The conscientious retiree: The relationship between conscientiousness, retirement, and volunteering

PubMed Central

Mike, Anissa; Jackson, Joshua J.; Oltmanns, Thomas F.

2015-01-01

The current study examined the relationship between conscientiousness, work status, and volunteering utilizing two large samples, the St. Louis Personality and Aging Network (SPAN) and the Health and Retirement Study (HRS). It was hypothesized that conscientious adults who were retired would be more likely to volunteer because, after retirement, they gain a substantial amount of free time, while losing an outlet for their industrious and achievement-striving tendencies. Cross-sectional and longitudinal analyses revealed that conscientious, retired individuals were more likely to volunteer than conscientious, working individuals. Further analyses revealed that facets of conscientiousness provide differential information from the general trait. These findings indicate that volunteering during retirement fills an important niche for high-striving, conscientious individuals. PMID:25843985

Cross-laboratory comparative study of the impact of experimental and regression methodologies on salmonella thermal inactivation parameters in ground beef

USDA-ARS?s Scientific Manuscript database

Isothermal inactivation studies are commonly used to quantify thermal inactivation kinetics of bacteria. Meta-analyses and comparisons utilizing results from multiple sources have revealed large variations in reported inactivation parameters for Salmonella, even in similar food materials. Different ...

Psychosocial and Cultural Factors Influencing Expectations of Menarche: A Study on Chinese Premenarcheal Teenage Girls

ERIC Educational Resources Information Center

Yeung, Dannii Y. L.; Tang, Catherine So-kum; Lee, Antoinette

2005-01-01

This study explored how psychosocial and cultural factors influenced expectations of menarche among 476 Chinese premenarcheal teenage girls. Results showed that participants' expectations of menarche were largely negative and heavily influenced by cultural beliefs about menstruation. Findings of hierarchical regression analyses revealed that…

Large-scale replication study reveals a limit on probabilistic prediction in language comprehension.

PubMed

Nieuwland, Mante S; Politzer-Ahles, Stephen; Heyselaar, Evelien; Segaert, Katrien; Darley, Emily; Kazanina, Nina; Von Grebmer Zu Wolfsthurn, Sarah; Bartolozzi, Federica; Kogan, Vita; Ito, Aine; Mézière, Diane; Barr, Dale J; Rousselet, Guillaume A; Ferguson, Heather J; Busch-Moreno, Simon; Fu, Xiao; Tuomainen, Jyrki; Kulakova, Eugenia; Husband, E Matthew; Donaldson, David I; Kohút, Zdenko; Rueschemeyer, Shirley-Ann; Huettig, Falk

2018-04-03

Do people routinely pre-activate the meaning and even the phonological form of upcoming words? The most acclaimed evidence for phonological prediction comes from a 2005 Nature Neuroscience publication by DeLong, Urbach and Kutas, who observed a graded modulation of electrical brain potentials (N400) to nouns and preceding articles by the probability that people use a word to continue the sentence fragment ('cloze'). In our direct replication study spanning 9 laboratories ( N =334), pre-registered replication-analyses and exploratory Bayes factor analyses successfully replicated the noun-results but, crucially, not the article-results. Pre-registered single-trial analyses also yielded a statistically significant effect for the nouns but not the articles. Exploratory Bayesian single-trial analyses showed that the article-effect may be non-zero but is likely far smaller than originally reported and too small to observe without very large sample sizes. Our results do not support the view that readers routinely pre-activate the phonological form of predictable words. © 2018, Nieuwland et al.

Large-scale replication study reveals a limit on probabilistic prediction in language comprehension

PubMed Central

Politzer-Ahles, Stephen; Heyselaar, Evelien; Segaert, Katrien; Darley, Emily; Kazanina, Nina; Von Grebmer Zu Wolfsthurn, Sarah; Bartolozzi, Federica; Kogan, Vita; Ito, Aine; Mézière, Diane; Barr, Dale J; Rousselet, Guillaume A; Ferguson, Heather J; Busch-Moreno, Simon; Fu, Xiao; Tuomainen, Jyrki; Kulakova, Eugenia; Husband, E Matthew; Donaldson, David I; Kohút, Zdenko; Rueschemeyer, Shirley-Ann; Huettig, Falk

2018-01-01

Do people routinely pre-activate the meaning and even the phonological form of upcoming words? The most acclaimed evidence for phonological prediction comes from a 2005 Nature Neuroscience publication by DeLong, Urbach and Kutas, who observed a graded modulation of electrical brain potentials (N400) to nouns and preceding articles by the probability that people use a word to continue the sentence fragment (‘cloze’). In our direct replication study spanning 9 laboratories (N=334), pre-registered replication-analyses and exploratory Bayes factor analyses successfully replicated the noun-results but, crucially, not the article-results. Pre-registered single-trial analyses also yielded a statistically significant effect for the nouns but not the articles. Exploratory Bayesian single-trial analyses showed that the article-effect may be non-zero but is likely far smaller than originally reported and too small to observe without very large sample sizes. Our results do not support the view that readers routinely pre-activate the phonological form of predictable words. PMID:29631695

A tale of two magmas: Petrological insights into mafic and intermediate Plinian volcanism at Volcán de Colima, Mexico

NASA Astrophysics Data System (ADS)

Crummy, J. M.; Savov, I. P.; Morgan, D. J.; Wilson, M.; Loughlin, S.; Navarro-Ochoa, C.

2012-12-01

Volcán de Colima in western Mexico explosively erupts basaltic to high-silica andesitic magmas. Detailed petrological and geochemical analyses of Holocene tephra fallout deposits reveal two distinct magma types: I. typical calc-alkaline series magmas; and II. mixed calc-alkaline - alkaline magmas. Group I magmas comprise basalt to high-silica andesite (50.7 to 60.4 wt.% SiO2) and typically contain phenocrysts of plagioclase + clinopyroxene + orthopyroxene + Fe-Ti oxides ± hornblende ± olivine. Crystallinity varies from 10-25 vol.% dominated by plagioclase in a groundmass comprising highly vesiculated glass with abundant microlites. Back-scatter electron (BSE) microscope images together with electron microprobe analyses (EPMA) reveal complex zoning patterns and compositional variations in plagioclase and pyroxene phenocrysts. Large scale resorption events with dissolution surfaces cross-cutting multiple growth zones, combined with large steps in An content of up to 20 mol.% in plagioclase, and Mg# varying from 0.74 to 0.86 in clinopyroxene and orthopyroxene, indicates destabilisation and recrystallisation in a more mafic melt: increases in Cr coincident with step increases in Mg# reveal mafic magma recharge. Many plagioclase and pyroxene phenocrysts record multiple magma recharge events; while small-scale oscillations reveal compositional fluctuations as a result of decompression and degassing. Group II magmas comprise basalt to basaltic-andesite (48.3 to 57.5 wt.% SiO2) and contain 10-15 vol.% crystals comprising clinopyroxene + olivine + phlogopite + plagioclase + Fe-Ti oxides ± hornblende ± orthopyroxene. The groundmass comprises highly vesiculated glass with abundant microlites of the same mineral phases. Clinopyroxene phenocrysts have magnesian cores (Mg# 0.88-0.89) that display strong dissolution with clear resorption and recrystallisation. EPMA analyses reveal large compositional differences with the surrounding growth zone (Mg# 0.80) indicating recrystallisation and re-equilibration within a compositionally different melt. This composition of the clinopyroxene is similar to that of the Group I magmas. Whole-rock geochemical and Sr and Nd isotopic analyses reveal strong trends in the Group II magmas towards the composition of monogenetic cinder cones composed of phlogopite-bearing alkaline lamprophyre situated to the north of Volcán de Colima. The alkaline magmas are thought to have formed from partial melting of metasomatically enriched veins within the lithospheric mantle. We suggest the high Mg clinopyroxene cores of the Group II magmas crystallised from such alkaline melts, which then mixed with the parental mantle-derived melts of the Group I magmas. Geothermometry and hygrometry based on mineral-mineral and mineral-melt equilibria reveal no correlation between variations in eruption temperature (930-1000°C) and magmatic H2O content (3-6 wt.%) with magma composition. This implies magma composition and volatile content are not controlling the highly explosive mafic and intermediate eruptions at Volcán de Colima, but rather, are driven by very fast ascent rates from source to surface.

Complete Genome Sequence of Biofilm-Forming Strain Staphylococcus haemolyticus S167.

PubMed

Hong, Jisoo; Kim, Jonguk; Kim, Byung-Yong; Park, Jin-Woo; Ryu, Jae-Gee; Roh, Eunjung

2016-06-16

Staphylococcus haemolyticus S167 has the ability to produce biofilms in large quantities. Genomic analyses revealed information on the biofilm-related genes of S. haemolyticus S167. Detailed studies of biofilm formation at the molecular level could provide a foundation for biofilm control research. Copyright © 2016 Hong et al.

Towards a Risk-Based Typology for Transnational Education

ERIC Educational Resources Information Center

Healey, Nigel Martin

2015-01-01

Transnational education (TNE) has been a growth area for UK universities over the last decade. The standard typology classifies TNE by the nature of the activity (i.e., distance learning, international branch campus, franchise, and validation). By analysing a large number of TNE partnerships around the world, this study reveals that the current…

Ethnic Variations in the Connection between Work-Induced Family Separation and Turnover Intent

ERIC Educational Resources Information Center

Behnke, Andrew O.; MacDermid, Shelley M.; Anderson, James C.; Weiss, Howard M.

2010-01-01

Using conservation of resources theory, this study examines the role of resources in the relationship between work-induced family separation and workers' intentions to leave their employment and how these relationships vary across ethnic groups. Analyses of a large representative sample of military members reveal that family separation is…

Comparative population genomics of fusarium graminearum reveals adaptive divergence among cereal head blight pathogens

USDA-ARS?s Scientific Manuscript database

During the last decade, a combination of molecular surveillance and population genetic analyses have significantly altered our understanding of Fusarium graminearum, the major FHB pathogen in North America. In addition to the native NA1 population (largely 15ADON toxin type) and the invasive NA2 pop...

Qualitative Analysis of Student Perceptions: ''Some Advisors Care. Some Don't.''

ERIC Educational Resources Information Center

Walker, Ruth V.; Zelin, Alexandra I.; Behrman, Carolyn; Strnad, Rachel

2017-01-01

University-based academic advising at a large, Great Lakes state institution was designed to support first-year students' transition to college. We conducted individual interviews and facilitated story circles with 162 students to determine their perceived effectiveness of advising. Analyses revealed four overarching themes: student difficulty…

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

PubMed

Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

2015-05-01

The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

Differential protein folding and chemical changes in lung tissues exposed to asbestos or particulates

PubMed Central

Pascolo, Lorella; Borelli, Violetta; Canzonieri, Vincenzo; Gianoncelli, Alessandra; Birarda, Giovanni; Bedolla, Diana E.; Salomé, Murielle; Vaccari, Lisa; Calligaro, Carla; Cotte, Marine; Hesse, Bernhard; Luisi, Fernando; Zabucchi, Giuliano; Melato, Mauro; Rizzardi, Clara

2015-01-01

Environmental and occupational inhalants may induce a large number of pulmonary diseases, with asbestos exposure being the most risky. The mechanisms are clearly related to chemical composition and physical and surface properties of materials. A combination of X-ray fluorescence (μXRF) and Fourier Transform InfraRed (μFTIR) microscopy was used to chemically characterize and compare asbestos bodies versus environmental particulates (anthracosis) in lung tissues from asbestos exposed and control patients. μXRF analyses revealed heterogeneously aggregated particles in the anthracotic structures, containing mainly Si, K, Al and Fe. Both asbestos and particulates alter lung iron homeostasis, with a more marked effect in asbestos exposure. μFTIR analyses revealed abundant proteins on asbestos bodies but not on anthracotic particles. Most importantly, the analyses demonstrated that the asbestos coating proteins contain high levels of β-sheet structures. The occurrence of conformational changes in the proteic component of the asbestos coating provides new insights into long-term asbestos effects. PMID:26159651

Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

PubMed

Eastman, Alexander W; Heinrichs, David E; Yuan, Ze-Chun

2014-10-03

Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

School Staff Responses to Gender-Based Bullying as Moral Interpretation: An Exploratory Study

ERIC Educational Resources Information Center

Anagnostopoulos, Dorothea; Buchanan, Nicole T.; Pereira, Christine; Lichty, Lauren F.

2009-01-01

Gender-based bullying is the most common form of violence that students encounter in U.S. public schools. Several large-scale surveys reveal its consequences for students. Fewer studies examine how school staff members make sense of and respond to such violence. The authors address this knowledge gap by presenting analyses of interviews conducted…

Elementary Teachers' Perspectives of Mathematics Problem Solving Strategies

ERIC Educational Resources Information Center

Bruun, Faye

2013-01-01

Participants in this study were asked to report what strategies were most often used in their attempts to foster their students' problem solving abilities. Participants included 70 second through fifth-grade elementary teachers from 42 schools in a large state of the south central region in the U.S. Data analyses of the interviews revealed that…

Within-Year Changes in Children's Intrinsic and Extrinsic Motivational Orientations: Contextual Predictors and Academic Outcomes

ERIC Educational Resources Information Center

Corpus, Jennifer Henderlong; McClintic-Gilbert, Megan S.; Hayenga, Amynta O.

2009-01-01

The present study was designed to investigate the nature, timing, and correlates of motivational change among a large sample (N = 1051) of third- through eighth-grade students. Analyses of within-year changes in students' motivational orientations revealed that both intrinsic and extrinsic motivations decreased from fall to spring, with declines…

Avenues to Prestige among Adolescents in Public and Religiously Affiliated High Schools

ERIC Educational Resources Information Center

Suitor, J. Jill; Powers, Rebecca S.; Brown, Rachel

2004-01-01

We used data from 1,733 college students to explore whether adolescents' avenues to prestige differ in public and private high schools. Students attending seven large universities during the 1997-98 academic year provided information on the ways in which adolescents in their high schools had gained prestige with peers. The analyses revealed no…

Implementation of School Choice Policy: Interpretation and Response by Parents of Students with Special Educational Needs.

ERIC Educational Resources Information Center

Bagley, Carl; Woods, Philip A.; Woods, Glenys

2001-01-01

Provides empirically based insights into preferences, perceptions, and responses of parents of students with special education needs to the 1990s restructured school system in England. Uses analyses of quantitative/qualitative data generated by a large-scale research study on school choice. Reveals depth and range of problems encountered by these…

Educators vs. Entrepreneurs: Traits and Bias in the Teaching of SWOT

ERIC Educational Resources Information Center

Clark, Andre

2011-01-01

A study of the marks allocated by 10 tutors to 263 students' SWOT (Strengths, Weaknesses, Opportunities, Threats) analyses on a range of business education courses reveals a largely hidden assumption regarding the balance of the four factors. To investigate the significance of this in light of the suggestion in the trait literature that…

Strategies for Effecting System-Wide Pedagogical Change: Identifying and Addressing the Gap between Organizational and Pedagogical Implementation

ERIC Educational Resources Information Center

Weinberger, Yehudith

2018-01-01

The study described here analyses a faculty-wide change designed to foster the communication proficiencies of students in a large teacher education college, gathering data from various sources over three years of the new agenda's implementation. Qualitative and quantitative data analysis revealed that implementation was progressing on two distinct…

One precursor, three apolipoproteins: the relationship between two crustacean lipoproteins, the large discoidal lipoprotein and the high density lipoprotein/β-glucan binding protein.

PubMed

Stieb, Stefanie; Roth, Ziv; Dal Magro, Christina; Fischer, Sabine; Butz, Eric; Sagi, Amir; Khalaila, Isam; Lieb, Bernhard; Schenk, Sven; Hoeger, Ulrich

2014-12-01

The novel discoidal lipoprotein (dLp) recently detected in the crayfish, differs from other crustacean lipoproteins in its large size, apoprotein composition and high lipid binding capacity, We identified the dLp sequence by transcriptome analyses of the hepatopancreas and mass spectrometry. Further de novo assembly of the NGS data followed by BLAST searches using the sequence of the high density lipoprotein/1-glucan binding protein (HDL-BGBP) of Astacus leptodactylus as query revealed a putative precursor molecule with an open reading frame of 14.7 kb and a deduced primary structure of 4889 amino acids. The presence of an N-terminal lipid bind- ing domain and a DUF 1943 domain suggests the relationship with the large lipid transfer proteins. Two-putative dibasic furin cleavage sites were identified bordering the sequence of the HDL-BGBP. When subjected to mass spectroscopic analyses, tryptic peptides of the large apoprotein of dLp matched the N-terminal part of the precursor, while the peptides obtained for its small apoprotein matched the C-terminal part. Repeating the analysis in the prawn Macrobrachium rosenbergii revealed a similar protein with identical domain architecture suggesting that our findings do not represent an isolated instance. Our results indicate that the above three apolipoproteins (i.e HDL-BGBP and both the large and the small subunit of dLp) are translated as a large precursor. Cleavage at the furin type sites releases two subunits forming a heterodimeric dLP particle, while the remaining part forms an HDL-BGBP whose relationship with other lipoproteins as well as specific functions are yet to be elucidated.

Stratospheric water vapour in the vicinity of the Arctic polar vortex

NASA Astrophysics Data System (ADS)

Maturilli, M.; Fierli, F.; Yushkov, V.; Lukyanov, A.; Khaykin, S.; Hauchecorne, A.

2006-07-01

The stratospheric water vapour mixing ratio inside, outside, and at the edge of the polar vortex has been accurately measured by the FLASH-B Lyman-Alpha hygrometer during the LAUTLOS campaign in Sodankylä, Finland, in January and February 2004. The retrieved H2O profiles reveal a detailed view on the Arctic lower stratospheric water vapour distribution, and provide a valuable dataset for the validation of model and satellite data. Analysing the measurements with the semi-lagrangian advection model MIMOSA, water vapour profiles typical for the polar vortex' interior and exterior have been identified, and laminae in the observed profiles have been correlated to filamentary structures in the potential vorticity field. Applying the validated MIMOSA transport scheme to specific humidity fields from operational ECMWF analyses, large discrepancies from the observed profiles arise. Although MIMOSA is able to reproduce weak water vapour filaments and improves the shape of the profiles compared to operational ECMWF analyses, both models reveal a dry bias of about 1 ppmv in the lower stratosphere above 400 K, accounting for a relative difference from the measurements in the order of 20%. The large dry bias in the analysis representation of stratospheric water vapour in the Arctic implies the need for future regular measurements of water vapour in the polar stratosphere to allow the validation and improvement of climate models.

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

PubMed Central

Sun, Keping; Kimball, Rebecca T.; Liu, Tong; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Lin, Aiqing; Feng, Jiang

2016-01-01

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization. PMID:27748429

Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment.

PubMed

Shaffer, John R; Li, Jinxi; Lee, Myoung Keun; Roosenboom, Jasmien; Orlova, Ekaterina; Adhikari, Kaustabh; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; González-José, Rolando; Pfeffer, Paige E; Wollenschlaeger, Christopher A; Hecht, Jacqueline T; Wehby, George L; Moreno, Lina M; Ding, Anan; Jin, Li; Yang, Yajun; Carlson, Jenna C; Leslie, Elizabeth J; Feingold, Eleanor; Marazita, Mary L; Hinds, David A; Cox, Timothy C; Wang, Sijia; Ruiz-Linares, Andrés; Weinberg, Seth M

2017-12-07

The genetic basis of earlobe attachment has been a matter of debate since the early 20 th century, such that geneticists argue both for and against polygenic inheritance. Recent genetic studies have identified a few loci associated with the trait, but large-scale analyses are still lacking. Here, we performed a genome-wide association study of lobe attachment in a multiethnic sample of 74,660 individuals from four cohorts (three with the trait scored by an expert rater and one with the trait self-reported). Meta-analysis of the three expert-rater-scored cohorts revealed six associated loci harboring numerous candidate genes, including EDAR, SP5, MRPS22, ADGRG6 (GPR126), KIAA1217, and PAX9. The large self-reported 23andMe cohort recapitulated each of these six loci. Moreover, meta-analysis across all four cohorts revealed a total of 49 significant (p < 5 × 10 -8 ) loci. Annotation and enrichment analyses of these 49 loci showed strong evidence of genes involved in ear development and syndromes with auricular phenotypes. RNA sequencing data from both human fetal ear and mouse second branchial arch tissue confirmed that genes located among associated loci showed evidence of expression. These results provide strong evidence for the polygenic nature of earlobe attachment and offer insights into the biological basis of normal and abnormal ear development. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A New Group of Hepadnaviruses Naturally Infecting Orangutans (Pongo pygmaeus)

PubMed Central

Warren, Kristin S.; Heeney, Jonathan L.; Swan, Ralph A.; Heriyanto; Verschoor, Ernst J.

1999-01-01

A high prevalence (42.6%) of hepatitis B virus (HBV) infection was suspected in 195 formerly captive orangutans due to a large number of serum samples which cross-reacted with human HBV antigens. It was assumed that such viral infections were contracted from humans during captivity. However, two wild orangutans were identified which were HBV surface antigen positive, indicating that HBV or related viruses may be occurring naturally in the orangutan populations. Sequence analyses of seven isolates revealed that orangutans were infected with hepadnaviruses but that these were clearly divergent from the six known human HBV genotypes and those of other nonhuman hepadnaviruses reported. Phylogenetic analyses revealed geographic clustering with Southeast Asian genotype C viruses and gibbon ape HBV. This implies a common origin of infection within this geographic region, with cross-species transmission of hepadnaviruses among hominoids. PMID:10438880

Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary.

PubMed

Tremblay, Louis A; Clark, Dana; Sinner, Jim; Ellis, Joanne I

2017-09-20

The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.

PubMed

Sharma, Rahul; Xia, Xiaojuan; Cano, Liliana M; Evangelisti, Edouard; Kemen, Eric; Judelson, Howard; Oome, Stan; Sambles, Christine; van den Hoogen, D Johan; Kitner, Miloslav; Klein, Joël; Meijer, Harold J G; Spring, Otmar; Win, Joe; Zipper, Reinhard; Bode, Helge B; Govers, Francine; Kamoun, Sophien; Schornack, Sebastian; Studholme, David J; Van den Ackerveken, Guido; Thines, Marco

2015-10-05

Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.

Large-scale genomic analyses link reproductive ageing to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

PubMed Central

Lunetta, Kathryn L.; Pervjakova, Natalia; Chasman, Daniel I.; Stolk, Lisette; Finucane, Hilary K.; Sulem, Patrick; Bulik-Sullivan, Brendan; Esko, Tõnu; Johnson, Andrew D.; Elks, Cathy E.; Franceschini, Nora; He, Chunyan; Altmaier, Elisabeth; Brody, Jennifer A.; Franke, Lude L.; Huffman, Jennifer E.; Keller, Margaux F.; McArdle, Patrick F.; Nutile, Teresa; Porcu, Eleonora; Robino, Antonietta; Rose, Lynda M.; Schick, Ursula M.; Smith, Jennifer A.; Teumer, Alexander; Traglia, Michela; Vuckovic, Dragana; Yao, Jie; Zhao, Wei; Albrecht, Eva; Amin, Najaf; Corre, Tanguy; Hottenga, Jouke-Jan; Mangino, Massimo; Smith, Albert V.; Tanaka, Toshiko; Abecasis, Goncalo; Andrulis, Irene L.; Anton-Culver, Hoda; Antoniou, Antonis C.; Arndt, Volker; Arnold, Alice M.; Barbieri, Caterina; Beckmann, Matthias W.; Beeghly-Fadiel, Alicia; Benitez, Javier; Bernstein, Leslie; Bielinski, Suzette J.; Blomqvist, Carl; Boerwinkle, Eric; Bogdanova, Natalia V.; Bojesen, Stig E.; Bolla, Manjeet K.; Borresen-Dale, Anne-Lise; Boutin, Thibaud S; Brauch, Hiltrud; Brenner, Hermann; Brüning, Thomas; Burwinkel, Barbara; Campbell, Archie; Campbell, Harry; Chanock, Stephen J.; Chapman, J. Ross; Chen, Yii-Der Ida; Chenevix-Trench, Georgia; Couch, Fergus J.; Coviello, Andrea D.; Cox, Angela; Czene, Kamila; Darabi, Hatef; De Vivo, Immaculata; Demerath, Ellen W.; Dennis, Joe; Devilee, Peter; Dörk, Thilo; dos-Santos-Silva, Isabel; Dunning, Alison M.; Eicher, John D.; Fasching, Peter A.; Faul, Jessica D.; Figueroa, Jonine; Flesch-Janys, Dieter; Gandin, Ilaria; Garcia, Melissa E.; García-Closas, Montserrat; Giles, Graham G.; Girotto, Giorgia G.; Goldberg, Mark S.; González-Neira, Anna; Goodarzi, Mark O.; Grove, Megan L.; Gudbjartsson, Daniel F.; Guénel, Pascal; Guo, Xiuqing; Haiman, Christopher A.; Hall, Per; Hamann, Ute; Henderson, Brian E.; Hocking, Lynne J.; Hofman, Albert; Homuth, Georg; Hooning, Maartje J.; Hopper, John L.; Hu, Frank B.; Huang, Jinyan; Humphreys, Keith; Hunter, David J.; Jakubowska, Anna; Jones, Samuel E.; Kabisch, Maria; Karasik, David; Knight, Julia A.; Kolcic, Ivana; Kooperberg, Charles; Kosma, Veli-Matti; Kriebel, Jennifer; Kristensen, Vessela; Lambrechts, Diether; Langenberg, Claudia; Li, Jingmei; Li, Xin; Lindström, Sara; Liu, Yongmei; Luan, Jian’an; Lubinski, Jan; Mägi, Reedik; Mannermaa, Arto; Manz, Judith; Margolin, Sara; Marten, Jonathan; Martin, Nicholas G.; Masciullo, Corrado; Meindl, Alfons; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L.; Müller-Nurasyid, Martina; Nalls, Michael; Neale, Ben M.; Nevanlinna, Heli; Neven, Patrick; Newman, Anne B.; Nordestgaard, Børge G.; Olson, Janet E.; Padmanabhan, Sandosh; Peterlongo, Paolo; Peters, Ulrike; Petersmann, Astrid; Peto, Julian; Pharoah, Paul D.P.; Pirastu, Nicola N.; Pirie, Ailith; Pistis, Giorgio; Polasek, Ozren; Porteous, David; Psaty, Bruce M.; Pylkäs, Katri; Radice, Paolo; Raffel, Leslie J.; Rivadeneira, Fernando; Rudan, Igor; Rudolph, Anja; Ruggiero, Daniela; Sala, Cinzia F.; Sanna, Serena; Sawyer, Elinor J.; Schlessinger, David; Schmidt, Marjanka K.; Schmidt, Frank; Schmutzler, Rita K.; Schoemaker, Minouk J.; Scott, Robert A.; Seynaeve, Caroline M.; Simard, Jacques; Sorice, Rossella; Southey, Melissa C.; Stöckl, Doris; Strauch, Konstantin; Swerdlow, Anthony; Taylor, Kent D.; Thorsteinsdottir, Unnur; Toland, Amanda E.; Tomlinson, Ian; Truong, Thérèse; Tryggvadottir, Laufey; Turner, Stephen T.; Vozzi, Diego; Wang, Qin; Wellons, Melissa; Willemsen, Gonneke; Wilson, James F.; Winqvist, Robert; Wolffenbuttel, Bruce B.H.R.; Wright, Alan F.; Yannoukakos, Drakoulis; Zemunik, Tatijana; Zheng, Wei; Zygmunt, Marek; Bergmann, Sven; Boomsma, Dorret I.; Buring, Julie E.; Ferrucci, Luigi; Montgomery, Grant W.; Gudnason, Vilmundur; Spector, Tim D.; van Duijn, Cornelia M; Alizadeh, Behrooz Z.; Ciullo, Marina; Crisponi, Laura; Easton, Douglas F.; Gasparini, Paolo P.; Gieger, Christian; Harris, Tamara B.; Hayward, Caroline; Kardia, Sharon L.R.; Kraft, Peter; McKnight, Barbara; Metspalu, Andres; Morrison, Alanna C.; Reiner, Alex P.; Ridker, Paul M.; Rotter, Jerome I.; Toniolo, Daniela; Uitterlinden, André G.; Ulivi, Sheila; Völzke, Henry; Wareham, Nicholas J.; Weir, David R.; Yerges-Armstrong, Laura M.; Price, Alkes L.; Stefansson, Kari; Visser, Jenny A.; Ong, Ken K.; Chang-Claude, Jenny; Murabito, Joanne M.; Perry, John R.B.; Murray, Anna

2015-01-01

Menopause timing has a substantial impact on infertility and risk of disease, including breast cancer, but the underlying mechanisms are poorly understood. We report a dual strategy in ~70,000 women to identify common and low-frequency protein-coding variation associated with age at natural menopause (ANM). We identified 44 regions with common variants, including two harbouring additional rare missense alleles of large effect. We found enrichment of signals in/near genes involved in delayed puberty, highlighting the first molecular links between the onset and end of reproductive lifespan. Pathway analyses revealed a major association with DNA damage-response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomisation analyses supported a causal effect of later ANM on breast cancer risk (~6% risk increase per-year, P=3×10−14), likely mediated by prolonged sex hormone exposure, rather than DDR mechanisms. PMID:26414677

Systems Analysis, Machineable Circulation Data and Library Users and Non-Users.

ERIC Educational Resources Information Center

Lubans, John, Jr.

A study to be made with computer-based circulation data of the non-use and use of a large academic library is discussed. A search of the literature reveals that computer-based circulation systems can be, but have not been, utilized to provide data bases for systematic analyses of library users and resources. The data gathered in the circulation…

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

The STD/MHD codes - Comparison of analyses with experiments at AEDC/HPDE, Reynolds Metal Co., and Hercules, Inc. [for MHD generator flows

NASA Technical Reports Server (NTRS)

Vetter, A. A.; Maxwell, C. D.; Swean, T. F., Jr.; Demetriades, S. T.; Oliver, D. A.; Bangerter, C. D.

1981-01-01

Data from sufficiently well-instrumented, short-duration experiments at AEDC/HPDE, Reynolds Metal Co., and Hercules, Inc., are compared to analyses with multidimensional and time-dependent simulations with the STD/MHD computer codes. These analyses reveal detailed features of major transient events, severe loss mechanisms, and anomalous MHD behavior. In particular, these analyses predicted higher-than-design voltage drops, Hall voltage overshoots, and asymmetric voltage drops before the experimental data were available. The predictions obtained with these analyses are in excellent agreement with the experimental data and the failure predictions are consistent with the experiments. The design of large, high-interaction or advanced MHD experiments will require application of sophisticated, detailed and comprehensive computational procedures in order to account for the critical mechanisms which led to the observed behavior in these experiments.

Alternative polyadenylation: New insights from global analyses

PubMed Central

Shi, Yongsheng

2012-01-01

Recent studies have revealed widespread mRNA alternative polyadenylation (APA) in eukaryotes and its dynamic spatial and temporal regulation. APA not only generates proteomic and functional diversity, but also plays important roles in regulating gene expression. Global deregulation of APA has been demonstrated in a variety of human diseases. Recent exciting advances in the field have been made possible in a large part by high throughput analyses using newly developed experimental tools. Here I review the recent progress in global studies of APA and the insights that have emerged from these and other studies that use more conventional methods. PMID:23097429

Optimization of large animal MI models; a systematic analysis of control groups from preclinical studies.

PubMed

Zwetsloot, P P; Kouwenberg, L H J A; Sena, E S; Eding, J E; den Ruijter, H M; Sluijter, J P G; Pasterkamp, G; Doevendans, P A; Hoefer, I E; Chamuleau, S A J; van Hout, G P J; Jansen Of Lorkeers, S J

2017-10-27

Large animal models are essential for the development of novel therapeutics for myocardial infarction. To optimize translation, we need to assess the effect of experimental design on disease outcome and model experimental design to resemble the clinical course of MI. The aim of this study is therefore to systematically investigate how experimental decisions affect outcome measurements in large animal MI models. We used control animal-data from two independent meta-analyses of large animal MI models. All variables of interest were pre-defined. We performed univariable and multivariable meta-regression to analyze whether these variables influenced infarct size and ejection fraction. Our analyses incorporated 246 relevant studies. Multivariable meta-regression revealed that infarct size and cardiac function were influenced independently by choice of species, sex, co-medication, occlusion type, occluded vessel, quantification method, ischemia duration and follow-up duration. We provide strong systematic evidence that commonly used endpoints significantly depend on study design and biological variation. This makes direct comparison of different study-results difficult and calls for standardized models. Researchers should take this into account when designing large animal studies to most closely mimic the clinical course of MI and enable translational success.

[Emerging novel therapeutic strategy for α-dystroglycanopathy by Large].

PubMed

Saito, Fumiaki

2011-11-01

The past decade of researches have revealed mutations of known or putative glycosyltransferases in several types of muscular dystrophy, including Fukuyama-type congenital muscular dystrophy. In these disorders, the function of α-dystroglycan is severely decreased, therefore they are called α-dystroglycanopathy. Recently, putative glycosyltransferase Large was shown to restore the defective function of α-dystroglycan, thus, it is an intriguing idea to apply this effect to the therapy of α-dystroglycanopathy. In the present study, we sought to test this possibility. Using several cultured cell lines, we confirmed that the overexpression of Large results in hyperglycosylation and marked enhancement of the function of α-dystroglycan. For this effect, the whole luminal domain of Large was shown to be necessary using several deletion constructs. We further generated transgenic mice overexpressing Large ubiquitously. In each tissue of the mice, the glycosylation of α-dystroglycan and its laminin binding activity was remarkably increased. Moreover, the morphological analyses on each tissue stained by H-E revealed no significant abnormality in the transgenic mice, suggesting no serious side effects by the overexpression of Large. Taken together, these results indicate that the restoration of the function of α-dystroglycan by Large should be an important molecular target to develop therapeutic strategies for α-dystroglycanopathy.

The Effects of Repetition on Children’s True and False Reports

PubMed Central

Evans, Angela D.; Brunet, Megan K.; Talwar, Victoria; Bala, Nicholas; Lindsay, Rod C.L.; Lee, Kang

2013-01-01

As children are often called upon to provide testimony in court proceedings, determining the veracity of their statements is an important issue. In the course of investigation by police and social workers, children are often repeatedly interviewed about their experiences, though the impact of this repetition on children’s true and false statements remains largely unexamined. The current study analysed semantic differences in children’s truthful and fabricated statements about an event they had or had not participated in. Results revealed that children’s truthful and fabricated reports differed in linguistic content, and that their language also varied with repetition. Discriminant analyses revealed that with repetition, children’s true and false reports became increasingly difficult to differentiate using linguistic markers, though true reports were consistently classified correctly at higher rates than false reports. The implications of these findings for legal procedures concerning child witnesses are discussed. PMID:24265592

Cathodoluminescence zoning and minor elements in forsterites from the Murchison (C2) and Allende (C3V) carbonaceous chondrites

NASA Technical Reports Server (NTRS)

Steele, I. M.; Smith, J. V.; Skirius, C.

1985-01-01

Cathodoluminescence has been applied to look for textural features of olivine in carbonaceous meteorites relevant to the unresolved dispute over the origin of the olivine, whether from a vapor or a liquid. Cathodoluminescence photographs of forsterite grains in Murchison (C2) and Allende (C3) meteorites presented here reveal a blue core with planar boundaries to a red or dark rim. High-precision electron microprobe analyses have been performed which reveal unusually large amounts of the 'minor' elements Al, Ti, and Ca in the blue cores of these forsterites, suggesting formation by crystallization at high temperatures from a source rich in these metals. Following conclusions drawn from previous analyses of olivine in meteorites, it is argued that the minor element signature should be able to characterize olivines in micrometeorites and in deep-sea particles.

Potential genotoxic effects of melted snow from an urban area revealed by the Allium cepa test.

PubMed

Blagojević, Jelena; Stamenković, Gorana; Vujosević, Mladen

2009-09-01

The presence of well-known atmospheric pollutants is regularly screened for in large towns but knowledge about the effects of mixtures of different pollutants and especially their genotoxic potential is largely missing. Since falling snow collects pollutants from the air, melted snow samples could be suitable for evaluating potential genotoxicity. For this purpose the Allium cepa anaphase-telophase test was used to analyse melted snow samples from Belgrade, the capital city of Serbia. Samples of snow were taken at two sites, characterized by differences in pollution intensity, in three successive years. At the more polluted site the analyses showed a very high degree of both toxicity and genotoxicity in the first year of the study corresponding to the effects of the known mutagen used as the positive control. At the other site the situation was much better but not without warning signals. The results showed that standard analyses for the presence of certain contaminants in the air do not give an accurate picture of the possible consequences of urban air pollution because the genotoxic potential remains hidden. The A. cepa test has been demonstrated to be very convenient for evaluation of air pollution through analyses of melted snow samples.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

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

Devos, Nicolas; Szövényi, Péter; Weston, David J.

In this study, the goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

DOE PAGES

Devos, Nicolas; Szövényi, Péter; Weston, David J.; ...

2016-02-22

In this study, the goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses.

Large‐scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions

PubMed Central

Saiki, Akiko; Fujiwara‐Tsukamoto, Yoko; Sakai, Yutaka; Isomura, Yoshikazu

2016-01-01

Key points There have been few systematic population‐wide analyses of relationships between spike synchrony within a period of several milliseconds and behavioural functions.In this study, we obtained a large amount of spike data from > 23,000 neuron pairs by multiple single‐unit recording from deep layer neurons in motor cortical areas in rats performing a forelimb movement task.The temporal changes of spike synchrony in the whole neuron pairs were statistically independent of behavioural changes during the task performance, although some neuron pairs exhibited correlated changes in spike synchrony.Mutual information analyses revealed that spike synchrony made a smaller contribution than spike rate to behavioural functions.The strength of spike synchrony between two neurons was statistically independent of the spike rate‐based preferences of the pair for behavioural functions. Abstract Spike synchrony within a period of several milliseconds in presynaptic neurons enables effective integration of functional information in the postsynaptic neuron. However, few studies have systematically analysed the population‐wide relationships between spike synchrony and behavioural functions. Here we obtained a sufficiently large amount of spike data among regular‐spiking (putatively excitatory) and fast‐spiking (putatively inhibitory) neuron subtypes (> 23,000 pairs) by multiple single‐unit recording from deep layers in motor cortical areas (caudal forelimb area, rostral forelimb area) in rats performing a forelimb movement task. After holding a lever, rats pulled the lever either in response to a cue tone (external‐trigger trials) or spontaneously without any cue (internal‐trigger trials). Many neurons exhibited functional spike activity in association with forelimb movements, and the preference of regular‐spiking neurons in the rostral forelimb area was more biased toward externally triggered movement than that in the caudal forelimb area. We found that a population of neuron pairs with spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population‐wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate‐based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large‐scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement. PMID:27488936

Ecstasy (MDMA) and memory function: a meta-analytic update.

PubMed

Laws, Keith R; Kokkalis, Joy

2007-08-01

A meta-analysis was conducted to examine the impact of recreational ecstasy use on short-term memory (STM), long-term memory (LTM), verbal and visual memory. We located 26 studies containing memory data for ecstasy and non-ecstasy users from which effect sizes could be derived. The analyses provided measures of STM and LTM in 610 and 439 ecstasy users and revealed moderate-to-large effect sizes (Cohen's d) of d = -0.63 and d = -0.87, respectively. The difference between STM versus LTM was non-significant. The effect size for verbal memory was large (d = -1.00) and significantly larger than the small effect size for visual memory (d = -0.27). Indeed, our analyses indicate that visual memory may be affected more by concurrent cannabis use. Finally, we found that the total lifetime number of ecstasy tablets consumed did not significantly predict memory performance. Copyright 2007 John Wiley & Sons, Ltd.

Towards resolving the complete fern tree of life.

PubMed

Lehtonen, Samuli

2011-01-01

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.

EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

PubMed

Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

2017-08-01

Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A Sunken Ship of the Desert at the River Danube in Tulln, Austria

PubMed Central

Galik, Alfred; Mohandesan, Elmira; Forstenpointner, Gerhard; Scholz, Ute Maria; Ruiz, Emily; Krenn, Martin; Burger, Pamela

2015-01-01

Rescue excavations recovered a skeleton that resurrect the contemporary dramatic history of Austria in the 17th century as troops besieged Vienna in the second Osmanic-Habsburg war. Unique for Central Europe is the evidence of a completely preserved camel skeleton uncovered in a large refuse pit. The male individual of slender stature indicates a few but characteristic pathological changes revealing not a beast of burden but probably a valuable riding animal. Anatomical and morphometrical analyses suggest a hybrid confirmed by the ancient DNA analyses resulting in the presence of a dromedary in the maternal and a Bactrian camel in the paternal line. PMID:25831121

Long-term growth-increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Treesearch

Bryan A. Black; Jason B. Dunham; Brett W. Blundon; Jayne Brim-Box; Alan J. Tepley

2014-01-01

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth-increment width chronologies for freshwater mussel species in the Pacific...

The Influence of Static and Dynamic Intrapersonal Factors on Longitudinal Patterns of Peer Victimization through Mid-adolescence: a Latent Transition Analysis.

PubMed

Haltigan, John D; Vaillancourt, Tracy

2018-01-01

Using 6 cycles (grade 5 through grade 10) of data obtained from a large prospective sample of Canadian school children (N = 700; 52.6% girls), we replicated previous findings concerning the empirical definition of peer victimization (i.e., being bullied) and examined static and dynamic intrapersonal factors associated with its emergence and experiential continuity through mid-adolescence. Latent class analyses consistently revealed a low victimization and an elevated victimization class across time, supporting previous work suggesting peer victimization was defined by degree rather than by type (e.g., physical). Using latent transition analyses (LTA), we found that child sex, parent-perceived pubertal development, and internalizing symptoms influenced the probability of transitioning from the low to the elevated victimization class across time. Higher-order extensions within the LTA modeling framework revealed a lasting effect of grade 5 victimization status on grade 10 victimization status and a large effect of chronic victimization on later parent-reported youth internalizing symptoms (net of prior parent-reported internalizing symptoms) in later adolescence (grade 11). Implications of the current findings for the experience of peer victimization, as well as the application of latent transition analysis as a useful approach for peer victimization research, are discussed.

Histological analysis on adhesive molecules of renal intravascular large B cell lymphoma treated with CHOP chemotherapy and rituximab.

PubMed

Kusaba, T; Hatta, T; Tanda, S; Kameyama, H; Tamagaki, K; Okigaki, M; Inaba, T; Shimazaki, C; Sasaki, S

2006-03-01

A 48-year-old man was admitted to our hospital for investigation of mild renal dysfunction. A blood examination revealed mild elevation of creatinine level (1.77 mg/dl). Urinary examination revealed mild protein excretion (0.54 g/day) and microhematuria; renal biopsy revealed the focal proliferation of large mononuclear cells with mitosis in glomerular capillaries. According to immunohistochemical analysis, the intravascular lymphomatous cells stained positively with anti-leukocyte common antigen (LCA: CD45) and CD20, indicating a B lymphocyte lineage. In electron microscopy, the glomerular capillary was filled with lymphoma cells and epithelial foot process fusion was noted. Immunohistochemical analysis on adhesive molecules revealed a lack of CD11a expression on lymphoma cells, but positive CD54 expression on endothelial cells. Systemic 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) revealed no abnormal uptake of isotopes. On the basis of these findings, we diagnosed intravascular diffuse large B cell lymphoma localized in the kidney. Despite treatment with rituximab and CHOP (prednisolone, doxorubicin, vincristine, cyclophosphamide) for 3 cycles at 1-month intervals, the renal dysfunction did not change. In histopathological analysis of the second biopsy, lymphoma cells disappeared, but focal segmental glomerulosclerosis and moderate interstitial fibrosis were noted. Electron microscopic findings revealed severe subendothelial edema with mesangial interposition, indicating severe endothelial damage. Epithelial foot process fusion was improved. These pathological analyses let us conclude that a lack of CD11a could be a candidate factor for prevention of the extravasation of lymphoma cells from blood vessels in our patient. We also presumed that the intraglomerular endothelial damage occurred due to chemotherapy-associated cell injury.

Serum Tumor Necrosis Factor-alpha associates with Myocardial Oxygen Demand and Exercise Tolerance in Postmenopausal Women.

PubMed

Carter, Stephen J; Bryan, David R; Neumeier, William H; Glasser, Stephen P; Hunter, Gary R

2018-01-01

The functional implications of serum tumor necrosis factor-alpha (TNF-α), a marker of oxidative stress, on hemodynamic parameters at rest and during physical exertion are unclear. The aims of this investigation were to examine the independent associations of TNF-α on myocardial oxygen demand at rest and during submaximal exercise, while also evaluating the association of TNF-α on exercise tolerance. Forty, postmenopausal women, provided blood samples and completed a modified-Balke protocol to measure maximal oxygen uptake (VO 2max ). Large artery compliance was measured by pulse contour analyses while rate-pressure product (RPP), an index of myocardial oxygen demand, was measured at rest and during two submaximal workloads (i.e., ≈55% and ≈75% VO 2max ). RPP was calculated by dividing the product of heart rate and systolic blood pressure (via auscultation) by 100. Exercise tolerance corresponded with the cessation of the graded exercise test. During higher-intensity exertion, ≈75% VO 2max , multiple linear regression revealed a positive association ( r = 0.43; p = 0.015) between TNF-α and RPP while adjusting for maximal heart rate, VO 2max , large artery compliance, and percent body fat. Path analyses revealed a significant indirect effect of large artery compliance on exercise tolerance through TNF-α, β = 0.13, CI [0.03, 0.35], indicating greater levels of TNF-α associated with poorer exercise tolerance. These data suggest TNF-α independently associates with myocardial oxygen demand during physical exertion, thus highlighting the utility of higher-intensity efforts to expose important phenomena not apparent at rest. TNF-α also appears to be indirectly associated with the link between large artery compliance and exercise tolerance.

Item Analyses of Memory Differences

PubMed Central

Salthouse, Timothy A.

2017-01-01

Objective Although performance on memory and other cognitive tests is usually assessed with a score aggregated across multiple items, potentially valuable information is also available at the level of individual items. Method The current study illustrates how analyses of variance with item as one of the factors, and memorability analyses in which item accuracy in one group is plotted as a function of item accuracy in another group, can provide a more detailed characterization of the nature of group differences in memory. Data are reported for two memory tasks, word recall and story memory, across age, ability, repetition, delay, and longitudinal contrasts. Results The item-level analyses revealed evidence for largely uniform differences across items in the age, ability, and longitudinal contrasts, but differential patterns across items in the repetition contrast, and unsystematic item relations in the delay contrast. Conclusion Analyses at the level of individual items have the potential to indicate the manner by which group differences in the aggregate test score are achieved. PMID:27618285

Examining gray matter structure associated with academic performance in a large sample of Chinese high school students.

PubMed

Wang, Song; Zhou, Ming; Chen, Taolin; Yang, Xun; Chen, Guangxiang; Wang, Meiyun; Gong, Qiyong

2017-04-18

Achievement in school is crucial for students to be able to pursue successful careers and lead happy lives in the future. Although many psychological attributes have been found to be associated with academic performance, the neural substrates of academic performance remain largely unknown. Here, we investigated the relationship between brain structure and academic performance in a large sample of high school students via structural magnetic resonance imaging (S-MRI) using voxel-based morphometry (VBM) approach. The whole-brain regression analyses showed that higher academic performance was related to greater regional gray matter density (rGMD) of the left dorsolateral prefrontal cortex (DLPFC), which is considered a neural center at the intersection of cognitive and non-cognitive functions. Furthermore, mediation analyses suggested that general intelligence partially mediated the impact of the left DLPFC density on academic performance. These results persisted even after adjusting for the effect of family socioeconomic status (SES). In short, our findings reveal a potential neuroanatomical marker for academic performance and highlight the role of general intelligence in explaining the relationship between brain structure and academic performance.

Fractal Analyses of High-Resolution Cloud Droplet Measurements.

NASA Astrophysics Data System (ADS)

Malinowski, Szymon P.; Leclerc, Monique Y.; Baumgardner, Darrel G.

1994-02-01

Fractal analyses of individual cloud droplet distributions using aircraft measurements along one-dimensional horizontal cross sections through clouds are performed. Box counting and cluster analyses are used to determine spatial scales of inhomogeneity of cloud droplet spacing. These analyses reveal that droplet spatial distributions do not exhibit a fractal behavior. A high variability in local droplet concentration in cloud volumes undergoing mixing was found. In these regions, thin filaments of cloudy air with droplet concentration close to those observed in cloud cores were found. Results suggest that these filaments may be anisotropic. Additional box counting analyses performed for various classes of cloud droplet diameters indicate that large and small droplets are similarly distributed, except for the larger characteristic spacing of large droplets.A cloud-clear air interface defined by a certain threshold of total droplet count (TDC) was investigated. There are indications that this interface is a convoluted surface of a fractal nature, at least in actively developing cumuliform clouds. In contrast, TDC in the cloud interior does not have fractal or multifractal properties. Finally a random Cantor set (RCS) was introduced as a model of a fractal process with an ill-defined internal scale. A uniform measure associated with the RCS after several generations was introduced to simulate the TDC records. Comparison of the model with real TDC records indicates similar properties of both types of data series.

The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization.

