orbiters (LEOs) are flown to separate non-gravitational forces acting on the satellite from influences of gravitational effects. Amongst others these instruments provide valuable information for improving our understanding of thermospheric properties like densities and winds. An unexpected result, for example, is the clear evidence of geomagnetic field control on the neutral upper atmosphere. The charged particles of the ionosphere act as mediators between the magnetic field and the thermosphere. In the framework of INSIGHT the climatology of the thermosphere will be established and the coupling between the ionosphere and thermosphere is studied. There are indications that the accelerometers are influenced by systematic errors not identified up to now. For GRACE it is one of the discussed reasons, why this mission so far did not reach the baseline accuracy. Beutler et al. 2010 discussed the limited use of the GRACE accelerometer measurements in comparison to stochastic pulses in gravity field recovery. Analysis of the accelerometer measurements show many structures in the high frequency region which can be traced back to switching processes of electric circuits in the spacecraft, like heater and magnetic torquer switching, or so called twangs, which can be associated with discharging of non-conducting surfaces of the satellite. As all observed signals have the same time dependency a common origin is very likely, namely the coupling of time variable electric currents into the accelerometer signal. In GOCE gravity field gradients non-gravitational signatures around the magnetic poles are found indicating that even at lower frequencies problems occur. INSIGHT will identify

Analytical insights into optimality and resonance in fish swimming

PubMed Central

Kohannim, Saba; Iwasaki, Tetsuya

2014-01-01

This paper provides analytical insights into the hypothesis that fish exploit resonance to reduce the mechanical cost of swimming. A simple body–fluid fish model, representing carangiform locomotion, is developed. Steady swimming at various speeds is analysed using optimal gait theory by minimizing bending moment over tail movements and stiffness, and the results are shown to match with data from observed swimming. Our analysis indicates the following: thrust–drag balance leads to the Strouhal number being predetermined based on the drag coefficient and the ratio of wetted body area to cross-sectional area of accelerated fluid. Muscle tension is reduced when undulation frequency matches resonance frequency, which maximizes the ratio of tail-tip velocity to bending moment. Finally, hydrodynamic resonance determines tail-beat frequency, whereas muscle stiffness is actively adjusted, so that overall body–fluid resonance is exploited. PMID:24430125

Insights on STEM Careers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wendelberger, Joanne Roth

2014-11-05

This presentation will provide career advice for individuals seeking to go beyond just having a job to building a successful career in the areas of Science, Technology, Engineering, and Mathematics. Careful planning can be used to turn a job into a springboard for professional advancement and personal satisfaction. Topics to be addressed include setting priorities, understanding career ladders, making tough choices, overcoming stereotypes and assumptions by others, networking, developing a professional identify, and balancing a career with family and other personal responsibilities. Insights on the transition from individual technical work to leadership will also be provided. The author will drawmore » upon experiences gained in academic, industrial, and government laboratory settings, as well as extensive professional service and community involvement.« less

Do health economic evaluations using observational data provide reliable assessment of treatment effects?

PubMed Central

2013-01-01

Economic evaluation in modern health care systems is seen as a transparent scientific framework that can be used to advance progress towards improvements in population health at the best possible value. Despite the perceived superiority that trial-based studies have in terms of internal validity, economic evaluations often employ observational data. In this review, the interface between econometrics and economic evaluation is explored, with emphasis placed on highlighting methodological issues relating to the evaluation of cost-effectiveness within a bivariate framework. Studies that satisfied the eligibility criteria exemplified the use of matching, regression analysis, propensity scores, instrumental variables, as well as difference-in-differences approaches. All studies were reviewed and critically appraised using a structured template. The findings suggest that although state-of-the-art econometric methods have the potential to provide evidence on the causal effects of clinical and policy interventions, their application in economic evaluation is subject to a number of limitations. These range from no credible assessment of key assumptions and scarce evidence regarding the relative performance of different methods, to lack of reporting of important study elements, such as a summary outcome measure and its associated sampling uncertainty. Further research is required to better understand the ways in which observational data should be analysed in the context of the economic evaluation framework. PMID:24229445

Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding.

PubMed

Chao, Ya-Ting; Chen, Wan-Chieh; Chen, Chun-Yi; Ho, Hsiu-Yin; Yeh, Chih-Hsin; Kuo, Yi-Tzu; Su, Chun-Lin; Yen, Shao-Hua; Hsueh, Hao-Yen; Yeh, Jen-Hau; Hsu, Hui-Lan; Tsai, Yi-Hui; Kuo, Tzu-Yen; Chang, Song-Bin; Chen, Kai-Yi; Shih, Ming-Che

2018-04-28

The Orchidaceae is a diverse and ecologically important plant family. Approximately 69% of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Inference of Surface Chemical and Physical Properties Using Mid-Infrared (MIR) Spectral Observations

NASA Technical Reports Server (NTRS)

Roush, Ted L.

2016-01-01

Reflected or emitted energy from solid surfaces in the solar system can provide insight into thermo-physical and chemical properties of the surface materials. Measurements have been obtained from instruments located on Earth-based telescopes and carried on several space missions. The characteristic spectral features commonly observed in Mid-Infrared (MIR) spectra of minerals will be reviewed, along with methods used for compositional interpretations of MIR emission spectra. The influence of surface grain size, and space weathering processes on MIR emissivity spectra will also be discussed. Methods used for estimating surface temperature, emissivity, and thermal inertias from MIR spectral observations will be reviewed.

Insight development in schizophrenia: the construction of dangerousness in relapse.

PubMed

Nordick, Wendy Gale; van Heugten, Kate

2014-05-01

Mental health professionals believe that lack of insight is a major problem in schizophrenia because it significantly interferes with adherence to medical treatment. Yet few researchers have attempted to ask people with schizophrenia for their views on how insight develops and impacts on their quality of life. We explored these questions in interviews and focus groups with 19 Canadian people who had been diagnosed with schizophrenia and identified as having good insight, and with New Zealand and Canadian treatment providers. We found that participants developed insight in three stages, which we labeled the period of chaos, the dynamic period, and the period of wisdom. Crises led participants to realize that their safety and their relationships with loved ones would continue to be dangerously imperiled unless they made sustained efforts to maintain wellness. We propose the Theory of Dangerousness to explain how participants developed and maintained their motivation to remain well.

Insight in schizophrenia: a review.

PubMed

Dam, Jesper

2006-01-01

The issue of insight in schizophrenia must be assumed to be one of the most important aspects of the clinical examination. Comprehensive studies have shown that between 50% and 80% of all patients suffering from schizophrenia do not believe that they have a disorder. In recent years, poor insight in schizophrenia has been the subject of increasing interest, as manifested in a number of studies discussed in the present review. Some of these studies focus on insight correlated to various parameters such as psychopathology, neuropsychology, clinical relevance and compliance. Other studies refer to more theoretical implications, among these the issue of defining the concept of insight: whether insight can be seen as a "primary" phenomenon in schizophrenia, and whether insight may be graduated, dimensioned or increased. Several authors have developed rating scales in an attempt to obtain a measure for the degree or dimension of insight. Here, the range of parameters employed gives an excellent impression of the complexity of the concept of insight. In the concluding discussion, a phenomenological aspect is brought in, in an attempt to place the concept of insight in relation to disturbances of the self in schizophrenia and to primary symptoms in schizophrenia, amongst these autism.

Overlap and distinction between measures of insight and self-stigma.

PubMed

Hasson-Ohayon, Ilanit

2018-05-24

Multiple studies on insight into one's illness and self-stigma among patients with serious mental illness and their relatives have shown that these constructs are related to one another and that they affect outcome. However, a critical exploration of the items used to assess both constructs raises questions with regard to the possible overlapping and centrality of items. The current study used five different samples to explore the possible overlap and distinction between insight and self-stigma, and to identify central items, via network analyses and principal component factor analysis. Findings from the network analyses showed overlap between insight and self-stigma exist with a relatively clearer observational distinction between the constructs among the two parent samples in comparison to the patient samples. Principal component factor analysis constrained to two factors showed that a relatively high percentage of items were not loaded on either factor, and in a few datasets, several insight items were loaded on the self-stigma scale and vice versa. The author discusses implications for research and calls for rethinking the way insight is assessed. Clinical implications are also discussed in reference to central items of social isolation, future worries and stereotype endorsement among the different study groups. Copyright © 2018 Elsevier B.V. All rights reserved.

Association between prefrontal N-acetylaspartate and insight in psychotic disorders.

PubMed

Larabi, Daouia I; Liemburg, Edith J; Pijnenborg, Gerdina H M; Sibeijn-Kuiper, Anita; de Vos, Annerieke E; Bais, Leonie; Knegtering, Henderikus; Ćurčić-Blake, Branislava; Aleman, André