PubMed

Nelson, David R; Khraiwesh, Basel; Fu, Weiqi; Alseekh, Saleh; Jaiswal, Ashish; Chaiboonchoe, Amphun; Hazzouri, Khaled M; O'Connor, Matthew J; Butterfoss, Glenn L; Drou, Nizar; Rowe, Jillian D; Harb, Jamil; Fernie, Alisdair R; Gunsalus, Kristin C; Salehi-Ashtiani, Kourosh

2017-06-17

To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007 , which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta).

PubMed

Devos, Nicolas; Szövényi, Péter; Weston, David J; Rothfels, Carl J; Johnson, Matthew G; Shaw, A Jonathan

2016-07-01

The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome. Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri

PubMed Central

Su, Andreas A. H.; Tripp, Vanessa; Randau, Lennart

2013-01-01

The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution. PMID:23620296

Laterodorsal Nucleus of the Thalamus: A Processor of Somatosensory Inputs

PubMed Central

BEZDUDNAYA, TATIANA; KELLER, ASAF

2009-01-01

The laterodorsal (LD) nucleus of the thalamus has been considered a “higher order” nucleus that provides inputs to limbic cortical areas. Although its functions are largely unknown, it is often considered to be involved in spatial learning and memory. Here we provide evidence that LD is part of a hitherto unknown pathway for processing somatosensory information. Juxtacellular and extracellular recordings from LD neurons reveal that they respond to vibrissa stimulation with short latency (median = 7 ms) and large magnitude responses (median = 1.2 spikes/stimulus). Most neurons (62%) had large receptive fields, responding to six and more individual vibrissae. Electrical stimulation of the trigeminal nucleus interpolaris (SpVi) evoked short latency responses (median = 3.8 ms) in vibrissa-responsive LD neurons. Labeling produced by anterograde and retrograde neuroanatomical tracers confirmed that LD neurons receive direct inputs from SpVi. Electrophysiological and neuroanatomical analyses revealed also that LD projects upon the cingulate and retrosplenial cortex, but has only sparse projections to the barrel cortex. These findings suggest that LD is part of a novel processing stream involved in spatial orientation and learning related to somatosensory cues. PMID:18273888

MAG-EPA reduces severity of DSS-induced colitis in rats.

PubMed

Morin, Caroline; Blier, Pierre U; Fortin, Samuel

2016-05-15

Ulcerative colitis (UC) is a chronic disease characterized by diffuse inflammation of the intestinal mucosa of the large bowel. Omega-3 (ω3) fatty acid supplementation has been associated with a decreased production of inflammatory cytokines involved in UC pathogenesis. The aim of this study was to determine the preventive and therapeutic potential of eicosapentaenoic acid monoglyceride (MAG-EPA) in an in vivo rats model of UC induced by dextran sulfate sodium (DSS). DSS rats were untreated or treated per os with MAG-EPA. Morphological, histological, and biochemical analyses were performed following MAG-EPA administrations. Morphological and histological analyses revealed that MAG-EPA pretreatment (12 days pre-DSS) and treatment (6 days post-DSS) exhibited strong activity in reducing severity of disease in DSS rats. Following MAG-EPA administrations, tissue levels of the proinflammatory cytokines TNF-α, IL-1β, and IL-6 were markedly lower compared with rats treated only with DSS. MAG-EPA per os administration decrease neutrophil infiltration in colon tissues, as depicted by myelohyperoxidase activity. Results also revealed a reduced activation of NF-κB pathways correlated with a decreased expression of COX-2 in colon homogenates derived from MAG-EPA-pretreated and treated rats. Tension measurements performed on colon tissues revealed that contractile responses to methacholine and relaxing effect induced by sodium nitroprusside were largely increased following MAG-EPA treatment. The combined treatment of MAG-EPA and vitamin E displayed an antagonistic effect on anti-inflammatory properties of MAG-EPA in DSS rats. Copyright © 2016 the American Physiological Society.

Functional evaluation of out-of-the-box text-mining tools for data-mining tasks

PubMed Central

Jung, Kenneth; LePendu, Paea; Iyer, Srinivasan; Bauer-Mehren, Anna; Percha, Bethany; Shah, Nigam H

2015-01-01

Objective The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications. Materials We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks. Results There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets. Conclusions For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. PMID:25336595

Computational domain length and Reynolds number effects on large-scale coherent motions in turbulent pipe flow

NASA Astrophysics Data System (ADS)

Feldmann, Daniel; Bauer, Christian; Wagner, Claus

2018-03-01

We present results from direct numerical simulations (DNS) of turbulent pipe flow at shear Reynolds numbers up to Reτ = 1500 using different computational domains with lengths up to ?. The objectives are to analyse the effect of the finite size of the periodic pipe domain on large flow structures in dependency of Reτ and to assess a minimum ? required for relevant turbulent scales to be captured and a minimum Reτ for very large-scale motions (VLSM) to be analysed. Analysing one-point statistics revealed that the mean velocity profile is invariant for ?. The wall-normal location at which deviations occur in shorter domains changes strongly with increasing Reτ from the near-wall region to the outer layer, where VLSM are believed to live. The root mean square velocity profiles exhibit domain length dependencies for pipes shorter than 14R and 7R depending on Reτ. For all Reτ, the higher-order statistical moments show only weak dependencies and only for the shortest domain considered here. However, the analysis of one- and two-dimensional pre-multiplied energy spectra revealed that even for larger ?, not all physically relevant scales are fully captured, even though the aforementioned statistics are in good agreement with the literature. We found ? to be sufficiently large to capture VLSM-relevant turbulent scales in the considered range of Reτ based on our definition of an integral energy threshold of 10%. The requirement to capture at least 1/10 of the global maximum energy level is justified by a 14% increase of the streamwise turbulence intensity in the outer region between Reτ = 720 and 1500, which can be related to VLSM-relevant length scales. Based on this scaling anomaly, we found Reτ⪆1500 to be a necessary minimum requirement to investigate VLSM-related effects in pipe flow, even though the streamwise energy spectra does not yet indicate sufficient scale separation between the most energetic and the very long motions.

A single active trehalose-6-P synthase (TPS) and a family of putative regulatory TPS-like proteins in Arabidopsis.

PubMed

Vandesteene, Lies; Ramon, Matthew; Le Roy, Katrien; Van Dijck, Patrick; Rolland, Filip

2010-03-01

Higher plants typically do not produce trehalose in large amounts, but their genome sequences reveal large families of putative trehalose metabolism enzymes. An important regulatory role in plant growth and development is also emerging for the metabolic intermediate trehalose-6-P (T6P). Here, we present an update on Arabidopsis trehalose metabolism and a resource for further detailed analyses. In addition, we provide evidence that Arabidopsis encodes a single trehalose-6-P synthase (TPS) next to a family of catalytically inactive TPS-like proteins that might fulfill specific regulatory functions in actively growing tissues.

A genomic regulatory network for development

NASA Technical Reports Server (NTRS)

Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar;

Origin of the cosmic network in ΛCDM: Nature vs nurture

NASA Astrophysics Data System (ADS)

Shandarin, Sergei; Habib, Salman; Heitmann, Katrin

2010-05-01

The large-scale structure of the Universe, as traced by the distribution of galaxies, is now being revealed by large-volume cosmological surveys. The structure is characterized by galaxies distributed along filaments, the filaments connecting in turn to form a percolating network. Our objective here is to quantitatively specify the underlying mechanisms that drive the formation of the cosmic network: By combining percolation-based analyses with N-body simulations of gravitational structure formation, we elucidate how the network has its origin in the properties of the initial density field (nature) and how its contrast is then amplified by the nonlinear mapping induced by the gravitational instability (nurture).

Family-based Association Analyses of Imputed Genotypes Reveal Genome-Wide Significant Association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

PubMed Central

Herold, Christine; Hooli, Basavaraj V.; Mullin, Kristina; Liu, Tian; Roehr, Johannes T; Mattheisen, Manuel; Parrado, Antonio R.; Bertram, Lars; Lange, Christoph; Tanzi, Rudolph E.

2015-01-01

The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1 and PSEN2 cause a subset of early-onset familial Alzheimer's disease (EOFAD). On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ε4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3,500 subjects from 1,070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value = 3.98·10−08), rs1347297 in the gene OSBPL6 (P-value = 4.53·10−08), and rs1513625 near PDCL3 (P-value = 4.28·10−08). In addition, rs72953347 in OSBPL6 (P-value = 6.36·10−07) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value: 4.76·10−07; rs62400067, P-value: 3.54·10−07). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance. PMID:26830138

GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks.

PubMed

Hosseini, S M Hadi; Hoeft, Fumiko; Kesler, Shelli R

2012-01-01

In recent years, graph theoretical analyses of neuroimaging data have increased our understanding of the organization of large-scale structural and functional brain networks. However, tools for pipeline application of graph theory for analyzing topology of brain networks is still lacking. In this report, we describe the development of a graph-analysis toolbox (GAT) that facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI) that facilitates construction and analysis of brain networks, comparison of regional and global topological properties between networks, analysis of network hub and modules, and analysis of resilience of the networks to random failure and targeted attacks. Area under a curve (AUC) and functional data analyses (FDA), in conjunction with permutation testing, is employed for testing the differences in network topologies; analyses that are less sensitive to the thresholding process. We demonstrated the capabilities of GAT by investigating the differences in the organization of regional gray-matter correlation networks in survivors of acute lymphoblastic leukemia (ALL) and healthy matched Controls (CON). The results revealed an alteration in small-world characteristics of the brain networks in the ALL survivors; an observation that confirm our hypothesis suggesting widespread neurobiological injury in ALL survivors. Along with demonstration of the capabilities of the GAT, this is the first report of altered large-scale structural brain networks in ALL survivors.

Non-metric multidimensional performance indicator scaling reveals seasonal and team dissimilarity within the National Rugby League.

PubMed

Woods, Carl T; Robertson, Sam; Sinclair, Wade H; Collier, Neil French

2018-04-01

Analysing the dissimilarity of seasonal and team profiles within elite sport may reveal the evolutionary dynamics of game-play, while highlighting the similarity of individual team profiles. This study analysed seasonal and team dissimilarity within the National Rugby League (NRL) between the 2005 to 2016 seasons. Longitudinal. Total seasonal values for 15 performance indicators were collected for every NRL team over the analysed period (n=190 observations). Non-metric multidimensional scaling was used to reveal seasonal and team dissimilarity. Compared to the 2005 to 2011 seasons, the 2012 to 2016 seasons were in a state of flux, with a relative dissimilarity in the positioning of team profiles on the ordination surface. There was an abrupt change in performance indicator characteristics following the 2012 season, with the 2014 season reflecting a large increase in the total count of 'all run metres' (d=1.21; 90% CI=0.56-1.83), 'kick return metres' (d=2.99; 90% CI=2.12-3.84) and decrease in 'missed tackles' (d=-2.43; 90% CI=-3.19 to -1.64) and 'tackle breaks' (d=-2.41; 90% CI=-3.17 to -1.62). Interpretation of team ordination plots showed that certain teams evolved in (dis)similar ways over the analysed period. It appears that NRL match-types evolved following the 2012 season and are in a current state of flux. The modification of coaching tactics and rule changes may have contributed to these observations. Coaches could use these results when designing prospective game strategies in the NRL. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Welcome to pandoraviruses at the ‘Fourth TRUC’ club

PubMed Central

Sharma, Vikas; Colson, Philippe; Chabrol, Olivier; Scheid, Patrick; Pontarotti, Pierre; Raoult, Didier

2015-01-01

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9–2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the ‘Fourth TRUC’ club, encompassing distinct life forms compared with cellular organisms. PMID:26042093

Welcome to pandoraviruses at the 'Fourth TRUC' club.

PubMed

Sharma, Vikas; Colson, Philippe; Chabrol, Olivier; Scheid, Patrick; Pontarotti, Pierre; Raoult, Didier

2015-01-01

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the 'Fourth TRUC' club, encompassing distinct life forms compared with cellular organisms.

Structural basis for amino acid export by DMT superfamily transporter YddG.

PubMed

Tsuchiya, Hirotoshi; Doki, Shintaro; Takemoto, Mizuki; Ikuta, Tatsuya; Higuchi, Takashi; Fukui, Keita; Usuda, Yoshihiro; Tabuchi, Eri; Nagatoishi, Satoru; Tsumoto, Kouhei; Nishizawa, Tomohiro; Ito, Koichi; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

2016-06-16

The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.

Vitamin A intoxication from reef fish liver consumption in Bermuda.

PubMed

Dewailly, E; Rouja, P; Schultz, E; Julien, P; Tucker, T

2011-09-01

We report three historical cases of severe vitamin A intoxication in anglers who had consumed reef fish liver caught in Bermuda. The subsequent analyses of 35 fish livers from seven different fish species revealed that very high concentrations of vitamin A exist in tropical fish liver, even in noncarnivorous fish species. Large variations in concentrations were observed between specimens and between species. The angling population and (especially) pregnant women should be advised of this potential health threat.

Comparative analysis of metazoan chromatin organization.

PubMed

Ho, Joshua W K; Jung, Youngsook L; Liu, Tao; Alver, Burak H; Lee, Soohyun; Ikegami, Kohta; Sohn, Kyung-Ah; Minoda, Aki; Tolstorukov, Michael Y; Appert, Alex; Parker, Stephen C J; Gu, Tingting; Kundaje, Anshul; Riddle, Nicole C; Bishop, Eric; Egelhofer, Thea A; Hu, Sheng'en Shawn; Alekseyenko, Artyom A; Rechtsteiner, Andreas; Asker, Dalal; Belsky, Jason A; Bowman, Sarah K; Chen, Q Brent; Chen, Ron A-J; Day, Daniel S; Dong, Yan; Dose, Andrea C; Duan, Xikun; Epstein, Charles B; Ercan, Sevinc; Feingold, Elise A; Ferrari, Francesco; Garrigues, Jacob M; Gehlenborg, Nils; Good, Peter J; Haseley, Psalm; He, Daniel; Herrmann, Moritz; Hoffman, Michael M; Jeffers, Tess E; Kharchenko, Peter V; Kolasinska-Zwierz, Paulina; Kotwaliwale, Chitra V; Kumar, Nischay; Langley, Sasha A; Larschan, Erica N; Latorre, Isabel; Libbrecht, Maxwell W; Lin, Xueqiu; Park, Richard; Pazin, Michael J; Pham, Hoang N; Plachetka, Annette; Qin, Bo; Schwartz, Yuri B; Shoresh, Noam; Stempor, Przemyslaw; Vielle, Anne; Wang, Chengyang; Whittle, Christina M; Xue, Huiling; Kingston, Robert E; Kim, Ju Han; Bernstein, Bradley E; Dernburg, Abby F; Pirrotta, Vincenzo; Kuroda, Mitzi I; Noble, William S; Tullius, Thomas D; Kellis, Manolis; MacAlpine, David M; Strome, Susan; Elgin, Sarah C R; Liu, Xiaole Shirley; Lieb, Jason D; Ahringer, Julie; Karpen, Gary H; Park, Peter J

2014-08-28

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.

Genome-environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica.

PubMed

Pluess, Andrea R; Frank, Aline; Heiri, Caroline; Lalagüe, Hadrien; Vendramin, Giovanni G; Oddou-Muratorio, Sylvie

2016-04-01

The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome-environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural Fagus sylvatica populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150 m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Bulky Trichomonad Genomes: Encoding a Swiss Army Knife.

PubMed

Barratt, Joel; Gough, Rory; Stark, Damien; Ellis, John

2016-10-01

The trichomonads are a remarkably successful lineage of ancient, predominantly parasitic protozoa. Recent molecular analyses have revealed extensive duplication of certain genetic loci in trichomonads. Consequently, their genomes are exceptionally large compared to other parasitic protozoa. Retention of these large gene expansions across different trichomonad families raises the question: do these duplications afford an advantage? Many duplicated genes are linked to the parasitic lifestyle and some are regulated differently to their paralogues, suggesting they have acquired new functions. It is proposed that these large genomes encode a Swiss army knife of sorts, packed with a multitude of tools for use in many different circumstances. This may have bestowed trichomonads with the extraordinary versatility that has undoubtedly contributed to their success. Copyright © 2016 Elsevier Ltd. All rights reserved.

Organizational factors affecting safety implementation in food companies in Thailand.

PubMed

Chinda, Thanwadee

2014-01-01

Thai food industry employs a massive number of skilled and unskilled workers. This may result in an industry with high incidences and accident rates. To improve safety and reduce the accident figures, this paper investigates factors influencing safety implementation in small, medium, and large food companies in Thailand. Five factors, i.e., management commitment, stakeholders' role, safety information and communication, supportive environment, and risk, are found important in helping to improve safety implementation. The statistical analyses also reveal that small, medium, and large food companies hold similar opinions on the risk factor, but bear different perceptions on the other 4 factors. It is also found that to improve safety implementation, the perceptions of safety goals, communication, feedback, safety resources, and supervision should be aligned in small, medium, and large companies.

Analytic and heuristic processing influences on adolescent reasoning and decision-making.

PubMed

Klaczynski, P A

2001-01-01

The normative/descriptive gap is the discrepancy between actual reasoning and traditional standards for reasoning. The relationship between age and the normative/descriptive gap was examined by presenting adolescents with a battery of reasoning and decision-making tasks. Middle adolescents (N = 76) performed closer to normative ideals than early adolescents (N = 66), although the normative/descriptive gap was large for both groups. Correlational analyses revealed that (1) normative responses correlated positively with each other, (2) nonnormative responses were positively interrelated, and (3) normative and nonnormative responses were largely independent. Factor analyses suggested that performance was based on two processing systems. The "analytic" system operates on "decontextualized" task representations and underlies conscious, computational reasoning. The "heuristic" system operates on "contextualized," content-laden representations and produces "cognitively cheap" responses that sometimes conflict with traditional norms. Analytic processing was more clearly linked to age and to intelligence than heuristic processing. Implications for cognitive development, the competence/performance issue, and rationality are discussed.

Retinotopic patterns of functional connectivity between V1 and large-scale brain networks during resting fixation

PubMed Central

Griffis, Joseph C.; Elkhetali, Abdurahman S.; Burge, Wesley K.; Chen, Richard H.; Bowman, Anthony D.; Szaflarski, Jerzy P.; Visscher, Kristina M.

2016-01-01

Psychophysical and neurobiological evidence suggests that central and peripheral vision are specialized for different functions. This specialization of function might be expected to lead to differences in the large-scale functional interactions of early cortical areas that represent central and peripheral visual space. Here, we characterize differences in whole-brain functional connectivity among sectors in primary visual cortex (V1) corresponding to central, near-peripheral, and far-peripheral vision during resting fixation. Importantly, our analyses reveal that eccentricity sectors in V1 have different functional connectivity with non-visual areas associated with large-scale brain networks. Regions associated with the fronto-parietal control network are most strongly connected with central sectors of V1, regions associated with the cingulo-opercular control network are most strongly connected with near-peripheral sectors of V1, and regions associated with the default mode and auditory networks are most strongly connected with far-peripheral sectors of V1. Additional analyses suggest that similar patterns are present during eyes-closed rest. These results suggest that different types of visual information may be prioritized by large-scale brain networks with distinct functional profiles, and provide insights into how the small-scale functional specialization within early visual regions such as V1 relates to the large-scale organization of functionally distinct whole-brain networks. PMID:27554527

Gas chromatography/chemical ionization triple quadrupole mass spectrometry analysis of anabolic steroids: ionization and collision-induced dissociation behavior.

PubMed

Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

2016-02-28

The detection of new anabolic steroid metabolites and new designer steroids is a challenging task in doping analysis. Switching from electron ionization gas chromatography triple quadrupole mass spectrometry (GC/EI-MS/MS) to chemical ionization (CI) has proven to be an efficient way to increase the sensitivity of GC/MS/MS analyses and facilitate the detection of anabolic steroids. CI also extends the possibilities of GC/MS/MS analyses as the molecular ion is retained in its protonated form due to the softer ionization. In EI it can be difficult to find previously unknown but expected metabolites due to the low abundance or absence of the molecular ion and the extensive (and to a large extent unpredictable) fragmentation. The main aim of this work was to study the CI and collision-induced dissociation (CID) behavior of a large number of anabolic androgenic steroids (AAS) as their trimethylsilyl derivatives in order to determine correlations between structures and CID fragmentation. Clarification of these correlations is needed for the elucidation of structures of unknown steroids and new metabolites. The ionization and CID behavior of 65 AAS have been studied using GC/CI-MS/MS with ammonia as the reagent gas. Glucuronidated AAS reference standards were first hydrolyzed to obtain their free forms. Afterwards, all the standards were derivatized to their trimethylsilyl forms. Full scan and product ion scan analyses were used to examine the ionization and CID behavior. Full scan and product ion scan analyses revealed clear correlations between AAS structure and the obtained mass spectra. These correlations were confirmed by analysis of multiple hydroxylated, methylated, chlorinated and deuterated analogs. AAS have been divided into three groups according to their ionization behavior and into seven groups according to their CID behavior. Correlations between fragmentation and structure were revealed and fragmentation pathways were postulated. Copyright © 2016 John Wiley & Sons, Ltd.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

PubMed Central

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A.; Smits, Theo H. M.; Venter, Stephanus N.; Coutinho, Teresa A.

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range. PMID:28959245

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

PubMed

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Does more education mean less disability in people with dementia? A large cross-sectional study in Taiwan

PubMed Central

Huang, Shih-Wei; Chi, Wen-Chou; Yen, Chia-Feng; Chang, Kwang-Hwa; Liao, Hua-Fang; Escorpizo, Reuben; Chang, Feng-Hang; Liou, Tsan-Hon

2017-01-01

Background WHO Disability Assessment Schedule 2.0 (WHODAS 2.0) is a feasible tool for assessing functional disability and analysing the risk of institutionalisation among elderly patients with dementia. However, the data for the effect of education on disability status in patients with dementia is lacking. The aim of this large-scale, population-based study was to analyse the effect of education on the disability status of elderly Taiwanese patients with dementia by using WHODAS 2.0. Methods From the Taiwan Data Bank of Persons with Disability, we enrolled 7698 disabled elderly (older than 65 years) patients diagnosed with dementia between July 2012 and January 2014. According to their education status, we categorised these patients with and without formal education (3849 patients each). We controlled for the demographic variables through propensity score matching. The standardised scores of these patients in the six domains of WHODAS 2.0 were evaluated by certified interviewers. Student’s t-test was used for comparing the WHODAS 2.0 scores of patients with dementia in the two aforementioned groups. Poisson regression was applied for analysing the association among all the investigated variables. Results Patients with formal education had low disability status in the domains of getting along and social participation than did patients without formal education. Poisson regression revealed that standardised scores in all domains of WHODAS 2.0—except self-care—were associated with education status. Conclusions This study revealed lower disability status in the WHODAS 2.0 domains of getting along and social participation for patients with dementia with formal education compared with those without formal education. For patients with disability and dementia without formal education, community intervention of social participation should be implemented to maintain better social interaction ability. PMID:28473510

Consensuses and discrepancies of basin-scale ocean heat content changes in different ocean analyses

NASA Astrophysics Data System (ADS)

Wang, Gongjie; Cheng, Lijing; Abraham, John; Li, Chongyin

2018-04-01

Inconsistent global/basin ocean heat content (OHC) changes were found in different ocean subsurface temperature analyses, especially in recent studies related to the slowdown in global surface temperature rise. This finding challenges the reliability of the ocean subsurface temperature analyses and motivates a more comprehensive inter-comparison between the analyses. Here we compare the OHC changes in three ocean analyses (Ishii, EN4 and IAP) to investigate the uncertainty in OHC in four major ocean basins from decadal to multi-decadal scales. First, all products show an increase of OHC since 1970 in each ocean basin revealing a robust warming, although the warming rates are not identical. The geographical patterns, the key modes and the vertical structure of OHC changes are consistent among the three datasets, implying that the main OHC variabilities can be robustly represented. However, large discrepancies are found in the percentage of basinal ocean heating related to the global ocean, with the largest differences in the Pacific and Southern Ocean. Meanwhile, we find a large discrepancy of ocean heat storage in different layers, especially within 300-700 m in the Pacific and Southern Oceans. Furthermore, the near surface analysis of Ishii and IAP are consistent with sea surface temperature (SST) products, but EN4 is found to underestimate the long-term trend. Compared with ocean heat storage derived from the atmospheric budget equation, all products show consistent seasonal cycles of OHC in the upper 1500 m especially during 2008 to 2012. Overall, our analyses further the understanding of the observed OHC variations, and we recommend a careful quantification of errors in the ocean analyses.

Analysis of grain characters in temperate grasses reveals distinctive patterns of endosperm organization associated with grain shape

PubMed Central

Drea, Sinéad

2012-01-01

Members of the core pooids represent the most important crops in temperate zones including wheat, barley, and oats. Their importance as crops is largely due to the grain, particularly the storage capabilities of the endosperm. In this study, a comprehensive survey of grain morphology and endosperm organization in representatives of wild and cultivated species throughout the core pooids was performed. As sister to the core pooid tribes Poeae, Aveneae, Triticeae, and Bromeae within the Pooideae subfamily, Brachypodium provides a taxonomically relevant reference point. Using macroscopic, histological, and molecular analyses distinct patterns of grain tissue organization in these species, focusing on the peripheral and modified aleurone, are described. The results indicate that aleurone organization is correlated with conventional grain quality characters such as grain shape and starch content. In addition to morphological and organizational variation, expression patterns of candidate gene markers underpinning this variation were examined. Features commonly associated with grains are largely defined by analyses on lineages within the Triticeae and knowledge of grain structure may be skewed as a result of the focus on wheat and barley. Specifically, the data suggest that the modified aleurone is largely restricted to species in the Triticeae tribe. PMID:23081982

Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box).

PubMed

Jordan, Rebecca; Dillon, Shannon K; Prober, Suzanne M; Hoffmann, Ary A

2016-12-01

In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Functional evaluation of out-of-the-box text-mining tools for data-mining tasks.

PubMed

Jung, Kenneth; LePendu, Paea; Iyer, Srinivasan; Bauer-Mehren, Anna; Percha, Bethany; Shah, Nigam H

2015-01-01

The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug-drug interactions, and learning used-to-treat relationships between drugs and indications. We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks. There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets. For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

PubMed Central

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms. PMID:28706512

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

PubMed

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Petrographic and petrological studies of lunar rocks. [from the Apollo 15 mission

NASA Technical Reports Server (NTRS)

Winzer, S. R.

1978-01-01

Thin sections and polished electron probe mounts of Apollo 15 glasscoated breccias 15255, 15286, 15466, and 15505 were examined optically and analyzed by sem/microprobe. Sections from breccias 15465 and 15466 were examined in detail, and chemical and mineralogical analyses of several larger lithic clasts, green glass, and partly crystallized green glass spheres are presented. Area analyses of 33 clasts from the above breccias were also done using the SEM/EDS system. Mineralogical and bulk chemical analyses of clasts from the Apollo 15 glass-coated breccias reveal a diverse set of potential rock types, including plutonic and extrusive igneous rocks and impact melts. Examination of the chemistry of the clasts suggests that many of these clasts, like those found in 61175, are impact melts. Their variability suggests formation by several small local impacts rather than by a large basin-forming event.

Beliefs about meditating among university students, faculty, and staff: a theory-based salient belief elicitation.

PubMed

Lederer, Alyssa M; Middlestadt, Susan E

2014-01-01

Stress impacts college students, faculty, and staff alike. Although meditation has been found to decrease stress, it is an underutilized strategy. This study used the Reasoned Action Approach (RAA) to identify beliefs underlying university constituents' decision to meditate. N=96 students, faculty, and staff at a large midwestern university during spring 2012. A survey measured the RAA global constructs and elicited the beliefs underlying intention to meditate. Thematic and frequency analyses and multiple regression were performed. Quantitative analyses showed that intention to meditate was significantly predicted (R2=.632) by attitude, perceived norm, and perceived behavioral control. Qualitative analyses revealed advantages (eg, reduced stress; feeling calmer), disadvantages (eg, takes time; will not work), and facilitating circumstances (eg, having more time; having quiet space) of meditating. Results of this theory-based research suggest how college health professionals can encourage meditation practice through individual, interpersonal, and environmental interventions.

Mining nutrigenetics patterns related to obesity: use of parallel multifactor dimensionality reduction.

PubMed

Karayianni, Katerina N; Grimaldi, Keith A; Nikita, Konstantina S; Valavanis, Ioannis K

2015-01-01

This paper aims to enlighten the complex etiology beneath obesity by analysing data from a large nutrigenetics study, in which nutritional and genetic factors associated with obesity were recorded for around two thousand individuals. In our previous work, these data have been analysed using artificial neural network methods, which identified optimised subsets of factors to predict one's obesity status. These methods did not reveal though how the selected factors interact with each other in the obtained predictive models. For that reason, parallel Multifactor Dimensionality Reduction (pMDR) was used here to further analyse the pre-selected subsets of nutrigenetic factors. Within pMDR, predictive models using up to eight factors were constructed, further reducing the input dimensionality, while rules describing the interactive effects of the selected factors were derived. In this way, it was possible to identify specific genetic variations and their interactive effects with particular nutritional factors, which are now under further study.

Tomographic local 2D analyses of the WISExSuperCOSMOS all-sky galaxy catalogue

NASA Astrophysics Data System (ADS)

Novaes, C. P.; Bernui, A.; Xavier, H. S.; Marques, G. A.

2018-05-01

The recent progress in obtaining larger and deeper galaxy catalogues is of fundamental importance for cosmological studies, especially to robustly measure the large scale density fluctuations in the Universe. The present work uses the Minkowski Functionals (MF) to probe the galaxy density field from the WISExSuperCOSMOS (WSC) all-sky catalogue by performing tomographic local analyses in five redshift shells (of thickness δz = 0.05) in the total range of 0.10 < z < 0.35. Here, for the first time, the MF are applied to 2D projections of the galaxy number count (GNC) fields with the purpose of looking for regions in the WSC catalogue with unexpected features compared to ΛCDM mock realisations. Our methodology reveals 1 - 3 regions of the GNC maps in each redshift shell with an uncommon behaviour (extreme regions), i.e., p-value < 1.4%. Indeed, the resulting MF curves show signatures that suggest the uncommon behaviour to be associated with the presence of over- or under-densities there, but contamination due to residual foregrounds is not discarded. Additionally, even though our analyses indicate a good agreement among data and simulations, we identify 1 highly extreme region, seemingly associated to a large clustered distribution of galaxies. Our results confirm the usefulness of the MF to analyse GNC maps from photometric galaxy datasets.

Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).

PubMed

Stervander, Martin; Alström, Per; Olsson, Urban; Ottosson, Ulf; Hansson, Bengt; Bensch, Staffan

2016-09-01

The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. Copyright © 2016 Elsevier Inc. All rights reserved.

Origin of the cosmic network in {Lambda}CDM: Nature vs nurture

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

Shandarin, Sergei; Habib, Salman; Heitmann, Katrin

The large-scale structure of the Universe, as traced by the distribution of galaxies, is now being revealed by large-volume cosmological surveys. The structure is characterized by galaxies distributed along filaments, the filaments connecting in turn to form a percolating network. Our objective here is to quantitatively specify the underlying mechanisms that drive the formation of the cosmic network: By combining percolation-based analyses with N-body simulations of gravitational structure formation, we elucidate how the network has its origin in the properties of the initial density field (nature) and how its contrast is then amplified by the nonlinear mapping induced by themore » gravitational instability (nurture).« less

Still searching for the engram.

PubMed

Eichenbaum, Howard

2016-09-01

For nearly a century, neurobiologists have searched for the engram-the neural representation of a memory. Early studies showed that the engram is widely distributed both within and across brain areas and is supported by interactions among large networks of neurons. Subsequent research has identified engrams that support memory within dedicated functional systems for habit learning and emotional memory, but the engram for declarative memories has been elusive. Nevertheless, recent years have brought progress from molecular biological approaches that identify neurons and networks that are necessary and sufficient to support memory, and from recording approaches and population analyses that characterize the information coded by large neural networks. These new directions offer the promise of revealing the engrams for episodic and semantic memories.

Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

PubMed Central

Kawakami, Eiryo; Singh, Vivek K; Matsubara, Kazuko; Ishii, Takashi; Matsuoka, Yukiko; Hase, Takeshi; Kulkarni, Priya; Siddiqui, Kenaz; Kodilkar, Janhavi; Danve, Nitisha; Subramanian, Indhupriya; Katoh, Manami; Shimizu-Yoshida, Yuki; Ghosh, Samik; Jere, Abhay; Kitano, Hiroaki

2016-01-01

Cellular stress responses require exquisite coordination between intracellular signaling molecules to integrate multiple stimuli and actuate specific cellular behaviors. Deciphering the web of complex interactions underlying stress responses is a key challenge in understanding robust biological systems and has the potential to lead to the discovery of targeted therapeutics for diseases triggered by dysregulation of stress response pathways. We constructed large-scale molecular interaction maps of six major stress response pathways in Saccharomyces cerevisiae (baker’s or budding yeast). Biological findings from over 900 publications were converted into standardized graphical formats and integrated into a common framework. The maps are posted at http://www.yeast-maps.org/yeast-stress-response/ for browse and curation by the research community. On the basis of these maps, we undertook systematic analyses to unravel the underlying architecture of the networks. A series of network analyses revealed that yeast stress response pathways are organized in bow–tie structures, which have been proposed as universal sub-systems for robust biological regulation. Furthermore, we demonstrated a potential role for complexes in stabilizing the conserved core molecules of bow–tie structures. Specifically, complex-mediated reversible reactions, identified by network motif analyses, appeared to have an important role in buffering the concentration and activity of these core molecules. We propose complex-mediated reactions as a key mechanism mediating robust regulation of the yeast stress response. Thus, our comprehensive molecular interaction maps provide not only an integrated knowledge base, but also a platform for systematic network analyses to elucidate the underlying architecture in complex biological systems. PMID:28725465

The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters.

PubMed

Patiño-Galindo, Juan Ángel; Torres-Puente, Manoli; Bracho, María Alma; Alastrué, Ignacio; Juan, Amparo; Navarro, David; Galindo, María José; Ocete, Dolores; Ortega, Enrique; Gimeno, Concepción; Belda, Josefina; Domínguez, Victoria; Moreno, Rosario; González-Candelas, Fernando

2017-09-14

HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups. The HIV epidemic in the CV is dominated by subtype B infections among local men who have sex with men (MSM). 270 transmission clusters were identified (>57% of the dataset), 12 of which included ≥10 patients; 11 of subtype B (9 affecting MSMs) and one (n = 21) of CRF14, affecting predominately intravenous drug users (IDUs). Dated phylogenies revealed these large clusters to have originated from the mid-80s to the early 00 s. Subtype B is more likely to form transmission clusters than non-B variants and MSMs to cluster than other risk groups. Multinomial analyses revealed an association between non-B variants, which are not established in the local population yet, and different foreign groups.

Greater widespread functional connectivity of the caudate in older adults who practice kripalu yoga and vipassana meditation than in controls

PubMed Central

Gard, Tim; Taquet, Maxime; Dixit, Rohan; Hölzel, Britta K.; Dickerson, Bradford C.; Lazar, Sara W.

2015-01-01

There has been a growing interest in understanding how contemplative practices affect brain functional organization. However, most studies have restricted their exploration to predefined networks. Furthermore, scientific comparisons of different contemplative traditions are largely lacking. Here we explored differences in whole brain resting state functional connectivity between experienced yoga practitioners, experienced meditators, and matched controls. Analyses were repeated in an independent sample of experienced meditators and matched controls. Analyses utilizing Network-Based Statistics (Zalesky et al., 2010) revealed difference components for yoga practitioners > controls and meditators > controls in which the right caudate was a central node. Follow up analyses revealed that yoga practitioners and meditators had significantly greater degree centrality in the caudate than controls. This greater degree centrality was not driven by single connections but by greater connectivity between the caudate and numerous brain regions. Findings of greater caudate connectivity in meditators than in controls was replicated in an independent dataset. These findings suggest that yoga and meditation practitioners have stronger functional connectivity within basal ganglia cortico-thalamic feedback loops than non-practitioners. Although we could not provide evidence for its mechanistic role, this greater connectivity might be related to the often reported effects of meditation and yoga on behavioral flexibility, mental health, and well-being. PMID:25852521

Laterodorsal nucleus of the thalamus: A processor of somatosensory inputs.

PubMed

Bezdudnaya, Tatiana; Keller, Asaf

2008-04-20

The laterodorsal (LD) nucleus of the thalamus has been considered a "higher order" nucleus that provides inputs to limbic cortical areas. Although its functions are largely unknown, it is often considered to be involved in spatial learning and memory. Here we provide evidence that LD is part of a hitherto unknown pathway for processing somatosensory information. Juxtacellular and extracellular recordings from LD neurons reveal that they respond to vibrissa stimulation with short latency (median = 7 ms) and large magnitude responses (median = 1.2 spikes/stimulus). Most neurons (62%) had large receptive fields, responding to six and more individual vibrissae. Electrical stimulation of the trigeminal nucleus interpolaris (SpVi) evoked short latency responses (median = 3.8 ms) in vibrissa-responsive LD neurons. Labeling produced by anterograde and retrograde neuroanatomical tracers confirmed that LD neurons receive direct inputs from SpVi. Electrophysiological and neuroanatomical analyses revealed also that LD projects upon the cingulate and retrosplenial cortex, but has only sparse projections to the barrel cortex. These findings suggest that LD is part of a novel processing stream involved in spatial orientation and learning related to somatosensory cues. (c) 2008 Wiley-Liss, Inc.

New developments in genetics of myositis.

PubMed

Rothwell, Simon; Lamb, Janine A; Chinoy, Hector

2016-11-01

This article reviews the advances that have been made in our understanding of the genetics of the idiopathic inflammatory myopathies (IIM) in the past 2 years, with a particular focus on polymyositis, dermatomyositis and inclusion body myositis. Two large human leukocyte antigen (HLA) imputation studies have confirmed a strong association with the 8.1 ancestral haplotype in clinical subgroups of myositis and suggest multiple independent associations on this haplotype. Risk in these genes may be due to specific amino acid positions within the peptide-binding grooves of HLA molecules. A large genetic study in 2566 IIM patients revealed associations such as PTPN22, STAT4, UBE2L3 and BLK, which overlap with risk variants reported in other seropositive autoimmune diseases. There is also evidence of different genetic architectures in clinical subgroups of IIM. Candidate gene studies in the Japanese and Chinese populations have replicated previous IIM associations which suggest common aetiology between ethnicities. International collaborations have facilitated large genetic studies in IIM that have revealed much about the genetics of this rare complex disease both within the HLA region and genome-wide. Future approaches, such as sequencing and trans-ethnic meta-analyses, will advance our knowledge of IIM genetics.

The 2016 Kumamoto-Oita earthquake sequence: aftershock seismicity gap and dynamic triggering in volcanic areas

NASA Astrophysics Data System (ADS)

Uchide, Takahiko; Horikawa, Haruo; Nakai, Misato; Matsushita, Reiken; Shigematsu, Norio; Ando, Ryosuke; Imanishi, Kazutoshi

2016-11-01

The 2016 Kumamoto-Oita earthquake sequence involving three large events ( M w ≥ 6) in the central Kyushu Island, southwest Japan, activated seismicities in two volcanic areas with unusual and puzzling spatial gaps after the largest earthquake ( M w 7.0) of April 16, 2016. We attempt to reveal the seismic process during the sequence by following seismological data analyses. Our hypocenter relocation result implies that the large events ruptured different faults of a complex fault system. A slip inversion analysis of the largest event indicates a large slip in the seismicity gap (Aso gap) in the caldera of Mt. Aso, which probably released accumulated stress and resulted in little aftershock production. We identified that the largest event dynamically triggered a mid-M6 event at Yufuin (80 km northeast of the epicenter), which is consistent with existence of the 20-km long zone where seismicity was activated and surface offset was observed. These findings will help us study the contribution of the identified complexity in fault geometries and the geotherm in the volcanic areas to the revealed seismic process and consequently improve our understanding of the seismo-volcano tectonics.[Figure not available: see fulltext.

The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

PubMed Central

Nelson, David R; Khraiwesh, Basel; Fu, Weiqi; Alseekh, Saleh; Jaiswal, Ashish; Chaiboonchoe, Amphun; Hazzouri, Khaled M; O’Connor, Matthew J; Butterfoss, Glenn L; Drou, Nizar; Rowe, Jillian D; Harb, Jamil; Fernie, Alisdair R; Gunsalus, Kristin C; Salehi-Ashtiani, Kourosh

2017-01-01

To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline. DOI: http://dx.doi.org/10.7554/eLife.25783.001 PMID:28623667

Neurocognitive Functioning in Patients with 22q11.2 Deletion Syndrome: A Meta-Analytic Review.

PubMed

Moberg, Paul J; Richman, Mara J; Roalf, David R; Morse, Chelsea L; Graefe, Anna C; Brennan, Laura; Vickers, Kayci; Tsering, Wangchen; Kamath, Vidyulata; Turetsky, Bruce I; Gur, Ruben C; Gur, Raquel E

2018-06-19

The 22q11.2 deletion syndrome (22q11.2DS) is a known risk factor for development of schizophrenia and is characterized by a complex neuropsychological profile. To date, a quantitative meta-analysis examining cognitive functioning in 22q11.2DS has not been conducted. A systematic review of cross-sectional studies comparing neuropsychological performance of individuals with 22q11.2DS with age-matched healthy typically developing and sibling comparison subjects was carried out. Potential moderators were analyzed. Analyses included 43 articles (282 effects) that met inclusion criteria. Very large and heterogeneous effects were seen for global cognition (d = - 1.21) and in specific neuropsychological domains (intellectual functioning, achievement, and executive function; d range = - 0.51 to - 2.43). Moderator analysis revealed a significant role for type of healthy comparison group used (typically developing or siblings), demographics (age, sex) and clinical factors (externalizing behavior). Results revealed significant differences between pediatric and adult samples, with isolated analysis within the pediatric sample yielding large effects in several neuropsychological domains (intellectual functioning, achievement, visual memory; d range = - 0.56 to - 2.50). Large cognitive deficits in intellectual functioning and specific neuropsychological variables in individuals with 22q11.2DS represent a robust finding, but these deficits are influenced by several factors, including type of comparison group utilized, age, sex, and clinical status. These findings highlight the clinical relevance of characterizing cognitive functioning in 22q11.2DS and the importance of considering demographic and clinical moderators in future analyses.

Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1.

PubMed

Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

2015-02-01

Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 +/- 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

Comparative genomics reveals insights into avian genome evolution and adaptation

PubMed Central

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

Genomic signatures of adaptation to wine biological ageing conditions in biofilm-forming flor yeasts.

PubMed

Coi, A L; Bigey, F; Mallet, S; Marsit, S; Zara, G; Gladieux, P; Galeote, V; Budroni, M; Dequin, S; Legras, J L

2017-04-01

The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological ageing are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and population structure analysis based on single nucleotide polymorphisms revealed a group of flor yeasts separated from wine yeasts. A combination of methods revealed several highly differentiated regions between wine and flor yeasts, and analyses using codon-substitution models for detecting molecular adaptation identified sites under positive selection in the high-affinity transporter gene ZRT1. The cross-population composite likelihood ratio revealed selective sweeps at three regions, including in the hexose transporter gene HXT7, the yapsin gene YPS6 and the membrane protein coding gene MTS27. Our analyses also revealed that the biological ageing environment has led to the accumulation of numerous mutations in proteins from several networks, including Flo11 regulation and divalent metal transport. Together, our findings suggest that the tuning of FLO11 expression and zinc transport networks are a distinctive feature of the genetic changes underlying the domestication of flor yeasts. Our study highlights the multiplicity of genomic changes underlying yeast adaptation to man-made habitats and reveals that flor/wine yeast lineage can serve as a useful model for studying the genomics of adaptive divergence. © 2017 John Wiley & Sons Ltd.

Influence of strain on dislocation core in silicon

NASA Astrophysics Data System (ADS)

Pizzagalli, L.; Godet, J.; Brochard, S.

2018-05-01

First principles, density functional-based tight binding and semi-empirical interatomic potentials calculations are performed to analyse the influence of large strains on the structure and stability of a 60? dislocation in silicon. Such strains typically arise during the mechanical testing of nanostructures like nanopillars or nanoparticles. We focus on bi-axial strains in the plane normal to the dislocation line. Our calculations surprisingly reveal that the dislocation core structure largely depends on the applied strain, for strain levels of about 5%. In the particular case of bi-axial compression, the transformation of the dislocation to a locally disordered configuration occurs for similar strain magnitudes. The formation of an opening, however, requires larger strains, of about 7.5%. Furthermore, our results suggest that electronic structure methods should be favoured to model dislocation cores in case of large strains whenever possible.

Preparation of γ-LiV2O5 from polyoxovanadate cluster Li7[V15O36(CO3)] as a high-performance cathode material and its reaction mechanism revealed by operando XAFS

NASA Astrophysics Data System (ADS)

Wang, Heng; Isobe, Jin; Shimizu, Takeshi; Matsumura, Daiju; Ina, Toshiaki; Yoshikawa, Hirofumi

2017-08-01

γ-phase LiV2O5, which shows superior electrochemical performance as cathode material in Li-ion batteries, was prepared by annealing the polyoxovanadate cluster Li7 [V15O36(CO3)]. The reaction mechanism was studied using operando X-ray absorption fine structure (XAFS), powder X-ray diffraction (PXRD), and X-ray photoelectron spectroscopy (XPS) analyses. The X-ray absorption near edge structure (XANES) and XPS results reveal that γ-LiV2O5 undergoes two-electron redox reaction per V2O5 pyramid unit, resulting in a large reversible capacity of 260 Ah/kg. The extended X-ray absorption fine structure (EXAFS) and PXRD analyses also suggest that the V-V distance slightly increases, due to the reduction of V5+ to V4+ during Li ion intercalation as the material structure is maintained. As a result, γ-LixV2O5 shows highly reversible electrochemical reaction with x = 0.1-1.9.

Comparative Analysis of Super-Shedder Strains of Escherichia coli O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells

PubMed Central

Cote, Rebecca; Katani, Robab; Moreau, Matthew R.; Kudva, Indira T.; Arthur, Terrance M.; DebRoy, Chitrita; Mwangi, Michael M.; Albert, Istvan; Raygoza Garay, Juan Antonio; Li, Lingling; Brandl, Maria T.; Carter, Michelle Q.; Kapur, Vivek

2015-01-01

Shiga toxin-producing Escherichia coli O157:H7 (O157) are significant foodborne pathogens and pose a serious threat to public health worldwide. The major reservoirs of O157 are asymptomatic cattle which harbor the organism in the terminal recto-anal junction (RAJ). Some colonized animals, referred to as “super-shedders” (SS), are known to shed O157 in exceptionally large numbers (>104 CFU/g of feces). Recent studies suggest that SS cattle play a major role in the prevalence and transmission of O157, but little is known about the molecular mechanisms associated with super-shedding. Whole genome sequence analysis of an SS O157 strain (SS17) revealed a genome of 5,523,849 bp chromosome with 5,430 open reading frames and two plasmids, pO157 and pSS17, of 94,645 bp and 37,446 bp, respectively. Comparative analyses showed that SS17 is clustered with spinach-associated O157 outbreak strains, and belongs to the lineage I/II, clade 8, D group, and genotype 1, a subgroup of O157 with predicted hyper-virulence. A large number of non-synonymous SNPs and other polymorphisms were identified in SS17 as compared with other O157 strains (EC4115, EDL933, Sakai, TW14359), including in key adherence- and virulence-related loci. Phenotypic analyses revealed a distinctive and strongly adherent aggregative phenotype of SS17 on bovine RAJ stratified squamous epithelial (RSE) cells that was conserved amongst other SS isolates. Molecular genetic and functional analyses of defined mutants of SS17 suggested that the strongly adherent aggregative phenotype amongst SS isolates is LEE-independent, and likely results from a novel mechanism. Taken together, our study provides a rational framework for investigating the molecular mechanisms associated with SS, and strong evidence that SS O157 isolates have distinctive features and use a LEE-independent mechanism for hyper-adherence to bovine rectal epithelial cells. PMID:25664460

Differential Expression Patterns in Chemosensory and Non-Chemosensory Tissues of Putative Chemosensory Genes Identified by Transcriptome Analysis of Insect Pest the Purple Stem Borer Sesamia inferens (Walker)

PubMed Central

Zhang, Ya-Nan; Jin, Jun-Yan; Jin, Rong; Xia, Yi-Han; Zhou, Jing-Jiang; Deng, Jian-Yu; Dong, Shuang-Lin

2013-01-01

Background A large number of insect chemosensory genes from different gene subfamilies have been identified and annotated, but their functional diversity and complexity are largely unknown. A systemic examination of expression patterns in chemosensory organs could provide important information. Methodology/Principal Findings We identified 92 putative chemosensory genes by analysing the transcriptome of the antennae and female sex pheromone gland of the purple stem borer Sesamia inferens, among them 87 are novel in this species, including 24 transcripts encoding for odorant binding proteins (OBPs), 24 for chemosensory proteins (CSPs), 2 for sensory neuron membrane proteins (SNMPs), 39 for odorant receptors (ORs) and 3 for ionotropic receptors (IRs). The transcriptome analyses were validated and quantified with a detailed global expression profiling by Reverse Transcription-PCR for all 92 transcripts and by Quantitative Real Time RT-PCR for selected 16 ones. Among the chemosensory gene subfamilies, CSP transcripts are most widely and evenly expressed in different tissues and stages, OBP transcripts showed a clear antenna bias and most of OR transcripts are only detected in adult antennae. Our results also revealed that some OR transcripts, such as the transcripts of SNMP2 and 2 IRs were expressed in non-chemosensory tissues, and some CSP transcripts were antenna-biased expression. Furthermore, no chemosensory transcript is specific to female sex pheromone gland and very few are found in the heads. Conclusion Our study revealed that there are a large number of chemosensory genes expressed in S. inferens, and some of them displayed unusual expression profile in non-chemosensory tissues. The identification of a large set of putative chemosensory genes of each subfamily from a single insect species, together with their different expression profiles provide further information in understanding the functions of these chemosensory genes in S. inferens as well as other insects. PMID:23894529

Differential expression patterns in chemosensory and non-chemosensory tissues of putative chemosensory genes identified by transcriptome analysis of insect pest the purple stem borer Sesamia inferens (Walker).