2017-01-01

Insight is impaired in most patients with psychosis and has been associated with poorer prognosis. The exact neural basis of impaired insight is still unknown, but it may involve disrupted prefrontal neural connectivity. Numerous studies have indeed found white matter (WM) abnormalities in psychosis. The association between prefrontal WM abnormalities and insight has not been studied yet by means of proton magnetic resonance spectroscopy ( 1 H-MRS). 1 H-MRS can be used to measure N-acetylaspartate (NAA), which is considered to be a marker of neuronal integrity. We measured insight with the Birchwood Insight Scale (BIS) as well as item G12 of the Positive and Negative Syndrome Scale (PANSS) in 88 patients with psychosis. Prefrontal WM concentrations of NAA and ratios of NAA to creatine (Cr) were assessed with 1 H-MRS. Nonparametric partial correlational analyses were conducted between NAA concentrations and insight controlling for illness duration, standardized antipsychotic dose, symptom scores, voxel grey matter content and voxel cerebrospinal fluid content. We found a significant correlation between reduced NAA/Cr ratios and poorer insight as measured with the BIS, which remained significant after additional correction for full width at half maximum, signal/noise and age. This is the first study reporting a relationship between lower prefrontal concentrations of a marker of neuronal integrity and impaired insight, providing further evidence that prefrontal pathology may play an important role in impaired insight in psychosis. This may be explained by the involvement of the prefrontal cortex in several executive and metacognitive functions, such as cognitive flexibility and perspective taking. Copyright © 2016 Elsevier B.V. All rights reserved.

Discovery of cyclotides in the fabaceae plant family provides new insights into the cyclization, evolution, and distribution of circular proteins.

PubMed

Poth, Aaron G; Colgrave, Michelle L; Philip, Reynold; Kerenga, Bomai; Daly, Norelle L; Anderson, Marilyn A; Craik, David J

2011-04-15

Cyclotides are plant proteins whose defining structural features are a head-to-tail cyclized backbone and three interlocking disulfide bonds, which in combination are known as a cyclic cystine knot. This unique structural motif confers cyclotides with exceptional resistance to proteolysis. Their endogenous function is thought to be as plant defense agents, associated with their insecticidal and larval growth-inhibitory properties. However, in addition, an array of pharmaceutically relevant biological activities has been ascribed to cyclotides, including anti-HIV, anthelmintic, uterotonic, and antimicrobial effects. So far, >150 cyclotides have been elucidated from members of the Rubiaceae, Violaceae, and Cucurbitaceae plant families, but their wider distribution among other plant families remains unclear. Clitoria ternatea (Butterfly pea) is a member of plant family Fabaceae and through its usage in traditional medicine to aid childbirth bears similarity to Oldenlandia affinis, from which many cyclotides have been isolated. Using a combination of nanospray and matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) analyses, we examined seed extracts of C. ternatea and discovered cyclotides in the Fabaceae, the third-largest family of flowering plants. We characterized 12 novel cyclotides, thus expanding knowledge of cyclotide distribution and evolution within the plant kingdom. The discovery of cyclotides containing novel sequence motifs near the in planta cyclization site has provided new insights into cyclotide biosynthesis. In particular, MS analyses of the novel cyclotides from C. ternatea suggest that Asn to Asp variants at the cyclization site are more common than previously recognized. Moreover, this study provides impetus for the examination of other economically and agriculturally significant species within Fabaceae, now the largest plant family from which cyclotides have been described.

Helioseismology Observations of Solar Cycles and Dynamo Modeling

NASA Astrophysics Data System (ADS)

Kosovichev, A. G.; Guerrero, G.; Pipin, V.

2017-12-01

Helioseismology observations from the SOHO and SDO, obtained in 1996-2017, provide unique insight into the dynamics of the Sun's deep interior for two solar cycles. The data allow us to investigate variations of the solar interior structure and dynamics, and compare these variations with dynamo models and simulations. We use results of the local and global helioseismology data processing pipelines at the SDO Joint Science Operations Center (Stanford University) to study solar-cycle variations of the differential rotation, meridional circulation, large-scale flows and global asphericity. By comparing the helioseismology results with the evolution of surface magnetic fields we identify characteristic changes associated the initiation and development of Solar Cycles 23 and 24. For the physical interpretation of observed variations, the results are compared with the current mean-field dynamo models and 3D MHD dynamo simulations. It is shown that the helioseismology inferences provide important constraints on the solar dynamo mechanism, may explain the fundamental difference between the two solar cycles, and also give information about the next solar cycle.

Transcriptomic analyses on muscle tissues of Litopenaeus vannamei provide the first profile insight into the response to low temperature stress.

PubMed

Huang, Wen; Ren, Chunhua; Li, Hongmei; Huo, Da; Wang, Yanhong; Jiang, Xiao; Tian, Yushun; Luo, Peng; Chen, Ting; Hu, Chaoqun

2017-01-01

The Pacific white shrimp (Litopenaeus vannamei) is an important cultured crustacean species worldwide. However, little is known about the molecular mechanism of this species involved in the response to cold stress. In this study, four separate RNA-Seq libraries of L. vannamei were generated from 13°C stress and control temperature. Total 29,662 of Unigenes and overall of 19,619 annotated genes were obtained. Three comparisons were carried out among the four libraries, in which 72 of the top 20% of differentially-expressed genes were obtained, 15 GO and 5 KEGG temperature-sensitive pathways were fished out. Catalytic activity (GO: 0003824) and Metabolic pathways (ko01100) were the most annotated GO and KEGG pathways in response to cold stress, respectively. In addition, Calcium, MAPK cascade, Transcription factor and Serine/threonine-protein kinase signal pathway were picked out and clustered. Serine/threonine-protein kinase signal pathway might play more important roles in cold adaptation, while other three signal pathway were not widely transcribed. Our results had summarized the differentially-expressed genes and suggested the major important signaling pathways and related genes. These findings provide the first profile insight into the molecular basis of L. vannamei response to cold stress.

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus

PubMed Central

Wu, Wei; Yang, Yu-Lan; He, Wei-Ming; Rouard, Mathieu; Li, Wei-Ming; Xu, Meng; Roux, Nicolas; Ge, Xue-Jun

2016-01-01

Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding. PMID:27531320

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus.

PubMed

Wu, Wei; Yang, Yu-Lan; He, Wei-Ming; Rouard, Mathieu; Li, Wei-Ming; Xu, Meng; Roux, Nicolas; Ge, Xue-Jun

2016-08-17

Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.

An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B.

PubMed

Rallapalli, P M; Kemball-Cook, G; Tuddenham, E G; Gomez, K; Perkins, S J

2013-07-01

Factor IX (FIX) is important in the coagulation cascade, being activated to FIXa on cleavage. Defects in the human F9 gene frequently lead to hemophilia B. To assess 1113 unique F9 mutations corresponding to 3721 patient entries in a new and up-to-date interactive web database alongside the FIXa protein structure. The mutations database was built using MySQL and structural analyses were based on a homology model for the human FIXa structure based on closely-related crystal structures. Mutations have been found in 336 (73%) out of 461 residues in FIX. There were 812 unique point mutations, 182 deletions, 54 polymorphisms, 39 insertions and 26 others that together comprise a total of 1113 unique variants. The 64 unique mild severity mutations in the mature protein with known circulating protein phenotypes include 15 (23%) quantitative type I mutations and 41 (64%) predominantly qualitative type II mutations. Inhibitors were described in 59 reports (1.6%) corresponding to 25 unique mutations. The interactive database provides insights into mechanisms of hemophilia B. Type II mutations are deduced to disrupt predominantly those structural regions involved with functional interactions. The interactive features of the database will assist in making judgments about patient management. © 2013 International Society on Thrombosis and Haemostasis.

Transcriptomic analyses on muscle tissues of Litopenaeus vannamei provide the first profile insight into the response to low temperature stress

PubMed Central

Huang, Wen; Ren, Chunhua; Li, Hongmei; Huo, Da; Wang, Yanhong; Jiang, Xiao; Tian, Yushun; Luo, Peng; Hu, Chaoqun

2017-01-01

The Pacific white shrimp (Litopenaeus vannamei) is an important cultured crustacean species worldwide. However, little is known about the molecular mechanism of this species involved in the response to cold stress. In this study, four separate RNA-Seq libraries of L. vannamei were generated from 13°C stress and control temperature. Total 29,662 of Unigenes and overall of 19,619 annotated genes were obtained. Three comparisons were carried out among the four libraries, in which 72 of the top 20% of differentially-expressed genes were obtained, 15 GO and 5 KEGG temperature-sensitive pathways were fished out. Catalytic activity (GO: 0003824) and Metabolic pathways (ko01100) were the most annotated GO and KEGG pathways in response to cold stress, respectively. In addition, Calcium, MAPK cascade, Transcription factor and Serine/threonine-protein kinase signal pathway were picked out and clustered. Serine/threonine-protein kinase signal pathway might play more important roles in cold adaptation, while other three signal pathway were not widely transcribed. Our results had summarized the differentially-expressed genes and suggested the major important signaling pathways and related genes. These findings provide the first profile insight into the molecular basis of L. vannamei response to cold stress. PMID:28575089

Using climate models to estimate the quality of global observational data sets.

PubMed

Massonnet, François; Bellprat, Omar; Guemas, Virginie; Doblas-Reyes, Francisco J

2016-10-28

Observational estimates of the climate system are essential to monitoring and understanding ongoing climate change and to assessing the quality of climate models used to produce near- and long-term climate information. This study poses the dual and unconventional question: Can climate models be used to assess the quality of observational references? We show that this question not only rests on solid theoretical grounds but also offers insightful applications in practice. By comparing four observational products of sea surface temperature with a large multimodel climate forecast ensemble, we find compelling evidence that models systematically score better against the most recent, advanced, but also most independent product. These results call for generalized procedures of model-observation comparison and provide guidance for a more objective observational data set selection. Copyright © 2016, American Association for the Advancement of Science.

Post-donation telephonic interview of blood donors providing an insight into delayed adverse reactions: First attempt in India.