PubMed

Zhang, Ya-Nan; Jin, Jun-Yan; Jin, Rong; Xia, Yi-Han; Zhou, Jing-Jiang; Deng, Jian-Yu; Dong, Shuang-Lin

2013-01-01

A large number of insect chemosensory genes from different gene subfamilies have been identified and annotated, but their functional diversity and complexity are largely unknown. A systemic examination of expression patterns in chemosensory organs could provide important information. We identified 92 putative chemosensory genes by analysing the transcriptome of the antennae and female sex pheromone gland of the purple stem borer Sesamia inferens, among them 87 are novel in this species, including 24 transcripts encoding for odorant binding proteins (OBPs), 24 for chemosensory proteins (CSPs), 2 for sensory neuron membrane proteins (SNMPs), 39 for odorant receptors (ORs) and 3 for ionotropic receptors (IRs). The transcriptome analyses were validated and quantified with a detailed global expression profiling by Reverse Transcription-PCR for all 92 transcripts and by Quantitative Real Time RT-PCR for selected 16 ones. Among the chemosensory gene subfamilies, CSP transcripts are most widely and evenly expressed in different tissues and stages, OBP transcripts showed a clear antenna bias and most of OR transcripts are only detected in adult antennae. Our results also revealed that some OR transcripts, such as the transcripts of SNMP2 and 2 IRs were expressed in non-chemosensory tissues, and some CSP transcripts were antenna-biased expression. Furthermore, no chemosensory transcript is specific to female sex pheromone gland and very few are found in the heads. Our study revealed that there are a large number of chemosensory genes expressed in S. inferens, and some of them displayed unusual expression profile in non-chemosensory tissues. The identification of a large set of putative chemosensory genes of each subfamily from a single insect species, together with their different expression profiles provide further information in understanding the functions of these chemosensory genes in S. inferens as well as other insects.

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

PubMed Central

Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

2016-01-01

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

Coping with occupational stress: the role of optimism and coping flexibility.

PubMed

Reed, Daniel J

2016-01-01

The current study aimed at measuring whether coping flexibility is a reliable and valid construct in a UK sample and subsequently investigating the association between coping flexibility, optimism, and psychological health - measured by perceived stress and life satisfaction. A UK university undergraduate student sample (N=95) completed an online questionnaire. The study is among the first to examine the validity and reliability of the English version of a scale measuring coping flexibility in a Western population and is also the first to investigate the association between optimism and coping flexibility. The results revealed that the scale had good reliability overall; however, factor analysis revealed no support for the existing two-factor structure of the scale. Coping flexibility and optimism were found to be strongly correlated, and hierarchical regression analyses revealed that the interaction between them predicted a large proportion of the variance in both perceived stress and life satisfaction. In addition, structural equation modeling revealed that optimism completely mediated the relationship between coping flexibility and both perceived stress and life satisfaction. The findings add to the occupational stress literature to further our understanding of how optimism is important in psychological health. Furthermore, given that optimism is a personality trait, and consequently relatively stable, the study also provides preliminary support for the potential of targeting coping flexibility to improve psychological health in Western populations. These findings must be replicated, and further analyses of the English version of the Coping Flexibility Scale are needed.

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field.

PubMed

Crépeau, Valentin; Cambon Bonavita, Marie-Anne; Lesongeur, Françoise; Randrianalivelo, Henintsoa; Sarradin, Pierre-Marie; Sarrazin, Jozée; Godfroy, Anne

2011-06-01

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge) were investigated using molecular approaches. DNA and RNA were extracted from mat samples overlaying hydrothermal deposits and Bathymodiolus azoricus mussel assemblages. We constructed and analyzed libraries of 16S rRNA gene sequences and sequences of functional genes involved in autotrophic carbon fixation [forms I and II RuBisCO (cbbL/M), ATP-citrate lyase B (aclB)]; methane oxidation [particulate methane monooxygenase (pmoA)] and sulfur oxidation [adenosine-5'-phosphosulfate reductase (aprA) and soxB]. To gain new insights into the relationships between mats and mussels, we also used new domain-specific 16S rRNA gene primers targeting Bathymodiolus sp. symbionts. All identified archaeal sequences were affiliated with a single group: the marine group 1 Thaumarchaeota. In contrast, analyses of bacterial sequences revealed much higher diversity, although two phyla Proteobacteria and Bacteroidetes were largely dominant. The 16S rRNA gene sequence library revealed that species affiliated to Beggiatoa Gammaproteobacteria were the dominant active population. Analyses of DNA and RNA functional gene libraries revealed a diverse and active chemolithoautotrophic population. Most of these sequences were affiliated with Gammaproteobacteria, including hydrothermal fauna symbionts, Thiotrichales and Methylococcales. PCR and reverse transcription-PCR using 16S rRNA gene primers targeted to Bathymodiolus sp. symbionts revealed sequences affiliated with both methanotrophic and thiotrophic endosymbionts. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Building rainfall thresholds for large-scales landslides by extracting occurrence time of landslides from seismic records

NASA Astrophysics Data System (ADS)

Yen, Hsin-Yi; Lin, Guan-Wei

2017-04-01

Understanding the rainfall condition which triggers mass moment on hillslope is the key to forecast rainfall-induced slope hazards, and the exact time of landslide occurrence is one of the basic information for rainfall statistics. In the study, we focused on large-scale landslides (LSLs) with disturbed area larger than 10 ha and conducted a string of studies including the recognition of landslide-induced ground motions and the analyses of different terms of rainfall thresholds. More than 10 heavy typhoons during the periods of 2005-2014 in Taiwan induced more than hundreds of LSLs and provided the opportunity to characterize the rainfall conditions which trigger LSLs. A total of 101 landslide-induced seismic signals were identified from the records of Taiwan seismic network. These signals exposed the occurrence time of landslide to assess rainfall conditions. Rainfall analyses showed that LSLs occurred when cumulative rainfall exceeded 500 mm. The results of rainfall-threshold analyses revealed that it is difficult to distinct LSLs from small-scale landslides (SSLs) by the I-D and R-D methods, but the I-R method can achieve the discrimination. Besides, an enhanced three-factor threshold considering deep water content was proposed as the rainfall threshold for LSLs.

Label-free imaging of mammalian cell nucleoli by Raman microspectroscopy.

PubMed

Schulze, H Georg; Konorov, Stanislav O; Piret, James M; Blades, Michael W; Turner, Robin F B

2013-06-21

The nucleolus is a prominent subnuclear structure whose major function is the transcription and assembly of ribosome subunits. The size of the nucleolus varies with the cell cycle, proliferation rate and stress. Changes in nucleolar size, number, chemical composition, and shape can be used to characterize malignant cells. We used spontaneous Raman microscopy as a label-free technique to examine nucleolar spatial and chemical features. Raman images of the 1003 cm(-1) phenylalanine band revealed large, well-defined subnuclear protein structures in MFC-7 breast cancer cells. The 783 cm(-1) images showed that nucleic acids were similarly distributed, but varied more in intensity, forming observable high-intensity regions. High subnuclear RNA concentrations were observed within some of these regions as shown by 809 cm(-1) Raman band images. Principal component analyses of sub-images and library spectra validated the subnuclear presence of RNA. They also revealed that an actin-like protein covaried with DNA within the nucleolus, a combination that accounted for 64% or more of the spectral variance. Embryonic stem cells are another rapidly proliferating cell type, but their nucleoli were not as large or well defined. Estimating the size of the larger MCF-7 nucleolus was used to show the utility of Raman microscopy for morphometric analyses. It was concluded that imaging based on Raman microscopy provides a promising new method for the study of nucleolar function and organization, in the evaluation of drug and experimental effects on the nucleolus, and in clinical diagnostics and prognostics.

Explosive detonation causes an increase in soil porosity leading to increased TNT transformation.

PubMed

Yu, Holly A; Nic Daeid, Niamh; Dawson, Lorna A; DeTata, David A; Lewis, Simon W

2017-01-01

Explosives are a common soil contaminant at a range of sites, including explosives manufacturing plants and areas associated with landmine detonations. As many explosives are toxic and may cause adverse environmental effects, a large body of research has targeted the remediation of explosives residues in soil. Studies in this area have largely involved spiking 'pristine' soils using explosives solutions. Here we investigate the fate of explosives present in soils following an actual detonation process and compare this to the fate of explosives spiked into 'pristine' undetonated soils. We also assess the effects of the detonations on the physical properties of the soils. Our scanning electron microscopy analyses reveal that detonations result in newly-fractured planes within the soil aggregates, and novel micro Computed Tomography analyses of the soils reveal, for the first time, the effect of the detonations on the internal architecture of the soils. We demonstrate that detonations cause an increase in soil porosity, and this correlates to an increased rate of TNT transformation and loss within the detonated soils, compared to spiked pristine soils. We propose that this increased TNT transformation is due to an increased bioavailability of the TNT within the now more porous post-detonation soils, making the TNT more easily accessible by soil-borne bacteria for potential biodegradation. This new discovery potentially exposes novel remediation methods for explosive contaminated soils where actual detonation of the soil significantly promotes subsequent TNT degradation. This work also suggests previously unexplored ramifications associated with high energy soil disruption.

Brain regions implicated in inhibitory control and appetite regulation are activated in response to food portion size and energy density in children.

PubMed

English, L K; Fearnbach, S N; Lasschuijt, M; Schlegel, A; Anderson, K; Harris, S; Wilson, S J; Fisher, J O; Savage, J S; Rolls, B J; Keller, K L

2016-10-01

Large portions of energy-dense foods drive energy intake but the brain mechanisms underlying this effect are not clear. Our main objective was to investigate brain function in response to food images varied by portion size (PS) and energy density (ED) in children using functional magnetic resonance imaging (fMRI). Blood-oxygen-level-dependent (BOLD) fMRI was completed in 36 children (ages 7-10 years) after a 2-h fast while viewing food images at two levels of PS (Large PS, Small PS) and two levels of ED (High ED, Low ED). Children rated perceived fullness pre- and post-fMRI, as well as liking of images on visual analog scales post-fMRI. Anthropometrics were completed 4 weeks before the fMRI. Large PS vs Small PS and High ED vs Low ED were compared with region-of-interest analyses using Brain Voyager v 2.8. Region-of-interest analyses revealed that activation in the right inferior frontal gyrus (P=0.03) was greater for Large PS vs Small PS. Activation was reduced for High ED vs Low ED in the left hypothalamus (P=0.03). Main effects were no longer significant after adjustment for pre-fMRI fullness and liking ratings (PS, P=0.92; ED, P=0.58). This is the first fMRI study to report increased activation to large portions in a brain region that is involved in inhibitory control. These findings may contribute to understanding why some children overeat when presented with large portions of palatable food.

Diffuse large B-cell lymphoma, not otherwise specified of the palate: A case report

PubMed Central

Pereira, Thaís SF.; Castro, Alexandre F.; Mesquita, Ricardo A.

2013-01-01

Diffuse large B-cell lymphoma (DLBCL) is the most frequent type of non-Hodgkin´s lymphoma found in oral and maxillofacial regions. A large number of cases may be biologically heterogeneous, which are commonly defined as DLBCL, not otherwise specified (NOS) by the World Health Organization (WHO-2008). The present case reports on an ulcer of raised and irregular edges, found on the border between the hard and soft palate, as the first and only manifestation of an extranodal non-Hodgkin lymphoma in an 85-year-old patient. Incisional biopsy was carried out, and the specimen revealed a proliferation of large lymphoid cells suggestive of diffuse large cell lymphoma. An immunohistochemical analysis was performed. EBV-RNA was assessed by in situ hybridization that also proved to be negative. Immunohistochemical and EBV analyses are important to avoid delays and inappropriate treatment strategies. Although advanced age is considered an adverse prognostic factor, early diagnosis did prove to be a key contributory factor in the cure of non-Hodgkin lymphoma. Key words:Diffuse large B-cell lymphoma, elderly, EBV. PMID:24455096

Still searching for the engram

PubMed Central

Eichenbaum, Howard

2016-01-01

For nearly a century neurobiologists have searched for the engram - the neural representation of a memory. Early studies showed that the engram is widely distributed both within and across brain areas and is supported by interactions among large networks of neurons. Subsequent research has identified engrams that support memory within dedicated functional systems for habit learning and emotional memory, but the engram for declarative memories has been elusive. Nevertheless, recent years have brought progress from molecular biological approaches that identify neurons and networks that are necessary and sufficient to support memory, and from recording approaches and population analyses that characterize the information coded by large neural networks. These new directions offer the promise of revealing the engrams for episodic and semantic memories. PMID:26944423

Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

PubMed Central

Trentmann, Oliver; Haferkamp, Ilka

2013-01-01

Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

Phylogenomic analyses reveal novel relationships among snake families.

PubMed

Streicher, Jeffrey W; Wiens, John J

2016-07-01

Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3776 nuclear loci from ultraconserved elements (1.40million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ∼100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups. Copyright © 2016 Elsevier Inc. All rights reserved.

Information Theoretic Approaches to Rapid Discovery of Relationships in Large Climate Data Sets

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.; Rossow, William B.; Clancy, Daniel (Technical Monitor)

2002-01-01

Mutual information as the asymptotic Bayesian measure of independence is an excellent starting point for investigating the existence of possible relationships among climate-relevant variables in large data sets, As mutual information is a nonlinear function of of its arguments, it is not beholden to the assumption of a linear relationship between the variables in question and can reveal features missed in linear correlation analyses. However, as mutual information is symmetric in its arguments, it only has the ability to reveal the probability that two variables are related. it provides no information as to how they are related; specifically, causal interactions or a relation based on a common cause cannot be detected. For this reason we also investigate the utility of a related quantity called the transfer entropy. The transfer entropy can be written as a difference between mutual informations and has the capability to reveal whether and how the variables are causally related. The application of these information theoretic measures is rested on some familiar examples using data from the International Satellite Cloud Climatology Project (ISCCP) to identify relation between global cloud cover and other variables, including equatorial pacific sea surface temperature (SST), over seasonal and El Nino Southern Oscillation (ENSO) cycles.

Molecular and FISH analyses of a 53-kbp intact DNA fragment inserted by biolistics in wheat (Triticum aestivum L.) genome.

PubMed

Partier, A; Gay, G; Tassy, C; Beckert, M; Feuillet, C; Barret, P

2017-10-01

A large, 53-kbp, intact DNA fragment was inserted into the wheat ( Triticum aestivum L.) genome. FISH analyses of individual transgenic events revealed multiple insertions of intact fragments. Transferring large intact DNA fragments containing clusters of resistance genes or complete metabolic pathways into the wheat genome remains a challenge. In a previous work, we showed that the use of dephosphorylated cassettes for wheat transformation enabled the production of simple integration patterns. Here, we used the same technology to produce a cassette containing a 44-kb Arabidopsis thaliana BAC, flanked by one selection gene and one reporter gene. This 53-kb linear cassette was integrated in the bread wheat (Triticum aestivum L.) genome by biolistic transformation. Our results showed that transgenic plants harboring the entire cassette were generated. The inheritability of the cassette was demonstrated in the T1 and T2 generation. Surprisingly, FISH analysis performed on T1 progeny of independent events identified double genomic insertions of intact fragments in non-homoeologous positions. Inheritability of these double insertions was demonstrated by FISH analysis of the T1 generation. Relative conclusions that can be drawn from molecular or FISH analysis are discussed along with future prospects of the engineering of large fragments for wheat transformation or genome editing.

Pollination syndromes in African Marantaceae.

PubMed

Ley, Alexandra C; Classen-Bockhoff, Regine

2009-07-01

The Marantaceae (550 spp.) is the most derived family in the order Zingiberales and exhibits a complex explosive pollination mechanism. To understand the evolutionary significance of this unique process of pollen transfer, comparative morphological and ecological studies were conducted in Gabon. During a total stay of 11 months, 31 species of Marantaceae were investigated at different sites in Gabon. The study included analyses of floral diversity, observations on the pollinator spectrum as well as ecological measurements (e.g. nectar sugar concentration and volume). Analyses reveal five flower types based on flower size and pigmentation, spatial arrangement of the floral tube and presence/absence of nectar guides and conspicuous outer staminodes. Each type is associated with a specific functional pollinator group leading to the description of distinct pollination syndromes. The 'small (horizontal)' flowers are predominantly pollinated by small bees (Thrinchostoma spp., Allodapula ornaticeps), the 'large (horizontal)' and 'medium-sized (horizontal)' flowers by medium-sized bees (Amegilla vivida, Thrinchostoma bicometes), the 'locked (horizontal)' flowers by large bees (Xylocopa nigrita, X. varipes) and the '(large) vertical' flowers by sunbirds. The longevity of Marantaceae individuals and the omnipresence of their pollinators allowed the specialization to a given functional pollinator group. Intermediate ecological values, however, make occasional pollinator overlaps possible, indicating potential pathways of pollinator shifts. Similar radiation tendencies observed on other continents hint at similar selective pressures and evolutionary constraints.

Ellipticity of near-threshold harmonics from stretched molecules.

PubMed

Li, Weiyan; Dong, Fulong; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-11-30

We study the ellipticity of near-threshold harmonics (NTH) from aligned molecules with large internuclear distances numerically and analytically. The calculated harmonic spectra show a broad plateau for NTH which is several orders of magnitude higher than that for high-order harmonics. In particular, the NTH plateau shows high ellipticity at small and intermediate orientation angles. Our analyses reveal that the main contributions to the NTH plateau come from the transition of the electron from continuum states to these two lowest bound states of the system, which are strongly coupled together by the laser field. Besides continuum states, higher excited states also play a role in the NTH plateau, resulting in a large phase difference between parallel and perpendicular harmonics and accordingly high ellipticity of the NTH plateau. The NTH plateau with high intensity and large ellipticity provides a promising manner for generating strong elliptically-polarized extreme-ultraviolet (EUV) pulses.

Laser-induced plasmonic colours on metals

NASA Astrophysics Data System (ADS)

Guay, Jean-Michel; Calà Lesina, Antonino; Côté, Guillaume; Charron, Martin; Poitras, Daniel; Ramunno, Lora; Berini, Pierre; Weck, Arnaud

2017-07-01

Plasmonic resonances in metallic nanoparticles have been used since antiquity to colour glasses. The use of metal nanostructures for surface colourization has attracted considerable interest following recent developments in plasmonics. However, current top-down colourization methods are not ideally suited to large-scale industrial applications. Here we use a bottom-up approach where picosecond laser pulses can produce a full palette of non-iridescent colours on silver, gold, copper and aluminium. We demonstrate the process on silver coins weighing up to 5 kg and bearing large topographic variations (~1.5 cm). We find that colours are related to a single parameter, the total accumulated fluence, making the process suitable for high-throughput industrial applications. Statistical image analyses of laser-irradiated surfaces reveal various nanoparticle size distributions. Large-scale finite-difference time-domain computations based on these nanoparticle distributions reproduce trends seen in reflectance measurements, and demonstrate the key role of plasmonic resonances in colour formation.

Laser-induced plasmonic colours on metals

PubMed Central

Guay, Jean-Michel; Calà Lesina, Antonino; Côté, Guillaume; Charron, Martin; Poitras, Daniel; Ramunno, Lora; Berini, Pierre; Weck, Arnaud

2017-01-01

Plasmonic resonances in metallic nanoparticles have been used since antiquity to colour glasses. The use of metal nanostructures for surface colourization has attracted considerable interest following recent developments in plasmonics. However, current top-down colourization methods are not ideally suited to large-scale industrial applications. Here we use a bottom-up approach where picosecond laser pulses can produce a full palette of non-iridescent colours on silver, gold, copper and aluminium. We demonstrate the process on silver coins weighing up to 5 kg and bearing large topographic variations (∼1.5 cm). We find that colours are related to a single parameter, the total accumulated fluence, making the process suitable for high-throughput industrial applications. Statistical image analyses of laser-irradiated surfaces reveal various nanoparticle size distributions. Large-scale finite-difference time-domain computations based on these nanoparticle distributions reproduce trends seen in reflectance measurements, and demonstrate the key role of plasmonic resonances in colour formation. PMID:28719576

New features of the Moon revealed and identified by CLTM-s01

NASA Astrophysics Data System (ADS)

Huang, Qian; Ping, Jinsong; Su, Xiaoli; Shu, Rong; Tang, Geshi

2009-12-01

Previous analyses showed a clear asymmetry in the topography, geological material distribution, and crustal thickness between the nearside and farside of the Moon. Lunar detecting data, such as topography and gravity, have made it possible to interpret this hemisphere dichotomy. The high-resolution lunar topographic model CLTM-s01 has revealed that there still exist four unknown features, namely, quasi-impact basin Sternfeld-Lewis (20°S, 232°E), confirmed impact basin Fitzgerald-Jackson (25°N, 191°E), crater Wugang (13°N, 189°E) and volcanic deposited highland Yutu (14°N, 308°E). Furthermore, we analyzed and identified about eleven large-scale impact basins that have been proposed since 1994, and classified them according to their circular characteristics.

Fossil evidence for evolution of the shape and color of penguin feathers.

PubMed

Clarke, Julia A; Ksepka, Daniel T; Salas-Gismondi, Rodolfo; Altamirano, Ali J; Shawkey, Matthew D; D'Alba, Liliana; Vinther, Jakob; DeVries, Thomas J; Baby, Patrice

2010-11-12

Penguin feathers are highly modified in form and function, but there have been no fossils to inform their evolution. A giant penguin with feathers was recovered from the late Eocene (~36 million years ago) of Peru. The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage. Analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray and reddish-brown. In contrast, the dark black-brown color of extant penguin feathers is generated by large, ellipsoidal melanosomes previously unknown for birds. The nanostructure of penguin feathers was thus modified after earlier macrostructural modifications of feather shape linked to aquatic flight.

Comparative genomics reveals insights into avian genome evolution and adaptation.

PubMed

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

2014-12-12

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Copyright © 2014, American Association for the Advancement of Science.

Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment

PubMed Central

Milani, Christian; Turroni, Francesca; Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Ferrario, Chiara; van Sinderen, Douwe

2015-01-01

Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome. PMID:26590291

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

PubMed

Ray, Jessica L; Althammer, Julia; Skaar, Katrine S; Simonelli, Paolo; Larsen, Aud; Stoecker, Diane; Sazhin, Andrey; Ijaz, Umer Z; Quince, Christopher; Nejstgaard, Jens C; Frischer, Marc; Pohnert, Georg; Troedsson, Christofer

2016-11-01

In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances. © 2016 John Wiley & Sons Ltd.

DISRUPTION OF LARGE-SCALE NEURAL NETWORKS IN NON-FLUENT/AGRAMMATIC VARIANT PRIMARY PROGRESSIVE APHASIA ASSOCIATED WITH FRONTOTEMPORAL DEGENERATION PATHOLOGY

PubMed Central

Grossman, Murray; Powers, John; Ash, Sherry; McMillan, Corey; Burkholder, Lisa; Irwin, David; Trojanowski, John Q.

2012-01-01

Non-fluent/agrammatic primary progressive aphasia (naPPA) is a progressive neurodegenerative condition most prominently associated with slowed, effortful speech. A clinical imaging marker of naPPA is disease centered in the left inferior frontal lobe. We used multimodal imaging to assess large-scale neural networks underlying effortful expression in 15 patients with sporadic naPPA due to frontotemporal lobar degeneration (FTLD) spectrum pathology. Effortful speech in these patients is related in part to impaired grammatical processing, and to phonologic speech errors. Gray matter (GM) imaging shows frontal and anterior-superior temporal atrophy, most prominently in the left hemisphere. Diffusion tensor imaging reveals reduced fractional anisotropy in several white matter (WM) tracts mediating projections between left frontal and other GM regions. Regression analyses suggest disruption of three large-scale GM-WM neural networks in naPPA that support fluent, grammatical expression. These findings emphasize the role of large-scale neural networks in language, and demonstrate associated language deficits in naPPA. PMID:23218686

Large area optical mapping of surface contact angle.

PubMed

Dutra, Guilherme; Canning, John; Padden, Whayne; Martelli, Cicero; Dligatch, Svetlana

2017-09-04

Top-down contact angle measurements have been validated and confirmed to be as good if not more reliable than side-based measurements. A range of samples, including industrially relevant materials for roofing and printing, has been compared. Using the top-down approach, mapping in both 1-D and 2-D has been demonstrated. The method was applied to study the change in contact angle as a function of change in silver (Ag) nanoparticle size controlled by thermal evaporation. Large area mapping reveals good uniformity for commercial Aspen paper coated with black laser printer ink. A demonstration of the forensic and chemical analysis potential in 2-D is shown by uncovering the hidden CsF initials made with mineral oil on the coated Aspen paper. The method promises to revolutionize nanoscale characterization and industrial monitoring as well as chemical analyses by allowing rapid contact angle measurements over large areas or large numbers of samples in ways and times that have not been possible before.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography.

PubMed

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-05-02

The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) is an IP 3 -gated ion channel that releases calcium ions (Ca 2+ ) from the endoplasmic reticulum. The IP 3 -binding sites in the large cytosolic domain are distant from the Ca 2+ conducting pore, and the allosteric mechanism of how IP 3 opens the Ca 2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP 3 R in the absence and presence of IP 3 Analyses of two distinct space group crystals uncovered an IP 3 -dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP 3 R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP 3 -controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP 3 binding to the Ca 2+ channel.

Large-Scale Discovery of Disease-Disease and Disease-Gene Associations

PubMed Central

Gligorijevic, Djordje; Stojanovic, Jelena; Djuric, Nemanja; Radosavljevic, Vladan; Grbovic, Mihajlo; Kulathinal, Rob J.; Obradovic, Zoran

2016-01-01

Data-driven phenotype analyses on Electronic Health Record (EHR) data have recently drawn benefits across many areas of clinical practice, uncovering new links in the medical sciences that can potentially affect the well-being of millions of patients. In this paper, EHR data is used to discover novel relationships between diseases by studying their comorbidities (co-occurrences in patients). A novel embedding model is designed to extract knowledge from disease comorbidities by learning from a large-scale EHR database comprising more than 35 million inpatient cases spanning nearly a decade, revealing significant improvements on disease phenotyping over current computational approaches. In addition, the use of the proposed methodology is extended to discover novel disease-gene associations by including valuable domain knowledge from genome-wide association studies. To evaluate our approach, its effectiveness is compared against a held-out set where, again, it revealed very compelling results. For selected diseases, we further identify candidate gene lists for which disease-gene associations were not studied previously. Thus, our approach provides biomedical researchers with new tools to filter genes of interest, thus, reducing costly lab studies. PMID:27578529

The silver lining of a mind in the clouds: interesting musings are associated with positive mood while mind-wandering

PubMed Central

Franklin, Michael S.; Mrazek, Michael D.; Anderson, Craig L.; Smallwood, Jonathan; Kingstone, Alan; Schooler, Jonathan W.

2013-01-01

The negative effects of mind-wandering on performance and mood have been widely documented. In a recent well-cited study, Killingsworth and Gilbert (2010) conducted a large experience sampling study revealing that all off-task episodes, regardless of content, have equal to or lower happiness ratings, than on-task episodes. We present data from a similarly implemented experience sampling study with additional mind-wandering content categories. Our results largely conform to those of the Killingsworth and Gilbert (2010) study, with mind-wandering generally being associated with a more negative mood. However, subsequent analyses reveal situations in which a more positive mood is reported after being off-task. Specifically when off-task episodes are rated for interest, the high interest episodes are associated with an increase in positive mood compared to all on-task episodes. These findings both identify a situation in which mind-wandering may have positive effects on mood, and suggest the possible benefits of encouraging individuals to shift their off-task musings to the topics they find most engaging. PMID:24009599

Validation of the Transient Structural Response of a Threaded Assembly: Phase I

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

Doebling, Scott W.; Hemez, Francois M.; Robertson, Amy N.

2004-04-01

This report explores the application of model validation techniques in structural dynamics. The problem of interest is the propagation of an explosive-driven mechanical shock through a complex threaded joint. The study serves the purpose of assessing whether validating a large-size computational model is feasible, which unit experiments are required, and where the main sources of uncertainty reside. The results documented here are preliminary, and the analyses are exploratory in nature. The results obtained to date reveal several deficiencies of the analysis, to be rectified in future work.

Analysis of rockbolt performance at the Waste Isolation Pilot Plant

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

Terrill, L.J.; Francke, C.T.; Saeb, S.

Rockbolt failures at the Waste Isolation Pilot Plant have been recorded since 1990 and are categorized in terms of mode of failure. The failures are evaluated in terms of physical location of installation within the mine, local excavation geometry and stratigraphy, proximity to other excavations or shafts, and excavation age. The database of failures has revealed discrete ares of the mine containing relatively large numbers of failures. The results of metallurgical analyses and standard rockbolt load testing have generally been in agreement with the in situ evaluations.

Structure and variability of the Western Maine Coastal Current

USGS Publications Warehouse

Churchill, J.H.; Pettigrew, N.R.; Signell, R.P.

2005-01-01

Analyses of CTD and moored current meter data from 1998 and 2000 reveal a number of mechanisms influencing the flow along the western coast of Maine. On occasions, the Eastern Maine Coastal Current extends into the western Gulf of Maine where it takes the form of a deep (order 100 m deep) and broad (order 20 km wide) southwestward flow with geostrophic velocities exceeding 20 cm s -1. This is not a coastally trapped flow, however. In fields of geostrophic velocity, computed from shipboard-CTD data, the core of this current is roughly centered at the 100 m isobath and its onshore edge is no closer than 10 km from the coast. Geostrophic velocity fields also reveal a relatively shallow (order 10 m deep) baroclinic flow adjacent to the coast. This flow is also directed to the southwest and appears to be principally comprised of local river discharge. Analyses of moored current meter data reveal wind-driven modulations of the coastal flow that are consistent with expectations from simple theoretical models. However, a large fraction of the near-shore current variance does not appear to be directly related to wind forcing. Sea-surface temperature imagery, combined with analysis of the moored current meter data, suggests that eddies and meanders within the coastal flow may at times dominate the near-shore current variance. ?? 2005 Elsevier Ltd. All rights reserved.

Comparative genomic and proteomic analyses of PE/PPE multigene family of Mycobacterium tuberculosis H37Rv and H37Ra reveal novel and interesting differences with implications in virulence

PubMed Central

Kohli, Sakshi; Singh, Yadvir; Sharma, Khushbu; Mittal, Aditya; Ehtesham, Nasreen Z.; Hasnain, Seyed E.

2012-01-01

Tuberculosis, caused by Mycobacterium tuberculosis, remains a leading infectious disease taking one human life every 15 s globally. The two well-characterized strains H37Rv and H37Ra, derived from the same parental strain M. tuberculosis H37, show dramatically different pathogenic phenotypes. PE/PPE gene family, comprising of 176 open reading frames and present exclusively in genus Mycobacterium, accounts for ∼10% of the M. tuberculosis genome. Our comprehensive in silico analyses of PE/PPE family of H37Ra and virulent H37Rv strains revealed genetic differences between these strains in terms of several single nucleotide variations and InDels and these manifested in changes in physico-chemical properties, phosphorylation sites, and protein: protein interacting domains of the corresponding proteomes. Similar comparisons using the 13 sigma factor genes, 36 members of the mammalian cell entry family, 13 mycobacterial membrane protein large family members and 11 two-component signal transduction systems along with 5 orphaned response regulators and 2 orphaned sensor kinases failed to reveal very significant difference between H37Rv and H37Ra, reinforcing the importance of PE/PPE genes. Many of these changes between H37Rv and H37Ra can be correlated to differences in pathogenesis and virulence of the two strains. PMID:22618876

Individual-based analyses reveal limited functional overlap in a coral reef fish community.

PubMed

Brandl, Simon J; Bellwood, David R

2014-05-01

Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on coral reefs, as algal removal appears to depend strongly on species-specific microhabitat utilization patterns of herbivores. Furthermore, the results emphasize the capacity of the individual-based analyses to reveal variation in the functional niches of species, even in high-diversity systems such as coral reefs, demonstrating its potential applicability to other high-diversity ecosystems. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Isotropy analyses of the Planck convergence map

NASA Astrophysics Data System (ADS)

Marques, G. A.; Novaes, C. P.; Bernui, A.; Ferreira, I. S.

2018-01-01

The presence of matter in the path of relic photons causes distortions in the angular pattern of the cosmic microwave background (CMB) temperature fluctuations, modifying their properties in a slight but measurable way. Recently, the Planck Collaboration released the estimated convergence map, an integrated measure of the large-scale matter distribution that produced the weak gravitational lensing (WL) phenomenon observed in Planck CMB data. We perform exhaustive analyses of this convergence map calculating the variance in small and large regions of the sky, but excluding the area masked due to Galactic contaminations, and compare them with the features expected in the set of simulated convergence maps, also released by the Planck Collaboration. Our goal is to search for sky directions or regions where the WL imprints anomalous signatures to the variance estimator revealed through a χ2 analyses at a statistically significant level. In the local analysis of the Planck convergence map, we identified eight patches of the sky in disagreement, in more than 2σ, with what is observed in the average of the simulations. In contrast, in the large regions analysis we found no statistically significant discrepancies, but, interestingly, the regions with the highest χ2 values are surrounding the ecliptic poles. Thus, our results show a good agreement with the features expected by the Λ cold dark matter concordance model, as given by the simulations. Yet, the outliers regions found here could suggest that the data still contain residual contamination, like noise, due to over- or underestimation of systematic effects in the simulation data set.

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters

PubMed Central

Sapriel, Guillaume; Quinet, Michelle; Heijde, Marc; Jourdren, Laurent; Tanty, Véronique; Luo, Guangzuo; Le Crom, Stéphane; Lopez, Pascal Jean

2009-01-01

Background Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. Methodology/Principal Findings Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. Conclusions/Significance Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins. PMID:19829693

Ecological characteristics of Simulium breeding sites in West Africa.

PubMed

Cheke, Robert A; Young, Stephen; Garms, Rolf

2017-03-01

Twenty-nine taxa of Simulium were identified amongst 527 collections of larvae and pupae from untreated rivers and streams in Liberia (362 collections in 1967-71 & 1989), Togo (125 in 1979-81), Benin (35 in 1979-81) and Ghana (5 in 1980-81). Presence or absence of associations between different taxa were used to group them into six clusters using Ward agglomerative hierarchical cluster analysis. Environmental data associated with the pre-imaginal habitats were then analysed in relation to the six clusters by one way ANOVA. The results revealed significant effects in determining the clusters of maximum river width (all P<0.001 unless stated otherwise), water temperature, dry bulb air temperature, relative humidity, altitude, type of water (on a range from trickle to large river), water level, slope, current, vegetation, light conditions, discharge, length of breeding area, environs, terrain, river bed type (P<0.01), and the supports to which the insects were attached (P<0.01). When four non-significant contributors (wet bulb temperature, river features, height of waterfall and depth) were excluded and the reduced data-set analysed by principal components analysis (PCA), the first two principal components (PCs) accounted for 87% of the variance, with geographical features dominant in PC1 and hydrological characteristics in PC2. The analyses also revealed the ecological characteristics of each taxon's pre-imaginal habitats, which are discussed with particular reference to members of the Simulium damnosum species complex, whose breeding site distributions were further analysed by canonical correspondence analysis (CCA), a method also applied to the data on non-vector species. Copyright © 2016 Elsevier B.V. All rights reserved.

Unexplored Character Diversity in Onychophora (Velvet Worms): A Comparative Study of Three Peripatid Species

PubMed Central

Oliveira, Ivo de Sena; Franke, Franziska Anni; Hering, Lars; Schaffer, Stefan; Rowell, David M.; Weck-Heimann, Andreas; Monge-Nájera, Julián; Morera-Brenes, Bernal; Mayer, Georg

2012-01-01

Low character variation among onychophoran species has been an obstacle for taxonomic and phylogenetic studies in the past, however we have identified a number of new and informative characters using morphological, molecular, and chromosomal techniques. Our analyses involved a detailed examination of Epiperipatus biolleyi from Costa Rica, Eoperipatus sp. from Thailand, and a new onychophoran species and genus from Costa Rica, Principapillatus hitoyensis gen. et sp. nov.. Scanning electron microscopy on embryos and specimens of varying age revealed novel morphological characters and character states, including the distribution of different receptor types along the antennae, the arrangement and form of papillae on the head, body and legs, the presence and shape of interpedal structures and fields of modified scales on the ventral body surface, the arrangement of lips around the mouth, the number, position and structure of crural tubercles and anal gland openings, and the presence and shape of embryonic foot projections. Karyotypic analyses revealed differences in the number and size of chromosomes among the species studied. The results of our phylogenetic analyses using mitochondrial COI and 12S rRNA gene sequences are in line with morphological and karyotype data. However, our data show a large number of unexplored, albeit informative, characters in the Peripatidae. We suggest that analysing these characters in additional species would help unravel species diversity and phylogeny in the Onychophora, and that inconsistencies among most diagnostic features used for the peripatid genera in the literature could be addressed by identifying a suite of characters common to all peripatids. PMID:23284667

Are self-directed parenting interventions sufficient for externalising behaviour problems in childhood? A systematic review and meta-analysis.

PubMed

Tarver, Joanne; Daley, David; Lockwood, Joanna; Sayal, Kapil

2014-12-01

Externalising behaviour in childhood is a prevalent problem in the field of child and adolescent mental health. Parenting interventions are widely accepted as efficacious treatment options for reducing externalising behaviour, yet practical and psychological barriers limit their accessibility. This review aims to establish the evidence base of self-directed (SD) parenting interventions for externalising behaviour problems. Electronic searches of PubMed, Web of Knowledge, Psychinfo, Embase and CENTRAL databases and manual searches of reference lists of relevant reviews identified randomised controlled trials and cluster randomised controlled trials examining the efficacy of SD interventions compared to no-treatment or active control groups. A random-effect meta-analysis estimated pooled standard mean difference (SMD) for SD interventions on measures of externalising child behaviour. Secondary analyses examined their effect on measures of parenting behaviour, parental stress and mood and parenting efficacy. Eleven eligible trials were included in the analyses. SD interventions had a large effect on parent report of externalising child behaviour (SMD = 1.01, 95 % CI: 0.77-1.24); although this effect was not upheld by analyses of observed child behaviour. Secondary analyses revealed effects of small to moderate magnitude on measures of parenting behaviour, parental mood and stress and parenting efficacy. An analysis comparing SD interventions with therapist-led parenting interventions revealed no significant difference on parent-reported measures of externalising child behaviour. SD interventions are associated with improvements in parental perception of externalising child behaviour and parental behaviour and well-being. Future research should further investigate the relative efficacy and cost-effectiveness of SD interventions compared to therapist-led interventions.

In-frame Val216-Ser217 deletion of KIT in mild piebaldism causes aberrant secretion and SCF response.

PubMed

Hattori, Mai; Ishikawa, Osamu; Oikawa, Daisuke; Amano, Hiroo; Yasuda, Masahito; Kaira, Kyoichi; Ishida-Yamamoto, Akemi; Nakano, Hajime; Sawamura, Daisuke; Terawaki, Shin-Ichi; Wakamatsu, Kaori; Tokunaga, Fuminori; Shimizu, Akira

2018-03-21

Piebaldism is a pigmentary disorder characterized by a white forelock and depigmented patches. Although the loss-of-function mutations in the KIT gene underlie the disease, the intracellular dynamics of the mutant KIT are largely unknown. We herein report a Japanese family with piebaldism in which the affected members showed a mild phenotype. The objective of this study is to investigate the functions and intracellular dynamics of the mutant KIT protein. We performed genetic analyses of the KIT gene using peripheral blood cells. We analyzed the intracellular localization of the mutant KIT protein in HEK293T cells transfected with wild-type (Wt) and/or mutant KIT genes. Immunoprecipitation analyses, immunoblotting and immunofluorescence studies were performed using antibodies against KIT and downstream signaling proteins. Glycosidase digestion analysis was performed to clarify the intracellular localization of KIT protein. A genetic analysis revealed a novel heterozygous mutation c.645_650delTGTGTC which results in the in-frame deletion of Val 216 and Ser 217 in the extracellular domain of KIT. Immunoprecipitation analyses confirmed that the wild and mutant KIT formed a heterodimer after treatment with stem cell factor (SCF); however, the phosphorylation of the downstream signaling factors was decreased. In an immunofluorescence study, the mutant KIT accumulated predominantly in the endoplasmic reticulum (ER) and was sparsely expressed on the cell surface. A glycosidase digestion study revealed that the mutant KIT is predominantly localized in the ER. These data reveal an aberrant function and intracellular localization of mutant KIT protein in piebaldism. Copyright © 2018 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

PubMed Central

Yuan, Bo; Liu, Pengfei; Gupta, Aditya; Beck, Christine R.; Tejomurtula, Anusha; Campbell, Ian M.; Gambin, Tomasz; Simmons, Alexandra D.; Withers, Marjorie A.; Harris, R. Alan; Rogers, Jeffrey; Schwartz, David C.; Lupski, James R.

2015-01-01

Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. PMID:26641089

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels.

PubMed

Spracklen, Cassandra N; Chen, Peng; Kim, Young Jin; Wang, Xu; Cai, Hui; Li, Shengxu; Long, Jirong; Wu, Ying; Wang, Ya Xing; Takeuchi, Fumihiko; Wu, Jer-Yuarn; Jung, Keum-Ji; Hu, Cheng; Akiyama, Koichi; Zhang, Yonghong; Moon, Sanghoon; Johnson, Todd A; Li, Huaixing; Dorajoo, Rajkumar; He, Meian; Cannon, Maren E; Roman, Tamara S; Salfati, Elias; Lin, Keng-Hung; Guo, Xiuqing; Sheu, Wayne H H; Absher, Devin; Adair, Linda S; Assimes, Themistocles L; Aung, Tin; Cai, Qiuyin; Chang, Li-Ching; Chen, Chien-Hsiun; Chien, Li-Hsin; Chuang, Lee-Ming; Chuang, Shu-Chun; Du, Shufa; Fan, Qiao; Fann, Cathy S J; Feranil, Alan B; Friedlander, Yechiel; Gordon-Larsen, Penny; Gu, Dongfeng; Gui, Lixuan; Guo, Zhirong; Heng, Chew-Kiat; Hixson, James; Hou, Xuhong; Hsiung, Chao Agnes; Hu, Yao; Hwang, Mi Yeong; Hwu, Chii-Min; Isono, Masato; Juang, Jyh-Ming Jimmy; Khor, Chiea-Chuen; Kim, Yun Kyoung; Koh, Woon-Puay; Kubo, Michiaki; Lee, I-Te; Lee, Sun-Ju; Lee, Wen-Jane; Liang, Kae-Woei; Lim, Blanche; Lim, Sing-Hui; Liu, Jianjun; Nabika, Toru; Pan, Wen-Harn; Peng, Hao; Quertermous, Thomas; Sabanayagam, Charumathi; Sandow, Kevin; Shi, Jinxiu; Sun, Liang; Tan, Pok Chien; Tan, Shu-Pei; Taylor, Kent D; Teo, Yik-Ying; Toh, Sue-Anne; Tsunoda, Tatsuhiko; van Dam, Rob M; Wang, Aili; Wang, Feijie; Wang, Jie; Wei, Wen Bin; Xiang, Yong-Bing; Yao, Jie; Yuan, Jian-Min; Zhang, Rong; Zhao, Wanting; Chen, Yii-Der Ida; Rich, Stephen S; Rotter, Jerome I; Wang, Tzung-Dau; Wu, Tangchun; Lin, Xu; Han, Bok-Ghee; Tanaka, Toshihiro; Cho, Yoon Shin; Katsuya, Tomohiro; Jia, Weiping; Jee, Sun-Ha; Chen, Yuan-Tsong; Kato, Norihiro; Jonas, Jost B; Cheng, Ching-Yu; Shu, Xiao-Ou; He, Jiang; Zheng, Wei; Wong, Tien-Yin; Huang, Wei; Kim, Bong-Jo; Tai, E-Shyong; Mohlke, Karen L; Sim, Xueling

2017-05-01

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

[Dopplerography of the large hepatic veins in the diagnosis of tricuspid valve insufficiency].

PubMed

Korytnikov, K I; Martyniuk, A D; Pustovit, L K

1991-01-01

During pulse dopplerography of the large hepatic veins in patients with tricuspid valve failure, the differences in the shape of the spectrum of Doppler's frequencies were revealed as dependent on cardiac rhythm. In sinus rhythm, the curve of the systolic flow is recordable beneath the baseline, in atrial fibrillation, over the baseline. In scanning of the large hepatic veins in patients with tricuspid valve failure, the shape of the curves of the spectrum of Doppler's frequencies coincides with the shape of the curves of liver pulsation. Tricuspid valve failure in sinus rhythm leads to a decrease of the maximum velocity of the systolic flow in the hepatic veins. There is a close correlation between the maximum velocity of the systolic flow of tricuspid regurgitation and the maximum velocity of the systolic flow in the large hepatic veins. Pulse dopplerography of the large hepatic veins is a safe enough method of the diagnosis of tricuspid valve failure and can be used in difficult cases when analysing the tricuspid blood flow from standard projections.

Confirmation of TNIP1 but not RHOB and PSORS1C1 as systemic sclerosis risk factors in a large independent replication study

PubMed Central

Bossini-Castillo, Lara; Martin, Jose Ezequiel; Broen, Jasper; Simeon, Carmen P; Beretta, Lorenzo; Gorlova, Olga Y; Vonk, Madelon C; Ortego-Centeno, Norberto; Espinosa, Gerard; Carreira, Patricia; García de la Peña, Paloma; Oreiro, Natividad; Román-Ivorra, José Andrés; Castillo, María Jesús; González-Gay, Miguel A; Sáez-Comet, Luis; Castellví, Ivan; Schuerwegh, Annemie J; Voskuyl, Alexandre E; Hoffmann-Vold, Anna-Maria; Hesselstrand, Roger; Nordin, Annika; Lunardi, Claudio; Scorza, Raffaella; van Laar, Jacob M; Shiels, Paul G; Herrick, Ariane; Worthington, Jane; Fonseca, Carmen; Denton, Christopher; Tan, Filemon K; Arnett, Frank C; Assassi, Shervin; Koeleman, Bobby P; Mayes, Maureen D; Radstake, Timothy R D J; Martin, Javier

2013-01-01

Introduction A recent genome-wide association study in European systemic sclerosis (SSc) patients identified three loci (PSORS1C1, TNIP1 and RHOB) as novel genetic risk factors for the disease. The aim of this study was to replicate the previously mentioned findings in a large multicentre independent SSc cohort of Caucasian ancestry. Methods 4389 SSc patients and 7611 healthy controls from different European countries and the USA were included in the study. Six single nucleotide polymorphisms (SNP): rs342070, rs13021401 (RHOB), rs2233287, rs4958881, rs3792783 (TNIP1) and rs3130573 (PSORS1C1) were analysed. Overall significance was calculated by pooled analysis of all the cohorts. Haplotype analyses and conditional logistic regression analyses were carried out to explore further the genetic structure of the tested loci. Results Pooled analyses of all the analysed SNPs in TNIP1 revealed significant association with the whole disease (rs2233287 pMH=1.94×10−4, OR 1.19; rs4958881 pMH=3.26×10−5, OR 1.19; rs3792783 pMH=2.16×10−4, OR 1.19). These associations were maintained in all the subgroups considered. PSORS1C1 comparison showed association with the complete set of patients and all the subsets except for the anti-centromere-positive patients. However, the association was dependent on different HLA class II alleles. The variants in the RHOB gene were not associated with SSc or any of its subsets. Conclusions These data confirmed the influence of TNIP1 on an increased susceptibility to SSc and reinforced this locus as a common autoimmunity risk factor. PMID:22896740

Genomic and Transcriptomic Analyses to Identify Pathways Involved in Nanoparticle Generation in the Ubiquitous Marine Bacterium Alteromonas macleodii Under Elevated Copper Conditions

NASA Astrophysics Data System (ADS)

Cusick, K. D.; Dale, J.; Little, B.; Cockrell, A.; Biffinger, J.