PubMed

Tiwari, Aseem K; Aggarwal, Geet; Dara, Ravi C; Arora, Dinesh; Srivastava, Khushboo; Raina, Vimarsh

2017-04-01

Blood donor experiences both immediate adverse reactions (IAR) and delayed adverse reactions (DAR). With limited published data available on the incidence of DAR, a study was conducted to estimate incidence and profile of DAR through telephonic interview. Study was conducted over a 45-day period for consecutive volunteer whole blood donations at tertiary care hospital. Donors were divided into first-time, repeat and regular and were monitored for IAR. They were given written copy of post-donation advice. Donors were contacted telephonically three weeks post-donation and enquired about general wellbeing and specific DAR in accordance with a standard n international (International Society of Blood Transfusion) standard format. Donors participated in the study of which 1.6% donors experienced an IAR. Much larger number reported DAR (10.3% vs.1.6% p<0.0001). Further, DAR was presented as a variegated profile with bruise, painful arms and fatigue being the commonest. DARs were more common in females than males (25% vs. 10.3%, p<0.02). Localized DAR like bruise and painful arms were more common in younger donors (age <50 years) whereas systemic DAR like fatigue was common in older donors (>50 years). First time (12.3%) and repeat donors (13.5%) had similar frequency of DAR but were lower among regular donors (6.7%). DARs are more common than IAR and are of different profile. Post-donation interview has provided an insight into donor experiences and can be used as a valuable tool in donor hemovigilance. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Genomic Survey of SCPP Family Genes in Fishes Provides Novel Insights into the Evolution of Fish Scales.

PubMed

Lv, Yunyun; Kawasaki, Kazuhiko; Li, Jia; Li, Yanping; Bian, Chao; Huang, Yu; You, Xinxin; Shi, Qiong

2017-11-16

The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi . According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes. In addition, most of these SCPP genes, with the exception of SPP1 , individually form one or two gene cluster(s) on each corresponding genome. Furthermore, we constructed phylogenetic trees using maximum likelihood method to estimate their evolution. The phylogenetic topology mostly supports two subclasses in some species, such as Cyprinus carpio , Sinocyclocheilus anshuiensis , S. grahamin , and S. rhinocerous , but not in the other examined fishes. By comparing the gene structures of recently reported candidate genes, SCPP1 and SCPP5 , for determining scale phenotypes, we found that the hypothesis is suitable for Astyanax mexicanus , but denied by S. anshuiensis , even though they are both sparsely scaled for cave adaptation. Thus, we conclude that, although different fish species display similar scale phenotypes, the underlying genetic changes however might be diverse. In summary, this paper accelerates the recognition of the SCPP family in teleosts for potential scale evolution.

Does the scale of our observational window affect our conclusions about correlations between endangered salmon populations and their habitat?

Treesearch

Blake E. Feist; E. Ashley Steel; David W. Jensen; Damon N.D. Sather

2010-01-01

Differences in the strength of species-habitat relationships across scales provide insights into the mechanisms that drive these relationships and guidance for designing in situ monitoring programs, conservation efforts and mechanistic studies. The scale of our observation can also impact the strength of perceived relationships between animals and habitat conditions....

Epicentral Determination from Macroseismic Data: Insights from Four Centuries of Observations (Invited)

NASA Astrophysics Data System (ADS)

Szeliga, W. M.; Martin, S.; Hough, S.; Bilham, R.

2009-12-01

A new compilation of more than 8300 newly interpreted intensity observations from 570 earthquakes on the Indian subcontinent between 1636 and 2009 provides a rich data base for examining the utility of recently developed methods for deriving magnitude and location from macroseismic data. Instrumentally determined locations and magnitudes are available for 144 of these earthquakes since 1900, and for a subset of these earthquakes we can calculate differences between instrumental- and intensity-derived parameters. Using a modification of the Bakun and Wentworth (1997) algorithm we find that epicenters determined from well-conditioned intensity distributions are typically within one fault length of those determined from instrumental data. This encouraging result, however, applies to fewer than one third of the events. For a larger number of earthquakes, intensity-derived epicenters are poorly constrained, due to scatter in intensity amplitude and/or to poor spatial coverage. This raises concerns about the accuracy of rupture parameters determined for pre-instrumental earthquakes in India and elsewhere. We find moreover, that where dense spatial intensity values are available, location is recovered reasonably well (e.g. Bhuj 2001, Kashmir 2005), but magnitude is over-estimated by as much as one magnitude unit. This suggests that epicentral locations for well-documented M>7 historical earthquakes might be relatively reliable, but their magnitude might be significantly inflated. The cause for these erroneous locations and magnitudes are examined and we outline the results of our search for numerical rules to determine whether a given set of intensities will provide accurate or misleading results.

Cognitive insight: A systematic review.