2016-02-01

Alteromonas macleodii is a ubiquitous marine bacterium that clusters by molecular analyses into two ecotypes: surface and deep-water. Our group isolated a marine bacterium from copper coupons that generates nanoparticles (NPs) at elevated copper concentrations. Sequencing of the 16S rRNA gene identified it as an A. macleodii strain. In phylogenetic analyses based on the gyrB gene, it clustered with other surface isolates; however, it formed a unique cluster separate from that of other surface isolates based on rpoB gene sequences. Copper is commonly employed as an antifouling agent on the hulls of ships, and so copper tolerance and NP generation is under investigation in this strain. The overall goals of this study were: (1) to determine if copper tolerance is the result of changes at the genetic or transcriptional level and (2) to identify the genes involved in NP formation. Sub-cultures were established from the initial isolate in which copper concentrations were increased in .25 mM increments through multiple generations. These sub-cultures were assayed for NP formation in seawater medium supplemented with 3-4 mM copper. Scanning electron microscopy revealed large aggregates of NPs on the exterior surface of all sub-cultures. Additionally, a portion of the cells in all sub-cultures displayed an elongated morphology in comparison to the wild-type. No NPs were observed in wild-type controls grown without the addition of increased copper. Metagenomic sequencing of natural populations of A. macleodii revealed extreme divergence in several large genomic regions whose content includes genes coding for exopolysaccharide production and metal resistance. High-throughput sequencing is being used to determine whether copper tolerance and NP generation is the result of genetic or transcriptional changes. These results will be extended to natural communities to gain insights into the role of bacterial NPs during conditions of elevated metal concentrations in coastal systems.

Does more education mean less disability in people with dementia? A large cross-sectional study in Taiwan.

PubMed

Huang, Shih-Wei; Chi, Wen-Chou; Yen, Chia-Feng; Chang, Kwang-Hwa; Liao, Hua-Fang; Escorpizo, Reuben; Chang, Feng-Hang; Liou, Tsan-Hon

2017-05-04

WHO Disability Assessment Schedule 2.0 (WHODAS 2.0) is a feasible tool for assessing functional disability and analysing the risk of institutionalisation among elderly patients with dementia. However, the data for the effect of education on disability status in patients with dementia is lacking. The aim of this large-scale, population-based study was to analyse the effect of education on the disability status of elderly Taiwanese patients with dementia by using WHODAS 2.0. From the Taiwan Data Bank of Persons with Disability, we enrolled 7698 disabled elderly (older than 65 years) patients diagnosed with dementia between July 2012 and January 2014. According to their education status, we categorised these patients with and without formal education (3849 patients each). We controlled for the demographic variables through propensity score matching. The standardised scores of these patients in the six domains of WHODAS 2.0 were evaluated by certified interviewers. Student's t - test was used for comparing the WHODAS 2.0 scores of patients with dementia in the two aforementioned groups. Poisson regression was applied for analysing the association among all the investigated variables. Patients with formal education had low disability status in the domains of getting along and social participation than did patients without formal education. Poisson regression revealed that standardised scores in all domains of WHODAS 2.0-except self-care-were associated with education status. This study revealed lower disability status in the WHODAS 2.0 domains of getting along and social participation for patients with dementia with formal education compared with those without formal education. For patients with disability and dementia without formal education, community intervention of social participation should be implemented to maintain better social interaction ability. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Quality of Relationships with Parents and Friends in Adolescence Predicts Metabolic Risk in Young Adulthood

PubMed Central

Ehrlich, Katherine B.; Hoyt, Lindsay T.; Sumner, Jennifer A.; McDade, Thomas W.; Adam, Emma K.

2015-01-01

Objective The present study was designed to examine whether family and peer relationships in adolescence predict the emergence of metabolic risk factors in young adulthood. Methods Participants from a large, nationally representative cohort study (N = 11,617 for these analyses) reported on their relationship experiences with parents and close friends during adolescence. Fourteen years later, interviewers collected blood samples, as well as anthropometric and blood pressure measurements. Blood samples were analyzed for HbA1c. Results Ordered logistic regressions revealed that for females, supportive parent-child relationships and close male friendships in adolescence were associated with reduced odds of having elevated metabolic risk markers in young adulthood. These effects remained significant even after controlling for baseline measures of body mass index (BMI) and health and demographic covariates. The protective effects of close relationships were not significant for males, however. Exploratory analyses with two-parent families revealed that supportive father-child relationships were especially protective for females. Conclusions These findings suggest that, for females, close and supportive relationships with parents and male friends in adolescence may reduce the risk of metabolic dysregulation in adulthood. PMID:25689301

Quality of relationships with parents and friends in adolescence predicts metabolic risk in young adulthood.

PubMed

Ehrlich, Katherine B; Hoyt, Lindsay Till; Sumner, Jennifer A; McDade, Thomas W; Adam, Emma K

2015-09-01

This study was designed to examine whether family and peer relationships in adolescence predict the emergence of metabolic risk factors in young adulthood. Participants from a large, nationally representative cohort study (N = 11,617 for these analyses) reported on their relationship experiences with parents and close friends during adolescence. Fourteen years later, interviewers collected blood samples, as well as anthropometric and blood pressure measurements. Blood samples were analyzed for HbA1c. Ordered logistic regressions revealed that for females, supportive parent-child relationships and close male friendships in adolescence were associated with reduced odds of having elevated metabolic risk markers in young adulthood. These effects remained significant even after controlling for baseline measures of body mass index (BMI) and health and demographic covariates. The protective effects of close relationships were not significant for males, however. Exploratory analyses with 2-parent families revealed that supportive father-child relationships were especially protective for females. These findings suggest that, for females, close and supportive relationships with parents and male friends in adolescence may reduce the risk of metabolic dysregulation in adulthood. (c) 2015 APA, all rights reserved).

Discovering Periodic Patterns in Historical News

PubMed Central

Dzogang, Fabon; Lansdall-Welfare, Thomas; Cristianini, Nello

2016-01-01

We address the problem of observing periodic changes in the behaviour of a large population, by analysing the daily contents of newspapers published in the United States and United Kingdom from 1836 to 1922. This is done by analysing the daily time series of the relative frequency of the 25K most frequent words for each country, resulting in the study of 50K time series for 31,755 days. Behaviours that are found to be strongly periodic include seasonal activities, such as hunting and harvesting. A strong connection with natural cycles is found, with a pronounced presence of fruits, vegetables, flowers and game. Periodicities dictated by religious or civil calendars are also detected and show a different wave-form than those provoked by weather. States that can be revealed include the presence of infectious disease, with clear annual peaks for fever, pneumonia and diarrhoea. Overall, 2% of the words are found to be strongly periodic, and the period most frequently found is 365 days. Comparisons between UK and US, and between modern and historical news, reveal how the fundamental cycles of life are shaped by the seasons, but also how this effect has been reduced in modern times. PMID:27824911

Uninsured Migrants: Health Insurance Coverage and Access to Care Among Mexican Return Migrants.

PubMed

Wassink, Joshua

2018-01-01

Despite an expansive body of research on health and access to medical care among Mexican immigrants in the United States, research on return migrants focuses primarily on their labor market mobility and contributions to local development. Motivated by recent scholarship that documents poor mental and physical health among Mexican return migrants, this study investigates return migrants' health insurance coverage and access to medical care. I use descriptive and multivariate techniques to analyze data from the 2009 and 2014 rounds of Mexico's National Survey of Demographic Dynamics (ENADID, combined n=632,678). Analyses reveal a large and persistent gap between recent return migrants and non-migrants, despite rising overall health coverage in Mexico. Multivariate analyses suggest that unemployment among recent arrivals contributes to their lack of insurance. Relative to non-migrants, recently returned migrants rely disproportionately on private clinics, pharmacies, self-medication, or have no regular source of care. Mediation analysis suggests that returnees' high rate of uninsurance contributes to their inadequate access to care. This study reveals limited access to medical care among the growing population of Mexican return migrants, highlighting the need for targeted policies to facilitate successful reintegration and ensure access to vital resources such as health care.

The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal

PubMed Central

Seim, Inge; Ma, Siming; Zhou, Xuming; Gerashchenko, Maxim V.; Lee, Sang-Goo; Suydam, Robert; George, John C.; Bickham, John W.; Gladyshev, Vadim N.

2014-01-01

Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases. PMID:25411232

Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

PubMed Central

Hoppe, Björn; Kahl, Tiemo; Karasch, Peter; Wubet, Tesfaye; Bauhus, Jürgen; Buscot, François; Krüger, Dirk

2014-01-01

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa. PMID:24505405

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi.

PubMed

Hoppe, Björn; Kahl, Tiemo; Karasch, Peter; Wubet, Tesfaye; Bauhus, Jürgen; Buscot, François; Krüger, Dirk

2014-01-01

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1

PubMed Central

Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio

2014-01-01

Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species. PMID:25501478

Severe hypoplasia of the omasal laminae in a Japanese Black steer with chronic bloat--a case report.

PubMed

Takagi, Mitsuhiro; Mukai, Shuhei; Fushimi, Yasuo; Matsushita, Kouhei; Miyoshi, Nobuaki; Yasuda, Nobuhiro; Kitajima, Hideo; Takamure, Senro; Matsushita, Toshihiko; Kitamura, Nobuo; Deguchi, Eisaburo

2007-12-01

An 11-month-old Japanese Black steer with chronic bloat underwent clinical and histological analyses. During the observation period, it showed normal appetite and fecal volume but persistent chronic bloat symptoms. Compared to controls, the steer's feces contained undigested large straws. Necropsy revealed normal rumen, reticulum, and abomasum but a small omasum. The rumen, reticulum, and abomasum mucosa was normal, with well-developed ruminal papillae. However, severe hypoplasia of the omasal laminae was observed along with hypoplasia reticular groove and ruminoreticular fold. The contents of the reticulum, omasum, and abomasums comprised undigested large sized hay particles. The omasum papillae showed no pathological abnormalities. This is a rare case of a steer with chronic bloat probably caused by severe hypoplasia of the omasal laminae.

Large craters on the meteoroid and space debris impact experiment

NASA Technical Reports Server (NTRS)

Humes, Donald H.

1992-01-01

Examination of 29.37 sq m of thick aluminum plates from the LDEF, which were exposed to the meteoroid and man-made orbital debris environments for 5.8 years, revealed 606 craters that were 0.5 mm in diameter or larger. Most were nearly hemispherical. There was a large variation in the number density of craters around the three axis gravity gradient stabilized spacecraft. A new model of the near-Earth meteoroid environment gives good agreement with the crater fluxes measured on the fourteen faces of the LDEF. The man-made orbital debris model of Kessler, which predicts that 16 pct. of the craters would be caused by man-made debris, is plausible. No chemical analyses of impactor residue that will distinguish between meteoroids and man-made debris is yet available.

An investigation on seismo-ionospheric precursors in various earthquake zones

NASA Astrophysics Data System (ADS)

Su, Y.; Liu, J. G.; Chen, M.

2011-12-01

Y. C. Su1, J. Y. Liu1 and M. Q. Chen1 1Institute of Space Science, National Central University, Chung-Li,Taiwan. This paper examines the relationships between the ionosphere and earthquakes occurring in different earthquake zones e.g. Malaysia area, Tibet plateau, mid-ocean ridge, Andes, etc., to reveal the possible seismo-ionospheric precursors for these area. Because the lithology, focal mechanism of earthquakes and electrodynamics in the ionosphere at different area are different, it is probable to have diverse ionospheric reactions before large earthquakes occurring in these areas. In addition to statistical analyses on increase or decrease anomalies of the ionospheric electron density few days before large earthquakes, we focus on the seismo-ionospheric precursors for oceanic and land earthquakes as well as for earthquakes with different focal mechanisms.

Variation in the population structure of Yukon River chum and coho salmon: Evaluating the potential impact of localized habitat degradation

USGS Publications Warehouse

Olsen, J.B.; Spearman, William J.; Sage, G.K.; Miller, S.J.; Flannery, B.G.; Wenburg, J.K.

2004-01-01

We used microsatellite and mitochondrial DNA-restriction fragment length polymorphism (mtDNA-RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity because of habitat degradation from a gold mine near a Yukon River tributary could differ between the two species. For each species, collections were made from two tributaries in both the Innoko and Tanana rivers, which are tributaries to the lower and middle Yukon River. The results revealed a large difference in the degree and spatial distribution of population structure between the two species. For chum salmon, the microsatellite loci (F-statistic [FST] = 0.021) and mtDNA (F ST = -0.008) revealed a low degree of interpopulation genetic diversity on a relatively large geographic scale. This large-scale population structure should minimize, although not eliminate, the risk of genetic diversity loss due to localized habitat degradation. For coho salmon, the microsatellites (FST = 0.091) and mtDNA (FST = 0.586) revealed a high degree of interpopulation genetic diversity on a relatively small geographic scale. This small-scale population structure suggests that coho salmon are at a relatively high risk of losing genetic diversity due to lo-calized habitat degradation. Our study underscores the importance of a multispecies approach for evaluating the potential impact of land-use activities on the genetic diversity of Pacific salmon.

Stress in 1st-year women teachers: the context of social support and coping.

PubMed

Schonfeld, I S

2001-05-01

The effects of adverse work environments were examined in the context of other risk/protective factors in this extension of a short-term longitudinal study involving 184 newly appointed women teachers. Regression analyses revealed that-adjusting for preemployment levels of the outcomes and negative affectivity-social support and adversity in the fall work environment were among the factors that affected spring depressive symptoms, self-esteem, job satisfaction, and motivation to teach. Support from nonwork sources was directly related to future improved symptom levels and self-esteem; supervisor and colleague support were directly related to future job satisfaction. Effects of occupational coping, professional efficacy, locus of control, and school factors (e.g., special vs. regular education) were largely nonsignificant. Structural equation analyses indicated that adverse working conditions began to seriously affect the women soon after they started teaching.

First-principles study on phase transition and ferroelectricity in lithium niobate and tantalate

NASA Astrophysics Data System (ADS)

Toyoura, Kazuaki; Ohta, Masataka; Nakamura, Atsutomo; Matsunaga, Katsuyuki

2015-08-01

The phase transitions and ferroelectricity of LiNbO3 and LiTaO3 have been investigated theoretically from first principles. The phonon analyses and the molecular dynamics simulations revealed that the ferroelectric phase transition is not conventional displacive type but order-disorder type with strong correlation between cation displacements. According to the evaluated potential energy surfaces around the paraelectric structures, the large difference in ferroelectricity between the two oxides results from the little difference in short-range interionic interaction between Nb-O and Ta-O. As the results of the crystal orbital overlap population analyses, the different short-range interaction originates from the difference in covalency between Nb4d-O2p and Ta5d-O2p orbitals, particularly dxz-px/dyz-py orbitals (π orbitals), from the electronic point of view.

Explosive detonation causes an increase in soil porosity leading to increased TNT transformation

PubMed Central

Yu, Holly A.; Nic Daeid, Niamh; Dawson, Lorna A.; DeTata, David A.; Lewis, Simon W.

2017-01-01

Explosives are a common soil contaminant at a range of sites, including explosives manufacturing plants and areas associated with landmine detonations. As many explosives are toxic and may cause adverse environmental effects, a large body of research has targeted the remediation of explosives residues in soil. Studies in this area have largely involved spiking ‘pristine’ soils using explosives solutions. Here we investigate the fate of explosives present in soils following an actual detonation process and compare this to the fate of explosives spiked into ‘pristine’ undetonated soils. We also assess the effects of the detonations on the physical properties of the soils. Our scanning electron microscopy analyses reveal that detonations result in newly-fractured planes within the soil aggregates, and novel micro Computed Tomography analyses of the soils reveal, for the first time, the effect of the detonations on the internal architecture of the soils. We demonstrate that detonations cause an increase in soil porosity, and this correlates to an increased rate of TNT transformation and loss within the detonated soils, compared to spiked pristine soils. We propose that this increased TNT transformation is due to an increased bioavailability of the TNT within the now more porous post-detonation soils, making the TNT more easily accessible by soil-borne bacteria for potential biodegradation. This new discovery potentially exposes novel remediation methods for explosive contaminated soils where actual detonation of the soil significantly promotes subsequent TNT degradation. This work also suggests previously unexplored ramifications associated with high energy soil disruption. PMID:29281650

Relationship Between Large-Scale Functional and Structural Covariance Networks in Idiopathic Generalized Epilepsy

PubMed Central

Zhang, Zhiqiang; Mantini, Dante; Xu, Qiang; Wang, Zhengge; Chen, Guanghui; Jiao, Qing; Zang, Yu-Feng

2013-01-01

Abstract The human brain can be modeled as a network, whose structure can be revealed by either anatomical or functional connectivity analyses. Little is known, so far, about the topological features of the large-scale interregional functional covariance network (FCN) in the brain. Further, the relationship between the FCN and the structural covariance network (SCN) has not been characterized yet, in the intact as well as in the diseased brain. Here, we studied 59 patients with idiopathic generalized epilepsy characterized by tonic–clonic seizures and 59 healthy controls. We estimated the FCN and the SCN by measuring amplitude of low-frequency fluctuations (ALFF) and gray matter volume (GMV), respectively, and then we conducted graph theoretical analyses. Our ALFF-based FCN and GMV-based results revealed that the normal human brain is characterized by specific topological properties such as small worldness and highly-connected hub regions. The patients had an altered overall topology compared to the controls, suggesting that epilepsy is primarily a disorder of the cerebral network organization. Further, the patients had altered nodal characteristics in the subcortical and medial temporal regions and default-mode regions, for both the FCN and SCN. Importantly, the correspondence between the FCN and SCN was significantly larger in patients than in the controls. These results support the hypothesis that the SCN reflects shared long-term trophic mechanisms within functionally synchronous systems. They can also provide crucial information for understanding the interactions between the whole-brain network organization and pathology in generalized tonic–clonic seizures. PMID:23510272

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

PubMed Central

Huang, Chien-Hsun; Sun, Renran; Hu, Yi; Zeng, Liping; Zhang, Ning; Cai, Liming; Zhang, Qiang; Koch, Marcus A.; Al-Shehbaz, Ihsan; Edger, Patrick P.; Pires, J. Chris; Tan, Dun-Yan; Zhong, Yang; Ma, Hong

2016-01-01

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae. PMID:26516094

Trajectories and Predictors of Response to the Challenging Horizons Program for Adolescents With ADHD.

PubMed

Langberg, Joshua M; Evans, Steven W; Schultz, Brandon K; Becker, Stephen P; Altaye, Mekibib; Girio-Herrera, Erin

2016-05-01

The Challenging Horizons After School Program is one of the only psychosocial interventions developed specifically for adolescents with attention-deficit/hyperactivity disorder (ADHD) that has demonstrated efficacy in multiple randomized controlled trials. To date, however, all research with the intervention has evaluated outcomes at the group level, and it is unclear whether all adolescents respond similarly, or if the intervention is particularly well suited for certain adolescents with ADHD. This type of information is needed to guide stakeholders in making informed choices as part of dissemination and implementation efforts. The purpose of this study was to evaluate trajectories of response to intervention for a large sample of middle-school age adolescents with ADHD (grades 6-8) who received the after-school intervention (N=112). An additional goal of the study was to evaluate potential predictors of response trajectories, focusing on determining what factors best distinguished between intervention responders and nonresponders. Latent trajectory analyses consistently revealed four or five distinct classes. Depending on the outcome, between 16% and 46% of participants made large improvements, moving into the normal range of functioning, and between 26% and 65% of participants made small or negligible improvements. Multivariate predictor analyses revealed that a strong counselor/adolescent working alliance rated from the adolescent perspective and lower levels of parenting stress and parent-adolescent conflict consistently predicted an increased likelihood of intervention response. Implications of these findings for disseminating the after school intervention and for further intervention development are discussed. Copyright © 2016. Published by Elsevier Ltd.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

PubMed

Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

2009-02-01

The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

PubMed

Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

2015-01-01

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1

PubMed Central

Villandre, Luc; Günthard, Huldrych F.; Kouyos, Roger; Stadler, Tanja

2016-01-01

Background Transmission patterns of sexually-transmitted infections (STIs) could relate to the structure of the underlying sexual contact network, whose features are therefore of interest to clinicians. Conventionally, we represent sexual contacts in a population with a graph, that can reveal the existence of communities. Phylogenetic methods help infer the history of an epidemic and incidentally, may help detecting communities. In particular, phylogenetic analyses of HIV-1 epidemics among men who have sex with men (MSM) have revealed the existence of large transmission clusters, possibly resulting from within-community transmissions. Past studies have explored the association between contact networks and phylogenies, including transmission clusters, producing conflicting conclusions about whether network features significantly affect observed transmission history. As far as we know however, none of them thoroughly investigated the role of communities, defined with respect to the network graph, in the observation of clusters. Methods The present study investigates, through simulations, community detection from phylogenies. We simulate a large number of epidemics over both unweighted and weighted, undirected random interconnected-islands networks, with islands corresponding to communities. We use weighting to modulate distance between islands. We translate each epidemic into a phylogeny, that lets us partition our samples of infected subjects into transmission clusters, based on several common definitions from the literature. We measure similarity between subjects’ island membership indices and transmission cluster membership indices with the adjusted Rand index. Results and Conclusion Analyses reveal modest mean correspondence between communities in graphs and phylogenetic transmission clusters. We conclude that common methods often have limited success in detecting contact network communities from phylogenies. The rarely-fulfilled requirement that network communities correspond to clades in the phylogeny is their main drawback. Understanding the link between transmission clusters and communities in sexual contact networks could help inform policymaking to curb HIV incidence in MSMs. PMID:26863322

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

PubMed Central

Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S.; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Stone, Eric A.; Rosenbloom, Kate R.; Kent, W. James; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Hinrichs, Angie; Trumbower, Heather; Clawson, Hiram; Zweig, Ann; Kuhn, Robert M.; Barber, Galt; Harte, Rachel; Karolchik, Donna; Field, Matthew A.; Moore, Richard A.; Matthewson, Carrie A.; Schein, Jacqueline E.; Marra, Marco A.; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend

2007-01-01

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. PMID:17567995

Negative density-dependent dispersal in the American black bear (Ursus americanus) revealed by noninvasive sampling and genotyping

PubMed Central

Roy, Justin; Yannic, Glenn; Côté, Steeve D; Bernatchez, Louis

2012-01-01

Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432

Depression as a mediator between family factors and peer-bullying victimization in Latino adolescents.

PubMed

Yabko, Brandon A; Hokoda, Audrey; Ulloa, Emilio C

2008-01-01

The purpose of this study was to assess the mediating role of depression in three different relationships: (a) sibling bullying and peer victimization, (b) mothers' power-assertive parenting and peer victimization, and (c) fathers' power-assertive parenting and peer victimization. Results from 242 Latino middle school adolescents from a large southwestern city bordering Mexico revealed that both boys' and girls' peer victimization were related to familial factors and depression. Regression analyses for boys revealed that depression mediated three relationships: (a) sibling bullying and peer victimization, (b) mothers' power-assertive parenting and peer victimization, and (c) fathers' power-assertive parenting and peer victimization. Depression also mediated the relationship between fathers' power-assertive parenting and girls' victimization by peers. The findings support the development of family-based interventions for peer victimization that include curriculum addressing depression.

Study of the mechanical behavior of a 2-D carbon-carbon composite

NASA Technical Reports Server (NTRS)

Avery, W. B.; Herakovich, C. T.

1987-01-01

The out-of-plane fracture of a 2-D carbon-carbon composite was observed and characterized to gain an understanding of the factors influencing the stress distribution in such a laminate. Finite element analyses of a two-ply carbon-carbon composite under in-plane, out-of-plane, and thermal loading were performed. Under in-plane loading all components of stress were strong functions of geometry. Additionally, large thermal stresses were predicted. Out-of-plane tensile tests revealed that failure was interlaminar, and that cracks propagated along the fiber-matrix interface. An elasticity solution was utilized to analyze an orthotropic fiber in an isotropic matrix under uniform thermal load. The analysis reveals that the stress distributions in a transversely orthotropic fiber are radically different than those predicted assuming the fiber to be transversely isotropic.

Large-Scale Land Acquisition and Its Effects on the Water Balance in Investor and Host Countries

PubMed Central

Breu, Thomas; Bader, Christoph; Messerli, Peter; Heinimann, Andreas; Rist, Stephan; Eckert, Sandra

2016-01-01

This study examines the validity of the assumption that international large-scale land acquisition (LSLA) is motivated by the desire to secure control over water resources, which is commonly referred to as ‘water grabbing’. This assumption was repeatedly expressed in recent years, ascribing the said motivation to the Gulf States in particular. However, it must be considered of hypothetical nature, as the few global studies conducted so far focused primarily on the effects of LSLA on host countries or on trade in virtual water. In this study, we analyse the effects of 475 intended or concluded land deals recorded in the Land Matrix database on the water balance in both host and investor countries. We also examine how these effects relate to water stress and how they contribute to global trade in virtual water. The analysis shows that implementation of the LSLAs in our sample would result in global water savings based on virtual water trade. At the level of individual LSLA host countries, however, water use intensity would increase, particularly in 15 sub-Saharan states. From an investor country perspective, the analysis reveals that countries often suspected of using LSLA to relieve pressure on their domestic water resources—such as China, India, and all Gulf States except Saudi Arabia—invest in agricultural activities abroad that are less water-intensive compared to their average domestic crop production. Conversely, large investor countries such as the United States, Saudi Arabia, Singapore, and Japan are disproportionately externalizing crop water consumption through their international land investments. Statistical analyses also show that host countries with abundant water resources are not per se favoured targets of LSLA. Indeed, further analysis reveals that land investments originating in water-stressed countries have only a weak tendency to target areas with a smaller water risk. PMID:26943794

Regional-scale drivers of marine nematode distribution in Southern Ocean continental shelf sediments

NASA Astrophysics Data System (ADS)

Hauquier, Freija; Verleyen, Elie; Tytgat, Bjorn; Vanreusel, Ann

2018-07-01

Many marine meiofauna taxa seem to possess cosmopolitan species distributions, despite their endobenthic lifestyle and restricted long-distance dispersal capacities. In light of this paradox we used a metacommunity framework to study spatial turnover in free-living nematode distribution and assess the importance of local environmental conditions in explaining differences between communities in surface and subsurface sediments of the Southern Ocean continental shelf. We analysed nematode community structure in two sediment layers (0-3 cm and 3-5 cm) of locations maximum 2400 km apart. We first focused on a subset of locations to evaluate whether the genus level is sufficiently taxonomically fine-grained to study large-scale patterns in nematode community structure. We subsequently used redundancy and variation partitioning analyses to quantify the unique and combined effects of local environmental conditions and spatial descriptors on genus-level community composition. Macroecological patterns in community structure were highly congruent at the genus and species level. Nematode community composition was highly divergent between both depth strata, likely as a result of local abiotic conditions. Variation in community structure between the different regions largely stemmed from turnover (i.e. genus/species replacement) rather than nestedness (i.e. genus/species loss). The level of turnover among communities increased with geographic distance and was more pronounced in subsurface layers compared to surface sediments. Variation partitioning analysis revealed that both environmental and spatial predictors significantly explained variation in community structure. Moreover, the shared fraction of both sets of variables was high, which suggested a substantial amount of spatially structured environmental variation. Additionally, the effect of space independent of environment was much higher than the effect of environment independent of space, which shows the importance of including spatial descriptors in meiofauna and nematode community ecology. Large-scale assessment of free-living nematode diversity and abundance in the Southern Ocean shelf zone revealed strong horizontal and vertical spatial structuring in response to local environmental conditions, in combination with (most likely) dispersal limitation.

Large-Scale Land Acquisition and Its Effects on the Water Balance in Investor and Host Countries.

PubMed

Breu, Thomas; Bader, Christoph; Messerli, Peter; Heinimann, Andreas; Rist, Stephan; Eckert, Sandra

2016-01-01

This study examines the validity of the assumption that international large-scale land acquisition (LSLA) is motivated by the desire to secure control over water resources, which is commonly referred to as 'water grabbing'. This assumption was repeatedly expressed in recent years, ascribing the said motivation to the Gulf States in particular. However, it must be considered of hypothetical nature, as the few global studies conducted so far focused primarily on the effects of LSLA on host countries or on trade in virtual water. In this study, we analyse the effects of 475 intended or concluded land deals recorded in the Land Matrix database on the water balance in both host and investor countries. We also examine how these effects relate to water stress and how they contribute to global trade in virtual water. The analysis shows that implementation of the LSLAs in our sample would result in global water savings based on virtual water trade. At the level of individual LSLA host countries, however, water use intensity would increase, particularly in 15 sub-Saharan states. From an investor country perspective, the analysis reveals that countries often suspected of using LSLA to relieve pressure on their domestic water resources--such as China, India, and all Gulf States except Saudi Arabia--invest in agricultural activities abroad that are less water-intensive compared to their average domestic crop production. Conversely, large investor countries such as the United States, Saudi Arabia, Singapore, and Japan are disproportionately externalizing crop water consumption through their international land investments. Statistical analyses also show that host countries with abundant water resources are not per se favoured targets of LSLA. Indeed, further analysis reveals that land investments originating in water-stressed countries have only a weak tendency to target areas with a smaller water risk.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

PubMed Central

Szczecińska, Monika

2016-01-01

Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers. Conclusions The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs. PMID:27833793

Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations.

PubMed

Liu, Jun-Jun; Shamoun, Simon Francis; Leal, Isabel; Kowbel, Robert; Sumampong, Grace; Zamany, Arezoo

2018-05-01

Characterization of genes involved in differentiation of pathogen species and isolates with variations of virulence traits provides valuable information to control tree diseases for meeting the challenges of sustainable forest health and phytosanitary trade issues. Lack of genetic knowledge and genomic resources hinders novel gene discovery, molecular mechanism studies and development of diagnostic tools in the management of forest pathogens. Here, we report on transcriptome profiling of Heterobasidion occidentale isolates with contrasting virulence levels. Comparative transcriptomic analysis identified orthologous groups exclusive to H. occidentale and its isolates, revealing biological processes involved in the differentiation of isolates. Further bioinformatics analyses identified an H. occidentale secretome, CYPome and other candidate effectors, from which genes with species- and isolate-specific expression were characterized. A large proportion of differentially expressed genes were revealed to have putative activities as cell wall modification enzymes and transcription factors, suggesting their potential roles in virulence and fungal pathogenesis. Next, large numbers of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected, including more than 14 000 interisolate non-synonymous SNPs. These polymorphic loci and species/isolate-specific genes may contribute to virulence variations and provide ideal DNA markers for development of diagnostic tools and investigation of genetic diversity. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Division of Labor in Vocabulary Structure: Insights From Corpus Analyses.

PubMed

Christiansen, Morten H; Monaghan, Padraic

2016-07-01

Psychologists have used experimental methods to study language for more than a century. However, only with the recent availability of large-scale linguistic databases has a more complete picture begun to emerge of how language is actually used, and what information is available as input to language acquisition. Analyses of such "big data" have resulted in reappraisals of key assumptions about the nature of language. As an example, we focus on corpus-based research that has shed new light on the arbitrariness of the sign: the longstanding assumption that the relationship between the sound of a word and its meaning is arbitrary. The results reveal a systematic relationship between the sound of a word and its meaning, which is stronger for early acquired words. Moreover, the analyses further uncover a systematic relationship between words and their lexical categories-nouns and verbs sound differently from each other-affecting how we learn new words and use them in sentences. Together, these results point to a division of labor between arbitrariness and systematicity in sound-meaning mappings. We conclude by arguing in favor of including "big data" analyses into the language scientist's methodological toolbox. Copyright © 2015 Cognitive Science Society, Inc.

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake.

PubMed

Jones, Adriane Clark; Hambright, K David; Caron, David A

2018-05-01

Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements.

PubMed

Longo, S J; Faircloth, B C; Meyer, A; Westneat, M W; Alfaro, M E; Wainwright, P C

2017-08-01

Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation. Copyright © 2017 Elsevier Inc. All rights reserved.

The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk

PubMed Central

Lemos, Mark; Xiao, Yanmei; Bjornson, Marta; Wang, Jin-zheng; Hicks, Derrick; de Souza, Amancio; Wang, Chang-Quan; Yang, Panyu; Ma, Shisong; Dinesh-Kumar, Savithramma; Dehesh, Katayoon

2016-01-01

The exquisite harmony between hormones and their corresponding signaling pathways is central to prioritizing plant responses to simultaneous and/or successive environmental trepidations. The crosstalk between jasmonic acid (JA) and salicylic acid (SA) is an established effective mechanism that optimizes and tailors plant adaptive responses. However, the underlying regulatory modules of this crosstalk are largely unknown. Global transcriptomic analyses of mutant plants (ceh1) with elevated levels of the stress-induced plastidial retrograde signaling metabolite 2-C-methyl-D-erythritol cyclopyrophosphate (MEcPP) revealed robustly induced JA marker genes, expected to be suppressed by the presence of constitutively high SA levels in the mutant background. Analyses of a range of genotypes with varying SA and MEcPP levels established the selective role of MEcPP-mediated signal(s) in induction of JA-responsive genes in the presence of elevated SA. Metabolic profiling revealed the presence of high levels of the JA precursor 12-oxo-phytodienoic acid (OPDA), but near wild type levels of JA in the ceh1 mutant plants. Analyses of coronatine-insensitive 1 (coi1)/ceh1 double mutant plants confirmed that the MEcPP-mediated induction is JA receptor COI1 dependent, potentially through elevated OPDA. These findings identify MEcPP as a previously unrecognized central regulatory module that induces JA-responsive genes in the presence of high SA, thereby staging a multifaceted plant response within the environmental context. PMID:26733689

Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge

PubMed Central

Vander Roost, Jan; Thorseth, Ingunn Hindenes

2017-01-01

Over the last decade it has become increasingly clear that Zetaproteobacteria are widespread in hydrothermal systems and that they contribute to the biogeochemical cycling of iron in these environments. However, how chemical factors control the distribution of Zetaproteobacteria and their co-occurring taxa remains elusive. Here we analysed iron mats from the Troll Wall Vent Field (TWVF) located at the Arctic Mid-Ocean Ridge (AMOR) in the Norwegian-Greenland Sea. The samples were taken at increasing distances from high-temperature venting chimneys towards areas with ultraslow low-temperature venting, encompassing a large variety in geochemical settings. Electron microscopy revealed the presence of biogenic iron stalks in all samples. Using 16S rRNA gene sequence profiling we found that relative abundances of Zetaproteobacteria in the iron mats varied from 0.2 to 37.9%. Biogeographic analyses of Zetaproteobacteria, using the ZetaHunter software, revealed the presence of ZetaOtus 1, 2 and 9, supporting the view that they are cosmopolitan. Relative abundances of co-occurring taxa, including Thaumarchaeota, Euryarchaeota and Proteobacteria, also varied substantially. From our results, combined with results from previous microbiological and geochemical analyses of the TWVF, we infer that the distribution of Zetaproteobacteria is connected to fluid-flow patterns and, ultimately, variations in chemical energy landscapes. Moreover, we provide evidence for iron-oxidizing members of Gallionellaceae being widespread in TWVF iron mats, albeit at low relative abundances. PMID:28931087

Relationships among race, education, criminal thinking, and recidivism: moderator and mediator effects.

PubMed

Walters, Glenn D

2014-02-01

Moderator and mediator relationships linking variables from three different theoretical traditions-race (subcultural theory), education (life-course theory), and criminal thinking (social learning theory)-and recidivism were examined in 1,101 released male federal prison inmates. Preliminary regression analyses indicated that racial status (White, Black, Hispanic) moderated the relationship between criminal thinking, as measured by the General Criminal Thinking (GCT) score of the Psychological Inventory of Criminal Thinking Styles (PICTS), and recidivism. Further analysis, however, revealed that it was not racial status, per se, that moderated the relationship between the PICTS and recidivism, but educational attainment. Whereas the PICTS was largely effective in predicting recidivism in inmates with 12 or more years of education, it was largely ineffective in predicting recidivism in inmates with fewer than 12 years of education. When education and the GCT score were compared as possible mediators of the race-recidivism relationship only the GCT successfully mediated this relationship. Sensitivity testing showed that the GCT mediating effect was moderately robust to violations of the sequential ignorability assumption on which causal mediation analysis rests. Moderator and mediator analyses are potentially important avenues through which theoretical constructs can be integrated and assessment strategies devised.

How 'healthy' are healthcare organizations? Exploring employee healthcare utilization rates among Dutch healthcare organizations.

PubMed

Bronkhorst, Babette

2017-08-01

Occupational health and safety research rarely makes use of data on employee healthcare utilization to gain insight into the physical and mental health of healthcare staff. This paper aims to fill this gap by examining the prevalence of two relevant types of healthcare utilization among staff working in healthcare organizations: physical therapy and mental healthcare utilization. The paper furthermore explores what role employee and organizational characteristics play in explaining differences in healthcare utilization between organizations. A Dutch healthcare insurance company provided healthcare utilization records for a sample of 417 organizations employing 136,804 healthcare workers in the Netherlands. The results showed that there are large differences between and within healthcare industries when it comes to employee healthcare utilization. Multivariate regression analyses revealed that employee characteristics such as age and gender distributions, and healthcare industry, explain some of the variance between healthcare organizations. Nevertheless, the results of the analyses showed that for all healthcare utilization indicators there is still a large amount of unexplained variance. Further research into the subject of organizational differences in employee healthcare utilization is needed, as finding possibilities to influence employee health and subsequent healthcare utilization is beneficial to employees, employers and society as a whole.

Indications of marine bioinvasion from network theory. An analysis of the global cargo ship network

NASA Astrophysics Data System (ADS)

Kölzsch, A.; Blasius, B.

2011-12-01

The transport of huge amounts of small aquatic organisms in the ballast tanks and at the hull of large cargo ships leads to ever increasing rates of marine bioinvasion. In this study, we apply a network theoretic approach to examine the introduction of invasive species into new ports by global shipping. This is the first stage of the invasion process where it is still possible to intervene with regulating measures. We compile a selection of widely used and newly developed network properties and apply these to analyse the structure and spread characteristics of the directed and weighted global cargo ship network (GCSN). Our results reveal that the GCSN is highly efficient, shows small world characteristics and is positive assortative, indicating that quick spread of invasive organisms between ports is likely. The GCSN shows strong community structure and contains two large communities, the Atlantic and Pacific trading groups. Ports that appear as connector hubs and are of high centralities are the Suez and Panama Canal, Singapore and Shanghai. Furthermore, from robustness analyses and the network's percolation behaviour, we evaluate differences of onboard and in-port ballast water treatment, set them into context with previous studies and advise bioinvasion management strategies.

OXTR polymorphism in depression and completed suicide-A study on a large population sample.

PubMed

Wasilewska, Krystyna; Pawlak, Aleksandra; Kostrzewa, Grażyna; Sobczyk-Kopcioł, Agnieszka; Kaczorowska, Aleksandra; Badowski, Jarosław; Brzozowska, Małgorzata; Drygas, Wojciech; Piwoński, Jerzy; Bielecki, Wojciech; Płoski, Rafał

2017-03-01

In the light of contradictory results concerning OXTR polymorphism rs53576 and depression, we decided to verify the potential association between the two on 1) a large, ethnically homogenous sample of 1185 individuals who completed the Beck Depression Inventory (BDI), as well as on 2) a sample of 763 suicide victims. In the population sample, AA males showed significantly lower BDI scores (p=0.005, p cor =0.030). Exploratory analyses suggested that this effect was limited to a subgroup within 0-9 BDI score range (p=0.0007, U-Mann Whitney test), whereas no main effect on depressive symptoms (BDI>9) was found. In the suicide sample no association with rs53576 genotype was present. Exploratory analyses in suicides revealed higher blood alcohol concentration (BAC) among AA than GG/GA males (p=0.014, U-Mann Whitney test). Our results show that the OXTR rs53576 variant modulates the mood in male individuals and may positively correlate with alcohol intake among male suicides, but is not associated with suicide or depression. The study adds to the growing knowledge on rs53576 genotype characteristics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Proteomic analysis of broccoli (Brassica oleracea) under high temperature and waterlogging stresses.

PubMed

Lin, Hsin-Hung; Lin, Kuan-Hung; Chen, Su-Ching; Shen, Yu-Hsing; Lo, Hsiao-Feng

2015-12-01

The production of broccoli (Brassica oleracea) is largely reduced by waterlogging and high temperature stresses. Heat-tolerant and heat-susceptible broccoli cultivars TSS-AVRDC-2 and B-75, respectively, were used for physiological and proteomic analyses. The objective of this study was to identify TSS-AVRDC-2 and B-75 proteins differentially regulated at different time periods in response to waterlogging at 40 °C for three days. TSS-AVRDC-2 exhibited significantly higher chlorophyll content, lower stomatal conductance, and better H 2 O 2 scavenging under stress in comparison to B-75. Two-dimensional liquid phase fractionation analyses revealed that Rubisco proteins in both varieties were regulated under stressing treatments, and that TSS-AVRDC-2 had higher levels of both Rubisco large and small subunit transcripts than B-75 when subjected to high temperature and/or waterlogging. This report utilizes physiological and proteomic approaches to discover changes in the protein expression profiles of broccoli in response to heat and waterlogging stresses. Higher levels of Rubisco proteins in TSS-AVRDC-2 could lead to increased carbon fixation efficiency to provide sufficient energy to enable stress tolerance under waterlogging at 40 °C.

Large-Scale functional network overlap is a general property of brain functional organization: Reconciling inconsistent fMRI findings from general-linear-model-based analyses

PubMed Central

Xu, Jiansong; Potenza, Marc N.; Calhoun, Vince D.; Zhang, Rubin; Yip, Sarah W.; Wall, John T.; Pearlson, Godfrey D.; Worhunsky, Patrick D.; Garrison, Kathleen A.; Moran, Joseph M.

2016-01-01

Functional magnetic resonance imaging (fMRI) studies regularly use univariate general-linear-model-based analyses (GLM). Their findings are often inconsistent across different studies, perhaps because of several fundamental brain properties including functional heterogeneity, balanced excitation and inhibition (E/I), and sparseness of neuronal activities. These properties stipulate heterogeneous neuronal activities in the same voxels and likely limit the sensitivity and specificity of GLM. This paper selectively reviews findings of histological and electrophysiological studies and fMRI spatial independent component analysis (sICA) and reports new findings by applying sICA to two existing datasets. The extant and new findings consistently demonstrate several novel features of brain functional organization not revealed by GLM. They include overlap of large-scale functional networks (FNs) and their concurrent opposite modulations, and no significant modulations in activity of most FNs across the whole brain during any task conditions. These novel features of brain functional organization are highly consistent with the brain’s properties of functional heterogeneity, balanced E/I, and sparseness of neuronal activity, and may help reconcile inconsistent GLM findings. PMID:27592153

Altération dans des sols de scories issues d'un atelier de fusion du plomb.

NASA Astrophysics Data System (ADS)

Sobanska, Sophie; Ledésert, Béatrice; Deneele, Dimitri; Laboudigue, Agnès

2000-08-01

A smelter located in northern France produces lead and zinc. Large amounts of metal bearing slag particles result from the process and constitute a main environmental problem. This work presents a characterization of the slag grains at the exit of the furnace and in the surrounding soils where they are frequently found. Their comparison shows an alteration in soils revealed by a strong increase of their porosity and a modification of their morphology. Chemical analyses indicate that Pb and Zn are released in the soils during the partial dissolution of the slag particles.

The association of serum prolactin concentration with inflammatory biomarkers - cross-sectional findings from the population-based Study of Health in Pomerania.

PubMed

Friedrich, Nele; Schneider, Harald J; Spielhagen, Christin; Markus, Marcello Ricardo Paulista; Haring, Robin; Grabe, Hans J; Buchfelder, Michael; Wallaschofski, Henri; Nauck, Matthias

2011-10-01

Prolactin (PRL) is involved in immune regulation and may contribute to an atherogenic phenotype. Previous results on the association of PRL with inflammatory biomarkers have been conflicting and limited by small patient studies. Therefore, we used data from a large population-based sample to assess the cross-sectional associations between serum PRL concentration and high-sensitivity C-reactive protein (hsCRP), fibrinogen, interleukin-6 (IL-6), and white blood cell (WBC) count. From the population-based Study of Health in Pomerania (SHIP), a total of 3744 subjects were available for the present analyses. PRL and inflammatory biomarkers were measured. Linear and logistic regression models adjusted for age, sex, body-mass-index, total cholesterol and glucose were analysed. Multivariable linear regression models revealed a positive association of PRL with WBC. Multivariable logistic regression analyses showed a significant association of PRL with increased IL-6 in non-smokers [highest vs lowest quintile: odds ratio 1·69 (95% confidence interval 1·10-2·58), P = 0·02] and smokers [OR 2·06 (95%-CI 1·10-3·89), P = 0·02]. Similar results were found for WBC in non-smokers [highest vs lowest quintile: OR 2·09 (95%-CI 1·21-3·61), P = 0·01)] but not in smokers. Linear and logistic regression analyses revealed no significant associations of PRL with hsCRP or fibrinogen. Serum PRL concentrations are associated with inflammatory biomarkers including IL-6 and WBC, but not hsCRP or fibrinogen. The suggested role of PRL in inflammation needs further investigation in future prospective studies. © 2011 Blackwell Publishing Ltd.

A review of trabecular bone functional adaptation: what have we learned from trabecular analyses in extant hominoids and what can we apply to fossils?

PubMed

Kivell, Tracy L

2016-04-01

Many of the unresolved debates in palaeoanthropology regarding evolution of particular locomotor or manipulative behaviours are founded in differing opinions about the functional significance of the preserved external fossil morphology. However, the plasticity of internal bone morphology, and particularly trabecular bone, allowing it to respond to mechanical loading during life means that it can reveal greater insight into how a bone or joint was used during an individual's lifetime. Analyses of trabecular bone have been commonplace for several decades in a human clinical context. In contrast, the study of trabecular bone as a method for reconstructing joint position, joint loading and ultimately behaviour in extant and fossil non-human primates is comparatively new. Since the initial 2D studies in the late 1970s and 3D analyses in the 1990 s, the utility of trabecular bone to reconstruct behaviour in primates has grown to incorporate experimental studies, expanded taxonomic samples and skeletal elements, and improved methodologies. However, this work, in conjunction with research on humans and non-primate mammals, has also revealed the substantial complexity inherent in making functional inferences from variation in trabecular architecture. This review addresses the current understanding of trabecular bone functional adaptation, how it has been applied to hominoids, as well as other primates and, ultimately, how this can be used to better interpret fossil hominoid and hominin morphology. Because the fossil record constrains us to interpreting function largely from bony morphology alone, and typically from isolated bones, analyses of trabecular structure, ideally in conjunction with that of cortical structure and external morphology, can offer the best resource for reconstructing behaviour in the past. © 2016 Anatomical Society.

Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae).

PubMed

Chen, Jin-Min; Poyarkov, Nikolay A; Suwannapoom, Chatmongkon; Lathrop, Amy; Wu, Yun-He; Zhou, Wei-Wei; Yuan, Zhi-Yong; Jin, Jie-Qiong; Chen, Hong-Man; Liu, He-Qun; Nguyen, Truong Quang; Nguyen, Sang Ngoc; Duong, Tang Van; Eto, Koshiro; Nishikawa, Kanto; Matsui, Masafumi; Orlov, Nikolai L; Stuart, Bryan L; Brown, Rafe M; Rowley, Jodi J L; Murphy, Robert W; Wang, Ying-Yong; Che, Jing

2018-07-01

Southeast Asia and southern China (SEA-SC) harbor a highly diverse and endemic flora and fauna that is under increasing threat. An understanding of the biogeographical history and drivers of this diversity is lacking, especially in some of the most diverse and threatened groups. The Asian leaf-litter frog genus Leptolalax Dubois 1980 is a forest-dependent genus distributed throughout SEA-SC, making it an ideal study group to examine specific biogeographic hypotheses. In addition, the diversity of this genus remains poorly understood, and the phylogenetic relationships among species of Leptolalax and closely related Leptobrachella Smith 1928 remain unclear. Herein, we evaluate species-level diversity based on 48 of the 53 described species from throughout the distribution of Leptolalax. Molecular analyses reveal many undescribed species, mostly in southern China and Indochina. Our well-resolved phylogeny based on multiple nuclear DNA markers shows that Leptolalax is not monophyletic with respect to Leptobrachella and, thus, we assign the former to being a junior synonym of the latter. Similarly, analyses reject monophyly of the two subgenera of Leptolalax. The diversification pattern of the group is complex, involving a high degree of sympatry and prevalence of microendemic species. Northern Sundaland (Borneo) and eastern Indochina (Vietnam) appear to have played pivotal roles as geographical centers of diversification, and paleoclimatic changes and tectonic movements seem to have driven the major divergence of clades. Analyses fail to reject an "upstream" colonization hypothesis, and, thus, the genus appears to have originated in Sundaland and then colonized mainland Asia. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns in the genus. Copyright © 2018 Elsevier Inc. All rights reserved.

Marine aerosol source regions to Prince of Wales Icefield, Ellesmere Island, and influence from the tropical Pacific, 1979-2001

NASA Astrophysics Data System (ADS)

Criscitiello, Alison S.; Marshall, Shawn J.; Evans, Matthew J.; Kinnard, Christophe; Norman, Ann-Lise; Sharp, Martin J.

2016-08-01

Using a coastal ice core collected from Prince of Wales (POW) Icefield on Ellesmere Island, we investigate source regions of sea ice-modulated chemical species (methanesulfonic acid (MSA) and chloride (Cl-)) to POW Icefield and the influence of large-scale atmospheric variability on the transport of these marine aerosols (1979-2001). Our key findings are (1) MSA in the POW Icefield core is derived primarily from productivity in the sea ice zone of Baffin Bay and the Labrador Sea, with influence from waters within the North Water (NOW) polynya, (2) sea ice formation processes within the NOW polynya may be a significant source of sea-salt aerosols to the POW core site, in addition to offshore open water source regions primarily in Hudson Bay, and (3) the tropical Pacific influences the source and transport of marine aerosols to POW Icefield through its remote control on regional winds and sea ice variability. Regression analyses during times of MSA deposition reveal sea level pressure (SLP) anomalies favorable for opening of the NOW polynya and subsequent oceanic dimethyl sulfide production. Regression analyses during times of Cl- deposition reveal SLP anomalies that indicate a broader oceanic region of sea-salt sources to the core site. These results are supported by Scanning Multichannel Microwave Radiometer- and Special Sensor Microwave/Imager-based sea ice reconstructions and air mass transport density analyses and suggest that the marine biogenic record may capture local polynya variability, while sea-salt transport to the site from larger offshore source regions in Baffin Bay is likely. Regression analyses show a link to tropical dynamics via an atmospheric Rossby wave.

MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.

PubMed

Ardin, Maude; Cahais, Vincent; Castells, Xavier; Bouaoun, Liacine; Byrnes, Graham; Herceg, Zdenko; Zavadil, Jiri; Olivier, Magali

2016-04-18

The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called MutSpec. MutSpec includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the COSMIC database and other sources. MutSpec offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. MutSpec may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. MutSpec offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. MutSpec can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.

Analyses and forecasts with LAWS winds

NASA Technical Reports Server (NTRS)

Wang, Muyin; Paegle, Jan

1994-01-01

Horizontal fluxes of atmospheric water vapor are studied for summer months during 1989 and 1992 over North and South America based on analyses from European Center for Medium Range Weather Forecasts, US National Meteorological Center, and United Kingdom Meteorological Office. The calculations are performed over 20 deg by 20 deg box-shaped midlatitude domains located to the east of the Rocky Mountains in North America, and to the east of the Andes Mountains in South America. The fluxes are determined from operational center gridded analyses of wind and moisture. Differences in the monthly mean moisture flux divergence determined from these analyses are as large as 7 cm/month precipitable water equivalent over South America, and 3 cm/month over North America. Gridded analyses at higher spatial and temporal resolution exhibit better agreement in the moisture budget study. However, significant discrepancies of the moisture flux divergence computed from different gridded analyses still exist. The conclusion is more pessimistic than Rasmusson's estimate based on station data. Further analysis reveals that the most significant sources of error result from model surface elevation fields, gaps in the data archive, and uncertainties in the wind and specific humidity analyses. Uncertainties in the wind analyses are the most important problem. The low-level jets, in particular, are substantially different in the different data archives. Part of the reason for this may be due to the way the different analysis models parameterized physical processes affecting low-level jets. The results support the inference that the noise/signal ratio of the moisture budget may be improved more rapidly by providing better wind observations and analyses than by providing better moisture data.

Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.

PubMed

Choudhury, Baharul I; Khan, Mohammed L; Dayanandan, Selvadurai

2014-12-29

Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

Lipid and DNA biomarker analyses of Narragansett Bay Sediments: Evaluating the UK'37 proxy in an Estuarine Environment

NASA Astrophysics Data System (ADS)

George, S. E.; Herbert, T.; Amaral-Zettler, L. A.; Richter, N.

2017-12-01

Long chain polyunsaturated alkenone (LCA) lipid biomarkers produced by haptophyte phytoplankton species within the Order Isochrysidales (Phylum Haptophyta) have proven exceptionally useful in paleotemperature studies by means of the Uk'37 and Uk37 indices. Two closely-related Group III haptophytes, Emiliania huxleyi and Gephyrocapsa oceanica are the primary alkenone synthesizers in the modern ocean, while freshwater systems host the distinct Group I phylotype, sometimes called the Greenland phylotype, in reference to the location of its original discovery. Group I haptophytes produce large quantities of the distinct C37:4 ketone, which acts as a chemical `fingerprint' in sediments. The utility of alkenones as a paleotemperature proxy in estuarine environments has remained largely untested, representing an under-utilized opportunity to construct high-resolution paleotemperature records from environments at the intersection of fluvial and marine systems. This uncertainty is due, in part, to the presence of multiple haptophyte groups in estuaries, resulting in a mixed alkenone signature. To determine the community composition of alkenone-producing haptophytes within Narragansett Bay, four geographically separated cores from within the Bay were analyzed for alkenones as well as haptophyte rRNA biomarker gene presence. Haptophyte rRNA genes (small and large subunit) were recovered from surface and near-subsurface samples, and in conjunction with alkenone profiles, reveal recent haptophyte community structure and alkenone production regimes throughout the Bay. A surprising result is the recovery of rRNA biomarker genes with a 100% match to the open-ocean alkenone producer E. huxleyi in locations away from large fresh water inputs to the Bay. Results of these analyses elucidate the effect of salinity and nutrient dynamics on alkenone-producing haptophyte communities and enhance applicability of long chain polyunsaturated alkenones as lipid biomarkers in estuarine environments. Future work will enhance Uk'37 analyses of Narragansett Bay sediments to better resolve historically and climatically significant events in the region, such as European settlement, the Industrial Revolution, and 20th century warming and eutrophication.

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation.

PubMed

Dillinger, Stefan; Straub, Tobias; Németh, Attila

2017-01-01

Mammalian chromosomes are organized in structural and functional domains of 0.1-10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10-50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization.

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation

PubMed Central

Dillinger, Stefan

2017-01-01

Mammalian chromosomes are organized in structural and functional domains of 0.1–10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10–50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization. PMID:28575119

Does Choice of Head Size and Neck Geometry Affect Stem Migration in Modular Large-Diameter Metal-on-Metal Total Hip Arthroplasty? A Preliminary Analysis

PubMed Central

Georgiou, CS; Evangelou, KG; Theodorou, EG; Provatidis, CG; Megas, PD

2012-01-01

Due to their theoretical advantages, hip systems combining modular necks and large diameter femoral heads have gradually gained popularity. However, among others, concerns regarding changes in the load transfer patterns were raised. Recent stress analyses have indeed shown that the use of modular necks and big femoral heads causes significant changes in the strain distribution along the femur. Our original hypothesis was that these changes may affect early distal migration of a modular stem. We examined the effect of head diameter and neck geometry on migration at two years of follow-up in a case series of 116 patients (125 hips), who have undergone primary Metal-on-Metal total hip arthroplasty with the modular grit-blasted Profemur®E stem combined with large-diameter heads (>36 mm). We found that choice of neck geometry and head diameter has no effect on stem migration. A multivariate regression analysis including the potential confounding variables of the body mass index, bone quality, canal fill and stem positioning revealed only a negative correlation between subsidence and canal fill in midstem area. Statistical analysis, despite its limitations, did not confirm our hypothesis that choice of neck geometry and/or head diameter affects early distal migration of a modular stem. However, the importance of correct stem sizing was revealed. PMID:23284597

Does Choice of Head Size and Neck Geometry Affect Stem Migration in Modular Large-Diameter Metal-on-Metal Total Hip Arthroplasty? A Preliminary Analysis.

PubMed

Georgiou, Cs; Evangelou, Kg; Theodorou, Eg; Provatidis, Cg; Megas, Pd

2012-01-01

Due to their theoretical advantages, hip systems combining modular necks and large diameter femoral heads have gradually gained popularity. However, among others, concerns regarding changes in the load transfer patterns were raised. Recent stress analyses have indeed shown that the use of modular necks and big femoral heads causes significant changes in the strain distribution along the femur. Our original hypothesis was that these changes may affect early distal migration of a modular stem. We examined the effect of head diameter and neck geometry on migration at two years of follow-up in a case series of 116 patients (125 hips), who have undergone primary Metal-on-Metal total hip arthroplasty with the modular grit-blasted Profemur®E stem combined with large-diameter heads (>36 mm). We found that choice of neck geometry and head diameter has no effect on stem migration. A multivariate regression analysis including the potential confounding variables of the body mass index, bone quality, canal fill and stem positioning revealed only a negative correlation between subsidence and canal fill in midstem area. Statistical analysis, despite its limitations, did not confirm our hypothesis that choice of neck geometry and/or head diameter affects early distal migration of a modular stem. However, the importance of correct stem sizing was revealed.

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Analysis of exceptionally large tremors in two gold mining districts of South Africa

USGS Publications Warehouse

McGarr, A.; Bicknell, J.; Sembera, E.; Green, R.W.E.

1989-01-01

An investigation of ground motion, recorded using broad-band, wide dynamic-range digital seismographs, of large mine tremors from two South African mining districts with different geologic settings, reveals some essential differences in both seismic source and ground motion parameters. In the Klerksdorp district where the strata are offset by major throughgoing normal faults, the largest tremors, with magnitudes ranging as high as 5.2, tend to be associated with slip on these pre-existing faults. Moreover, the seismic source and ground motion parameters are quite similar to those of natural crustal earthquakes. In the Carletonville district, by contrast, where substantial faults do not exist, the large-magnitude tremors appear to result from the failure of relatively intact rock and cause seismic stress drops and ground motion parameters higher than normally observed for natural shocks. Additionally, there appears to be an upper magnitude limit of about 4 in the Carletonville district. Detailed analyses of an exceptionally large event recorded locally from each of these districts serve to highlight these contrasts. ?? 1989 Birkha??user Verlag.

A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family

PubMed Central

Yao, Qing; Lu, Qiuhe; Wan, Xiaobo; Song, Feng; Xu, Yue; Hu, Mo; Zamyatina, Alla; Liu, Xiaoyun; Huang, Niu; Zhu, Ping; Shao, Feng

2014-01-01

A large group of bacterial virulence autotransporters including AIDA-I from diffusely adhering E. coli (DAEC) and TibA from enterotoxigenic E. coli (ETEC) require hyperglycosylation for functioning. Here we demonstrate that TibC from ETEC harbors a heptosyltransferase activity on TibA and AIDA-I, defining a large family of bacterial autotransporter heptosyltransferases (BAHTs). The crystal structure of TibC reveals a characteristic ring-shape dodecamer. The protomer features an N-terminal β-barrel, a catalytic domain, a β-hairpin thumb, and a unique iron-finger motif. The iron-finger motif contributes to back-to-back dimerization; six dimers form the ring through β-hairpin thumb-mediated hand-in-hand contact. The structure of ADP-D-glycero-β-D-manno-heptose (ADP-D,D-heptose)-bound TibC reveals a sugar transfer mechanism and also the ligand stereoselectivity determinant. Electron-cryomicroscopy analyses uncover a TibC–TibA dodecamer/hexamer assembly with two enzyme molecules binding to one TibA substrate. The complex structure also highlights a high efficient hyperglycosylation of six autotransporter substrates simultaneously by the dodecamer enzyme complex. DOI: http://dx.doi.org/10.7554/eLife.03714.001 PMID:25310236

Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species.

PubMed

Kindler, Carolin; Chèvre, Maxime; Ursenbacher, Sylvain; Böhme, Wolfgang; Hille, Axel; Jablonski, Daniel; Vamberger, Melita; Fritz, Uwe

2017-08-07

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

PubMed Central

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-01-01

The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and the allosteric mechanism of how IP3 opens the Ca2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP3R in the absence and presence of IP3. Analyses of two distinct space group crystals uncovered an IP3-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP3R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP3-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP3 binding to the Ca2+ channel. PMID:28416699

Parent-school relationships and children's academic and social outcomes in public school pre-kindergarten.

PubMed

Powell, Douglas R; Son, Seung-Hee; File, Nancy; San Juan, Robert R

2010-08-01

Two dimensions of parent-school relationships, parental school involvement and parents' perceptions of teacher responsiveness to child/parent, were examined in state-funded pre-kindergarten classrooms in a large urban school district. Children's social and academic outcomes were individually assessed in the fall and spring. Hierarchical Linear Modeling analyses revealed that parental school involvement positively predicted children's social skills (d=.55) and mathematics skills (d=.36), and negatively predicted problem behaviors (d=.47). Perceived teacher responsiveness to child/parent was positively related to children's early reading (d=.43), and social skills (d=.43), and negatively to problem behaviors (d=.61). All analyses controlled for quality of teacher interaction with children in the classroom, parental home involvement, parental education level, and child race/ethnicity. Copyright 2010 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.

PubMed

Nakato, Ryuichiro; Shirahige, Katsuhiko

2017-03-01

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field. © The Author 2016. Published by Oxford University Press.

The structure of DSM-IV-TR personality disorder diagnoses in NESARC: a reanalysis.

PubMed

Trull, Timothy J; Vergés, Alvaro; Wood, Phillip K; Sher, Kenneth J

2013-12-01

Cox, Clara, Worobec, and Grant (2012) recently presented results from a series of analyses aimed at identifying the factor structure underlying the DSM-IV-TR (APA, 2000) personality diagnoses assessed in the large NESARC study. Cox et al. (2012) concluded that the best fitting model was one that modeled three lower-order factors (the three clusters of PDs as outlined by DSM-IV-TR), which in turn loaded on a single PD higher-order factor. Our reanalyses of the NESARC Wave 1 and Wave 2 data for personality disorder diagnoses revealed that the best fitting model was that of a general PD factor that spans each of the ten DSM-IV PD diagnoses, and our reanalyses do not support the three-cluster hierarchical structure outlined by Cox et al. (2012) and DSM-IV-TR. Finally, we note the importance of modeling the Wave 2 assessment method factor in analyses of NESARC PD data.

Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

PubMed Central

Kuhn, Jens H.; Andersen, Kristian G.; Baize, Sylvain; Bào, Yīmíng; Bavari, Sina; Berthet, Nicolas; Blinkova, Olga; Brister, J. Rodney; Clawson, Anna N.; Fair, Joseph; Gabriel, Martin; Garry, Robert F.; Gire, Stephen K.; Goba, Augustine; Gonzalez, Jean-Paul; Günther, Stephan; Happi, Christian T.; Jahrling, Peter B.; Kapetshi, Jimmy; Kobinger, Gary; Kugelman, Jeffrey R.; Leroy, Eric M.; Maganga, Gael Darren; Mbala, Placide K.; Moses, Lina M.; Muyembe-Tamfum, Jean-Jacques; N’Faly, Magassouba; Nichol, Stuart T.; Omilabu, Sunday A.; Palacios, Gustavo; Park, Daniel J.; Paweska, Janusz T.; Radoshitzky, Sheli R.; Rossi, Cynthia A.; Sabeti, Pardis C.; Schieffelin, John S.; Schoepp, Randal J.; Sealfon, Rachel; Swanepoel, Robert; Towner, Jonathan S.; Wada, Jiro; Wauquier, Nadia; Yozwiak, Nathan L.; Formenty, Pierre

2014-01-01

In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures. PMID:25421896

First-principles study on phase transition and ferroelectricity in lithium niobate and tantalate

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

Toyoura, Kazuaki, E-mail: toyoura@numse.nagoya-u.ac.jp; Ohta, Masataka; Nakamura, Atsutomo

2015-08-14

The phase transitions and ferroelectricity of LiNbO{sub 3} and LiTaO{sub 3} have been investigated theoretically from first principles. The phonon analyses and the molecular dynamics simulations revealed that the ferroelectric phase transition is not conventional displacive type but order-disorder type with strong correlation between cation displacements. According to the evaluated potential energy surfaces around the paraelectric structures, the large difference in ferroelectricity between the two oxides results from the little difference in short-range interionic interaction between Nb-O and Ta-O. As the results of the crystal orbital overlap population analyses, the different short-range interaction originates from the difference in covalency betweenmore » Nb4d-O2p and Ta5d-O2p orbitals, particularly d{sub xz}-p{sub x}/d{sub yz}-p{sub y} orbitals (π orbitals), from the electronic point of view.« less

Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses.

PubMed

Aho, Vilma; Ollila, Hanna M; Kronholm, Erkki; Bondia-Pons, Isabel; Soininen, Pasi; Kangas, Antti J; Hilvo, Mika; Seppälä, Ilkka; Kettunen, Johannes; Oikonen, Mervi; Raitoharju, Emma; Hyötyläinen, Tuulia; Kähönen, Mika; Viikari, Jorma S A; Härmä, Mikko; Sallinen, Mikael; Olkkonen, Vesa M; Alenius, Harri; Jauhiainen, Matti; Paunio, Tiina; Lehtimäki, Terho; Salomaa, Veikko; Orešič, Matej; Raitakari, Olli T; Ala-Korpela, Mika; Porkka-Heiskanen, Tarja

2016-04-22

Sleep loss and insufficient sleep are risk factors for cardiometabolic diseases, but data on how insufficient sleep contributes to these diseases are scarce. These questions were addressed using two approaches: an experimental, partial sleep restriction study (14 cases and 7 control subjects) with objective verification of sleep amount, and two independent epidemiological cohorts (altogether 2739 individuals) with questions of sleep insufficiency. In both approaches, blood transcriptome and serum metabolome were analysed. Sleep loss decreased the expression of genes encoding cholesterol transporters and increased expression in pathways involved in inflammatory responses in both paradigms. Metabolomic analyses revealed lower circulating large HDL in the population cohorts among subjects reporting insufficient sleep, while circulating LDL decreased in the experimental sleep restriction study. These findings suggest that prolonged sleep deprivation modifies inflammatory and cholesterol pathways at the level of gene expression and serum lipoproteins, inducing changes toward potentially higher risk for cardiometabolic diseases.

Notum deacylates Wnts to suppress signalling activity

PubMed Central

Howell, Steve; Chang, Tao-Hsin; Liu, Yan; Feizi, Ten; Bineva, Ganka; O’Reilly, Nicola; Snijders, Ambrosius P.; Jones, E. Yvonne; Vincent, Jean-Paul

2015-01-01

Signalling by Wnts is finely balanced to ensure normal development and tissue homeostasis while avoiding diseases such as cancer. This is achieved in part by Notum, a highly conserved secreted feedback antagonist. Notum has been thought to act as a phospholipase, shedding glypicans and associated Wnts from the cell surface. However, this view fails to explain specificity since glypicans bind many extracellular ligands. Here we provide genetic evidence in Drosophila that Notum requires glypicans to suppress Wnt signalling, but does not cleave their glycophosphatidylinositol anchor. Structural analyses reveal glycosaminoglycan binding sites on Notum, which likely help Notum colocalise with Wnts. They also identify, at the active site of human and Drosophila Notum, a large hydrophobic pocket that accommodates palmitoleate. Kinetic and mass spectrometric analyses of human proteins show that Notum is a carboxylesterase that removes an essential palmitoleate moiety from Wnts and thus constitutes the first known extracellular protein deacylase. PMID:25731175

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III

PubMed Central

Bezerra, Gustavo A.; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramić, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

2012-01-01

Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies. PMID:22493238

Examination of Sex Differences in a Large Sample of Young Children with Autism Spectrum Disorder and Typical Development

PubMed Central

Reinhardt, Vanessa P.; Wetherby, Amy M.; Schatschneider, Christopher

2014-01-01

Despite consistent and substantive research documenting a large male to female ratio in Autism Spectrum Disorder (ASD), only a modest body of research exists examining sex differences in characteristics. This study examined sex differences in developmental functioning and early social communication in children with ASD as compared to children with typical development. Sex differences in adaptive behavior and autism symptoms were also examined in children with ASD. Participants (n = 511) were recruited from the Florida State University FIRST WORDS® Project and University of Michigan Autism and Communication Disorders Center. Analyses did not reveal significant effects of sex or a diagnostic group by sex interaction, suggesting a similar phenotype in males and females early in development. Further research is needed to examine sex differences across development. PMID:25189824

Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices.

PubMed

Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

2016-01-01

How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women's shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

PubMed

Gerstein, Mark B; Lu, Zhi John; Van Nostrand, Eric L; Cheng, Chao; Arshinoff, Bradley I; Liu, Tao; Yip, Kevin Y; Robilotto, Rebecca; Rechtsteiner, Andreas; Ikegami, Kohta; Alves, Pedro; Chateigner, Aurelien; Perry, Marc; Morris, Mitzi; Auerbach, Raymond K; Feng, Xin; Leng, Jing; Vielle, Anne; Niu, Wei; Rhrissorrakrai, Kahn; Agarwal, Ashish; Alexander, Roger P; Barber, Galt; Brdlik, Cathleen M; Brennan, Jennifer; Brouillet, Jeremy Jean; Carr, Adrian; Cheung, Ming-Sin; Clawson, Hiram; Contrino, Sergio; Dannenberg, Luke O; Dernburg, Abby F; Desai, Arshad; Dick, Lindsay; Dosé, Andréa C; Du, Jiang; Egelhofer, Thea; Ercan, Sevinc; Euskirchen, Ghia; Ewing, Brent; Feingold, Elise A; Gassmann, Reto; Good, Peter J; Green, Phil; Gullier, Francois; Gutwein, Michelle; Guyer, Mark S; Habegger, Lukas; Han, Ting; Henikoff, Jorja G; Henz, Stefan R; Hinrichs, Angie; Holster, Heather; Hyman, Tony; Iniguez, A Leo; Janette, Judith; Jensen, Morten; Kato, Masaomi; Kent, W James; Kephart, Ellen; Khivansara, Vishal; Khurana, Ekta; Kim, John K; Kolasinska-Zwierz, Paulina; Lai, Eric C; Latorre, Isabel; Leahey, Amber; Lewis, Suzanna; Lloyd, Paul; Lochovsky, Lucas; Lowdon, Rebecca F; Lubling, Yaniv; Lyne, Rachel; MacCoss, Michael; Mackowiak, Sebastian D; Mangone, Marco; McKay, Sheldon; Mecenas, Desirea; Merrihew, Gennifer; Miller, David M; Muroyama, Andrew; Murray, John I; Ooi, Siew-Loon; Pham, Hoang; Phippen, Taryn; Preston, Elicia A; Rajewsky, Nikolaus; Rätsch, Gunnar; Rosenbaum, Heidi; Rozowsky, Joel; Rutherford, Kim; Ruzanov, Peter; Sarov, Mihail; Sasidharan, Rajkumar; Sboner, Andrea; Scheid, Paul; Segal, Eran; Shin, Hyunjin; Shou, Chong; Slack, Frank J; Slightam, Cindie; Smith, Richard; Spencer, William C; Stinson, E O; Taing, Scott; Takasaki, Teruaki; Vafeados, Dionne; Voronina, Ksenia; Wang, Guilin; Washington, Nicole L; Whittle, Christina M; Wu, Beijing; Yan, Koon-Kiu; Zeller, Georg; Zha, Zheng; Zhong, Mei; Zhou, Xingliang; Ahringer, Julie; Strome, Susan; Gunsalus, Kristin C; Micklem, Gos; Liu, X Shirley; Reinke, Valerie; Kim, Stuart K; Hillier, LaDeana W; Henikoff, Steven; Piano, Fabio; Snyder, Michael; Stein, Lincoln; Lieb, Jason D; Waterston, Robert H

2010-12-24

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

A National Analysis of Medicaid Home and Community Based Services Waivers for People With Intellectual and Developmental Disabilities: FY 2015.

PubMed

Friedman, Carli

2017-10-01

Medicaid Home and Community Based Services (HCBS) 1915(c) waivers are the largest source of funding for the long term services and supports of people with intellectual and developmental disabilities (IDD). National-level analyses of HCBS IDD waivers are crucial because of the large variance across states, the recent CMS rule and regulation changes (CMS 2249-F/2296-F), and the ever changing economic and political landscape. Therefore, the aim of this study was to examine state waiver priorities for people with IDD. In FY 2015, 111 waivers projected spending $25.6 billion for approximately 630,000 people with IDD. The services with the most funding were residential habilitation, supports to live in one's own home, and day habilitation. However, our analysis revealed large discrepancies across states and services.

The inviscid stability of supersonic flow past heated or cooled axisymmetric bodies

NASA Technical Reports Server (NTRS)

Shaw, Stephen J.; Duck, Peter W.

1992-01-01

The inviscid, linear, nonaxisymmetric, temporal stability of the boundary layer associated with the supersonic flow past axisymmetric bodies (with particular emphasis on long thin, straight circular cylinders), subject to heated or cooled wall conditions is investigated. The eigenvalue problem is computed in some detail for a particular Mach number or 3.8, revealing that the effect of curvature and the choice of wall conditions both have a significant effect on the stability of the flow. Both the asymptotic, large azimuthal wavenumber solution and the asymptotic, far downstream solution are obtained for the stability analysis and compared with numerical results. Additionally, asymptotic analyses valid for large radii of curvature with cooled/heated wall conditions are presented. In general, important differences were found to exist between the wall temperature conditions imposed and the adiabatic wall conditions considered previously.

Iridium enrichment in airborne particles from kilauea volcano: january 1983.

PubMed

Zoller, W H; Parrington, J R; Kotra, J M

1983-12-09

Airborne particulate matter from the January 1983 eruption of Kilauea volcano was inadvertently collected on air filters at Mauna Loa Observatory at a sampling station used to observe particles in global circulation. Analyses of affected samples revealed unusually large concentrations of selenium, arsenic, indium, gold, and sulfur, as expected for volcanic emissions. Strikingly large concentrations of iridium were also observed, the ratio of iridium to aluminum being 17,000 times its value in Hawaiian basalt. Since iridium enrichments have not previously been observed in volcanic emissions, the results for Kilauea suggest that it is part of an unusual volcanic system which may be fed by magma from the mantle. The iridium enrichment appears to be linked with the high fluorine content of the volcanic gases, which suggests that the iridium is released as a volatile IrF(6).

A large-scale evaluation of the KiVa antibullying program: grades 4-6.

PubMed

Kärnä, Antti; Voeten, Marinus; Little, Todd D; Poskiparta, Elisa; Kaljonen, Anne; Salmivalli, Christina

2011-01-01

This study demonstrates the effectiveness of the KiVa antibullying program using a large sample of 8,237 youth from Grades 4-6 (10-12 years). Altogether, 78 schools were randomly assigned to intervention (39 schools, 4,207 students) and control conditions (39 schools, 4,030 students). Multilevel regression analyses revealed that after 9 months of implementation, the intervention had consistent beneficial effects on 7 of the 11 dependent variables, including self- and peer-reported victimization and self-reported bullying. The results indicate that the KiVa program is effective in reducing school bullying and victimization in Grades 4-6. Despite some evidence against school-based interventions, the results suggest that well-conceived school-based programs can reduce victimization. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc.

The inviscid stability of supersonic flow past heated or cooled axisymmetric bodies

NASA Technical Reports Server (NTRS)

Shaw, Stephen J.; Duck, Peter W.

1990-01-01

The inviscid, linear, nonaxisymmetric, temporal stability of the boundary layer associated with the supersonic flow past axisymmetric bodies (with particular emphasis on long thin, straight circular cylinders), subject to heated or cooled wall conditions is investigated. The eigenvalue problem is computed in some detail for a particular Mach number or 3.8, revealing that the effect of curvature and the choice of wall conditions both have a significant effect on the stability of the flow. Both the asymptotic, large azimuthal wavenumber solution and the asymptotic, far downstream solution are obtained for the stability analysis and compared with numerical results. Additionally, asymptotic analyses valid for large radii of curvature with cooled/heated wall conditions, are presented. In general, important differences were found to exist between the wall temperature conditions imposed and the adiabatic wall conditions considered previously.

Large-deformation and high-strength amorphous porous carbon nanospheres

NASA Astrophysics Data System (ADS)

Yang, Weizhu; Mao, Shimin; Yang, Jia; Shang, Tao; Song, Hongguang; Mabon, James; Swiech, Wacek; Vance, John R.; Yue, Zhufeng; Dillon, Shen J.; Xu, Hangxun; Xu, Baoxing

2016-04-01

Carbon is one of the most important materials extensively used in industry and our daily life. Crystalline carbon materials such as carbon nanotubes and graphene possess ultrahigh strength and toughness. In contrast, amorphous carbon is known to be very brittle and can sustain little compressive deformation. Inspired by biological shells and honeycomb-like cellular structures in nature, we introduce a class of hybrid structural designs and demonstrate that amorphous porous carbon nanospheres with a thin outer shell can simultaneously achieve high strength and sustain large deformation. The amorphous carbon nanospheres were synthesized via a low-cost, scalable and structure-controllable ultrasonic spray pyrolysis approach using energetic carbon precursors. In situ compression experiments on individual nanospheres show that the amorphous carbon nanospheres with an optimized structure can sustain beyond 50% compressive strain. Both experiments and finite element analyses reveal that the buckling deformation of the outer spherical shell dominates the improvement of strength while the collapse of inner nanoscale pores driven by twisting, rotation, buckling and bending of pore walls contributes to the large deformation.

Suicidal ideation among individuals whose parents have divorced: findings from a representative Canadian community survey.

PubMed

Fuller-Thomson, Esme; Dalton, Angela D

2011-05-15

This study used a large, nationally representative sample to examine the gender-specific association between parental divorce and the cumulative lifetime incidence of suicidal ideation. Known risk factors for suicidal ideation, such as childhood stressors, socioeconomic factors, adult health behaviors and stressors, marital status, and any history of mood and/or anxiety disorders were controlled. Gender-specific analyses revealed that for men, the parental divorce-suicidal ideation relationship remained statistically significant even when the above-listed cluster of risk factors were included in the analyses (odds ratio (OR)=2.36, 95% confidence interval (CI)=1.56, 3.58). For women, the association between parental divorce and suicidal ideation was reduced to non-significance when other adverse childhood experiences were included in the analyses (full adjustment OR=1.04, 95% CI=0.72, 1.50). These findings indicate a need for screening of suicidal ideation among individuals, particularly men and those with mood and/or anxiety disorders, who have experienced parental divorce. Future research should focus on the mechanisms linking parental divorce and suicidal ideation. Copyright © 2010 Elsevier Ltd. All rights reserved.

A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape

PubMed Central

Ried, Janina S.; Jeff M., Janina; Chu, Audrey Y.; Bragg-Gresham, Jennifer L.; van Dongen, Jenny; Huffman, Jennifer E.; Ahluwalia, Tarunveer S.; Cadby, Gemma; Eklund, Niina; Eriksson, Joel; Esko, Tõnu; Feitosa, Mary F.; Goel, Anuj; Gorski, Mathias; Hayward, Caroline; Heard-Costa, Nancy L.; Jackson, Anne U.; Jokinen, Eero; Kanoni, Stavroula; Kristiansson, Kati; Kutalik, Zoltán; Lahti, Jari; Luan, Jian'an; Mägi, Reedik; Mahajan, Anubha; Mangino, Massimo; Medina-Gomez, Carolina; Monda, Keri L.; Nolte, Ilja M.; Pérusse, Louis; Prokopenko, Inga; Qi, Lu; Rose, Lynda M.; Salvi, Erika; Smith, Megan T.; Snieder, Harold; Stančáková, Alena; Ju Sung, Yun; Tachmazidou, Ioanna; Teumer, Alexander; Thorleifsson, Gudmar; van der Harst, Pim; Walker, Ryan W.; Wang, Sophie R.; Wild, Sarah H.; Willems, Sara M.; Wong, Andrew; Zhang, Weihua; Albrecht, Eva; Couto Alves, Alexessander; Bakker, Stephan J. L.; Barlassina, Cristina; Bartz, Traci M.; Beilby, John; Bellis, Claire; Bergman, Richard N.; Bergmann, Sven; Blangero, John; Blüher, Matthias; Boerwinkle, Eric; Bonnycastle, Lori L.; Bornstein, Stefan R.; Bruinenberg, Marcel; Campbell, Harry; Chen, Yii-Der Ida; Chiang, Charleston W. K.; Chines, Peter S.; Collins, Francis S; Cucca, Fracensco; Cupples, L Adrienne; D'Avila, Francesca; de Geus, Eco J .C.; Dedoussis, George; Dimitriou, Maria; Döring, Angela; Eriksson, Johan G.; Farmaki, Aliki-Eleni; Farrall, Martin; Ferreira, Teresa; Fischer, Krista; Forouhi, Nita G.; Friedrich, Nele; Gjesing, Anette Prior; Glorioso, Nicola; Graff, Mariaelisa; Grallert, Harald; Grarup, Niels; Gräßler, Jürgen; Grewal, Jagvir; Hamsten, Anders; Harder, Marie Neergaard; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew Tym; Havulinna, Aki S.; Heliövaara, Markku; Hillege, Hans; Hofman, Albert; Holmen, Oddgeir; Homuth, Georg; Hottenga, Jouke-Jan; Hui, Jennie; Husemoen, Lise Lotte; Hysi, Pirro G.; Isaacs, Aaron; Ittermann, Till; Jalilzadeh, Shapour; James, Alan L.; Jørgensen, Torben; Jousilahti, Pekka; Jula, Antti; Marie Justesen, Johanne; Justice, Anne E.; Kähönen, Mika; Karaleftheri, Maria; Tee Khaw, Kay; Keinanen-Kiukaanniemi, Sirkka M.; Kinnunen, Leena; Knekt, Paul B.; Koistinen, Heikki A.; Kolcic, Ivana; Kooner, Ishminder K.; Koskinen, Seppo; Kovacs, Peter; Kyriakou, Theodosios; Laitinen, Tomi; Langenberg, Claudia; Lewin, Alexandra M.; Lichtner, Peter; Lindgren, Cecilia M.; Lindström, Jaana; Linneberg, Allan; Lorbeer, Roberto; Lorentzon, Mattias; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Manunta, Paolo; Leach, Irene Mateo; McArdle, Wendy L.; Mcknight, Barbara; Mohlke, Karen L.; Mihailov, Evelin; Milani, Lili; Mills, Rebecca; Montasser, May E.; Morris, Andrew P.; Müller, Gabriele; Musk, Arthur W.; Narisu, Narisu; Ong, Ken K.; Oostra, Ben A.; Osmond, Clive; Palotie, Aarno; Pankow, James S.; Paternoster, Lavinia; Penninx, Brenda W.; Pichler, Irene; Pilia, Maria G.; Polašek, Ozren; Pramstaller, Peter P.; Raitakari, Olli T; Rankinen, Tuomo; Rao, D. C.; Rayner, Nigel W.; Ribel-Madsen, Rasmus; Rice, Treva K.; Richards, Marcus; Ridker, Paul M.; Rivadeneira, Fernando; Ryan, Kathy A.; Sanna, Serena; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Sebert, Sylvain; Southam, Lorraine; Sparsø, Thomas Hempel; Steinthorsdottir, Valgerdur; Stirrups, Kathleen; Stolk, Ronald P.; Strauch, Konstantin; Stringham, Heather M.; Swertz, Morris A.; Swift, Amy J.; Tönjes, Anke; Tsafantakis, Emmanouil; van der Most, Peter J.; Van Vliet-Ostaptchouk, Jana V.; Vandenput, Liesbeth; Vartiainen, Erkki; Venturini, Cristina; Verweij, Niek; Viikari, Jorma S.; Vitart, Veronique; Vohl, Marie-Claude; Vonk, Judith M.; Waeber, Gérard; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Winkler, Thomas W.; Wright, Alan F.; Yerges-Armstrong, Laura M.; Hua Zhao, Jing; Carola Zillikens, M.; Boomsma, Dorret I.; Bouchard, Claude; Chambers, John C.; Chasman, Daniel I.; Cusi, Daniele; Gansevoort, Ron T.; Gieger, Christian; Hansen, Torben; Hicks, Andrew A.; Hu, Frank; Hveem, Kristian; Jarvelin, Marjo-Riitta; Kajantie, Eero; Kooner, Jaspal S.; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lakka, Timo A.; Lehtimäki, Terho; Metspalu, Andres; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Palmer, Lyle J.; Pedersen, Oluf; Perola, Markus; Peters, Annette; Psaty, Bruce M.; Puolijoki, Hannu; Rauramaa, Rainer; Rudan, Igor; Salomaa, Veikko; Schwarz, Peter E. H.; Shudiner, Alan R.; Smit, Jan H.; Sørensen, Thorkild I. A.; Spector, Timothy D.; Stefansson, Kari; Stumvoll, Michael; Tremblay, Angelo; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; Völker, Uwe; Vollenweider, Peter; Wareham, Nicholas J.; Watkins, Hugh; Wilson, James F.; Zeggini, Eleftheria; Abecasis, Goncalo R.; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; van Duijn, Cornelia M.; Fox, Caroline; Groop, Leif C.; Heid, Iris M.; Hunter, David J.; Kaplan, Robert C.; McCarthy, Mark I.; North, Kari E.; O'Connell, Jeffrey R.; Schlessinger, David; Thorsteinsdottir, Unnur; Strachan, David P.; Frayling, Timothy; Hirschhorn, Joel N.; Müller-Nurasyid, Martina; Loos, Ruth J. F.

2016-01-01

Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways. PMID:27876822

Individual differences affecting caffeine intake. Analysis of consumption behaviours for different times of day and caffeine sources.

PubMed

Penolazzi, Barbara; Natale, Vincenzo; Leone, Luigi; Russo, Paolo Maria

2012-06-01

The main purpose of the present study was to investigate the individual variables contributing to determine the high variability in the consumption behaviours of caffeine, a psychoactive substance which is still poorly investigated in comparison with other drugs. The effects of a large set of specific personality traits (i.e., Impulsivity, Sensation Seeking, Anxiety, Reward Sensitivity and Circadian Preference) were compared along with some relevant socio-demographic variables (i.e., gender and age) and cigarette smoking behaviour. Analyses revealed that daily caffeine intake was significantly higher for males, older people, participants smoking more cigarettes and showing higher scores on Impulsivity, Sensation Seeking and a facet of Reward Sensitivity. However, more detailed analyses showed that different patterns of individual variables predicted caffeine consumption when the times of day and the caffeine sources were considered. The present results suggest that such detailed analyses are required to detect the critical predictive variables that could be obscured when only total caffeine intake during the entire day is considered. Copyright © 2012 Elsevier Ltd. All rights reserved.

Oort spike comets with large perihelion distances

NASA Astrophysics Data System (ADS)

Królikowska, Małgorzata; Dybczyński, Piotr A.

2017-12-01

The complete sample of large-perihelion nearly-parabolic comets discovered during the period 1901-2010 is studied, starting with their orbit determination. Next, an orbital evolution that includes three perihelion passages (previous-observed-next) is investigated in which a full model of Galactic perturbations and perturbations from passing stars is incorporated. We show that the distribution of planetary perturbations suffered by actual large-perihelion comets during their passage through the Solar system has a deep, unexpected minimum around zero, which indicates a lack of 'almost unperturbed' comets. Using a series of simulations we show that this deep well is moderately resistant to some diffusion of the orbital elements of the analysed comets. It seems reasonable to assert that the observed stream of these large-perihelion comets experienced a series of specific planetary configurations when passing through the planetary zone. An analysis of the past dynamics of these comets clearly shows that dynamically new comets can appear only when their original semimajor axes are greater than 20 000 au. On the other hand, dynamically old comets are completely absent for semimajor axes longer than 40 000 au. We demonstrate that the observed 1/aori-distribution exhibits a local minimum separating dynamically new from dynamically old comets. Long-term dynamical studies reveal a wide variety of orbital behaviour. Several interesting examples of the action of passing stars are also described, in particular the impact of Gliese 710, which will pass close to the Sun in the future. However, none of the obtained stellar perturbations is sufficient to change the dynamical status of the analysed comets.

Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

NASA Astrophysics Data System (ADS)

Palmblad, Magnus; van Eck, Nees Jan

2018-03-01

We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

PubMed

Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

2006-06-01

Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

Colorado Learning Difficulties Questionnaire:Validation of a parent-report screening measure

PubMed Central

Willcutt, Erik G.; Boada, Richard; Riddle, Margaret W.; Chhabildas, Nomita; DeFries, John C.; Pennington, Bruce F.

2011-01-01

This study evaluated the internal structure and convergent and discriminant evidence for the Colorado Learning Difficulties Questionnaire (CLDQ), a 20-item parent-report rating scale that was developed to provide a brief screening measure for learning difficulties. CLDQ ratings were obtained from parents of children in two large community samples and two samples from clinics that specialize in the assessment of learning disabilities and related disorders (total N = 8,004). Exploratory and confirmatory factor analyses revealed five correlated but separable dimensions that were labeled reading, math, social cognition, social anxiety, and spatial difficulties. Results revealed strong convergent and discriminant evidence for the CLDQ Reading scale, suggesting that this scale may provide a useful method to screen for reading difficulties in both research studies and clinical settings. Results are also promising for the other four CLDQ scales, but additional research is needed to refine each of these measures. PMID:21574721

The ecological origins of snakes as revealed by skull evolution.

PubMed

Da Silva, Filipe O; Fabre, Anne-Claire; Savriama, Yoland; Ollonen, Joni; Mahlow, Kristin; Herrel, Anthony; Müller, Johannes; Di-Poï, Nicolas

2018-01-25

The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.

A Winter Precipitation Reconstruction (CE 1810-2012) in the Southeastern Tibetan Plateau and Its Relationship to Salween River Streamflow Variations

NASA Astrophysics Data System (ADS)

Chen, Feng; Yuan, Yujiang; Fan, Zexin; Yu, Shulong

2018-01-01

We established a tree-ring width series from one Yunnan Douglas fir (Pseudotsuga forrestii) stand near the Mingyong glacier terminus of Meili Snow Mountain, southeastern Tibetan Plateau. Correlation analyses indicated that radial growth of Yunnan Douglas firs is largely controlled by variations in winter (November-March) precipitation. The precipitation reconstruction model accounts for 37% of the actual precipitation variance during the common period 1954-2012. Spatial correlations with the gridded precipitation data reveal that the winter precipitation reconstruction represents regional precipitation changes over the southeastern Tibetan Plateau. By comparing our results with other regional tree-ring records, a distinctive amount of common dry and humid periods were found. Our winter precipitation reconstruction shows profound similarities with Salween river streamflow signals as well as regional glacial activity. Cross-wavelet analysis reveals solar and ENSO influences on precipitation and streamflow variations in the southeastern Tibetan Plateau.

Hybridization Reveals the Evolving Genomic Architecture of Speciation

PubMed Central

Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

2014-01-01

SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

The domestication and evolutionary ecology of apples.

PubMed

Cornille, Amandine; Giraud, Tatiana; Smulders, Marinus J M; Roldán-Ruiz, Isabel; Gladieux, Pierre

2014-02-01

The cultivated apple is a major fruit crop in temperate zones. Its wild relatives, distributed across temperate Eurasia and growing in diverse habitats, represent potentially useful sources of diversity for apple breeding. We review here the most recent findings on the genetics and ecology of apple domestication and its impact on wild apples. Genetic analyses have revealed a Central Asian origin for cultivated apple, together with an unexpectedly large secondary contribution from the European crabapple. Wild apple species display strong population structures and high levels of introgression from domesticated apple, and this may threaten their genetic integrity. Recent research has revealed a major role of hybridization in the domestication of the cultivated apple and has highlighted the value of apple as an ideal model for unraveling adaptive diversification processes in perennial fruit crops. We discuss the implications of this knowledge for apple breeding and for the conservation of wild apples. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial diversity of culturable heterotrophs in the rhizosphere of salt marsh grass, Porteresia coarctata (Tateoka) in a mangrove ecosystem.

PubMed

Bharathkumar, Srinivasan; Paul, Diby; Nair, Sudha

2008-02-01

A study was conducted to understand the complexity of bacterial diversity of rhizosphere of Porteresia coarctata based on culture dependent method. A large number of bacteria were isolated on nutrient agar medium supplemented with 1% NaCl and the dominant ones were further analyzed with PCR-RFLP method. The sequence analyses of the dominant strains revealed that most of the sequences belonged to members of gamma proteobacteria, firmicutes, bacteroidetes and uncultured bacteria. The phylogenetic analysis of 16S rRNA gene sequences revealed close relationships to a wide range of clones or bacterial species of various divisions. These results afford an understanding of the role of rhizobacteria in alleviating salt stress in Porteresia coarctata expected to contribute towards long-term goal of improving plant-microbe interactions for salinity affected fields. (c) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Virus genomes reveal factors that spread and sustained the Ebola epidemic

PubMed Central

Dudas, Gytis; Carvalho, Luiz Max; Bedford, Trevor; Tatem, Andrew J.; Baele, Guy; Faria, Nuno R.; Park, Daniel J.; Ladner, Jason T.; Arias, Armando; Asogun, Danny; Bielejec, Filip; Caddy, Sarah L.; Cotten, Matthew; D’Ambrozio, Jonathan; Dellicour, Simon; Di Caro, Antonino; Diclaro, JosephW.; Duraffour, Sophie; Elmore, Michael J.; Fakoli, Lawrence S.; Faye, Ousmane; Gilbert, Merle L.; Gevao, Sahr M.; Gire, Stephen; Gladden-Young, Adrianne; Gnirke, Andreas; Goba, Augustine; Grant, Donald S.; Haagmans, Bart L.; Hiscox, Julian A.; Jah, Umaru; Kargbo, Brima; Kugelman, Jeffrey R.; Liu, Di; Lu, Jia; Malboeuf, Christine M.; Mate, Suzanne; Matthews, David A.; Matranga, Christian B.; Meredith, Luke W.; Qu, James; Quick, Joshua; Pas, Suzan D.; Phan, My VT; Pollakis, Georgios; Reusken, Chantal B.; Sanchez-Lockhart, Mariano; Schaffner, Stephen F.; Schieffelin, John S.; Sealfon, Rachel S.; Simon-Loriere, Etienne; Smits, Saskia L.; Stoecker, Kilian; Thorne, Lucy; Tobin, Ekaete Alice; Vandi, Mohamed A.; Watson, Simon J.; West, Kendra; Whitmer, Shannon; Wiley, Michael R.; Winnicki, Sarah M.; Wohl, Shirlee; Wölfel, Roman; Yozwiak, Nathan L.; Andersen, Kristian G.; Blyden, Sylvia O.; Bolay, Fatorma; Carroll, MilesW.; Dahn, Bernice; Diallo, Boubacar; Formenty, Pierre; Fraser, Christophe; Gao, George F.; Garry, Robert F.; Goodfellow, Ian; Günther, Stephan; Happi, Christian T.; Holmes, Edward C.; Kargbo, Brima; Keïta, Sakoba; Kellam, Paul; Koopmans, Marion P. G.; Kuhn, Jens H.; Loman, Nicholas J.; Magassouba, N’Faly; Naidoo, Dhamari; Nichol, Stuart T.; Nyenswah, Tolbert; Palacios, Gustavo; Pybus, Oliver G.; Sabeti, Pardis C.; Sall, Amadou; Ströher, Ute; Wurie, Isatta; Suchard, Marc A.; Lemey, Philippe; Rambaut, Andrew

2017-01-01

The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already set the seeds for an international epidemic, rendering these measures ineffective in curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing they were susceptible to significant outbreaks but at lower risk of introductions. Finally, we reveal this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform interventions in future epidemics. PMID:28405027

Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness

PubMed Central

Davis, Brian W.; Schoenebeck, Jeffrey J.

2017-01-01

Domestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during the formation and maintenance of modern breeds. While previous studies focused on the identification of alleles that contribute to small skeletal size, little is known about the underlying genetics controlling large size. We first performed a genome-wide association study (GWAS) using the Illumina Canine HD 170,000 single nucleotide polymorphism (SNP) array which compared 165 large-breed dogs from 19 breeds (defined as having a Standard Breed Weight (SBW) >41 kg [90 lb]) to 690 dogs from 69 small breeds (SBW ≤41 kg). We identified two loci on the canine X chromosome that were strongly associated with large body size at 82–84 megabases (Mb) and 101–104 Mb. Analyses of whole genome sequencing (WGS) data from 163 dogs revealed two indels in the Insulin Receptor Substrate 4 (IRS4) gene at 82.2 Mb and two additional mutations, one SNP and one deletion of a single codon, in Immunoglobulin Superfamily member 1 gene (IGSF1) at 102.3 Mb. IRS4 and IGSF1 are members of the GH/IGF1 and thyroid pathways whose roles include determination of body size. We also found one highly associated SNP in the 5’UTR of Acyl-CoA Synthetase Long-chain family member 4 (ACSL4) at 82.9 Mb, a gene which controls the traits of muscling and back fat thickness. We show by analysis of sequencing data from 26 wolves and 959 dogs representing 102 domestic dog breeds that skeletal size and body mass in large dog breeds are strongly associated with variants within IRS4, ACSL4 and IGSF1. PMID:28257443

Comparative RNA-Seq transcriptome analyses reveal distinct metabolic pathways in diabetic nerve and kidney disease.