PubMed

Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

2017-07-01

Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

Genomic Insights into Growth and Its Disorders: An Update

PubMed Central

de Bruin, Christiaan; Dauber, Andrew

2016-01-01

Purpose of review To provide an update of the most striking new developments in the field of growth genetics over the past 12 months Recent findings A number of large genome-wide association studies have identified new genetic loci and pathways associated to human growth and adult height as well as related traits and comorbidities. New genetic etiologies of primordial dwarfism and several short stature syndromes have been elucidated. Moreover, a breakthrough finding of Xq26 microduplications as a cause of pituitary gigantism was made. Several new developments in imprinted growth-related genes (including the first human mutation in IGF-II) and novel insights into the epigenetic regulation of growth have been reported. Summary Genomic investigations continue to provide new insights into the genetic basis of human growth as well as its disorders. PMID:26702851

Large-Amplitude Electrostatic Waves Observed at a Supercritical Interplanetary Shock

NASA Technical Reports Server (NTRS)

Wilson, L. B., III; Cattell, C. A.; Kellogg, P. J.; Goetz, K.; Kersten, K.; Kasper, J. C.; Szabo, A.; Wilber, M.

2010-01-01

We present the first observations at an interplanetary shock of large-amplitude (> 100 mV/m pk-pk) solitary waves and large-amplitude (approx.30 mV/m pk-pk) waves exhibiting characteristics consistent with electron Bernstein waves. The Bernstein-like waves show enhanced power at integer and half-integer harmonics of the cyclotron frequency with a broadened power spectrum at higher frequencies, consistent with the electron cyclotron drift instability. The Bernstein-like waves are obliquely polarized with respect to the magnetic field but parallel to the shock normal direction. Strong particle heating is observed in both the electrons and ions. The observed heating and waveforms are likely due to instabilities driven by the free energy provided by reflected ions at this supercritical interplanetary shock. These results offer new insights into collisionless shock dissipation and wave-particle interactions in the solar wind.

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Stu Spath, InSight program manager, Lockheed Martin Space, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Tom Hoffman, InSight project manager, NASA JPL, right, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Bruce Banerdt, InSight principal investigator, NASA JPL, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Cortical thickness and low insight into symptoms in enduring schizophrenia.

PubMed

Emami, Seema; Guimond, Synthia; Mallar Chakravarty, M; Lepage, Martin

2016-01-01

Poor insight is a common, multidimensional phenomenon in patients with schizophrenia, associated with poorer outcomes and treatment non-adherence. Yet scant research has investigated the neuronal correlates of insight into symptoms (IS), a dimension of insight that may be particularly significant in enduring schizophrenia. Sixty-six patients with enduring schizophrenia (duration >4years) and 33 healthy controls completed MRI scanning and IQ, depression, and anxiety assessments. The Scale to Assess Insight-Expanded (SAI-E) measured insight into patients' four most prominent symptoms and patients were classified into two groups: low IS (0-2; n=33), and high IS (>2; n=33). We evaluated the association between cortical thickness (CT) and insight into symptoms using two methods: (1) a between-patients region-of-interest analysis in the insula, superior temporal gyrus (STG) and frontal lobe; and (2) a whole-brain exploratory regression between patient and controls. Brain regions were segmented using a neuroanatomical atlas and vertex-wise CT analyses were conducted with CIVET, covaried for age and sex. ROI analysis revealed thinner insula cortex in patients with low IS (p<0.05, surviving FDR correction). Patients with low IS also showed significantly thinner right insula, STG, and parahippocampal cortex compared to healthy controls (p<0.05, surviving FDR correction). Regions of observed CT reductions have been hypothesized to subserve self-monitoring, error awareness, and ability to identify hallucinations. Results highlight an important association between right insula abnormalities and impaired IS in schizophrenia. The diverse clinical presentation of patients further suggests an independent relationship between symptomology and insight-related differences in CT that has been previously unexplored in enduring schizophrenia. Copyright © 2015 Elsevier B.V. All rights reserved.

Quality of pharmaceutical care at the pharmacy counter: patients’ experiences versus video observation

PubMed Central

Koster, Ellen S; Blom, Lyda; Overbeeke, Marloes R; Philbert, Daphne; Vervloet, Marcia; Koopman, Laura; van Dijk, Liset