PubMed

Hinder, Lucy M; Park, Meeyoung; Rumora, Amy E; Hur, Junguk; Eichinger, Felix; Pennathur, Subramaniam; Kretzler, Matthias; Brosius, Frank C; Feldman, Eva L

2017-09-01

Treating insulin resistance with pioglitazone normalizes renal function and improves small nerve fibre function and architecture; however, it does not affect large myelinated nerve fibre function in mouse models of type 2 diabetes (T2DM), indicating that pioglitazone affects the body in a tissue-specific manner. To identify distinct molecular pathways regulating diabetic peripheral neuropathy (DPN) and nephropathy (DN), as well those affected by pioglitazone, we assessed DPN and DN gene transcript expression in control and diabetic mice with or without pioglitazone treatment. Differential expression analysis and self-organizing maps were then used in parallel to analyse transcriptome data. Differential expression analysis showed that gene expression promoting cell death and the inflammatory response was reversed in the kidney glomeruli but unchanged or exacerbated in sciatic nerve by pioglitazone. Self-organizing map analysis revealed that mitochondrial dysfunction was normalized in kidney and nerve by treatment; however, conserved pathways were opposite in their directionality of regulation. Collectively, our data suggest inflammation may drive large fibre dysfunction, while mitochondrial dysfunction may drive small fibre dysfunction in T2DM. Moreover, targeting both of these pathways is likely to improve DN. This study supports growing evidence that systemic metabolic changes in T2DM are associated with distinct tissue-specific metabolic reprogramming in kidney and nerve and that these changes play a critical role in DN and small fibre DPN pathogenesis. These data also highlight the potential dangers of a 'one size fits all' approach to T2DM therapeutics, as the same drug may simultaneously alleviate one complication while exacerbating another. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

PubMed Central

2013-01-01

Background Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. Methods The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Results Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Conclusions Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma. PMID:24373183

A Reading Attempt of the Urban Memory of Eskisehir Osmangazi University Meselik Campus via Cognitive Mapping

NASA Astrophysics Data System (ADS)

Alptekin, Orkun

2017-10-01

University campuses have a small city view containing basic city functions such as work, accommodation, rest and transportation. They are spaces of social life that occupy large areas, have population density and different activities, change and grow with the cities they live in, and memorize the past accumulations. In this context, it is necessary for campuses to form and protect their own memories like cities. Campus memory is the ability of individuals to keep, maintain and - when necessary- reveal the experiences, sensations, comprehensions gathered from physical environment. "Cognitive mapping" is used to reveal the physical and emotional relationship that individuals make with the city and the individual-city interaction. Cognitive maps are created graphically using verbal and geometric items on paper by remembering these coded urban images. In this study, to determine the urban images belonging to Eskisehir Osmangazi University Meselik Campus, architecture students who have a short period experience of the campus were asked to note the areas they interact with the campus on the cognitive map. Campus memory items are identified by analysing the cognitive maps of the individuals who experienced the campus. In the direction of the obtained data, the campus area was re-read with five basic elements of Lynch: paths, districts, edges, nodes, and landmarks. As a result of these analyses, it is seen that religious structure, which is a large symbolic structure, located next to the main entrance in the settlement and health care facilities defined as landmarks are located in the memory of most of the individuals. Then, paths, nodes, districts, edges and educational buildings are listed respectively in cognitive maps.

From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement.

PubMed

Zhou, Chuanen; Han, Lu; Pislariu, Catalina; Nakashima, Jin; Fu, Chunxiang; Jiang, Qingzhen; Quan, Li; Blancaflor, Elison B; Tang, Yuhong; Bouton, Joseph H; Udvardi, Michael; Xia, Guangmin; Wang, Zeng-Yu

2011-11-01

Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop.

From Model to Crop: Functional Analysis of a STAY-GREEN Gene in the Model Legume Medicago truncatula and Effective Use of the Gene for Alfalfa Improvement1[W][OA

PubMed Central

Zhou, Chuanen; Han, Lu; Pislariu, Catalina; Nakashima, Jin; Fu, Chunxiang; Jiang, Qingzhen; Quan, Li; Blancaflor, Elison B.; Tang, Yuhong; Bouton, Joseph H.; Udvardi, Michael; Xia, Guangmin; Wang, Zeng-Yu

2011-01-01

Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop. PMID:21957014

Turtle Functions Downstream of Cut in Differentially Regulating Class Specific Dendrite Morphogenesis in Drosophila

PubMed Central

Sulkowski, Mikolaj J.; Iyer, Srividya Chandramouli; Kurosawa, Mathieu S.; Iyer, Eswar Prasad R.; Cox, Daniel N.

2011-01-01

Background Dendritic morphology largely determines patterns of synaptic connectivity and electrochemical properties of a neuron. Neurons display a myriad diversity of dendritic geometries which serve as a basis for functional classification. Several types of molecules have recently been identified which regulate dendrite morphology by acting at the levels of transcriptional regulation, direct interactions with the cytoskeleton and organelles, and cell surface interactions. Although there has been substantial progress in understanding the molecular mechanisms of dendrite morphogenesis, the specification of class-specific dendritic arbors remains largely unexplained. Furthermore, the presence of numerous regulators suggests that they must work in concert. However, presently, few genetic pathways regulating dendrite development have been defined. Methodology/Principal Findings The Drosophila gene turtle belongs to an evolutionarily conserved class of immunoglobulin superfamily members found in the nervous systems of diverse organisms. We demonstrate that Turtle is differentially expressed in Drosophila da neurons. Moreover, MARCM analyses reveal Turtle acts cell autonomously to exert class specific effects on dendritic growth and/or branching in da neuron subclasses. Using transgenic overexpression of different Turtle isoforms, we find context-dependent, isoform-specific effects on mediating dendritic branching in class II, III and IV da neurons. Finally, we demonstrate via chromatin immunoprecipitation, qPCR, and immunohistochemistry analyses that Turtle expression is positively regulated by the Cut homeodomain transcription factor and via genetic interaction studies that Turtle is downstream effector of Cut-mediated regulation of da neuron dendrite morphology. Conclusions/Significance Our findings reveal that Turtle proteins differentially regulate the acquisition of class-specific dendrite morphologies. In addition, we have established a transcriptional regulatory interaction between Cut and Turtle, representing a novel pathway for mediating class specific dendrite development. PMID:21811639

Kinematic, dynamic, and thermodynamic impacts of hook-echo hydrometeors, including explorations into the utilization of polarimetric radar data

NASA Astrophysics Data System (ADS)

Askelson, Mark Anthony

Recent studies have revealed that the thermodynamic properties of the rear flank downdraft (RFD) may dictate whether or not a supercell becomes tornadic. Since hydrometeors are thought to be an important driving force for the RFD, it is postulated that they may be important to its thermodynamic properties and, possibly, to tornadogenesis. The role hook-echo hydrometeors play in driving RFDs is investigated by estimating hook-echo hydrometeor types and amounts from polarimetric radar data and by using that information to drive a relatively simple downdraft model. Soundings for the individual cases are used to initialize the downdraft model in order to replicate the environments of the storms as closely as possible. Since this effort and others like it require the quantitative utilization of radar data, issues pertaining to this are explored. In addition to analyses of coordinate transformation equations and an innovative objective analysis technique for weather radar data, the difficult problem of response functions for arbitrary weight functions and data distributions was considered. A novel approach to this problem revealed that the local response function for distance dependent weighted averaging schemes is the complex conjugate of the normalized Fourier transform of the effective weight function. This facilitates new research avenues, especially regarding analyses of irregularly spaced data. Simulations of hydrometeor driven RFDs show that hydrometeor fields inferred from radar data are able to drive significant downdrafts without the influence of vertical perturbation pressure gradients. Moreover, they reveal that above the boundary layer supercell environments are relatively resistant to downdrafts whereas within the boundary layer they are generally supportive of downdrafts. It appears that in many supercell environments relatively large hail (≥1 cm in diameter) or vertical perturbation pressure gradients may be needed to drive deep midlevel downdrafts that penetrate into the boundary layer. Because the boundary layer is an important downdraft generation/intensification layer, its thetae profile appears to be important to the surface RFD thetae deficit and, consequently, to tornadogenesis. To further examine these issues, analyses using idealized soundings that represent multiple possible RFD environments and analyses of the complete set of VORTEX cases are planned.

Rare copy number variants in patients with congenital conotruncal heart defects.

PubMed

Xie, Hongbo M; Werner, Petra; Stambolian, Dwight; Bailey-Wilson, Joan E; Hakonarson, Hakon; White, Peter S; Taylor, Deanne M; Goldmuntz, Elizabeth

2017-03-01

Previous studies using different cardiac phenotypes, technologies and designs suggest a burden of large, rare or de novo copy number variants (CNVs) in subjects with congenital heart defects. We sought to identify disease-related CNVs, candidate genes, and functional pathways in a large number of cases with conotruncal and related defects that carried no known genetic syndrome. Cases and control samples were divided into two cohorts and genotyped to assess each subject's CNV content. Analyses were performed to ascertain differences in overall CNV prevalence and to identify enrichment of specific genes and functional pathways in conotruncal cases relative to healthy controls. Only findings present in both cohorts are presented. From 973 total conotruncal cases, a burden of rare CNVs was detected in both cohorts. Candidate genes from rare CNVs found in both cohorts were identified based on their association with cardiac development or disease, and/or their reported disruption in published studies. Functional and pathway analyses revealed significant enrichment of terms involved in either heart or early embryonic development. Our study tested one of the largest cohorts specifically with cardiac conotruncal and related defects. These results confirm and extend previous findings that CNVs contribute to disease risk for congenital heart defects in general and conotruncal defects in particular. As disease heterogeneity renders identification of single recurrent genes or loci difficult, functional pathway and gene regulation network analyses appear to be more informative. Birth Defects Research 109:271-295, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).

PubMed

Foster, Charles S P; Henwood, Murray J; Ho, Simon Y W

2018-05-25

Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics. Copyright © 2018 Elsevier Inc. All rights reserved.

Structure and stability of genetic variance-covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three-spined stickleback.

PubMed

Siren, J; Ovaskainen, O; Merilä, J

2017-10-01

The genetic variance-covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G-matrices is limited for two reasons. First, phenotypes are high-dimensional, whereas traditional statistical methods are tuned to estimate and analyse low-dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high-dimensional G-matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half-sib breeding design of three-spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low-temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability-as well as the similarity among G-matrices-may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G-matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G-matrices, the BSFG method can improve predicted evolutionary responses to selection. © 2017 John Wiley & Sons Ltd.

Extensive Geographic Mosaicism in Avian Influenza Viruses from Gulls in the Northern Hemisphere

PubMed Central

Wille, Michelle; Robertson, Gregory J.; Whitney, Hugh; Bishop, Mary Anne; Runstadler, Jonathan A.; Lang, Andrew S.

2011-01-01

Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence of low frequency reassortment between these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages of the PB1 and PA segments in North America are of Eurasian origin. Large-scale analyses of intercontinental reassortment have shown that viruses isolated from Charadriiformes (gulls, terns, and shorebirds) are the major contributor of these outsider events. To clarify the role of gulls in AIV dynamics, specifically in movement of genes between geographic regions, we have sequenced six gull AIV isolated in Alaska and analyzed these along with 142 other available gull virus sequences. Basic investigations of host species and the locations and times of isolation reveal biases in the available sequence information. Despite these biases, our analyses reveal a high frequency of geographic reassortment in gull viruses isolated in America. This intercontinental gene mixing is not found in the viruses isolated from gulls in Eurasia. This study demonstrates that gulls are important as vectors for geographically reassorted viruses, particularly in America, and that more surveillance effort should be placed on this group of birds. PMID:21697989

Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish

PubMed Central

Tian, Fei; Zhao, Kai

2017-01-01

Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways. Interestingly, we identified two candidate genes contributed to normal skeletal development. The altered expression of these gene groups could potentially be associated with the developmental issues of deformity and induced larval death. Our results have three important implications: first, these findings provide strong evidences to support our hypothesis that G. przewalskii possess ability to build heat-tolerance against the controversial issue. Second, this study shows that transcriptional and post-transcriptional regulations are extensively involved in thermal acclimation. Third, the integrated mRNA and microRNA transcriptome analyses provide a large number of valuable genetic resources for future studies on environmental stress response in G. przewalskii and as a case study in Tibetan Schizothoracine fish. PMID:29045433

Siblings of Military Servicemembers: A Qualitative Exploration of Individual and Family Systems Reactions

PubMed Central

Rodriguez, Aubrey J.; Margolin, Gayla

2012-01-01

How does having a sibling in the military affect young adults? Despite increasing attention to the challenges faced by spouses and children of servicemembers, the siblings of servicemembers have been largely ignored. This qualitative investigation uses unstructured narratives to explore siblings’ perceptions of changes in their lives and changes in the family of origin associated with having a family member enlist in the United States military. Thematic analyses revealed an acute period of conflict followed by reorganization, awareness of the parents’ distress, changes in the emotional climate of the family, shifts in family roles, admiration for the military sibling, and increased meaning and purpose for the family following the servicemember’s enlistment. Computer-assisted text analyses revealed both positive and negative emotional content associated with the siblings’ military service. For professional psychologists who come into contact with siblings of servicemembers, it is important to recognize that military enlistment can have ripple effects and complicate other common individual and family stresses. More generally, it is important to provide siblings and the family of origin with information about what to expect during and after the servicemember’s enlistment, especially since these families may lack support and contact from others going through similar transitions. PMID:22815592

Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans.

PubMed

Gómez-Carballa, Alberto; Pardo-Seco, Jacobo; Amigo, Jorge; Martinón-Torres, Federico; Salas, Antonio

2015-01-01

Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000). Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran. Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

Rigid and flexible control of eating behavior in a college population.

PubMed

Timko, C Alix; Perone, Julie

2005-02-01

The objective of this study was to explore the relationship between rigid control (RC) and flexible control (FC) of eating behavior and their relationship to traditional weight, eating, and affective measurements in a large heterogeneous population. Participants were 639 underweight to obese male and female college students. Multiple regression analyses (MRA) revealed that high RC was associated with high Body Mass Index (BMI) and high Disinhibition (DIS), and high FC was associated with low BMI and low DIS in women. In men, high RC was associated with high BMI and high DIS, whereas FC was not related to BMI or DIS. Multiple regression analyses of BMI on RC and FC in the female subsample revealed that the control variables interact in such a way that the relationship between RC and BMI is stronger when FC is lower. In men, there was no interaction between these variables. This study is the first full replication of Westenhoefer's Gezugeltes Essen und Storbarkeit des Ebetaverhaltens: 2. Auflage. Gottingen: Verlag fur Psychologie () findings regarding RC and FC and their relationship to weight (BMI) and Disinhibition (DIS) in women. This is also the only second study to use the expanded, more reliable versions of the RC and FC scales. Overall, high RC in women and men was associated with greater eating and affective pathology.

Quantitative methods for analysing cumulative effects on fish migration success: a review.

PubMed

Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

2012-07-01

It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans

PubMed Central

Pardo-Seco, Jacobo; Amigo, Jorge; Martinón-Torres, Federico

2015-01-01

Background Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000). Results Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran. Conclusions Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks. PMID:25786119

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets

PubMed Central

Xia, Zhen; Clark, Peter; Huynh, Tien; Loher, Phillipe; Zhao, Yue; Chen, Huang-Wen; Rigoutsos, Isidore; Zhou, Ruhong

2012-01-01

To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 ‘hinge’ and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs. PMID:22888400

A novel mouse model of Niemann-Pick type C disease carrying a D1005G-Npc1 mutation comparable to commonly observed human mutations.

PubMed

Maue, Robert A; Burgess, Robert W; Wang, Bing; Wooley, Christine M; Seburn, Kevin L; Vanier, Marie T; Rogers, Maximillian A; Chang, Catherine C; Chang, Ta-Yuan; Harris, Brent T; Graber, David J; Penatti, Carlos A A; Porter, Donna M; Szwergold, Benjamin S; Henderson, Leslie P; Totenhagen, John W; Trouard, Theodore P; Borbon, Ivan A; Erickson, Robert P

2012-02-15

We have identified a point mutation in Npc1 that creates a novel mouse model (Npc1(nmf164)) of Niemann-Pick type C1 (NPC) disease: a single nucleotide change (A to G at cDNA bp 3163) that results in an aspartate to glycine change at position 1005 (D1005G). This change is in the cysteine-rich luminal loop of the NPC1 protein and is highly similar to commonly occurring human mutations. Genetic and molecular biological analyses, including sequencing the Npc1(spm) allele and identifying a truncating mutation, confirm that the mutation in Npc1(nmf164) mice is distinct from those in other existing mouse models of NPC disease (Npc1(nih), Npc1(spm)). Analyses of lifespan, body and spleen weight, gait and other motor activities, as well as acoustic startle responses all reveal a more slowly developing phenotype in Npc1(nmf164) mutant mice than in mice with the null mutations (Npc1(nih), Npc1(spm)). Although Npc1 mRNA levels appear relatively normal, Npc1(nmf164) brain and liver display dramatic reductions in Npc1 protein, as well as abnormal cholesterol metabolism and altered glycolipid expression. Furthermore, histological analyses of liver, spleen, hippocampus, cortex and cerebellum reveal abnormal cholesterol accumulation, glial activation and Purkinje cell loss at a slower rate than in the Npc1(nih) mouse model. Magnetic resonance imaging studies also reveal significantly less demyelination/dysmyelination than in the null alleles. Thus, although prior mouse models may correspond to the severe infantile onset forms of NPC disease, Npc1(nmf164) mice offer many advantages as a model for the late-onset, more slowly progressing forms of NPC disease that comprise the large majority of human cases.

A novel mouse model of Niemann–Pick type C disease carrying a D1005G-Npc1 mutation comparable to commonly observed human mutations

PubMed Central

Maue, Robert A.; Burgess, Robert W.; Wang, Bing; Wooley, Christine M.; Seburn, Kevin L.; Vanier, Marie T.; Rogers, Maximillian A.; Chang, Catherine C.; Chang, Ta-Yuan; Harris, Brent T.; Graber, David J.; Penatti, Carlos A.A.; Porter, Donna M.; Szwergold, Benjamin S.; Henderson, Leslie P.; Totenhagen, John W.; Trouard, Theodore P.; Borbon, Ivan A.; Erickson, Robert P.

2012-01-01

We have identified a point mutation in Npc1 that creates a novel mouse model (Npc1nmf164) of Niemann–Pick type C1 (NPC) disease: a single nucleotide change (A to G at cDNA bp 3163) that results in an aspartate to glycine change at position 1005 (D1005G). This change is in the cysteine-rich luminal loop of the NPC1 protein and is highly similar to commonly occurring human mutations. Genetic and molecular biological analyses, including sequencing the Npc1spm allele and identifying a truncating mutation, confirm that the mutation in Npc1nmf164 mice is distinct from those in other existing mouse models of NPC disease (Npc1nih, Npc1spm). Analyses of lifespan, body and spleen weight, gait and other motor activities, as well as acoustic startle responses all reveal a more slowly developing phenotype in Npc1nmf164 mutant mice than in mice with the null mutations (Npc1nih, Npc1spm). Although Npc1 mRNA levels appear relatively normal, Npc1nmf164 brain and liver display dramatic reductions in Npc1 protein, as well as abnormal cholesterol metabolism and altered glycolipid expression. Furthermore, histological analyses of liver, spleen, hippocampus, cortex and cerebellum reveal abnormal cholesterol accumulation, glial activation and Purkinje cell loss at a slower rate than in the Npc1nih mouse model. Magnetic resonance imaging studies also reveal significantly less demyelination/dysmyelination than in the null alleles. Thus, although prior mouse models may correspond to the severe infantile onset forms of NPC disease, Npc1nmf164 mice offer many advantages as a model for the late-onset, more slowly progressing forms of NPC disease that comprise the large majority of human cases. PMID:22048958

Activity-Dependence of Synaptic Vesicle Dynamics

PubMed Central

Forte, Luca A.

2017-01-01

The proper function of synapses relies on efficient recycling of synaptic vesicles. The small size of synaptic boutons has hampered efforts to define the dynamical states of vesicles during recycling. Moreover, whether vesicle motion during recycling is regulated by neural activity remains largely unknown. We combined nanoscale-resolution tracking of individual synaptic vesicles in cultured hippocampal neurons from rats of both sexes with advanced motion analyses to demonstrate that the majority of recently endocytosed vesicles undergo sequences of transient dynamical states including epochs of directed, diffusional, and stalled motion. We observed that vesicle motion is modulated in an activity-dependent manner, with dynamical changes apparent in ∼20% of observed boutons. Within this subpopulation of boutons, 35% of observed vesicles exhibited acceleration and 65% exhibited deceleration, accompanied by corresponding changes in directed motion. Individual vesicles observed in the remaining ∼80% of boutons did not exhibit apparent dynamical changes in response to stimulation. More quantitative transient motion analyses revealed that the overall reduction of vesicle mobility, and specifically of the directed motion component, is the predominant activity-evoked change across the entire bouton population. Activity-dependent modulation of vesicle mobility may represent an important mechanism controlling vesicle availability and neurotransmitter release. SIGNIFICANCE STATEMENT Mechanisms governing synaptic vesicle dynamics during recycling remain poorly understood. Using nanoscale resolution tracking of individual synaptic vesicles in hippocampal synapses and advanced motion analysis tools we demonstrate that synaptic vesicles undergo complex sets of dynamical states that include epochs of directed, diffusive, and stalled motion. Most importantly, our analyses revealed that vesicle motion is modulated in an activity-dependent manner apparent as the reduction in overall vesicle mobility in response to stimulation. These results define the vesicle dynamical states during recycling and reveal their activity-dependent modulation. Our study thus provides fundamental new insights into the principles governing synaptic function. PMID:28954868

Pacific Ocean-wide profile of CYP1A1 expression, stable carbon and nitrogen isotope ratios, and organic contaminant burden in sperm whale skin biopsies.

PubMed

Godard-Codding, Céline A J; Clark, Rebecca; Fossi, Maria Cristina; Marsili, Letizia; Maltese, Silvia; West, Adam G; Valenzuela, Luciano; Rowntree, Victoria; Polyak, Ildiko; Cannon, John C; Pinkerton, Kim; Rubio-Cisneros, Nadia; Mesnick, Sarah L; Cox, Stephen B; Kerr, Iain; Payne, Roger; Stegeman, John J

2011-03-01

Ocean pollution affects marine organisms and ecosystems as well as humans. The International Oceanographic Commission recommends ocean health monitoring programs to investigate the presence of marine contaminants and the health of threatened species and the use of multiple and early-warning biomarker approaches. We explored the hypothesis that biomarker and contaminant analyses in skin biopsies of the threatened sperm whale (Physeter macrocephalus) could reveal geographical trends in exposure on an oceanwide scale. We analyzed cytochrome P450 1A1 (CYP1A1) expression (by immunohistochemistry), stable nitrogen and carbon isotope ratios (as general indicators of trophic position and latitude, respectively), and contaminant burdens in skin biopsies to explore regional trends in the Pacific Ocean. Biomarker analyses revealed significant regional differences within the Pacific Ocean. CYP1A1 expression was highest in whales from the Galapagos, a United Nations Educational, Scientific, and Cultural Organization World Heritage marine reserve, and was lowest in the sampling sites farthest away from continents. We examined the possible influence of the whales' sex, diet, or range and other parameters on regional variation in CYP1A1 expression, but data were inconclusive. In general, CYP1A1 expression was not significantly correlated with contaminant burdens in blubber. However, small sample sizes precluded detailed chemical analyses, and power to detect significant associations was limited. Our large-scale monitoring study was successful at identifying regional differences in CYP1A1 expression, providing a baseline for this known biomarker of exposure to aryl hydrocarbon receptor agonists. However, we could not identify factors that explained this variation. Future oceanwide CYP1A1 expression profiles in cetacean skin biopsies are warranted and could reveal whether globally distributed chemicals occur at biochemically relevant concentrations on a global basis, which may provide a measure of ocean integrity.

Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago.

PubMed

Andrews, Kimberly R; Moriwake, Virginia N; Wilcox, Christie; Grau, E Gordon; Kelley, Christopher; Pyle, Richard L; Bowen, Brian W

2014-01-01

The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. "marshi" (formerly E. carbunculus; N = 770) with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans.

Phylogeographic Analyses of Submesophotic Snappers Etelis coruscans and Etelis “marshi” (Family Lutjanidae) Reveal Concordant Genetic Structure across the Hawaiian Archipelago

PubMed Central

Andrews, Kimberly R.; Moriwake, Virginia N.; Wilcox, Christie; Grau, E. Gordon; Kelley, Christopher; Pyle, Richard L.; Bowen, Brian W.

2014-01-01

The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200–360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. “marshi” (formerly E. carbunculus; N = 770) with 436–490 bp of mtDNA cytochrome b and 10–11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans. PMID:24722193

Cryptic Species in Tropic Sands - Interactive 3D Anatomy, Molecular Phylogeny and Evolution of Meiofaunal Pseudunelidae (Gastropoda, Acochlidia)

PubMed Central

Neusser, Timea P.; Jörger, Katharina M.; Schrödl, Michael

2011-01-01

Background Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics. Results The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution. Conclusions Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are recommended for all taxonomic approaches and biodiversity surveys on soft-bodied and small-sized invertebrates. With increasing taxon sampling and details studied, the evolution of acochlidian panpulmonates is even more complex than expected. PMID:21912592

Allelic differences in a vacuolar invertase affect Arabidopsis growth at early plant development.

PubMed

Leskow, Carla Coluccio; Kamenetzky, Laura; Dominguez, Pia Guadalupe; Díaz Zirpolo, José Antonio; Obata, Toshihiro; Costa, Hernán; Martí, Marcelo; Taboga, Oscar; Keurentjes, Joost; Sulpice, Ronan; Ishihara, Hirofumi; Stitt, Mark; Fernie, Alisdair Robert; Carrari, Fernando

2016-07-01

Improving carbon fixation in order to enhance crop yield is a major goal in plant sciences. By quantitative trait locus (QTL) mapping, it has been demonstrated that a vacuolar invertase (vac-Inv) plays a key role in determining the radical length in Arabidopsis. In this model, variation in vac-Inv activity was detected in a near isogenic line (NIL) population derived from a cross between two divergent accessions: Landsberg erecta (Ler) and Cape Verde Island (CVI), with the CVI allele conferring both higher Inv activity and longer radicles. The aim of the current work is to understand the mechanism(s) underlying this QTL by analyzing structural and functional differences of vac-Inv from both accessions. Relative transcript abundance analyzed by quantitative real-time PCR (qRT-PCR) showed similar expression patterns in both accessions; however, DNA sequence analyses revealed several polymorphisms that lead to changes in the corresponding protein sequence. Moreover, activity assays revealed higher vac-Inv activity in genotypes carrying the CVI allele than in those carrying the Ler allele. Analyses of purified recombinant proteins showed a similar K m for both alleles and a slightly higher V max for that of Ler. Treatment of plant extracts with foaming to release possible interacting Inv inhibitory protein(s) led to a large increase in activity for the Ler allele, but no changes for genotypes carrying the CVI allele. qRT-PCR analyses of two vac-Inv inhibitors in seedlings from parental and NIL genotypes revealed different expression patterns. Taken together, these results demonstrate that the vac-Inv QTL affects root biomass accumulation and also carbon partitioning through a differential regulation of vac-Inv inhibitors at the mRNA level. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

PubMed Central

Milrot, Elad; Mutsafi, Yael; Ben-Dor, Shifra; Levin, Yishai; Savidor, Alon; Kartvelishvily, Elena

2016-01-01

ABSTRACT The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed “viral factories,” where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as “production lines” of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses. IMPORTANCE Large dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed “viral factories,” are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles. PMID:27581975

Pacific Ocean–Wide Profile of CYP1A1 Expression, Stable Carbon and Nitrogen Isotope Ratios, and Organic Contaminant Burden in Sperm Whale Skin Biopsies

PubMed Central

Godard-Codding, Céline A.J.; Clark, Rebecca; Fossi, Maria Cristina; Marsili, Letizia; Maltese, Silvia; West, Adam G.; Valenzuela, Luciano; Rowntree, Victoria; Polyak, Ildiko; Cannon, John C.; Pinkerton, Kim; Rubio-Cisneros, Nadia; Mesnick, Sarah L.; Cox, Stephen B.; Kerr, Iain; Payne, Roger; Stegeman, John J.

2011-01-01

Background Ocean pollution affects marine organisms and ecosystems as well as humans. The International Oceanographic Commission recommends ocean health monitoring programs to investigate the presence of marine contaminants and the health of threatened species and the use of multiple and early-warning biomarker approaches. Objective We explored the hypothesis that biomarker and contaminant analyses in skin biopsies of the threatened sperm whale (Physeter macrocephalus) could reveal geographical trends in exposure on an oceanwide scale. Methods We analyzed cytochrome P450 1A1 (CYP1A1) expression (by immunohistochemistry), stable nitrogen and carbon isotope ratios (as general indicators of trophic position and latitude, respectively), and contaminant burdens in skin biopsies to explore regional trends in the Pacific Ocean. Results Biomarker analyses revealed significant regional differences within the Pacific Ocean. CYP1A1 expression was highest in whales from the Galapagos, a United Nations Educational, Scientific, and Cultural Organization World Heritage marine reserve, and was lowest in the sampling sites farthest away from continents. We examined the possible influence of the whales’ sex, diet, or range and other parameters on regional variation in CYP1A1 expression, but data were inconclusive. In general, CYP1A1 expression was not significantly correlated with contaminant burdens in blubber. However, small sample sizes precluded detailed chemical analyses, and power to detect significant associations was limited. Conclusions Our large-scale monitoring study was successful at identifying regional differences in CYP1A1 expression, providing a baseline for this known biomarker of exposure to aryl hydrocarbon receptor agonists. However, we could not identify factors that explained this variation. Future oceanwide CYP1A1 expression profiles in cetacean skin biopsies are warranted and could reveal whether globally distributed chemicals occur at biochemically relevant concentrations on a global basis, which may provide a measure of ocean integrity. PMID:21134820

Psychosocial factors at work and self reported health: comparative results of cross sectional and prospective analyses of the French GAZEL cohort

PubMed Central

Niedhammer, I; Chea, M

2003-01-01

Background: Psychosocial factors at work have been found to be significant contributors to health, especially cardiovascular health. Aims: To explore the relation between psychosocial factors at work and self reported health, using cross sectional and prospective analyses for a large occupational cohort of men and women. Methods: Psychosocial factors at work were evaluated using the Karasek questionnaire, designed to measure psychological demands, decision latitude, social support, and physical demands. Self reported health was used as health outcome. Covariates included chronic diseases, and sociodemographic, occupational, and behavioural factors. The cross sectional and prospective analyses concerned respectively 11 447 and 7664 workers. Men and women were analysed separately. Results: Cross sectional analysis revealed significant associations between psychological demands, decision latitude, social support, and physical demands, and self reported health for both men and women. Prospective analysis showed that high psychological demands for both genders, low decision authority for men, and low social support and high physical demands for women were predictive of poor self reported health. These results were independent of potential confounding variables. Conclusions: Results highlight the predictive effects of psychosocial factors at work on self reported health in a one year follow up study. They also underline the need for longitudinal study design and separate analyses for men and women in the field of psychosocial factors at work. PMID:12819285

Patterns of medicinal plant use: an examination of the Ecuadorian Shuar medicinal flora using contingency table and binomial analyses.

PubMed

Bennett, Bradley C; Husby, Chad E

2008-03-28

Botanical pharmacopoeias are non-random subsets of floras, with some taxonomic groups over- or under-represented. Moerman [Moerman, D.E., 1979. Symbols and selectivity: a statistical analysis of Native American medical ethnobotany, Journal of Ethnopharmacology 1, 111-119] introduced linear regression/residual analysis to examine these patterns. However, regression, the commonly-employed analysis, suffers from several statistical flaws. We use contingency table and binomial analyses to examine patterns of Shuar medicinal plant use (from Amazonian Ecuador). We first analyzed the Shuar data using Moerman's approach, modified to better meet requirements of linear regression analysis. Second, we assessed the exact randomization contingency table test for goodness of fit. Third, we developed a binomial model to test for non-random selection of plants in individual families. Modified regression models (which accommodated assumptions of linear regression) reduced R(2) to from 0.59 to 0.38, but did not eliminate all problems associated with regression analyses. Contingency table analyses revealed that the entire flora departs from the null model of equal proportions of medicinal plants in all families. In the binomial analysis, only 10 angiosperm families (of 115) differed significantly from the null model. These 10 families are largely responsible for patterns seen at higher taxonomic levels. Contingency table and binomial analyses offer an easy and statistically valid alternative to the regression approach.

Phylogeography of the large white-bellied rat Niviventer excelsior suggests the influence of Pleistocene glaciations in the Hengduan mountains.

PubMed

Chen, Weicai; Liu, Shaoying; Liu, Yang; Hao, Haibang; Zeng, Bo; Chen, Shunde; Peng, Hongyuan; Yue, Bisong; Zhang, Xiuyue

2010-06-01

The Hengduan Mountains, situated in the southeastern Tibetan Plateau, have undergone dramatic geological and climatic changes over the Pleistocene epoch. Several studies have revealed that the mountains served as a refugium during the ice age. The large white-bellied rat Niviventer excelsior is a rodent endemic to the Hengduan Mountains, which makes it an appropriate species for investigating the influence of glacial movements on the genetic structure of mammals. In this study, we sequenced the partial mitochondrial DNA control region from 72 N. excelsior specimens collected from 20 localities. The results revealed very high levels of haplotype diversity (h = 0.947) and nucleotide diversity (pi = 0.101) in this species. No common haplotype was found to be shared in samples from all geographic regions. Demographic analyses suggested that N. excelsior populations had not been subject to either expansion or bottleneck. The phylogenetic relationships among the haplotypes have no correlation with their geographical origins, while topology revealed two major clades. We speculate that the populations of N. excelsior may have been restricted to two separate refugia during the Last Glacial Maximum (0.60-0.17 Mya), with one west and one east of the Shaluli Mountains. Between the two major refugia, there existed a more widely distributed network subrefugia, which conserved genetic variations in N. excelsior. These results indicated that complex topographic configuration in the Hengduan Mountains provided a network of refugia to maintain the high level of genetic diversity in Pleistocene glaciations.

Novel Autism Subtype-Dependent Genetic Variants Are Revealed by Quantitative Trait and Subphenotype Association Analyses of Published GWAS Data

PubMed Central

Hu, Valerie W.; Addington, Anjene; Hyman, Alexander

2011-01-01

The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders. PMID:21556359

Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

PubMed

Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

2016-04-01

Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Diagnosing AIRS Sampling with CloudSat Cloud Classes

NASA Technical Reports Server (NTRS)

Fetzer, Eric; Yue, Qing; Guillaume, Alexandre; Kahn, Brian

2011-01-01

AIRS yield and sampling vary with cloud state. Careful utilization of collocated multiple satellite sensors is necessary. Profile differences between AIRS and ECMWF model analyses indicate that AIRS has high sampling and excellent accuracy for certain meteorological conditions. Cloud-dependent sampling biases may have large impact on AIRS L2 and L3 data in climate research. MBL clouds / lower tropospheric stability relationship is one example. AIRS and CloudSat reveal a reasonable climatology in the MBL cloud regime despite limited sampling in stratocumulus. Thermodynamic parameters such as EIS derived from AIRS data map these cloud conditions successfully. We are working on characterizing AIRS scenes with mixed cloud types.

RNA antitoxins.

PubMed

Gerdes, Kenn; Wagner, E Gerhart H

2007-04-01

Recent genomic analyses revealed a surprisingly large number of toxin-antitoxin loci in free-living prokaryotes. The antitoxins are proteins or antisense RNAs that counteract the toxins. Two antisense RNA-regulated toxin-antitoxin gene families, hok/sok and ldr, are unrelated sequence-wise but have strikingly similar properties at the level of gene and RNA organization. Recently, two SOS-induced toxins were found to be regulated by RNA antitoxins. One such toxin, SymE, exhibits similarity with MazE antitoxin and, surprisingly, inhibits translation. Thus, it is possible that an ancestral antitoxin gene evolved into the present toxin gene (symE) whose translation is repressed by an RNA antitoxin (SymR).

Affective outcomes of virtual reality exposure therapy for anxiety and specific phobias: a meta-analysis.

PubMed

Parsons, Thomas D; Rizzo, Albert A

2008-09-01

Virtual reality exposure therapy (VRET) is an increasingly common treatment for anxiety and specific phobias. Lacking is a quantitative meta-analysis that enhances understanding of the variability and clinical significance of anxiety reduction outcomes after VRET. Searches of electronic databases yielded 52 studies, and of these, 21 studies (300 subjects) met inclusion criteria. Although meta-analysis revealed large declines in anxiety symptoms following VRET, moderator analyses were limited due to inconsistent reporting in the VRET literature. This highlights the need for future research studies that report uniform and detailed information regarding presence, immersion, anxiety and/or phobia duration, and demographics.

The influence of vaccine-critical websites on perceiving vaccination risks.

PubMed

Betsch, Cornelia; Renkewitz, Frank; Betsch, Tilmann; Ulshöfer, Corina

2010-04-01

This large-scale Internet-experiment tests whether vaccine-critical pages raise perceptions of the riskiness of vaccinations and alter vaccination intentions. We manipulated the information environment (vaccine-critical website, control, both) and the focus of search (on vaccination risks, omission risks, no focus). Our analyses reveal that accessing vaccine-critical websites for five to 10 minutes increases the perception of risk of vaccinating and decreases the perception of risk of omitting vaccinations as well as the intentions to vaccinate. In line with the 'risk-as-feelings' approach, the affect elicited by the vaccine-critical websites was positively related to changes in risk perception.

Development of a local size hierarchy causes regular spacing of trees in an even-aged Abies forest: analyses using spatial autocorrelation and the mark correlation function.

PubMed

Suzuki, Satoshi N; Kachi, Naoki; Suzuki, Jun-Ichirou

2008-09-01

During the development of an even-aged plant population, the spatial distribution of individuals often changes from a clumped pattern to a random or regular one. The development of local size hierarchies in an Abies forest was analysed for a period of 47 years following a large disturbance in 1959. In 1980 all trees in an 8 x 8 m plot were mapped and their height growth after the disturbance was estimated. Their mortality and growth were then recorded at 1- to 4-year intervals between 1980 and 2006. Spatial distribution patterns of trees were analysed by the pair correlation function. Spatial correlations between tree heights were analysed with a spatial autocorrelation function and the mark correlation function. The mark correlation function was able to detect a local size hierarchy that could not be detected by the spatial autocorrelation function alone. The small-scale spatial distribution pattern of trees changed from clumped to slightly regular during the 47 years. Mortality occurred in a density-dependent manner, which resulted in regular spacing between trees after 1980. The spatial autocorrelation and mark correlation functions revealed the existence of tree patches consisting of large trees at the initial stage. Development of a local size hierarchy was detected within the first decade after the disturbance, although the spatial autocorrelation was not negative. Local size hierarchies that developed persisted until 2006, and the spatial autocorrelation became negative at later stages (after about 40 years). This is the first study to detect local size hierarchies as a prelude to regular spacing using the mark correlation function. The results confirm that use of the mark correlation function together with the spatial autocorrelation function is an effective tool to analyse the development of a local size hierarchy of trees in a forest.

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

PubMed Central

Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

2017-01-01

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar.

PubMed

Summerer, Monika; Horst, Jürgen; Erhart, Gertraud; Weißensteiner, Hansi; Schönherr, Sebastian; Pacher, Dominic; Forer, Lukas; Horst, David; Manhart, Angelika; Horst, Basil; Sanguansermsri, Torpong; Kloss-Brandstätter, Anita

2014-01-28

Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. Our aim was to search for genetic footprints of Myanmar's geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia.

Observations and controls on the occurrence of inherited zircon in Concord-type granitoids, New Hampshire

USGS Publications Warehouse

Harrison, T.M.; Aleinikoff, J.N.; Compston, W.

1987-01-01

U-Pb analyses of zircons separated from two Concord-type plutons near Sunapee and Dixville Notch, New Hampshire, reveal differences in the pattern and magnitude of zircon inheritance which are related to differences in melt chemistry. The Sunapee pluton contains only slightly more Zr than required to saturate the melt at the peak temperature of 700 ?? 30??C. Traces of inherited zircon in this separate are inferred to be present as small, largely resorbed grains. In contrast, the Long Mountain pluton, near Dixville Notch, contains about 240% more Zr than required to saturate the melt. Thus, more than half of the Zr existed as stable, inherited zircon crystals during the partial fusion event, consistent with the observation of substantial inheritance in all grain size fractions. Ion probe intra-grain analyses of zircon from the Long Mountain pluton indicate a complex pattern of inheritance with contributions from at least two Proterozoic terrenes and caution against simple interpretations of upper and lower intercepts of chords containing an inherited component. Ion probe analyses of zircons from the Sunapee pluton reveal clear evidence of U loss which results in incorrect apparent conventional U-Pb ages. Ages of crystallization for the Long Mountain and Sunapee pluton are ~350 and 354 ?? 5 Ma, respectively. A Sm/Nd measurement for the Long Mountain pluton yields a depleted mantle model age of 1.5 Ga, consistent with the observed inheritance pattern. In contrast, a Sm/Nd model age for the Sunapee pluton is improbably old due to minor monazite fractionation. ?? 1987.

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

PubMed

Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

2017-07-18

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk.

PubMed

Lemos, Mark; Xiao, Yanmei; Bjornson, Marta; Wang, Jin-Zheng; Hicks, Derrick; Souza, Amancio de; Wang, Chang-Quan; Yang, Panyu; Ma, Shisong; Dinesh-Kumar, Savithramma; Dehesh, Katayoon

2016-03-01

The exquisite harmony between hormones and their corresponding signaling pathways is central to prioritizing plant responses to simultaneous and/or successive environmental trepidations. The crosstalk between jasmonic acid (JA) and salicylic acid (SA) is an established effective mechanism that optimizes and tailors plant adaptive responses. However, the underlying regulatory modules of this crosstalk are largely unknown. Global transcriptomic analyses of mutant plants (ceh1) with elevated levels of the stress-induced plastidial retrograde signaling metabolite 2-C-methyl-D-erythritol cyclopyrophosphate (MEcPP) revealed robustly induced JA marker genes, expected to be suppressed by the presence of constitutively high SA levels in the mutant background. Analyses of a range of genotypes with varying SA and MEcPP levels established the selective role of MEcPP-mediated signal(s) in induction of JA-responsive genes in the presence of elevated SA. Metabolic profiling revealed the presence of high levels of the JA precursor 12-oxo-phytodienoic acid (OPDA), but near wild type levels of JA in the ceh1 mutant plants. Analyses of coronatine-insensitive 1 (coi1)/ceh1 double mutant plants confirmed that the MEcPP-mediated induction is JA receptor COI1 dependent, potentially through elevated OPDA. These findings identify MEcPP as a previously unrecognized central regulatory module that induces JA-responsive genes in the presence of high SA, thereby staging a multifaceted plant response within the environmental context. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Pollination syndromes in African Marantaceae

PubMed Central

Ley, Alexandra C.; Claßen-Bockhoff, Regine

2009-01-01

Background and Aims The Marantaceae (550 spp.) is the most derived family in the order Zingiberales and exhibits a complex explosive pollination mechanism. To understand the evolutionary significance of this unique process of pollen transfer, comparative morphological and ecological studies were conducted in Gabon. Methods During a total stay of 11 months, 31 species of Marantaceae were investigated at different sites in Gabon. The study included analyses of floral diversity, observations on the pollinator spectrum as well as ecological measurements (e.g. nectar sugar concentration and volume). Key Results Analyses reveal five flower types based on flower size and pigmentation, spatial arrangement of the floral tube and presence/absence of nectar guides and conspicuous outer staminodes. Each type is associated with a specific functional pollinator group leading to the description of distinct pollination syndromes. The ‘small (horizontal)’ flowers are predominantly pollinated by small bees (Thrinchostoma spp., Allodapula ornaticeps), the ‘large (horizontal)’ and ‘medium-sized (horizontal)’ flowers by medium-sized bees (Amegilla vivida, Thrinchostoma bicometes), the ‘locked (horizontal)’ flowers by large bees (Xylocopa nigrita, X. varipes) and the ‘(large) vertical’ flowers by sunbirds. Conclusions The longevity of Marantaceae individuals and the omnipresence of their pollinators allowed the specialization to a given functional pollinator group. Intermediate ecological values, however, make occasional pollinator overlaps possible, indicating potential pathways of pollinator shifts. Similar radiation tendencies observed on other continents hint at similar selective pressures and evolutionary constraints. PMID:19443460

Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy.

PubMed

Sheng, Xihui; Wang, Ligang; Ni, Hemin; Wang, Lixian; Qi, Xiaolong; Xing, Shuhan; Guo, Yong

2016-01-01

The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of longissimus dorsi muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.

Converging flow and anisotropy cause large-scale folding in Greenland's ice sheet.

PubMed

Bons, Paul D; Jansen, Daniela; Mundel, Felicitas; Bauer, Catherine C; Binder, Tobias; Eisen, Olaf; Jessell, Mark W; Llorens, Maria-Gema; Steinbach, Florian; Steinhage, Daniel; Weikusat, Ilka

2016-04-29

The increasing catalogue of high-quality ice-penetrating radar data provides a unique insight in the internal layering architecture of the Greenland ice sheet. The stratigraphy, an indicator of past deformation, highlights irregularities in ice flow and reveals large perturbations without obvious links to bedrock shape. In this work, to establish a new conceptual model for the formation process, we analysed the radar data at the onset of the Petermann Glacier, North Greenland, and created a three-dimensional model of several distinct stratigraphic layers. We demonstrate that the dominant structures are cylindrical folds sub-parallel to the ice flow. By numerical modelling, we show that these folds can be formed by lateral compression of mechanically anisotropic ice, while a general viscosity contrast between layers would not lead to folding for the same boundary conditions. We conclude that the folds primarily form by converging flow as the mechanically anisotropic ice is channelled towards the glacier.

Converging flow and anisotropy cause large-scale folding in Greenland's ice sheet

NASA Astrophysics Data System (ADS)

Bons, Paul D.; Jansen, Daniela; Mundel, Felicitas; Bauer, Catherine C.; Binder, Tobias; Eisen, Olaf; Jessell, Mark W.; Llorens, Maria-Gema; Steinbach, Florian; Steinhage, Daniel; Weikusat, Ilka

2016-04-01

The increasing catalogue of high-quality ice-penetrating radar data provides a unique insight in the internal layering architecture of the Greenland ice sheet. The stratigraphy, an indicator of past deformation, highlights irregularities in ice flow and reveals large perturbations without obvious links to bedrock shape. In this work, to establish a new conceptual model for the formation process, we analysed the radar data at the onset of the Petermann Glacier, North Greenland, and created a three-dimensional model of several distinct stratigraphic layers. We demonstrate that the dominant structures are cylindrical folds sub-parallel to the ice flow. By numerical modelling, we show that these folds can be formed by lateral compression of mechanically anisotropic ice, while a general viscosity contrast between layers would not lead to folding for the same boundary conditions. We conclude that the folds primarily form by converging flow as the mechanically anisotropic ice is channelled towards the glacier.

Eavesdropping on the Arctic: Automated bioacoustics reveal dynamics in songbird breeding phenology.

PubMed

Oliver, Ruth Y; Ellis, Daniel P W; Chmura, Helen E; Krause, Jesse S; Pérez, Jonathan H; Sweet, Shannan K; Gough, Laura; Wingfield, John C; Boelman, Natalie T

2018-06-01

Bioacoustic networks could vastly expand the coverage of wildlife monitoring to complement satellite observations of climate and vegetation. This approach would enable global-scale understanding of how climate change influences phenomena such as migratory timing of avian species. The enormous data sets that autonomous recorders typically generate demand automated analyses that remain largely undeveloped. We devised automated signal processing and machine learning approaches to estimate dates on which songbird communities arrived at arctic breeding grounds. Acoustically estimated dates agreed well with those determined via traditional surveys and were strongly related to the landscape's snow-free dates. We found that environmental conditions heavily influenced daily variation in songbird vocal activity, especially before egg laying. Our novel approaches demonstrate that variation in avian migratory arrival can be detected autonomously. Large-scale deployment of this innovation in wildlife monitoring would enable the coverage necessary to assess and forecast changes in bird migration in the face of climate change.

Decadal and annual changes in biogenic opal and carbonate fluxes to the deep Sargasso Sea

USGS Publications Warehouse

Deuser, W.G.; Jickells, T.D.; Commeau, Judith A.

1995-01-01

Analyses of samples from a 14-year series of sediment-trap deployments in the deep Sargasso Sea reveal a significant trend in the ratio of the sinking fluxes of biogenic calcium carbonate and silica. Although there are pronounced seasonal cycles for both flux components, the overall opal/CaCO3 ratio changed by 50% from 1978 to 1991 (largely due to a decrease of opal flux), while total flux had no significant trend. These results suggest that plankton communities respond rapidly to subtle climate change, such as is evident in regional variations of wind speed, precipitation, wintertime ventilation and midwater temperatures. If the trends we observe in the makeup of sinking particulate matter occur on a large scale, they may in turn modify climate by modulating ocean-atmosphere CO2 exchange and albedo over the ocean.

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

An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens

PubMed Central

Rensing, Stefan A; Ick, Julia; Fawcett, Jeffrey A; Lang, Daniel; Zimmer, Andreas; Van de Peer, Yves; Reski, Ralf

2007-01-01

Background: Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past. Results: In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss Physcomitrella patens is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in P. patens reveal different biases of gene retention compared with seed plants. Conclusion: Metabolic genes seem to have been retained in excess following the genome duplication in P. patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants. PMID:17683536

Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices

PubMed Central

Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

2016-01-01

How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women’s shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context. PMID:27144595

The accident analysis of mobile mine machinery in Indian opencast coal mines.

PubMed

Kumar, R; Ghosh, A K

2014-01-01

This paper presents the analysis of large mining machinery related accidents in Indian opencast coal mines. The trends of coal production, share of mining methods in production, machinery deployment in open cast mines, size and population of machinery, accidents due to machinery, types and causes of accidents have been analysed from the year 1995 to 2008. The scrutiny of accidents during this period reveals that most of the responsible factors are machine reversal, haul road design, human fault, operator's fault, machine fault, visibility and dump design. Considering the types of machines, namely, dumpers, excavators, dozers and loaders together the maximum number of fatal accidents has been caused by operator's faults and human faults jointly during the period from 1995 to 2008. The novel finding of this analysis is that large machines with state-of-the-art safety system did not reduce the fatal accidents in Indian opencast coal mines.

Strigeid parasites of Circus buffoni from Argentina, with the description of a new species of Parastrigea Szidat, 1928.

PubMed

Drago, Fabiana B; Núñez, Verónica; Lunaschi, Lía I

2018-03-01

Studying the Helminthological Collection of Museo de La Plata (MLP-He), several specimens of digeneans, recovered parasitizing a long-winged harrier, Circus buffoni (Accipitridae) from Buenos Aires Argentina, were analysed. The morphological and morphometric analysis of these specimens revealed the presence of two strigeid species, one of them new for science. Parastrigea buffoni n. sp. is characterised by a forebody differentiated in a retractile cephalic region with a large opening and a balloon-shaped collar region or collerette, suckers located in cephalic region, holdfast organ with well development dorsal and ventral lips that can emerge through opening, a claviform hindbody, a large copulatory bursa with muscular ring (Ringnapf) and a genital cone well delimited, crossed by a sinuous hermaphroditic duct with internal rugae. The euryxenous parasite, Strigea falconis brasiliana, is briefly described, parasitizing a new host. This is the first record of helminths parasitizing long-winged harrier.

Evidence for accreted component in the Galactic discs

NASA Astrophysics Data System (ADS)

Xing, Q. F.; Zhao, G.

2018-06-01

We analyse the distribution of [Mg/Fe] abundance in the Galactic discs with F- and G-type dwarf stars selected from the Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST) archive. The sample stars are assigned into different stellar populations by using kinematic criteria. Our analysis reveals the chemical inhomogeneities in the Galactic thick disc. A few of metal-poor stars in the thick disc exhibit relatively low [Mg/Fe] abundance in respect to the standard thick-disc sample. The orbital eccentricities and maximum Galactocentric radii of low-α metal-poor stars are apparently greater than that of high-α thick-disc stars. The orbital parameters and chemical components of low-α stars in the thick disc suggest that they may have been formed in regions with low star formation rate that were located at large distances from the Galactic centre, such as infalling dwarf spheroidal galaxies.

Systematics of the Platyrrhinus helleri species complex (Chiroptera: Phyllostomidae), with descriptions of two new species

USGS Publications Warehouse

Velazco, Paúl M.; Gardner, Alfred L.; Patterson, Bruce D.

2010-01-01

Platyrrhinus is a diverse genus of small to large phyllostomid bats characterized by a comparatively narrow uropatagium thickly fringed with hair, a white dorsal stripe, comparatively large inner upper incisors that are convergent at the tips, and three upper and three lower molars. Eighteen species are currently recognized, the majority occurring in the Andes. Molecular, morphological, and morphometric analyses of specimens formerly identified as Platyrrhinus helleri support recognition of Platyrrhinus incarum as a separate species and reveal the presence of two species from western and northern South America that we describe herein as new (Platyrrhinus angustirostris sp. nov. from eastern Colombia and Ecuador, north-eastern Peru, and Venezuela and Platyrrhinus fusciventris sp. nov. from Guyana, Suriname, French Guiana, Trinidad and Tobago, northern Brazil, eastern Ecuador, and southern Venezuela). These two new species are sister taxa and, in turn, sister to Platyrrhinus incarum.

Nuclear and mitochondrial markers reveal evidence for genetically segregated cryptic speciation in giant Pacific octopuses from Prince William Sound, Alaska

USGS Publications Warehouse

Toussaint, Rebecca K.; Scheel, David; Sage, G.K.; Talbot, S.L.

2012-01-01

Multiple species of large octopus are known from the north Pacific waters around Japan, however only one large species is known in the Gulf of Alaska (the giant Pacific octopus, Enteroctopus dofleini). Current taxonomy of E. dofleini is based on geographic and morphological characteristics, although with advances in genetic technology that is changing. Here, we used two mitochondrial genes (cytochrome b and cytochrome oxidase I), three nuclear genes (rhodopsin, octopine dehydrogenase, and paired-box 6), and 18 microsatellite loci for phylogeographic and phylogenetic analyses of octopuses collected from across southcentral and the eastern Aleutian Islands (Dutch Harbor), Alaska. Our results suggest the presence of a cryptic Enteroctopus species that is allied to, but distinguished from E. dofleini in Prince William Sound, Alaska. Existence of an undescribed and previously unrecognized taxon raises important questions about the taxonomy of octopus in southcentral Alaska waters.

Statistical properties of edge plasma turbulence in the Large Helical Device

NASA Astrophysics Data System (ADS)

Dewhurst, J. M.; Hnat, B.; Ohno, N.; Dendy, R. O.; Masuzaki, S.; Morisaki, T.; Komori, A.

2008-09-01

Ion saturation current (Isat) measurements made by three tips of a Langmuir probe array in the Large Helical Device are analysed for two plasma discharges. Absolute moment analysis is used to quantify properties on different temporal scales of the measured signals, which are bursty and intermittent. Strong coherent modes in some datasets are found to distort this analysis and are consequently removed from the time series by applying bandstop filters. Absolute moment analysis of the filtered data reveals two regions of power-law scaling, with the temporal scale τ ≈ 40 µs separating the two regimes. A comparison is made with similar results from the Mega-Amp Spherical Tokamak. The probability density function is studied and a monotonic relationship between connection length and skewness is found. Conditional averaging is used to characterize the average temporal shape of the largest intermittent bursts.

Eye-Tracking Technology and the Dynamics of Natural Gaze Behavior in Sports: A Systematic Review of 40 Years of Research.

PubMed

Kredel, Ralf; Vater, Christian; Klostermann, André; Hossner, Ernst-Joachim

2017-01-01

Reviewing 60 studies on natural gaze behavior in sports, it becomes clear that, over the last 40 years, the use of eye-tracking devices has considerably increased. Specifically, this review reveals the large variance of methods applied, analyses performed, and measures derived within the field. The results of sub-sample analyses suggest that sports-related eye-tracking research strives, on the one hand, for ecologically valid test settings (i.e., viewing conditions and response modes), while on the other, for experimental control along with high measurement accuracy (i.e., controlled test conditions with high-frequency eye-trackers linked to algorithmic analyses). To meet both demands, some promising compromises of methodological solutions have been proposed-in particular, the integration of robust mobile eye-trackers in motion-capture systems. However, as the fundamental trade-off between laboratory and field research cannot be solved by technological means, researchers need to carefully weigh the arguments for one or the other approach by accounting for the respective consequences. Nevertheless, for future research on dynamic gaze behavior in sports, further development of the current mobile eye-tracking methodology seems highly advisable to allow for the acquisition and algorithmic analyses of larger amounts of gaze-data and further, to increase the explanatory power of the derived results.

A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station (Utah)

NASA Astrophysics Data System (ADS)

Direito, Susana O. L.; Ehrenfreund, Pascale; Marees, Andries; Staats, Martijn; Foing, Bernard; Röling, Wilfred F. M.

2011-07-01

Humankind's innate curiosity makes us wonder whether life is or was present on other planetary bodies such as Mars. The EuroGeoMars 2009 campaign was organized at the Mars Desert Research Station (MDRS) to perform multidisciplinary astrobiology research. MDRS in southeast Utah is situated in a cold arid desert with mineralogy and erosion processes comparable to those on Mars. Insight into the microbial community composition of this terrestrial Mars analogue provides essential information for the search for life on Mars: including sampling and life detection methodology optimization and what kind of organisms to expect. Soil samples were collected from different locations. Culture-independent molecular analyses directed at ribosomal RNA genes revealed the presence of all three domains of life (Archaea, Bacteria and Eukarya), but these were not detected in all samples. Spiking experiments revealed that this appears to relate to low DNA recovery, due to adsorption or degradation. Bacteria were most frequently detected and showed high alpha- and beta-diversity. Members of the Actinobacteria, Proteobacteria, Bacteroidetes and Gemmatimonadetes phyla were found in the majority of samples. Archaea alpha- and beta-diversity was very low. For Eukarya, a diverse range of organisms was identified, such as fungi, green algae and several phyla of Protozoa. Phylogenetic analysis revealed an extraordinary variety of putative extremophiles, mainly Bacteria but also Archaea and Eukarya. These comprised radioresistant, endolithic, chasmolithic, xerophilic, hypolithic, thermophilic, thermoacidophilic, psychrophilic, halophilic, haloalkaliphilic and alkaliphilic micro-organisms. Overall, our data revealed large difference in occurrence and diversity over short distances, indicating the need for high-sampling frequency at similar sites. DNA extraction methods need to be optimized to improve extraction efficiencies.

Geospatial Characterization of Fluvial Wood Arrangement in a Semi-confined Alluvial River

NASA Astrophysics Data System (ADS)

Martin, D. J.; Harden, C. P.; Pavlowsky, R. T.

2014-12-01

Large woody debris (LWD) has become universally recognized as an integral component of fluvial systems, and as a result, has become increasingly common as a river restoration tool. However, "natural" processes of wood recruitment and the subsequent arrangement of LWD within the river network are poorly understood. This research used a suite of spatial statistics to investigate longitudinal arrangement patterns of LWD in a low-gradient, Midwestern river. First, a large-scale GPS inventory of LWD, performed on the Big River in the eastern Missouri Ozarks, resulted in over 4,000 logged positions of LWD along seven river segments that covered nearly 100 km of the 237 km river system. A global Moran's I analysis indicates that LWD density is spatially autocorrelated and displays a clustering tendency within all seven river segments (P-value range = 0.000 to 0.054). A local Moran's I analysis identified specific locations along the segments where clustering occurs and revealed that, on average, clusters of LWD density (high or low) spanned 400 m. Spectral analyses revealed that, in some segments, LWD density is spatially periodic. Two segments displayed strong periodicity, while the remaining segments displayed varying degrees of noisiness. Periodicity showed a positive association with gravel bar spacing and meander wavelength, although there were insufficient data to statistically confirm the relationship. A wavelet analysis was then performed to investigate periodicity relative to location along the segment. The wavelet analysis identified significant (α = 0.05) periodicity at discrete locations along each of the segments. Those reaches yielding strong periodicity showed stronger relationships between LWD density and the geomorphic/riparian independent variables tested. Analyses consistently identified valley width and sinuosity as being associated with LWD density. The results of these analyses contribute a new perspective on the longitudinal distribution of LWD in a river system, which should help identify physical and/or riparian control mechanisms of LWD arrangement and support the development of models of LWD arrangement. Additionally, the spatial statistical tools presented here have shown to be valuable for identifying longitudinal patterns in river system components.

Instantaneous polarization analysis of ambient noise recordings in site response investigations

NASA Astrophysics Data System (ADS)

Del Gaudio, Vincenzo

2017-07-01

A new procedure is proposed for analyses of ambient noise aimed at investigating complex cases of site response to seismic shaking. Information on site response characterized by several resonance frequencies and by amplifications varying with direction can be obtained by analysing instantaneous polarization properties of ambient noise recordings. Through this kind of analysis, it is possible to identify Rayleigh wave packets emerging from incoherent background noise for very short intervals. Analysing noise recordings passed through narrow-band filters with different central frequencies, variations of Rayleigh wave properties depending on frequencies can be estimated. In particular, one can calculate: (i) the instantaneous ratios H/V between the amplitudes of horizontal and vertical components of the elliptical particle motion and (ii) the azimuthal direction of the vertical plane containing such a motion. These can be determined on a large number of recording samples, providing the basis for statistical estimates. A preferential concentration of H/V peak values at site-specific frequencies and directions can reveal directional resonance phenomena. Furthermore, peak amplitudes can be related to site amplification factors and provide constraints for subsurface velocity modelling. Some tests, carried out on data acquired at sites with known response properties, gave indications on how to select the parameters of the analysis that optimize its implementation. In particular, preliminary trials, conducted on a limited number of frequencies, allow the selection of the parameters that, while providing a large number of instantaneous H/V estimates for Rayleigh waves, minimize their scattering. The analysis can then be refined and an H/V curve as function of frequency can be obtained with a higher spectral resolution. First tests showed that cases of directional resonance can be more effectively recognized with this technique and more details can be revealed on its properties (e.g. secondary peaks) in comparison to the Nakamura's method currently employed for ordinary noise analysis. For sites characterized by isotropic response or by differently oriented directional maxima, however, the presence of noise sources with an anisotropic spatial distribution, which excite signals with inhomogeneous distribution of energy through the examined spectral band, can make the correct interpretation of data more difficult.

Saturation Mutagenesis of 5S rRNA in Saccharomyces cerevisiae

PubMed Central

Smith, Maria W.; Meskauskas, Arturas; Wang, Pinger; Sergiev, Petr V.; Dinman, Jonathan D.

2001-01-01

rRNAs are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs are actively involved in different ribosome functions. Our previous demonstration that yeast 5S rRNA mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. At the time, however, the highly repetitive nature of the genes encoding rRNAs precluded more detailed genetic and molecular analyses. A new genetic system allows all 5S rRNAs in the cell to be transcribed from a small, easily manipulated plasmid. The system is also amenable for the study of the other rRNAs, and provides an ideal genetic platform for detailed structural and functional studies. Saturation mutagenesis reveals regions of 5S rRNA that are required for cell viability, translational accuracy, and virus propagation. Unexpectedly, very few lethal alleles were identified, demonstrating the resilience of this molecule. Superimposition of genetic phenotypes on a physical map of 5S rRNA reveals the existence of phenotypic clusters of mutants, suggesting that specific regions of 5S rRNA are important for specific functions. Mapping these mutants onto the Haloarcula marismortui large subunit reveals that these clusters occur at important points of physical interaction between 5S rRNA and the different functional centers of the ribosome. Our analyses lead us to propose that one of the major functions of 5S rRNA may be to enhance translational fidelity by acting as a physical transducer of information between all of the different functional centers of the ribosome. PMID:11713264

Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

PubMed Central

BARKER, BRITTANY S.; ANDONIAN, KRIKOR; SWOPE, SARAH M.; LUSTER, DOUGLAS G.; DLUGOSCH, KATRINA M.

2017-01-01

Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species. Our analyses revealed clear population genomic structure of potential source populations in Eurasia, including deep differentiation of a lineage found in the southern Apennine and Balkan Peninsulas and divergence among populations in Asia, eastern Europe, and western Europe. We found strongest support for an evolutionary scenario in which western European populations were derived from an ancient admixture event between populations from eastern Europe and Asia, and subsequently served as the main genetic ‘bridgehead’ for introductions to the Americas. Introductions to California appear to be from a single source region, and multiple, independent introductions of divergent genotypes likely occurred into the Pacific Northwest. Plant size has evolved significantly at three points during range expansion, including a large size increase in the lineage responsible for the aggressive invasion of California’s interior. These results reveal a long history of colonization, admixture, and trait evolution in C. solstitialis, and suggest routes for improving evidence-based management decisions for one of the most ecologically and economically damaging invasive species in the western United States. PMID:28029713

Histomorphometry and cortical robusticity of the adult human femur.

PubMed

Miszkiewicz, Justyna Jolanta; Mahoney, Patrick

2018-01-13

Recent quantitative analyses of human bone microanatomy, as well as theoretical models that propose bone microstructure and gross anatomical associations, have started to reveal insights into biological links that may facilitate remodeling processes. However, relationships between bone size and the underlying cortical bone histology remain largely unexplored. The goal of this study is to determine the extent to which static indicators of bone remodeling and vascularity, measured using histomorphometric techniques, relate to femoral midshaft cortical width and robusticity. Using previously published and new quantitative data from 450 adult human male (n = 233) and female (n = 217) femora, we determine if these aspects of femoral size relate to bone microanatomy. Scaling relationships are explored and interpreted within the context of tissue form and function. Analyses revealed that the area and diameter of Haversian canals and secondary osteons, and densities of secondary osteons and osteocyte lacunae from the sub-periosteal region of the posterior midshaft femur cortex were significantly, but not consistently, associated with femoral size. Cortical width and bone robusticity were correlated with osteocyte lacunae density and scaled with positive allometry. Diameter and area of osteons and Haversian canals decreased as the width of cortex and bone robusticity increased, revealing a negative allometric relationship. These results indicate that microscopic products of cortical bone remodeling and vascularity are linked to femur size. Allometric relationships between more robust human femora with thicker cortical bone and histological products of bone remodeling correspond with principles of bone functional adaptation. Future studies may benefit from exploring scaling relationships between bone histomorphometric data and measurements of bone macrostructure.

Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

NASA Astrophysics Data System (ADS)

Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

2015-02-01

In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

Common variation in the LMNA gene (encoding lamin A/C) and type 2 diabetes: association analyses in 9,518 subjects.

PubMed

Owen, Katharine R; Groves, Christopher J; Hanson, Robert L; Knowler, William C; Shuldiner, Alan R; Elbein, Steven C; Mitchell, Braxton D; Froguel, Philippe; Ng, Maggie C Y; Chan, Juliana C; Jia, Weiping; Deloukas, Panos; Hitman, Graham A; Walker, Mark; Frayling, Timothy M; Hattersley, Andrew T; Zeggini, Eleftheria; McCarthy, Mark I

2007-03-01

Mutations in the LMNA gene (encoding lamin A/C) underlie familial partial lipodystrophy, a syndrome of monogenic insulin resistance and diabetes. LMNA maps to the well-replicated diabetes-linkage region on chromosome 1q, and there are reported associations between LMNA single nucleotide polymorphisms (SNPs) (particularly rs4641; H566H) and metabolic syndrome components. We examined the relationship between LMNA variation and type 2 diabetes (using six tag SNPs capturing >90% of common variation) in several large datasets. Analysis of 2,490 U.K. diabetic case and 2,556 control subjects revealed no significant associations at either genotype or haplotype level: the minor allele at rs4641 was no more frequent in case subjects (allelic odds ratio [OR] 1.07 [95% CI 0.98-1.17], P = 0.15). In 390 U.K. trios, family-based association analyses revealed nominally significant overtransmission of the major allele at rs12063564 (P = 0.01), which was not corroborated in other samples. Finally, genotypes for 2,817 additional subjects from the International 1q Consortium revealed no consistent case-control or family-based associations with LMNA variants. Across all our data, the OR for the rs4641 minor allele approached but did not attain significance (1.07 [0.99-1.15], P = 0.08). Our data do not therefore support a major effect of LMNA variation on diabetes risk. However, in a meta-analysis including other available data, there is evidence that rs4641 has a modest effect on diabetes susceptibility (1.10 [1.04-1.16], P = 0.001).

Self-organization of bacterial biofilms is facilitated by extracellular DNA

PubMed Central

Gloag, Erin S.; Turnbull, Lynne; Huang, Alan; Vallotton, Pascal; Wang, Huabin; Nolan, Laura M.; Mililli, Lisa; Hunt, Cameron; Lu, Jing; Osvath, Sarah R.; Monahan, Leigh G.; Cavaliere, Rosalia; Charles, Ian G.; Wand, Matt P.; Gee, Michelle L.; Prabhakar, Ranganathan; Whitchurch, Cynthia B.

2013-01-01

Twitching motility-mediated biofilm expansion is a complex, multicellular behavior that enables the active colonization of surfaces by many species of bacteria. In this study we have explored the emergence of intricate network patterns of interconnected trails that form in actively expanding biofilms of Pseudomonas aeruginosa. We have used high-resolution, phase-contrast time-lapse microscopy and developed sophisticated computer vision algorithms to track and analyze individual cell movements during expansion of P. aeruginosa biofilms. We have also used atomic force microscopy to examine the topography of the substrate underneath the expanding biofilm. Our analyses reveal that at the leading edge of the biofilm, highly coherent groups of bacteria migrate across the surface of the semisolid media and in doing so create furrows along which following cells preferentially migrate. This leads to the emergence of a network of trails that guide mass transit toward the leading edges of the biofilm. We have also determined that extracellular DNA (eDNA) facilitates efficient traffic flow throughout the furrow network by maintaining coherent cell alignments, thereby avoiding traffic jams and ensuring an efficient supply of cells to the migrating front. Our analyses reveal that eDNA also coordinates the movements of cells in the leading edge vanguard rafts and is required for the assembly of cells into the “bulldozer” aggregates that forge the interconnecting furrows. Our observations have revealed that large-scale self-organization of cells in actively expanding biofilms of P. aeruginosa occurs through construction of an intricate network of furrows that is facilitated by eDNA. PMID:23798445

Large space systems technology, 1981. [conferences

NASA Technical Reports Server (NTRS)

Boyer, W. J. (Compiler)

1982-01-01

A total systems approach including structures, analyses, controls, and antennas is presented as a cohesive, programmatic plan for large space systems. Specifically, program status, structures, materials, and analyses, and control of large space systems are addressed.

Biosocial correlates of inter-generational social mobility in a British cohort.

PubMed

Krzyżanowska, Monika; Mascie-Taylor, C G Nicholas

2013-07-01

The relationship between inter-generational social mobility of sons and daughters between 1958 and 1991 and biosocial variables, i.e. birth order, number of children in family, father's social class, region, educational attainment of child and father, educational and cognitive test scores (reading, mathematics, verbal and non-verbal IQ tests), was studied in a large British cohort study. The data used were collected as part of the British National Child Development Study (NCDS). The extent of social class mobility was determined inter-generationally and was categorized as none (no change in social class between the father's and index child's social class), upwardly mobile (where the index child moved up one or more social classes compared with their father) or downwardly mobile (where the index child moved down one or more social classes compared with their father). All of the biosocial variables were associated with social mobility when analysed separately. Multivariate analyses revealed that the most significant predictor of mobility categories in both sexes was education of the cohort member, followed by social class of the father. In both sexes mathematics score was a significant predicator, while in sons reading and non-verbal IQ scores were also important predictors. In the light of these results, it appears that social mobility in Britain takes place largely on meritocratic principles.

Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts

USGS Publications Warehouse

Graham, Matthew R.; Wood, Dustin A.; Henault, Jonathan A.; Valois, Zachary J.; Cushing, Paula E.

2017-01-01

Recent syntheses of phylogeographical data from terrestrial animals in the Mojave and Sonoran deserts have revealed a complex history of geologic and climatic vicariance events. We studied the phylogeography of Smeringurus vachoni to see how vicariance events may have impacted a large, endemic rock scorpion. Additionally, we used the phylogeographical data to examine the validity of two subspecies of S. vachoni that were described using unconventional morphological characters. Phylogenetic, network and SAMOVA analyses indicate that S. vachoni consists of 11 clades mostly endemic to isolated desert mountain ranges. Molecular clock estimates suggest that clades diversified between the Miocene and early Pleistocene. Species distribution models predict a contraction of suitable habitat during the last glacial maximum. Landscape interpolations and Migrate-n analyses highlight areas of gene flow across the Colorado River. Smeringurus vachoni does not comprise two subspecies. Instead, the species represents at least 11 mitochondrial clades that probably diversified by vicariance associated with Pleistocene climate changes and formation of ancient lakes along the Colorado River corridor. Gene flow appears to have occurred from west to east across the Colorado River during periodic river avulsions.

Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge.

PubMed

Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

2016-01-01

Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution.

Underpowered samples, false negatives, and unconscious learning.

PubMed

Vadillo, Miguel A; Konstantinidis, Emmanouil; Shanks, David R

2016-02-01

The scientific community has witnessed growing concern about the high rate of false positives and unreliable results within the psychological literature, but the harmful impact of false negatives has been largely ignored. False negatives are particularly concerning in research areas where demonstrating the absence of an effect is crucial, such as studies of unconscious or implicit processing. Research on implicit processes seeks evidence of above-chance performance on some implicit behavioral measure at the same time as chance-level performance (that is, a null result) on an explicit measure of awareness. A systematic review of 73 studies of contextual cuing, a popular implicit learning paradigm, involving 181 statistical analyses of awareness tests, reveals how underpowered studies can lead to failure to reject a false null hypothesis. Among the studies that reported sufficient information, the meta-analytic effect size across awareness tests was d z = 0.31 (95 % CI 0.24-0.37), showing that participants' learning in these experiments was conscious. The unusually large number of positive results in this literature cannot be explained by selective publication. Instead, our analyses demonstrate that these tests are typically insensitive and underpowered to detect medium to small, but true, effects in awareness tests. These findings challenge a widespread and theoretically important claim about the extent of unconscious human cognition.

The importance of within-system spatial variation in drivers of marine ecosystem regime shifts

PubMed Central

Fisher, J. A. D.; Casini, M.; Frank, K. T.; Möllmann, C.; Leggett, W. C.; Daskalov, G.

2015-01-01

Comparative analyses of the dynamics of exploited marine ecosystems have led to differing hypotheses regarding the primary causes of observed regime shifts, while many ecosystems have apparently not undergone regime shifts. These varied responses may be partly explained by the decade-old recognition that within-system spatial heterogeneity in key climate and anthropogenic drivers may be important, as recent theoretical examinations have concluded that spatial heterogeneity in environmental characteristics may diminish the tendency for regime shifts. Here, we synthesize recent, empirical within-system spatio-temporal analyses of some temperate and subarctic large marine ecosystems in which regime shifts have (and have not) occurred. Examples from the Baltic Sea, Black Sea, Bengula Current, North Sea, Barents Sea and Eastern Scotian Shelf reveal the largely neglected importance of considering spatial variability in key biotic and abiotic influences and species movements in the context of evaluating and predicting regime shifts. We highlight both the importance of understanding the scale-dependent spatial dynamics of climate influences and key predator–prey interactions to unravel the dynamics of regime shifts, and the utility of spatial downscaling of proposed mechanisms (as evident in the North Sea and Barents Sea) as a means of evaluating hypotheses originally derived from among-system comparisons.

Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge

PubMed Central

Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

2016-01-01

Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

Origin of sulfur for elemental sulfur concentration in salt dome cap rocks, Gulf Coast Basin, USA

NASA Astrophysics Data System (ADS)

Hill, J. M.; Kyle, R.; Loyd, S. J.

2017-12-01

Calcite cap rocks of the Boling and Main Pass salt domes contain large elemental sulfur accumulations. Isotopic and petrographic data indicate complex histories of cap rock paragenesis for both domes. Whereas paragenetic complexity is in part due to the open nature of these hydrodynamic systems, a comprehensive understanding of elemental sulfur sources and concentration mechanisms is lacking. Large ranges in traditional sulfur isotope compositions (δ34S) among oxidized and reduced sulfur-bearing phases has led some to infer that microbial sulfate reduction and/or influx of sulfide-rich formation waters occurred during calcite cap rock formation. Ultimately, traditional sulfur isotope analyses alone cannot distinguish among local microbial or exogenous sulfur sources. Recently, multiple sulfur isotope (32S, 33S, 34S, 36S) studies reveal small, but measurable differences in mass-dependent behavior of microbial and abiogenic processes. To distinguish between the proposed sulfur sources, multiple-sulfur-isotope analyses have been performed on native sulfur from the Boling and Main Pass cap rocks. Similarities or deviations from equilibrium relationships indicate which pathways were responsible for native sulfur precipitation. Pathway determination provides insight into Gulf Coast cap rock development and potentially highlights the conditions that led to anomalous sulfur enrichment in Boling and Main Pass Domes.

Big Cat Coalitions: A Comparative Analysis of Regional Brain Volumes in Felidae.

PubMed

Sakai, Sharleen T; Arsznov, Bradley M; Hristova, Ani E; Yoon, Elise J; Lundrigan, Barbara L

2016-01-01

Broad-based species comparisons across mammalian orders suggest a number of factors that might influence the evolution of large brains. However, the relationship between these factors and total and regional brain size remains unclear. This study investigated the relationship between relative brain size and regional brain volumes and sociality in 13 felid species in hopes of revealing relationships that are not detected in more inclusive comparative studies. In addition, a more detailed analysis was conducted of four focal species: lions ( Panthera leo ), leopards ( Panthera pardus ), cougars ( Puma concolor ), and cheetahs ( Acinonyx jubatus ). These species differ markedly in sociality and behavioral flexibility, factors hypothesized to contribute to increased relative brain size and/or frontal cortex size. Lions are the only truly social species, living in prides. Although cheetahs are largely solitary, males often form small groups. Both leopards and cougars are solitary. Of the four species, leopards exhibit the most behavioral flexibility, readily adapting to changing circumstances. Regional brain volumes were analyzed using computed tomography. Skulls ( n = 75) were scanned to create three-dimensional virtual endocasts, and regional brain volumes were measured using either sulcal or bony landmarks obtained from the endocasts or skulls. Phylogenetic least squares regression analyses found that sociality does not correspond with larger relative brain size in these species. However, the sociality/solitary variable significantly predicted anterior cerebrum (AC) volume, a region that includes frontal cortex. This latter finding is despite the fact that the two social species in our sample, lions and cheetahs, possess the largest and smallest relative AC volumes, respectively. Additionally, an ANOVA comparing regional brain volumes in four focal species revealed that lions and leopards, while not significantly different from one another, have relatively larger AC volumes than are found in cheetahs or cougars. Further, female lions possess a significantly larger AC volume than conspecific males; female lion values were also larger than those of the other three species (regardless of sex). These results may reflect greater complexity in a female lion's social world, but additional studies are necessary. These data suggest that within family comparisons may reveal variations not easily detected by broad comparative analyses.

Big Cat Coalitions: A Comparative Analysis of Regional Brain Volumes in Felidae

PubMed Central

Sakai, Sharleen T.; Arsznov, Bradley M.; Hristova, Ani E.; Yoon, Elise J.; Lundrigan, Barbara L.

2016-01-01

Broad-based species comparisons across mammalian orders suggest a number of factors that might influence the evolution of large brains. However, the relationship between these factors and total and regional brain size remains unclear. This study investigated the relationship between relative brain size and regional brain volumes and sociality in 13 felid species in hopes of revealing relationships that are not detected in more inclusive comparative studies. In addition, a more detailed analysis was conducted of four focal species: lions (Panthera leo), leopards (Panthera pardus), cougars (Puma concolor), and cheetahs (Acinonyx jubatus). These species differ markedly in sociality and behavioral flexibility, factors hypothesized to contribute to increased relative brain size and/or frontal cortex size. Lions are the only truly social species, living in prides. Although cheetahs are largely solitary, males often form small groups. Both leopards and cougars are solitary. Of the four species, leopards exhibit the most behavioral flexibility, readily adapting to changing circumstances. Regional brain volumes were analyzed using computed tomography. Skulls (n = 75) were scanned to create three-dimensional virtual endocasts, and regional brain volumes were measured using either sulcal or bony landmarks obtained from the endocasts or skulls. Phylogenetic least squares regression analyses found that sociality does not correspond with larger relative brain size in these species. However, the sociality/solitary variable significantly predicted anterior cerebrum (AC) volume, a region that includes frontal cortex. This latter finding is despite the fact that the two social species in our sample, lions and cheetahs, possess the largest and smallest relative AC volumes, respectively. Additionally, an ANOVA comparing regional brain volumes in four focal species revealed that lions and leopards, while not significantly different from one another, have relatively larger AC volumes than are found in cheetahs or cougars. Further, female lions possess a significantly larger AC volume than conspecific males; female lion values were also larger than those of the other three species (regardless of sex). These results may reflect greater complexity in a female lion’s social world, but additional studies are necessary. These data suggest that within family comparisons may reveal variations not easily detected by broad comparative analyses. PMID:27812324

Soybean kinome: functional classification and gene expression patterns

PubMed Central

Liu, Jinyi; Chen, Nana; Grant, Joshua N.; Cheng, Zong-Ming (Max); Stewart, C. Neal; Hewezi, Tarek

2015-01-01

The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants and plays a role in nearly all biological functions. While a large number of genes have been predicted to encode PKs in soybean, a comprehensive functional classification and global analysis of expression patterns of this large gene family is lacking. In this study, we identified the entire soybean PK repertoire or kinome, which comprised 2166 putative PK genes, representing 4.67% of all soybean protein-coding genes. The soybean kinome was classified into 19 groups, 81 families, and 122 subfamilies. The receptor-like kinase (RLK) group was remarkably large, containing 1418 genes. Collinearity analysis indicated that whole-genome segmental duplication events may have played a key role in the expansion of the soybean kinome, whereas tandem duplications might have contributed to the expansion of specific subfamilies. Gene structure, subcellular localization prediction, and gene expression patterns indicated extensive functional divergence of PK subfamilies. Global gene expression analysis of soybean PK subfamilies revealed tissue- and stress-specific expression patterns, implying regulatory functions over a wide range of developmental and physiological processes. In addition, tissue and stress co-expression network analysis uncovered specific subfamilies with narrow or wide interconnected relationships, indicative of their association with particular or broad signalling pathways, respectively. Taken together, our analyses provide a foundation for further functional studies to reveal the biological and molecular functions of PKs in soybean. PMID:25614662

A large hydrothermal reservoir beneath Taal Volcano (Philippines) revealed by magnetotelluric observations and its implications to the volcanic activity.

PubMed

Alanis, Paul K B; Yamaya, Yusuke; Takeuchi, Akihiro; Sasai, Yoichi; Okada, Yoshihiro; Nagao, Toshiyasu

2013-01-01

Taal Volcano is one of the most active volcanoes in the Philippines. The magnetotelluric 3D forward analyses indicate the existence of a large high resistivity anomaly (∼100 Ω·m) with a volume of at least 3 km×3 km×3 km, which is capped by a conductive layer (∼10 Ω·m), beneath the Main Crater. This high resistivity anomaly is hypothesized to be a large hydrothermal reservoir, consisting of the aggregate of interconnected cracks in rigid and dense host rocks, which are filled with hydrothermal fluids coming from a magma batch below the reservoir. The hydrothermal fluids are considered partly in gas phase and liquid phase. The presence of such a large hydrothermal reservoir and the stagnant magma below may have influences on the volcano's activity. Two possibilities are presented. First, the 30 January 1911 explosion event was a magmatic hydrothermal eruption rather than a base-surge associated with a phreato-magmatic eruption. Second, the earlier proposed four eruption series may be better interpreted by two cycles, each consisting of series of summit and flank eruptions.

A large hydrothermal reservoir beneath Taal Volcano (Philippines) revealed by magnetotelluric observations and its implications to the volcanic activity

PubMed Central

ALANIS, Paul K. B.; YAMAYA, Yusuke; TAKEUCHI, Akihiro; SASAI, Yoichi; OKADA, Yoshihiro; NAGAO, Toshiyasu

2013-01-01

Taal Volcano is one of the most active volcanoes in the Philippines. The magnetotelluric 3D forward analyses indicate the existence of a large high resistivity anomaly (∼100 Ω·m) with a volume of at least 3 km × 3 km × 3 km, which is capped by a conductive layer (∼10 Ω·m), beneath the Main Crater. This high resistivity anomaly is hypothesized to be a large hydrothermal reservoir, consisting of the aggregate of interconnected cracks in rigid and dense host rocks, which are filled with hydrothermal fluids coming from a magma batch below the reservoir. The hydrothermal fluids are considered partly in gas phase and liquid phase. The presence of such a large hydrothermal reservoir and the stagnant magma below may have influences on the volcano’s activity. Two possibilities are presented. First, the 30 January 1911 explosion event was a magmatic hydrothermal eruption rather than a base-surge associated with a phreato-magmatic eruption. Second, the earlier proposed four eruption series may be better interpreted by two cycles, each consisting of series of summit and flank eruptions. PMID:24126286

Computational dissection of human episodic memory reveals mental process-specific genetic profiles

PubMed Central

Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G.; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J.-F.

2015-01-01

Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory. PMID:26261317

A large-scale RNA interference screen identifies genes that regulate autophagy at different stages.

PubMed

Guo, Sujuan; Pridham, Kevin J; Virbasius, Ching-Man; He, Bin; Zhang, Liqing; Varmark, Hanne; Green, Michael R; Sheng, Zhi

2018-02-12

Dysregulated autophagy is central to the pathogenesis and therapeutic development of cancer. However, how autophagy is regulated in cancer is not well understood and genes that modulate cancer autophagy are not fully defined. To gain more insights into autophagy regulation in cancer, we performed a large-scale RNA interference screen in K562 human chronic myeloid leukemia cells using monodansylcadaverine staining, an autophagy-detecting approach equivalent to immunoblotting of the autophagy marker LC3B or fluorescence microscopy of GFP-LC3B. By coupling monodansylcadaverine staining with fluorescence-activated cell sorting, we successfully isolated autophagic K562 cells where we identified 336 short hairpin RNAs. After candidate validation using Cyto-ID fluorescence spectrophotometry, LC3B immunoblotting, and quantitative RT-PCR, 82 genes were identified as autophagy-regulating genes. 20 genes have been reported previously and the remaining 62 candidates are novel autophagy mediators. Bioinformatic analyses revealed that most candidate genes were involved in molecular pathways regulating autophagy, rather than directly participating in the autophagy process. Further autophagy flux assays revealed that 57 autophagy-regulating genes suppressed autophagy initiation, whereas 21 candidates promoted autophagy maturation. Our RNA interference screen identifies identified genes that regulate autophagy at different stages, which helps decode autophagy regulation in cancer and offers novel avenues to develop autophagy-related therapies for cancer.

Computational dissection of human episodic memory reveals mental process-specific genetic profiles.

PubMed

Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J-F

2015-09-01

Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory.

Predicting risky choices from brain activity patterns

PubMed Central

Helfinstein, Sarah M.; Schonberg, Tom; Congdon, Eliza; Karlsgodt, Katherine H.; Mumford, Jeanette A.; Sabb, Fred W.; Cannon, Tyrone D.; London, Edythe D.; Bilder, Robert M.; Poldrack, Russell A.

2014-01-01

Previous research has implicated a large network of brain regions in the processing of risk during decision making. However, it has not yet been determined if activity in these regions is predictive of choices on future risky decisions. Here, we examined functional MRI data from a large sample of healthy subjects performing a naturalistic risk-taking task and used a classification analysis approach to predict whether individuals would choose risky or safe options on upcoming trials. We were able to predict choice category successfully in 71.8% of cases. Searchlight analysis revealed a network of brain regions where activity patterns were reliably predictive of subsequent risk-taking behavior, including a number of regions known to play a role in control processes. Searchlights with significant predictive accuracy were primarily located in regions more active when preparing to avoid a risk than when preparing to engage in one, suggesting that risk taking may be due, in part, to a failure of the control systems necessary to initiate a safe choice. Additional analyses revealed that subject choice can be successfully predicted with minimal decrements in accuracy using highly condensed data, suggesting that information relevant for risky choice behavior is encoded in coarse global patterns of activation as well as within highly local activation within searchlights. PMID:24550270

Of mice and (Viking?) men: phylogeography of British and Irish house mice.

PubMed

Searle, Jeremy B; Jones, Catherine S; Gündüz, Islam; Scascitelli, Moira; Jones, Eleanor P; Herman, Jeremy S; Rambau, R Victor; Noble, Leslie R; Berry, R J; Giménez, Mabel D; Jóhannesdóttir, Fríoa

2009-01-22

The west European subspecies of house mouse (Mus musculus domesticus) has gained much of its current widespread distribution through commensalism with humans. This means that the phylogeography of M. m. domesticus should reflect patterns of human movements. We studied restriction fragment length polymorphism (RFLP) and DNA sequence variations in mouse mitochondrial (mt) DNA throughout the British Isles (328 mice from 105 localities, including previously published data). There is a major mtDNA lineage revealed by both RFLP and sequence analyses, which is restricted to the northern and western peripheries of the British Isles, and also occurs in Norway. This distribution of the 'Orkney' lineage fits well with the sphere of influence of the Norwegian Vikings and was probably generated through inadvertent transport by them. To form viable populations, house mice would have required large human settlements such as the Norwegian Vikings founded. The other parts of the British Isles (essentially most of mainland Britain) are characterized by house mice with different mtDNA sequences, some of which are also found in Germany, and which probably reflect both Iron Age movements of people and mice and earlier development of large human settlements. MtDNA studies on house mice have the potential to reveal novel aspects of human history.

Of mice and (Viking?) men: phylogeography of British and Irish house mice

PubMed Central

Searle, Jeremy B.; Jones, Catherine S.; Gündüz, İslam; Scascitelli, Moira; Jones, Eleanor P.; Herman, Jeremy S.; Rambau, R. Victor; Noble, Leslie R.; Berry, R.J.; Giménez, Mabel D.; Jóhannesdóttir, Fríða

2008-01-01

The west European subspecies of house mouse (Mus musculus domesticus) has gained much of its current widespread distribution through commensalism with humans. This means that the phylogeography of M. m. domesticus should reflect patterns of human movements. We studied restriction fragment length polymorphism (RFLP) and DNA sequence variations in mouse mitochondrial (mt) DNA throughout the British Isles (328 mice from 105 localities, including previously published data). There is a major mtDNA lineage revealed by both RFLP and sequence analyses, which is restricted to the northern and western peripheries of the British Isles, and also occurs in Norway. This distribution of the ‘Orkney’ lineage fits well with the sphere of influence of the Norwegian Vikings and was probably generated through inadvertent transport by them. To form viable populations, house mice would have required large human settlements such as the Norwegian Vikings founded. The other parts of the British Isles (essentially most of mainland Britain) are characterized by house mice with different mtDNA sequences, some of which are also found in Germany, and which probably reflect both Iron Age movements of people and mice and earlier development of large human settlements. MtDNA studies on house mice have the potential to reveal novel aspects of human history. PMID:18826939

Changes in hemp secondary fiber production related to technical fiber variability revealed by light microscopy and attenuated total reflectance Fourier transform infrared spectroscopy

PubMed Central

Fernandez-Tendero, Eva; Day, Arnaud; Legros, Sandrine; Habrant, Anouck; Hawkins, Simon

2017-01-01

Interest in hemp (Cannabis sativa L.) is increasing due to the development of a new range of industrial applications based on bast fibers. However the variability of bast fiber yield and quality represents an important barrier to further exploitation. Primary and secondary fiber content was examined in two commercial hemp varieties (Fedora 17, Santhica 27) grown under contrasted sowing density and irrigation conditions. Both growing conditions and hemp varieties impact stem tissue architecture with a large effect on the proportion of secondary fibers but not primary fibers. Attenuated total reflectance infrared spectroscopy allowed the discrimination of manually-isolated native primary fibers and secondary fibers but did not reveal any clustering according to growing conditions and variety. Infrared data were confirmed by wet chemistry analyses that revealed slight but significant differences between primary and secondary fiber cell wall composition. Infrared spectroscopy of technical fibers obtained after mechanical defibering revealed differences with native primary, but not secondary fibers and also discriminated samples obtained from plants grown under different conditions. Altogether the results suggested that the observed variability of hemp technical fibers could be partially explained by i) differences in secondary fiber production and ii) differential behavior during mechanical defibering resulting in unequal separation of primary and secondary fibers. PMID:28640922

Changes in hemp secondary fiber production related to technical fiber variability revealed by light microscopy and attenuated total reflectance Fourier transform infrared spectroscopy.

PubMed

Fernandez-Tendero, Eva; Day, Arnaud; Legros, Sandrine; Habrant, Anouck; Hawkins, Simon; Chabbert, Brigitte

2017-01-01

Interest in hemp (Cannabis sativa L.) is increasing due to the development of a new range of industrial applications based on bast fibers. However the variability of bast fiber yield and quality represents an important barrier to further exploitation. Primary and secondary fiber content was examined in two commercial hemp varieties (Fedora 17, Santhica 27) grown under contrasted sowing density and irrigation conditions. Both growing conditions and hemp varieties impact stem tissue architecture with a large effect on the proportion of secondary fibers but not primary fibers. Attenuated total reflectance infrared spectroscopy allowed the discrimination of manually-isolated native primary fibers and secondary fibers but did not reveal any clustering according to growing conditions and variety. Infrared data were confirmed by wet chemistry analyses that revealed slight but significant differences between primary and secondary fiber cell wall composition. Infrared spectroscopy of technical fibers obtained after mechanical defibering revealed differences with native primary, but not secondary fibers and also discriminated samples obtained from plants grown under different conditions. Altogether the results suggested that the observed variability of hemp technical fibers could be partially explained by i) differences in secondary fiber production and ii) differential behavior during mechanical defibering resulting in unequal separation of primary and secondary fibers.

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System

PubMed Central

2013-01-01

Armillaria mellea is a major plant pathogen. Yet, no large-scale “-omics” data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (n = 629 unique) and secreted (n = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (n = 111) was detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was 4-fold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases, and lignin peroxidases in the A. mellea proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms. PMID:23656496

Recurrent major depression and right hippocampal volume: A bivariate linkage and association study.

PubMed

Mathias, Samuel R; Knowles, Emma E M; Kent, Jack W; McKay, D Reese; Curran, Joanne E; de Almeida, Marcio A A; Dyer, Thomas D; Göring, Harald H H; Olvera, Rene L; Duggirala, Ravi; Fox, Peter T; Almasy, Laura; Blangero, John; Glahn, David C

2016-01-01

Previous work has shown that the hippocampus is smaller in the brains of individuals suffering from major depressive disorder (MDD) than those of healthy controls. Moreover, right hippocampal volume specifically has been found to predict the probability of subsequent depressive episodes. This study explored the utility of right hippocampal volume as an endophenotype of recurrent MDD (rMDD). We observed a significant genetic correlation between the two traits in a large sample of Mexican American individuals from extended pedigrees (ρg = -0.34, p = 0.013). A bivariate linkage scan revealed a significant pleiotropic quantitative trait locus on chromosome 18p11.31-32 (LOD = 3.61). Bivariate association analysis conducted under the linkage peak revealed a variant (rs574972) within an intron of the gene SMCHD1 meeting the corrected significance level (χ(2) = 19.0, p = 7.4 × 10(-5)). Univariate association analyses of each phenotype separately revealed that the same variant was significant for right hippocampal volume alone, and also revealed a suggestively significant variant (rs12455524) within the gene DLGAP1 for rMDD alone. The results implicate right-hemisphere hippocampal volume as a possible endophenotype of rMDD, and in so doing highlight a potential gene of interest for rMDD risk. © 2015 Wiley Periodicals, Inc.

Detecting temporal change in watershed nutrient yields

Treesearch

James D. Wickham; Timothy G. Wade; Kurt H. Riitters

2008-01-01

Meta-analyses reveal that nutrient yields tend to be higher for watersheds dominated by anthropogenic uses (e.g., urban, agriculture) and lower for watersheds dominated by natural vegetation. One implication of this pattern is that loss of natural vegetation will produce increases in watershed nutrient yields. Yet, the same meta-analyses also reveal that, absent land-...

Detecting Temporal Change in Watershed Nutrient Yields

Treesearch

James D. Wickham; Timothy G. Wade; Kurt H. Riitters

2008-01-01

Meta-analyses reveal that nutrient yields tend to be higher for watersheds dominated by anthropogenic uses (e.g., urban, agriculture) and lower for watersheds dominated by natural vegetation. One implication of this pattern is that loss of natural vegetation will produce increases in watershed nutrient yields. Yet, the same meta-analyses also reveal that, absent land-...

Comparing Distance vs. Campus-Based Delivery of Research Methods Courses

ERIC Educational Resources Information Center

Girod, Mark; Wojcikiewicz, Steve

2009-01-01

A causal-comparative pre-test, post-test design was used to investigate differences in learning in a research methods course for face-to-face and web-based delivery models. Analyses of participant achievement (N = 205) revealed almost no differences but post-hoc analyses revealed important differences in pedagogy between delivery models despite…

Diversity of mitochondrial large subunit rDNA haplotypes of Glomus intraradices in two agricultural field experiments and two semi-natural grasslands.

PubMed

Börstler, Boris; Thiéry, Odile; Sýkorová, Zuzana; Berner, Alfred; Redecker, Dirk

2010-04-01

Glomus intraradices, an arbuscular mycorrhizal fungus (AMF), is frequently found in a surprisingly wide range of ecosystems all over the world. It is used as model organism for AMF and its genome is being sequenced. Despite the ecological importance of AMF, little has been known about their population structure, because no adequate molecular markers have been available. In the present study we analyse for the first time the intraspecific genetic structure of an AMF directly from colonized roots in the field. A recently developed PCR-RFLP approach for the mitochondrial rRNA large subunit gene (mtLSU) of these obligate symbionts was used and complemented by sequencing and primers specific for a particularly frequent mtLSU haplotype. We analysed root samples from two agricultural field experiments in Switzerland and two semi-natural grasslands in France and Switzerland. RFLP type composition of G. intraradices (phylogroup GLOM A-1) differed strongly between agricultural and semi-natural sites and the G. intraradices populations of the two agricultural sites were significantly differentiated. RFLP type richness was higher in the agricultural sites compared with the grasslands. Detailed sequence analyses which resolved multiple sequence haplotypes within some RFLP types even revealed that there was no overlap of haplotypes among any of the study sites except between the two grasslands. Our results demonstrate a surprisingly high differentiation among semi-natural and agricultural field sites for G. intraradices. These findings will have major implications on our views of processes of adaptation and specialization in these plant/fungus associations.