2016-01-01

Introduction Consumer Quality Index questionnaires are used to assess quality of care from patients’ experiences. Objective To provide insight into the agreement about quality of pharmaceutical care, measured both by a patient questionnaire and video observations. Methods Pharmaceutical encounters in four pharmacies were video-recorded. Patients completed a questionnaire based upon the Consumer Quality Index Pharmaceutical Care after the encounter containing questions about patients’ experiences regarding information provision, medication counseling, and pharmacy staff’s communication style. An observation protocol was used to code the recorded encounters. Agreement between video observation and patients’ experiences was calculated. Results In total, 109 encounters were included for analysis. For the domains “medication counseling” and “communication style”, agreement between patients’ experiences and observations was very high (>90%). Less agreement (45%) was found for “information provision”, which was rated more positive by patients compared to the observations, especially for the topic, encouragement of patients’ questioning behavior. Conclusion A questionnaire is useful to assess the quality of medication counseling and pharmacy staff’s communication style, but might be less suitable to evaluate information provision and pharmacy staff’s encouragement of patients’ questioning behavior. Although patients may believe that they have received all necessary information to use their new medicine, some information on specific instructions was not addressed during the encounter. When using questionnaires to get insight into information provision, observations of encounters are very informative to validate the patient questionnaires and make necessary adjustments. PMID:27042025

Comparison of the Incorporation of DHA in Circulatory and Neural Tissue When Provided as Triacylglycerol (TAG), Monoacylglycerol (MAG) or Phospholipids (PL) Provides New Insight into Fatty Acid Bioavailability.

PubMed

Destaillats, Frédéric; Oliveira, Manuel; Bastic Schmid, Viktoria; Masserey-Elmelegy, Isabelle; Giuffrida, Francesca; Thakkar, Sagar K; Dupuis, Lénaïck; Gosoniu, Maria Laura; Cruz-Hernandez, Cristina

2018-05-15

Phospholipids (PL) or partial acylglycerols such as sn -1(3)-monoacylglycerol (MAG) are potent dietary carriers of long-chain polyunsaturated fatty acids (LC-PUFA) and have been reported to provide superior bioavailability when compared to conventional triacylglycerol (TAG). The main objective of the present study was to compare the incorporation of docosahexaenoic acid (DHA) in plasma, erythrocytes, retina and brain tissues in adult rats when provided as PL (PL-DHA) and MAG (MAG-DHA). Conventional dietary DHA oil containing TAG (TAG-DHA) as well as control chow diet were used to evaluate the potency of the two alternative DHA carriers over a 60-day feeding period. Fatty acid profiles were determined in erythrocytes and plasma lipids at time 0, 7, 14, 28, 35 and 49 days of the experimental period and in retina, cortex, hypothalamus, and hippocampus at 60 days. The assessment of the longitudinal evolution of DHA in erythrocyte and plasma lipids suggest that PL-DHA and MAG-DHA are efficient carriers of dietary DHA when compared to conventional DHA oil (TAG-DHA). Under these experimental conditions, both PL-DHA and MAG-DHA led to higher incorporations of DHA erythrocytes lipids compared to TAG-DHA group. After 60 days of supplementation, statistically significant increase in DHA level incorporated in neural tissues analyzed were observed in the DHA groups compared with the control. The mechanism explaining hypothetically the difference observed in circulatory lipids is discussed.

Comparison of the Incorporation of DHA in Circulatory and Neural Tissue When Provided as Triacylglycerol (TAG), Monoacylglycerol (MAG) or Phospholipids (PL) Provides New Insight into Fatty Acid Bioavailability

PubMed Central

Destaillats, Frédéric; Oliveira, Manuel; Bastic Schmid, Viktoria; Masserey-Elmelegy, Isabelle; Giuffrida, Francesca; Thakkar, Sagar K.; Dupuis, Lénaïck; Gosoniu, Maria Laura; Cruz-Hernandez, Cristina

2018-01-01

Phospholipids (PL) or partial acylglycerols such as sn-1(3)-monoacylglycerol (MAG) are potent dietary carriers of long-chain polyunsaturated fatty acids (LC-PUFA) and have been reported to provide superior bioavailability when compared to conventional triacylglycerol (TAG). The main objective of the present study was to compare the incorporation of docosahexaenoic acid (DHA) in plasma, erythrocytes, retina and brain tissues in adult rats when provided as PL (PL-DHA) and MAG (MAG-DHA). Conventional dietary DHA oil containing TAG (TAG-DHA) as well as control chow diet were used to evaluate the potency of the two alternative DHA carriers over a 60-day feeding period. Fatty acid profiles were determined in erythrocytes and plasma lipids at time 0, 7, 14, 28, 35 and 49 days of the experimental period and in retina, cortex, hypothalamus, and hippocampus at 60 days. The assessment of the longitudinal evolution of DHA in erythrocyte and plasma lipids suggest that PL-DHA and MAG-DHA are efficient carriers of dietary DHA when compared to conventional DHA oil (TAG-DHA). Under these experimental conditions, both PL-DHA and MAG-DHA led to higher incorporations of DHA erythrocytes lipids compared to TAG-DHA group. After 60 days of supplementation, statistically significant increase in DHA level incorporated in neural tissues analyzed were observed in the DHA groups compared with the control. The mechanism explaining hypothetically the difference observed in circulatory lipids is discussed. PMID:29762503

Dreaming and insight

PubMed Central

Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

2013-01-01

This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

Insight and analysis problem solving in microbes to machines.

PubMed

Clark, Kevin B

2015-11-01

A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright

Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants

PubMed Central

Hofberger, Johannes A.; Ramirez, Aldana M.; van den Bergh, Erik; Zhu, Xinguang; Bouwmeester, Harro J.; Schuurink, Robert C.; Schranz, M. Eric

2015-01-01

An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species. PMID

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Social media guest listen as Bruce Banerdt, InSight principal investigator, NASA JPL, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Fermi GBM Observations During the Second Observing Run of LIGO/Virgo

NASA Astrophysics Data System (ADS)

Goldstein, Adam; Fermi-GBM

2018-01-01

The Fermi Gamma-ray Burst Monitor (GBM) is a prolific detector of gamma-ray bursts (GRBs) and detects more short duration GRBs than any other instrument currently in operation. Short GRBs are thought to be associated with the mergers of binary neutron star systems (or neutron star-black hole systems), and are therefore considered likely counterparts to gravitational-wave detections from LIGO/Virgo. We report on the GBM observations during the second observing run of LIGO/Virgo and detail the physical and astrophysical insights that might be gleaned from a joint detection of a short GRB and a gravitational-wave source.

Satellite-derived SIF and CO2 Observations Show Coherent Responses to Interannual Climate Variations

NASA Astrophysics Data System (ADS)

Butterfield, Z.; Hogikyan, A.; Kulawik, S. S.; Keppel-Aleks, G.

2017-12-01

Gross primary production (GPP) is the single largest carbon flux in the Earth system, but its sensitivity to changes in climate is subject to significant uncertainty. Satellite measurements of solar-induced chlorophyll fluorescence (SIF) offer insight into spatial and temporal patterns in GPP at a global scale and, combined with other satellite-derived datasets, provide unprecedented opportunity to explore interactions between atmospheric CO2, GPP, and climate variability. To explore potential drivers of GPP in the Northern Hemisphere (NH), we compare monthly-averaged SIF data from the Global Ozone Monitoring Experiment 2 (GOME-2) with observed anomalies in temperature (T; CRU-TS), liquid water equivalent (LWE) from the Gravity Recovery and Climate Experiment (GRACE), and photosynthetically active radiation (PAR; CERES SYN1deg). Using observations from 2007 through 2015 for several NH regions, we calculate month-specific sensitivities of SIF to variability in T, LWE, and PAR. These sensitivities provide insight into the seasonal progression of how productivity is affected by climate variability and can be used to effectively model the observed SIF signal. In general, we find that high temperatures are beneficial to productivity in the spring, but detrimental in the summer. The influences of PAR and LWE are more heterogeneous between regions; for example, higher LWE in North American temperate forest leads to decreased springtime productivity, while exhibiting a contrasting effect in water-limited regions. Lastly, we assess the influence of variations in terrestrial productivity on atmospheric carbon using a new lower tropospheric CO2 product derived from the Greenhouse Gases Observing Satellite (GOSAT). Together, these data shed light on the drivers of interannual variability in the annual cycle of NH atmospheric CO2, and may provide improved constraints on projections of long-term carbon cycle responses to climate change.

Long, paired A'A/Pahoehoe flows of Mauna Loa: Volcanological significance and insights they provide into volcano plumbing systems

NASA Technical Reports Server (NTRS)

Rowland, Scott K.; Walker, George P. L.

1987-01-01

The long lava flows of Mauna Loa, Hawaii have been cited as Earth's closed analogs to the large Martian flows. It is therefore important to understand the flow mechanics and characteristics of the Mauna Loa flows and to make use of these in an attempt to gain insights into Martian eruptive processes. Two fundamentally different kinds of long lava flows can be distinguished on Hawaiian volcanoes as in Martian flows. The two kinds may have identical initial viscosities, chemical compositions, flow lengths, and flow volumes, but their flow mechanisms and thermal energy budgets are radically different. One travels a distance set by the discharge rate as envisaged by Walker and Wadge, and the other travels a distance set mainly by the eruption duration and ground slope. In the Mauna Loa lavas, yield strength becomes an important flow morphology control only in the distal part of a'a lavas. The occurrence of paired flows on Mauna Loa yields insights into the internal plumbing systems of the volcano, and it is significant that all of the volume of the a'a flow must be stored in a magma chamber before eruption, while none of the volume of the pahoehoe needs to be so stored. Differentiation between the two kinds of flows on images of Martian volcanoes is possible and hence an improved understanding of these huge structures is acquired.

INSIGHT: RFID and Bluetooth enabled automated space for the blind and visually impaired.