Analysis of sex and gender-specific research reveals a common increase in publications and marked differences between disciplines

PubMed Central

2010-01-01

Background The incorporation of sex and gender-specific analysis in medical research is increasing due to pressure from public agencies, funding bodies, and the clinical and research community. However, generations of knowledge and publication trends in this discipline are currently spread over distinct specialties and are difficult to analyze comparatively. Methods Using a text-mining approach, we have analysed sex and gender aspects in research within nine clinical subspecialties - Cardiology, Pulmonology, Nephrology, Endocrinology, Gastroenterology, Haematology, Oncology, Rheumatology, Neurology - using six paradigmatic diseases in each one. Articles have been classified into five pre-determined research categories - Epidemiology, Pathophysiology, Clinical research, Management and Outcomes. Additional information has been collected on the type of study (human/animal) and the number of subjects included. Of the 8,836 articles initially retrieved, 3,466 (39%) included sex and gender-specific research and have been further analysed. Results Literature incorporating sex/gender analysis increased over time and displays a stronger trend if compared to overall publication increase. All disciplines, but cardiology (22%), demonstrated an underrepresentation of research about gender differences in management, which ranges from 3 to 14%. While the use of animal models for identification of sex differences in basic research varies greatly among disciplines, studies involving human subjects are frequently conducted in large cohorts with more than 1,000 patients (24% of all human studies). Conclusions Heterogeneity characterizes sex and gender-specific research. Although large cohorts are often analysed, sex and gender differences in clinical management are insufficiently investigated leading to potential inequalities in health provision and outcomes. PMID:21067576

Protein homology model refinement by large-scale energy optimization.

PubMed

Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

2018-03-20

Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops.

PubMed

Cao, Ke; Zheng, Zhijun; Wang, Lirong; Liu, Xin; Zhu, Gengrui; Fang, Weichao; Cheng, Shifeng; Zeng, Peng; Chen, Changwen; Wang, Xinwei; Xie, Min; Zhong, Xiao; Wang, Xiaoli; Zhao, Pei; Bian, Chao; Zhu, Yinling; Zhang, Jiahui; Ma, Guosheng; Chen, Chengxuan; Li, Yanjun; Hao, Fengge; Li, Yong; Huang, Guodong; Li, Yuxiang; Li, Haiyan; Guo, Jian; Xu, Xun; Wang, Jun

2014-07-31

Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.

Size-dependent trophic patterns of pallid sturgeon and shovelnose sturgeon in a large river system

USGS Publications Warehouse

French, William E.; Graeb, Brian D. S.; Bertrand, Katie N.; Chipps, Steven R.; Klumb, Robert A.

2013-01-01

This study compared patterns of δ15N and δ13C enrichment of pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon S. platorynchus in the Missouri River, United States, to infer their trophic position in a large river system. We examined enrichment and energy flow for pallid sturgeon in three segments of the Missouri River (Montana/North Dakota, Nebraska/South Dakota, and Nebraska/Iowa) and made comparisons between species in the two downstream segments (Nebraska/South Dakota and Nebraska/Iowa). Patterns in isotopic composition for pallid sturgeon were consistent with gut content analyses indicating an ontogenetic diet shift from invertebrates to fish prey at sizes of >500-mm fork length (FL) in all three segments of the Missouri River. Isotopic patterns revealed shovelnose sturgeon did not experience an ontogenetic shift in diet and used similar prey resources as small (<500-mm FL) pallid sturgeon in the two downstream segments. We found stable isotope analysis to be an effective tool for evaluating the trophic position of sturgeons within a large river food web.

Preservation of large-scale chromatin structure in FISH experiments

PubMed Central

Hepperger, Claudia; Otten, Simone; von Hase, Johann

2006-01-01

The nuclear organization of specific endogenous chromatin regions can be investigated only by fluorescence in situ hybridization (FISH). One of the two fixation procedures is typically applied: (1) buffered formaldehyde or (2) hypotonic shock with methanol acetic acid fixation followed by dropping of nuclei on glass slides and air drying. In this study, we compared the effects of these two procedures and some variations on nuclear morphology and on FISH signals. We analyzed mouse erythroleukemia and mouse embryonic stem cells because their clusters of subcentromeric heterochromatin provide an easy means to assess preservation of chromatin. Qualitative and quantitative analyses revealed that formaldehyde fixation provided good preservation of large-scale chromatin structures, while classical methanol acetic acid fixation after hypotonic treatment severely impaired nuclear shape and led to disruption of chromosome territories, heterochromatin structures, and large transgene arrays. Our data show that such preparations do not faithfully reflect in vivo nuclear architecture. Electronic supplementary material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00412-006-0084-2 and is accessible for authorized users. PMID:17119992

A rice kinase-protein interaction map.

PubMed

Ding, Xiaodong; Richter, Todd; Chen, Mei; Fujii, Hiroaki; Seo, Young Su; Xie, Mingtang; Zheng, Xianwu; Kanrar, Siddhartha; Stevenson, Rebecca A; Dardick, Christopher; Li, Ying; Jiang, Hao; Zhang, Yan; Yu, Fahong; Bartley, Laura E; Chern, Mawsheng; Bart, Rebecca; Chen, Xiuhua; Zhu, Lihuang; Farmerie, William G; Gribskov, Michael; Zhu, Jian-Kang; Fromm, Michael E; Ronald, Pamela C; Song, Wen-Yuan

2009-03-01

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

Response to displaced neighbours in a territorial songbird with a large repertoire

NASA Astrophysics Data System (ADS)

Briefer, Elodie; Aubin, Thierry; Rybak, Fanny

2009-09-01

Neighbour recognition allows territory owners to modulate their territorial response according to the threat posed by each neighbour and thus to reduce the costs associated with territorial defence. Individual acoustic recognition of neighbours has been shown in numerous bird species, but few of them had a large repertoire. Here, we tested individual vocal recognition in a songbird with a large repertoire, the skylark Alauda arvensis. We first examined the physical basis for recognition in the song, and we then experimentally tested recognition by playing back songs of adjacent neighbours and strangers. Males showed a lower territorial response to adjacent neighbours than to strangers when we broadcast songs from the shared boundary. However, when we broadcast songs from the opposite boundary, males showed a similar response to neighbours and strangers, indicating a spatial categorisation of adjacent neighbours’ songs. Acoustic analyses revealed that males could potentially use the syntactical arrangement of syllables in sequences to identify the songs of their neighbours. Neighbour interactions in skylarks are thus subtle relationships that can be modulated according to the spatial position of each neighbour.

The effects of question-generation training on metacognitive knowledge, self regulation and learning approaches in science.

PubMed

Cano García, Francisco; García, Ángela; Berbén, A B G; Pichardo, M C; Justicia, Fernando

2014-01-01

Although much research has examined the impact of question generation on students' reading comprehension and learning from lectures, far less research has analysed its influence on how students learn and study science. The present study aims to bridge this knowledge gap. Using a quasi-experimental design, three complete ninth-grade science classes, with a total of 72 students, were randomly assigned to three conditions (groups): (G1) questioning-training by providing prompts; (G2) question-generation without any explicit instruction; and (G3) no question control. Participants' pre-test and post-test self-reported measures of metacognitive knowledge, self-regulation and learning approaches were collected and data analysed with multivariate and univariate analyses of covariance. (a) MANCOVA revealed a significant effect for group; (b) ANCOVAs showed the highest average gains for G1 and statistically significant between-group differences in the two components of metacognition: metacognitive knowledge and self-regulation; and (c) the direction of these differences seemed to vary in each of these components. Question-generation training influenced how students learned and studied, specifically their metacognition, and it had a medium to large effect size, which was somewhat related to the prompts used.

Single-cell analysis of population context advances RNAi screening at multiple levels

PubMed Central

Snijder, Berend; Sacher, Raphael; Rämö, Pauli; Liberali, Prisca; Mench, Karin; Wolfrum, Nina; Burleigh, Laura; Scott, Cameron C; Verheije, Monique H; Mercer, Jason; Moese, Stefan; Heger, Thomas; Theusner, Kristina; Jurgeit, Andreas; Lamparter, David; Balistreri, Giuseppe; Schelhaas, Mario; De Haan, Cornelis A M; Marjomäki, Varpu; Hyypiä, Timo; Rottier, Peter J M; Sodeik, Beate; Marsh, Mark; Gruenberg, Jean; Amara, Ali; Greber, Urs; Helenius, Ari; Pelkmans, Lucas

2012-01-01

Isogenic cells in culture show strong variability, which arises from dynamic adaptations to the microenvironment of individual cells. Here we study the influence of the cell population context, which determines a single cell's microenvironment, in image-based RNAi screens. We developed a comprehensive computational approach that employs Bayesian and multivariate methods at the single-cell level. We applied these methods to 45 RNA interference screens of various sizes, including 7 druggable genome and 2 genome-wide screens, analysing 17 different mammalian virus infections and four related cell physiological processes. Analysing cell-based screens at this depth reveals widespread RNAi-induced changes in the population context of individual cells leading to indirect RNAi effects, as well as perturbations of cell-to-cell variability regulators. We find that accounting for indirect effects improves the consistency between siRNAs targeted against the same gene, and between replicate RNAi screens performed in different cell lines, in different labs, and with different siRNA libraries. In an era where large-scale RNAi screens are increasingly performed to reach a systems-level understanding of cellular processes, we show that this is often improved by analyses that account for and incorporate the single-cell microenvironment. PMID:22531119

Tree of Life Reveals Clock-Like Speciation and Diversification

PubMed Central

Hedges, S. Blair; Marin, Julie; Suleski, Michael; Paymer, Madeline; Kumar, Sudhir

2015-01-01

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process. PMID:25739733

The influence of mid-latitude storm tracks on hot, cold, dry and wet extremes

PubMed Central

Lehmann, Jascha; Coumou, Dim

2015-01-01

Changes in mid-latitude circulation can strongly affect the number and intensity of extreme weather events. In particular, high-amplitude quasi-stationary planetary waves have been linked to prolonged weather extremes at the surface. In contrast, analyses of fast-traveling synoptic-scale waves and their direct influence on heat and cold extremes are scarce though changes in such waves have been detected and are projected for the 21st century. Here we apply regression analyses of synoptic activity with surface temperature and precipitation in monthly gridded observational data. We show that over large parts of mid-latitude continental regions, summer heat extremes are associated with low storm track activity. In winter, the occurrence of cold spells is related to low storm track activity over parts of eastern North America, Europe, and central- to eastern Asia. Storm tracks thus have a moderating effect on continental temperatures. Pronounced storm track activity favors monthly rainfall extremes throughout the year, whereas dry spells are associated with a lack thereof. Trend analyses reveal significant regional changes in recent decades favoring the occurrence of cold spells in the eastern US, droughts in California and heat extremes over Eurasia. PMID:26657163

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed

Condamine, Fabien L; Clapham, Matthew E; Kergoat, Gael J

2016-01-18

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed Central

Condamine, Fabien L.; Clapham, Matthew E.; Kergoat, Gael J.

2016-01-01

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders. PMID:26778170

Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco.

PubMed

Garcia, I; Rodgers, M; Pepin, R; Hsieh, T F; Matringe, M

1999-04-01

4-Hydroxyphenylpyruvate dioxygenase (4HPPD) catalyzes the formation of homogentisate (2,5-dihydroxyphenylacetate) from p-hydroxyphenylpyruvate and molecular oxygen. In plants this enzyme activity is involved in two distinct metabolic processes, the biosynthesis of prenylquinones and the catabolism of tyrosine. We report here the molecular and biochemical characterization of an Arabidopsis 4HPPD and the compartmentation of the recombinant protein in chlorophyllous tissues. We isolated a 1508-bp cDNA with one large open reading frame of 1338 bp. Southern analysis strongly suggested that this Arabidopsis 4HPPD is encoded by a single-copy gene. We investigated the biochemical characteristics of this 4HPPD by overproducing the recombinant protein in Escherichia coli JM105. The subcellular localization of the recombinant 4HPPD in chlorophyllous tissues was examined by overexpressing its complete coding sequence in transgenic tobacco (Nicotiana tabacum), using Agrobacterium tumefaciens transformation. We performed western analyses for the immunodetection of protein extracts from purified chloroplasts and total leaf extracts and for the immunocytochemistry on tissue sections. These analyses clearly revealed that 4HPPD was confined to the cytosol compartment, not targeted to the chloroplast. Western analyses confirmed the presence of a cytosolic form of 4HPPD in cultured green Arabidopsis cells.

Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

NASA Astrophysics Data System (ADS)

Maier, E.; Buckenmaier, A.; Tollrian, R.; Nürnberger, B.

2012-06-01

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.

Patterns and Correlates of Serostatus Disclosure to Sexual Partners by Perinatally-Infected Adolescents and Young Adults.

PubMed

Weintraub, Amy; Mellins, Claude A; Warne, Patricia; Dolezal, Curtis; Elkington, Katherine; Bucek, Amelia; Leu, Cheng-Shiun; Bamji, Mahrukh; Wiznia, Andrew; Abrams, Elaine J

2017-01-01

Similar to same-age peers, perinatally HIV-infected (PHIV+) youth in the US are engaging in sex, including condomless sex. Understanding decisions about serostatus disclosure to sexual partners is important to domestic and global HIV prevention efforts, since large numbers of PHIV+ children are entering adolescence and becoming sexually active. Using Social Action Theory (SAT) to inform variable selection, we examined correlates of disclosure among 98 PHIV+ adolescents/young adults in New York City. Over half of these youth reported not disclosing to any casual partners (59 %) or to any partners when using condoms (55 %). In bivariate analyses, increased disclosure was associated with older age; being female; earlier age of learning one's serostatus; and increased STD knowledge, disclosure intentions, and parent-child communication. Multiple regression analyses revealed a strong fit with the SAT model. As with adults, disclosure to sexual partners is difficult for PHIV+ youth and challenges prevention efforts. Effective interventions that help youth with disclosure decisions are needed to curb the epidemic.

The taxonomic status of genetically divergent populations of Lutzomyia longipalpis (Diptera: Psychodidae) based on the distribution of mitochondrial and isozyme variation.

PubMed

Arrivillaga, Jazzmin; Mutebi, John-Paul; Piñango, Hermes; Norris, Douglas; Alexander, Bruce; Feliciangeli, M Dora; Lanzaro, Gregory C

2003-09-01

The sand fly, Lutzomyia longipalpis (Lutz & Neiva) reputedly is a complex of cryptic species; however, there is currently no consensus as to the number of species in the complex or their geographic distributions. We conducted phylogenetic analyses of 31 populations from throughout the species range, using seven isozyme loci and genes in the mitochondrial genome. Analyses of these two independent sets of markers were largely concordant and revealed four distinct clades that support the existence of four species. The four clades have distinct geographic ranges: (1) Brazil (Species A = Lu. longipalpis sensu stricto), (2) Laran (Species B = Lu. pseudolongipalpis), (3) cis-Andean (Species C), and (4) trans-Andean (Species D). The cis-Andean clade may be subdivided further into two groups, one in Colombia and one in northwestern Venezuela, but their taxonomic status remains unresolved. Knowledge that Lu. longipalpis is a complex of species may ultimately shed light on anomalies in the epidemiology of visceral leishmaniasis in the New World.

Software development for the analysis of heartbeat sounds with LabVIEW in diagnosis of cardiovascular disease.

PubMed

Topal, Taner; Polat, Hüseyin; Güler, Inan

2008-10-01

In this paper, a time-frequency spectral analysis software (Heart Sound Analyzer) for the computer-aided analysis of cardiac sounds has been developed with LabVIEW. Software modules reveal important information for cardiovascular disorders, it can also assist to general physicians to come up with more accurate and reliable diagnosis at early stages. Heart sound analyzer (HSA) software can overcome the deficiency of expert doctors and help them in rural as well as urban clinics and hospitals. HSA has two main blocks: data acquisition and preprocessing, time-frequency spectral analyses. The heart sounds are first acquired using a modified stethoscope which has an electret microphone in it. Then, the signals are analysed using the time-frequency/scale spectral analysis techniques such as STFT, Wigner-Ville distribution and wavelet transforms. HSA modules have been tested with real heart sounds from 35 volunteers and proved to be quite efficient and robust while dealing with a large variety of pathological conditions.

High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations

PubMed Central

Stegelmann, Frank; Bullinger, Lars; Griesshammer, Martin; Holzmann, Karlheinz; Habdank, Marianne; Kuhn, Susanne; Maile, Carmen; Schauer, Stefanie; Döhner, Hartmut; Döhner, Konstanze

2010-01-01

Single-nucleotide polymorphism arrays allow for genome-wide profiling of copy-number alterations and copy-neutral runs of homozygosity at high resolution. To identify novel genetic lesions in myeloproliferative neoplasms, a large series of 151 clinically well characterized patients was analyzed in our study. Copy-number alterations were rare in essential thrombocythemia and polycythemia vera. In contrast, approximately one third of myelofibrosis patients exhibited small genomic losses (less than 5 Mb). In 2 secondary myelofibrosis cases the tumor suppressor gene NF1 in 17q11.2 was affected. Sequencing analyses revealed a mutation in the remaining NF1 allele of one patient. In terms of copy-neutral aberrations, no chromosomes other than 9p were recurrently affected. In conclusion, novel genomic aberrations were identified in our study, in particular in patients with myelofibrosis. Further analyses on single-gene level are necessary to uncover the mechanisms that are involved in the pathogenesis of myeloproliferative neoplasms. PMID:20015882

Differential Contribution of Low- and High-level Image Content to Eye Movements in Monkeys and Humans.

PubMed

Wilming, Niklas; Kietzmann, Tim C; Jutras, Megan; Xue, Cheng; Treue, Stefan; Buffalo, Elizabeth A; König, Peter

2017-01-01

Oculomotor selection exerts a fundamental impact on our experience of the environment. To better understand the underlying principles, researchers typically rely on behavioral data from humans, and electrophysiological recordings in macaque monkeys. This approach rests on the assumption that the same selection processes are at play in both species. To test this assumption, we compared the viewing behavior of 106 humans and 11 macaques in an unconstrained free-viewing task. Our data-driven clustering analyses revealed distinct human and macaque clusters, indicating species-specific selection strategies. Yet, cross-species predictions were found to be above chance, indicating some level of shared behavior. Analyses relying on computational models of visual saliency indicate that such cross-species commonalities in free viewing are largely due to similar low-level selection mechanisms, with only a small contribution by shared higher level selection mechanisms and with consistent viewing behavior of monkeys being a subset of the consistent viewing behavior of humans. © The Author 2017. Published by Oxford University Press.

Differential Contribution of Low- and High-level Image Content to Eye Movements in Monkeys and Humans

PubMed Central

Wilming, Niklas; Kietzmann, Tim C.; Jutras, Megan; Xue, Cheng; Treue, Stefan; Buffalo, Elizabeth A.; König, Peter

2017-01-01

Abstract Oculomotor selection exerts a fundamental impact on our experience of the environment. To better understand the underlying principles, researchers typically rely on behavioral data from humans, and electrophysiological recordings in macaque monkeys. This approach rests on the assumption that the same selection processes are at play in both species. To test this assumption, we compared the viewing behavior of 106 humans and 11 macaques in an unconstrained free-viewing task. Our data-driven clustering analyses revealed distinct human and macaque clusters, indicating species-specific selection strategies. Yet, cross-species predictions were found to be above chance, indicating some level of shared behavior. Analyses relying on computational models of visual saliency indicate that such cross-species commonalities in free viewing are largely due to similar low-level selection mechanisms, with only a small contribution by shared higher level selection mechanisms and with consistent viewing behavior of monkeys being a subset of the consistent viewing behavior of humans. PMID:28077512

Intra-Trackway Morphological Variations Due to Substrate Consistency: The El Frontal Dinosaur Tracksite (Lower Cretaceous, Spain)

PubMed Central

Razzolini, Novella L.; Vila, Bernat; Castanera, Diego; Falkingham, Peter L.; Barco, José Luis; Canudo, José Ignacio; Manning, Phillip L.; Galobart, Àngel

2014-01-01

An ichnological and sedimentological study of the El Frontal dinosaur tracksite (Early Cretaceous, Cameros basin, Soria, Spain) highlights the pronounced intra-trackway variation found in track morphologies of four theropod trackways. Photogrammetric 3D digital models revealed various and distinct intra-trackway morphotypes, which reflect changes in footprint parameters such as the pace length, the track length, depth, and height of displacement rims. Sedimentological analyses suggest that the original substrate was non-homogenous due to lateral changes in adjoining microfacies. Multidata analyses indicate that morphological differences in these deep and shallow tracks represent a part of a continuum of track morphologies and geometries produced by a gradient of substrate consistencies across the site. This implies that the large range of track morphologies at this site resulted from similar trackmakers crossing variable facies. The trackways at the El Frontal site present an exemplary case of how track morphology, and consequently potential ichnotaxa, can vary, even when produced by a single trackmaker. PMID:24699696

Anomalous chemical changes in well waters and possible relation to earthquakes

NASA Astrophysics Data System (ADS)

King, Chi-Yu; Evans, William C.; Presser, Theresa; Husk, Robert H.

Water level, temperature, salinity, electric conductivity, and pH have been measured periodically for several years at three water wells located along a 17-km segment of the San Andreas fault between San Juan Bautista and Cienega Winery in central California. Water samples were collected at the same time for subsequent chemical analyses in the laboratory. Some sudden large changes in salinity and conductivity were recorded in early March 1980 at the two wells near San Juan Bautista. These changes coincided approximately with the beginning of an episode of increased local seismicity, including a magnitude 4.8 earthquake on April 13. Analyses of water samples revealed corresponding changes in ion concentrations, especially of Na+, Ca++, Mg++, SO4--, HCO3-, F-, and Cl-. The observed changes may be the result of mixing of waters from different aquifers through cracks developed in the water barriers by a possible crustal strain episode that may have occurred in the study area.

Anomalous chemical changes in well waters and possible relation to earthquakes.

USGS Publications Warehouse

Chi-Yu, King; Evans, William C.; Presser, T.; Husk, R.H.

1981-01-01

Water level, temperature, salinity, electric conductivity, and pH have been measured periodically for several years at three water wells located along a 17km segment of the San Andreas fault between San Juan Bautista and Cienega Winery in central California. Water samples were collected at the same time for subsequent chemical analyses in the laboratory. Some sudden large changes in salinity and conductivity were recorded in early March 1980 at the two wells near San Juan Bautista. These changes coincided approximately with the beginning of an episode of increased local seismicity, including a magnitude 4.8 earthquake on April 13. Analyses of water samples revealed corresponding changes in ion concentrations, especially of Na+, Ca2+, Mg2+, 035SO42-, 046HCO3-, F-, and Cl-. The observed changes may be the result of mixing of waters from different aquifers through cracks developed in the water barriers by a possible crustal strain episode that may have occurred in the study area.-Authors

Differential relationships between set-shifting abilities and dimensions of insight in schizophrenia.

PubMed

Diez-Martin, J; Moreno-Ortega, M; Bagney, A; Rodriguez-Jimenez, R; Padilla-Torres, D; Sanchez-Morla, E M; Santos, J L; Palomo, T; Jimenez-Arriero, M A

2014-01-01

To assess insight in a large sample of patients with schizophrenia and to study its relationship with set shifting as an executive function. The insight of a sample of 161 clinically stable, community-dwelling patients with schizophrenia was evaluated by means of the Scale to Assess Unawareness of Mental Disorder (SUMD). Set shifting was measured using the Trail-Making Test time required to complete part B minus the time required to complete part A (TMT B-A). Linear regression analyses were performed to investigate the relationships of TMT B-A with different dimensions of general insight. Regression analyses revealed a significant association between TMT B-A and two of the SUMD general components: 'awareness of mental disorder' and 'awareness of the efficacy of treatment'. The 'awareness of social consequences' component was not significantly associated with set shifting. Our results show a significant relation between set shifting and insight, but not in the same manner for the different components of the SUMD general score. Copyright © 2013 S. Karger AG, Basel.

Range contractions of the world's large carnivores

PubMed Central

2017-01-01

The majority of the world's terrestrial large carnivores have undergone substantial range contractions and many of these species are currently threatened with extinction. However, there has been little effort to fully quantify the extent of large carnivore range contractions, which hinders our ability to understand the roles and relative drivers of such trends. Here we present and analyse a newly constructed and comprehensive set of large carnivore range contraction maps. We reveal the extent to which ranges have contracted since historical times and identify regions and biomes where range contractions have been particularly large. In summary, large carnivores that have experienced the greatest range contractions include the red wolf (Canis rufus) (greater than 99%), Ethiopian wolf (Canis simensis) (99%), tiger (Panthera tigris) (95%) and lion (Panthera leo) (94%). In general, the greatest range contractions occurred in Southeastern Asia and Africa. Motivated by the ecological importance of intact large carnivore guilds, we also examined the spatial extent of intact large carnivore guilds both for the entire world and regionally. We found that intact carnivore guilds occupy just 34% of the world's land area. This compares to 96% in historic times. Spatial modelling of range contractions showed that contractions were significantly more likely in regions with high rural human population density, cattle density or cropland. Our results offer new insights into how best to prevent further range contractions for the world's largest carnivores, which will assist efforts to conserve these species and their important ecological effects. PMID:28791136

Range contractions of the world's large carnivores.

PubMed

Wolf, Christopher; Ripple, William J

2017-07-01

The majority of the world's terrestrial large carnivores have undergone substantial range contractions and many of these species are currently threatened with extinction. However, there has been little effort to fully quantify the extent of large carnivore range contractions, which hinders our ability to understand the roles and relative drivers of such trends. Here we present and analyse a newly constructed and comprehensive set of large carnivore range contraction maps. We reveal the extent to which ranges have contracted since historical times and identify regions and biomes where range contractions have been particularly large. In summary, large carnivores that have experienced the greatest range contractions include the red wolf ( Canis rufus ) (greater than 99%), Ethiopian wolf ( Canis simensis ) (99%), tiger ( Panthera tigris ) (95%) and lion ( Panthera leo ) (94%). In general, the greatest range contractions occurred in Southeastern Asia and Africa. Motivated by the ecological importance of intact large carnivore guilds, we also examined the spatial extent of intact large carnivore guilds both for the entire world and regionally. We found that intact carnivore guilds occupy just 34% of the world's land area. This compares to 96% in historic times. Spatial modelling of range contractions showed that contractions were significantly more likely in regions with high rural human population density, cattle density or cropland. Our results offer new insights into how best to prevent further range contractions for the world's largest carnivores, which will assist efforts to conserve these species and their important ecological effects.

Diachronic investigations of mitochondrial and Y-chromosomal genetic markers in pre-Columbian Andean highlanders from South Peru.

PubMed

Fehren-Schmitz, Lars; Warnberg, Ole; Reindel, Markus; Seidenberg, Verena; Tomasto-Cagigao, Elsa; Isla-Cuadrado, Johny; Hummel, Susanne; Herrmann, Bernd

2011-03-01

This study examines the reciprocal effects of cultural evolution, and population dynamics in pre-Columbian southern Peru by the analysis of DNA from pre-Columbian populations that lived in the fringe area between the Andean highlands and the Pacific coast. The main objective is to reveal whether the transition from the Middle Horizon (MH: 650-1000 AD) to the Late Intermediate Period (LIP: 1000-1400 AD) was accompanied or influenced by population dynamic processes. Tooth samples from 90 individuals from several archaeological sites, dating to the MH and LIP, in the research area were collected to analyse mitochodrial, and Y-chromosomal genetic markers. Coding region polymorphisms were successfully analysed and replicated for 72 individuals, as were control region sequences for 65 individuals and Y-chromosomal single nucleotide polymorphisms (SNPs) for 19 individuals, and these were compared to a large set of ancient and modern indigenous South American populations. The diachronic comparison of the upper valley samples from both time periods reveals no genetic discontinuities accompanying the cultural dynamic processes. A high genetic affinity for other ancient and modern highland populations can be observed, suggesting genetic continuity in the Andean highlands at the latest from the MH. A significant matrilineal differentiation to ancient Peruvian coastal populations can be observed suggesting a differential population history. © 2010 The Authors Annals of Human Genetics © 2010 Blackwell Publishing Ltd/University College London.

Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress

PubMed Central

Schmid, Christoph; Bauer, Sibylle; Müller, Benedikt; Bartelheimer, Maik

2013-01-01

Root-root interactions are much more sophisticated than previously thought, yet the mechanisms of belowground neighbor perception remain largely obscure. Genome-wide transcriptome analyses allow detailed insight into plant reactions to environmental cues. A root interaction trial was set up to explore both morphological and whole genome transcriptional responses in roots of Arabidopsis thaliana in the presence or absence of an inferior competitor, Hieracium pilosella. Neighbor perception was indicated by Arabidopsis roots predominantly growing away from the neighbor (segregation), while solitary plants placed more roots toward the middle of the pot. Total biomass remained unaffected. Database comparisons in transcriptome analysis revealed considerable similarity between Arabidopsis root reactions to neighbors and reactions to pathogens. Detailed analyses of the functional category “biotic stress” using MapMan tools found the sub-category “pathogenesis-related proteins” highly significantly induced. A comparison to a study on intraspecific competition brought forward a core of genes consistently involved in reactions to neighbor roots. We conclude that beyond resource depletion roots perceive neighboring roots or their associated microorganisms by a relatively uniform mechanism that involves the strong induction of pathogenesis-related proteins. In an ecological context the findings reveal that belowground neighbor detection may occur independently of resource depletion, allowing for a time advantage for the root to prepare for potential interactions. PMID:23967000

Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands.

PubMed

Correa, Sandra Bibiana; Arujo, Joisiane K; Penha, Jerry; Nunes da Cunha, Catia; Bobier, Karen E; Anderson, Jill T

2016-08-31

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence-absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore-fruit interactions. © 2016 The Author(s).

Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma

PubMed Central

Seliger, Barbara; Dressler, Sven P.; Wang, Ena; Kellner, Roland; Recktenwald, Christian V.; Lottspeich, Friedrich; Marincola, Francesco M.; Baumgärtner, Maja; Atkins, Derek; Lichtenfels, Rudolf

2012-01-01

Results obtained from expression profilings of renal cell carcinoma using different “ome”-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to upregulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%) and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely 3 candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain and ubiquitin carboxyl-terminal hydrolase L1 the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors. PMID:19235166

Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands

PubMed Central

Arujo, Joisiane K.; Penha, Jerry; Nunes da Cunha, Catia

2016-01-01

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence–absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore–fruit interactions. PMID:27581879

Multivariate pattern analysis of MEG and EEG: A comparison of representational structure in time and space.

PubMed

Cichy, Radoslaw Martin; Pantazis, Dimitrios

2017-09-01

Multivariate pattern analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data can reveal the rapid neural dynamics underlying cognition. However, MEG and EEG have systematic differences in sampling neural activity. This poses the question to which degree such measurement differences consistently bias the results of multivariate analysis applied to MEG and EEG activation patterns. To investigate, we conducted a concurrent MEG/EEG study while participants viewed images of everyday objects. We applied multivariate classification analyses to MEG and EEG data, and compared the resulting time courses to each other, and to fMRI data for an independent evaluation in space. We found that both MEG and EEG revealed the millisecond spatio-temporal dynamics of visual processing with largely equivalent results. Beyond yielding convergent results, we found that MEG and EEG also captured partly unique aspects of visual representations. Those unique components emerged earlier in time for MEG than for EEG. Identifying the sources of those unique components with fMRI, we found the locus for both MEG and EEG in high-level visual cortex, and in addition for MEG in low-level visual cortex. Together, our results show that multivariate analyses of MEG and EEG data offer a convergent and complimentary view on neural processing, and motivate the wider adoption of these methods in both MEG and EEG research. Copyright © 2017 Elsevier Inc. All rights reserved.

A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite

PubMed Central

Lee, Ann-Ying; Chen, Chun-Yi; Chang, Yao-Chien Alex; Chao, Ya-Ting; Shih, Ming-Che

2013-01-01

Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns. PMID:24265826

3-Hydroxyisobutyrate Dehydrogenase Is Involved in Both, Valine and Isoleucine Degradation in Arabidopsis thaliana.

PubMed

Schertl, Peter; Danne, Lennart; Braun, Hans-Peter

2017-09-01

In plants, amino acid catabolism is especially relevant in metabolic stress situations (e.g. limited carbohydrate availability during extended darkness). Under these conditions, amino acids are used as alternative substrates for respiration. Complete oxidation of the branched-chain amino acids (BCAAs) leucine, isoleucine (Ile), and valine (Val) in the mitochondria efficiently allows the formation of ATP by oxidative phosphorylation. However, the metabolic pathways for BCAA breakdown are largely unknown so far in plants. A systematic search for Arabidopsis ( Arabidopsis thaliana ) genes encoding proteins resembling enzymes involved in BCAA catabolism in animals, fungi, and bacteria as well as proteomic analyses of mitochondrial fractions from Arabidopsis allowed the identification of a putative 3-hydroxyisobutyrate dehydrogenase, AtHDH1 (At4g20930), involved in Val degradation. Systematic substrate screening analyses revealed that the protein uses 3-hydroxyisobutyrate but additionally 3-hydroxypropionate as substrates. This points to a role of the enzyme not only in Val but possibly also in Ile metabolism. At4g20930 knockdown plants were characterized to test this conclusion. Root toxicity assays revealed increased root growth inhibition of the mutants if cultivated in the presence of Val or Ile but not in the presence of leucine. We conclude that AtHDH1 has a dual role in BCAA metabolism in plants. © 2017 American Society of Plant Biologists. All Rights Reserved.

Varved sediments from Lake Czechowskie (Poland) reveal gradual increase in Atlantic influence during the Holocene

NASA Astrophysics Data System (ADS)

Ott, Florian; Brauer, Achim; Słowiński, Michał; Wulf, Sabine; Putyrskaya, Victoria; Plessen, Birgit; Błaszkiewicz, Miroslaw

2015-04-01

Detailed micro-facies and geochemical analyses have been carried out for the predominantly varved Holocene sediment record of Lake Czechowskie (north-central Poland). The chronology has been established by a multiple dating approach comprising varve counting, AMS 14C dating, 137Cs activity concentration measurements and tephrochronology. The combination of independent dating techniques revealed well-constrained time scales even in phases lacking annual laminations and allows reliable high-resolution archive synchronization. Quantitative (varve thickness variations) and qualitative (sublayer structure) varve parameters as well as geochemical composition have been obtained to gain a comprehensive view of climatic and environmental evolution during the last 11500 years in northern Poland. Five major sedimentological changes have been identified, encompassing transitions from varved to non-varved sediments (and vice versa) at 10.100 and 7.300 cal a BP, respectively, changes in general varve pattern at 6.500 and 4.200 cal a BP and distinct increase of varve thickness accompanied by increased annual variability since 2.800 cal a BP. These changes reflect large-scale reorganization of the climate system throughout the Holocene with increasing influences of the North Atlantic climate system in Poland. Moreover, the observed changes suggest different thresholds and trigger mechanisms over the investigated time period. This study is a contribution to the Virtual Institute of Integrated Climate and Landscape Evolution Analyses - ICLEA - of the Helmholtz Association, grant number VH-VI-415.

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

PubMed Central

Wei, Chih-Hsuan; Hakala, Kai; Pyysalo, Sampo; Ananiadou, Sophia; Kao, Hung-Yu; Lu, Zhiyong; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip

2013-01-01

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license. PMID:23613707

Extracting climate signals from large hydrological data cubes using multivariate statistics - an example for the Mediterranean basin

NASA Astrophysics Data System (ADS)

Kauer, Agnes; Dorigo, Wouter; Bauer-Marschallinger, Bernhard

2017-04-01

Global warming is expected to change ocean-atmosphere oscillation patterns, e.g. the El Nino Southern Oscillation, and may thus have a substantial impact on water resources over land. Yet, the link between climate oscillations and terrestrial hydrology has large uncertainties. In particular, the climate in the Mediterranean basin is expected to be sensitive to global warming as it may increase insufficient and irregular water supply and lead to more frequent and intense droughts and heavy precipitation events. The ever increasing need for water in tourism and agriculture reinforce the problem. Therefore, the monitoring and better understanding of the hydrological cycle are crucial for this area. This study seeks to quantify the effect of regional climate modes, e.g. the Northern Atlantic Oscillation (NAO) on the hydrological cycle in the Mediterranean. We apply Empirical Orthogonal Functions (EOF) to a wide range of hydrological datasets to extract the major modes of variation over the study period. We use more than ten datasets describing precipitation, soil moisture, evapotranspiration, and changes in water mass with study periods ranging from one to three decades depending on the dataset. The resulting EOFs are then examined for correlations with regional climate modes using Spearman rank correlation analysis. This is done for the entire time span of the EOFs and for monthly and seasonally sampled data. We find relationships between the hydrological datasets and the climate modes NAO, Arctic Oscillation (AO), Eastern Atlantic (EA), and Tropical Northern Atlantic (TNA). Analyses of monthly and seasonally sampled data reveal high correlations especially in the winter months. However, the spatial extent of the data cube considered for the analyses have a large impact on the results. Our statistical analyses suggest an impact of regional climate modes on the hydrological cycle in the Mediterranean area and may provide valuable input for evaluating process-oriented climate models. The study is supported by WACMOS-MED project of the European Space Agency.

Default mode network abnormalities in posttraumatic stress disorder: A novel network-restricted topology approach.

PubMed

Akiki, Teddy J; Averill, Christopher L; Wrocklage, Kristen M; Scott, J Cobb; Averill, Lynnette A; Schweinsburg, Brian; Alexander-Bloch, Aaron; Martini, Brenda; Southwick, Steven M; Krystal, John H; Abdallah, Chadi G

2018-08-01

Disruption in the default mode network (DMN) has been implicated in numerous neuropsychiatric disorders, including posttraumatic stress disorder (PTSD). However, studies have largely been limited to seed-based methods and involved inconsistent definitions of the DMN. Recent advances in neuroimaging and graph theory now permit the systematic exploration of intrinsic brain networks. In this study, we used resting-state functional magnetic resonance imaging (fMRI), diffusion MRI, and graph theoretical analyses to systematically examine the DMN connectivity and its relationship with PTSD symptom severity in a cohort of 65 combat-exposed US Veterans. We employed metrics that index overall connectivity strength, network integration (global efficiency), and network segregation (clustering coefficient). Then, we conducted a modularity and network-based statistical analysis to identify DMN regions of particular importance in PTSD. Finally, structural connectivity analyses were used to probe whether white matter abnormalities are associated with the identified functional DMN changes. We found decreased DMN functional connectivity strength to be associated with increased PTSD symptom severity. Further topological characterization suggests decreased functional integration and increased segregation in subjects with severe PTSD. Modularity analyses suggest a spared connectivity in the posterior DMN community (posterior cingulate, precuneus, angular gyrus) despite overall DMN weakened connections with increasing PTSD severity. Edge-wise network-based statistical analyses revealed a prefrontal dysconnectivity. Analysis of the diffusion networks revealed no alterations in overall strength or prefrontal structural connectivity. DMN abnormalities in patients with severe PTSD symptoms are characterized by decreased overall interconnections. On a finer scale, we found a pattern of prefrontal dysconnectivity, but increased cohesiveness in the posterior DMN community and relative sparing of connectivity in this region. The DMN measures established in this study may serve as a biomarker of disease severity and could have potential utility in developing circuit-based therapeutics. Published by Elsevier Inc.

A reanalysis of cluster randomized trials showed interrupted time-series studies were valuable in health system evaluation.

PubMed

Fretheim, Atle; Zhang, Fang; Ross-Degnan, Dennis; Oxman, Andrew D; Cheyne, Helen; Foy, Robbie; Goodacre, Steve; Herrin, Jeph; Kerse, Ngaire; McKinlay, R James; Wright, Adam; Soumerai, Stephen B

2015-03-01

There is often substantial uncertainty about the impacts of health system and policy interventions. Despite that, randomized controlled trials (RCTs) are uncommon in this field, partly because experiments can be difficult to carry out. An alternative method for impact evaluation is the interrupted time-series (ITS) design. Little is known, however, about how results from the two methods compare. Our aim was to explore whether ITS studies yield results that differ from those of randomized trials. We conducted single-arm ITS analyses (segmented regression) based on data from the intervention arm of cluster randomized trials (C-RCTs), that is, discarding control arm data. Secondarily, we included the control group data in the analyses, by subtracting control group data points from intervention group data points, thereby constructing a time series representing the difference between the intervention and control groups. We compared the results from the single-arm and controlled ITS analyses with results based on conventional aggregated analyses of trial data. The findings were largely concordant, yielding effect estimates with overlapping 95% confidence intervals (CI) across different analytical methods. However, our analyses revealed the importance of a concurrent control group and of taking baseline and follow-up trends into account in the analysis of C-RCTs. The ITS design is valuable for evaluation of health systems interventions, both when RCTs are not feasible and in the analysis and interpretation of data from C-RCTs. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

How is communication of vaccines in traditional media: a systematic review.

PubMed

Catalan-Matamoros, Daniel; Peñafiel-Saiz, Carmen

2018-06-01

Taking into account that a key determinant in public approval of vaccinations is how the media constructs and frames messages about vaccination programmes, our aim is to review communication studies exploring media coverage of vaccines within traditional media venues. Using a registered protocol (PROSPERO: 42017072849), a systematic review was conducted that searched in three international electronic databases (PubMed, Scopus, and the International Bibliography of Social Science) for articles published between 2007 and 2017 following content-analysis methods. The characteristics and outcomes were systematically identified and described. The search yielded 24 eligible studies that were further analysed in the review. Media coverage of vaccines has been largely studied during the last decade. Findings revealed that 62% ( n = 15) of studies analysed the human papillomavirus vaccine, 87% ( n = 21) examined newspapers, and 62% ( n = 15) examined North American media. In relation to media content analyses, 75% found negative messages on vaccines and 83% identified a lack of accurate information. This systematic review suggests an agenda for further research. There is a significant need to analyse other types of traditional media beyond newspapers. Future studies should focus on other geographical areas such as low-income countries and on analysing visual materials and digital media. We found that negative messages and inaccurate information are common in media coverage on vaccines; therefore, further research focusing on these topics is needed. Officials in public health organizations should develop a close collaboration with the media to improve public communication on vaccines.

Study on structural characteristics of pillared clay modified phosphate fertilizers and its increase efficiency mechanism*

PubMed Central

Wu, Ping-xiao; Liao, Zong-wen

2005-01-01

Three types of new high-efficiency phosphate fertilizers were made when pillared clays at certain proportions were added into ground phosphate rock. Chemical analyses showed that their soluble phosphorus content decreased more than that of superphosphate. Pot experiment showed that, under equal weights, the new fertilizers increased their efficiency by a large margin over that of superphosphate. Researches on their structures by means of XRD, IR and EPR spectrum revealed that their crystal structures changed considerably, improving their activity and preventing the fixation of available phosphorus in the soil, and consequently, greatly improved the bioavailability and became the main cause of the increase of biomass. PMID:15682504

Polar nature of stress-induced twin walls in ferroelastic CaTiO3

NASA Astrophysics Data System (ADS)

Yokota, H.; Niki, S.; Haumont, R.; Hicher, P.; Uesu, Y.

2017-08-01

A compressive uniaxial mechanical stress is applied on ferroelastic CaTiO3 (CTO), and a change in the domain structure is observed under a polarization microscope and a second harmonic generation (SHG) microscope. New twin walls (TWs) appear perpendicular to the original TWs under stress. The SHG microscope observations and analyses confirm that this type of stress-induced TWs is polar, similar to the original TWs, and is crystallographically prominent with monoclinic symmetry m. A quantitative estimation of this stress-induced effect reveals that CTO is hard ferroelastic in the sense that the TW movement requires a large stress. A possible application of this phenomenon is discussed.

Immigrants' health in Europe: a cross-classified multilevel approach to examine origin country, destination country, and community effects.

PubMed

Huijts, Tim; Kraaykamp, Gerbert

2012-01-01

In this study, we examined origin, destination, and community effects on first- and second-generation immigrants' health in Europe. We used information from the European Social Surveys (2002–2008) on 19,210 immigrants from 123 countries of origin, living in 31 European countries. Cross-classified multilevel regression analyses reveal that political suppression in the origin country and living in countries with large numbers of immigrant peers have a detrimental influence on immigrants' health. Originating from predominantly Islamic countries and good average health among natives in the destination country appear to be beneficial. Additionally, the results point toward health selection mechanisms into migration.

Concrete lunar base investigation

NASA Technical Reports Server (NTRS)

Lin, T. D.; Senseney, Jonathan A.; Arp, Larry Dean; Lindbergh, Charles

1989-01-01

This paper presents results of structural analyses and a preliminary design of a precast, prestressed concrete lunar based subjected to one atmosphere internal pressure. The proposed infrastructure measures 120 ft in diameter and 72 ft in height, providing 33,000 sq ft of work area for scientific and industrial operations. Three loading conditions were considered in the design: (1) during construction; (2) under pressurization; and (3) during an air-leak scenario. A floating foundation, capable of rigid body rotation and translation as the lunar soil beneath it yields, was developed to support the infrastructure and to ensure the air-tightness of the system. Results reveal that it is feasible to use precast, prestressed concrete for construction of large lunar bases on the moon.

Fatal Case of Deer Tick Virus Encephalitis

PubMed Central

Tavakoli, Norma P.; Wang, Heng; Dupuis, Michelle; Hull, Rene; Ebel, Gregory D.; Gilmore, Emily J.; Faust, Phyllis L.

2010-01-01

SUMMARY Deer tick virus is related to Powassan virus, a tickborne encephalitis virus. A 62-year-old man presented with a meningoencephalitis syndrome and eventually died. Analyses of tissue samples obtained during surgery and at autopsy revealed a widespread necrotizing meningoencephalitis. Nucleic acid was extracted from formalin-fixed tissue, and the presence of deer tick virus was verified on a flavivirus-specific polymerase-chain-reaction (PCR) assay, followed by sequence confirmation. Immunohistochemical analysis with antisera specific for deer tick virus identified numerous immunoreactive neurons, with prominent involvement of large neurons in the brain stem, cerebellum, basal ganglia, thalamus, and spinal cord. This case demonstrates that deer tick virus can be a cause of fatal encephalitis. PMID:19439744

Fatal case of deer tick virus encephalitis.

PubMed

Tavakoli, Norma P; Wang, Heng; Dupuis, Michelle; Hull, Rene; Ebel, Gregory D; Gilmore, Emily J; Faust, Phyllis L

2009-05-14

Deer tick virus is related to Powassan virus, a tickborne encephalitis virus. A 62-year-old man presented with a meningoencephalitis syndrome and eventually died. Analyses of tissue samples obtained during surgery and at autopsy revealed a widespread necrotizing meningoencephalitis. Nucleic acid was extracted from formalin-fixed tissue, and the presence of deer tick virus was verified on a flavivirus-specific polymerase-chain-reaction (PCR) assay, followed by sequence confirmation. Immunohistochemical analysis with antisera specific for deer tick virus identified numerous immunoreactive neurons, with prominent involvement of large neurons in the brain stem, cerebellum, basal ganglia, thalamus, and spinal cord. This case demonstrates that deer tick virus can be a cause of fatal encephalitis. 2009 Massachusetts Medical Society

Concrete lunar base investigation

NASA Technical Reports Server (NTRS)

Lin, T. D.; Senseny, Jonathan A.; Arp, Larry D.; Lindbergh, Charles

1992-01-01

This paper presents results of structural analyses and a preliminary design of a precast, prestressed concrete lunar base subjected to 1-atm internal pressure. The proposed infrastructure measures 120 ft in diameter and 72 ft in height, providing 33,000 sq ft of work area for scientific and industrial operations. Three loading conditions were considered in the design (1) during construction, (2) under pressurization, and (3) during an air-leak scenario. A floating foundation, capable of rigid body rotation and translation as the lunar soil beneath it yields, was developed to support the infrastructure and to ensure the airtightness of the system. Results reveal that it is feasible to use precast, prestressed concrete for construction of large lunar bases on the Moon.

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions.

PubMed

van Haaften, Rachel I M; Luceri, Cristina; van Erk, Arie; Evelo, Chris T A

2009-06-01

Omics technology used for large-scale measurements of gene expression is rapidly evolving. This work pointed out the need of an extensive bioinformatics analyses for array quality assessment before and after gene expression clustering and pathway analysis. A study focused on the effect of red wine polyphenols on rat colon mucosa was used to test the impact of quality control and normalisation steps on the biological conclusions. The integration of data visualization, pathway analysis and clustering revealed an artifact problem that was solved with an adapted normalisation. We propose a possible point to point standard analysis procedure, based on a combination of clustering and data visualization for the analysis of microarray data.

Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

PubMed

Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

2015-02-15

WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

PubMed

DeAtley, K L; Rincon, G; Farber, C R; Medrano, J F; Luna-Nevarez, P; Enns, R M; VanLeeuwen, D M; Silver, G A; Thomas, M G

2011-07-01

ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (P<0.05) birth weight, yet cattle with the large/large genotype had approximately 5.1% greater (P<0.05) percentage of fat within LM and more LM per BW than cattle with small/large or small/small genotypes. Genotype-to-phenotype relationships were not detected in multibreed analyses. The ETH10 locus appears to be associated with growth and carcass traits in Angus and Brangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5. © 2011 American Society of Animal Science. All rights reserved.

Physiological and Metagenomic Analyses of Microbial Mats Involved in Self-Purification of Mine Waters Contaminated with Heavy Metals

PubMed Central

Drewniak, Lukasz; Krawczyk, Pawel S.; Mielnicki, Sebastian; Adamska, Dorota; Sobczak, Adam; Lipinski, Leszek; Burec-Drewniak, Weronika; Sklodowska, Aleksandra

2016-01-01

Two microbial mats found inside two old (gold and uranium) mines in Zloty Stok and Kowary located in SW Poland seem to form a natural barrier that traps heavy metals leaking from dewatering systems. We performed complex physiological and metagenomic analyses to determine which microorganisms are the main driving agents responsible for self-purification of the mine waters and identify metabolic processes responsible for the observed features. SEM and energy dispersive X-ray microanalysis showed accumulation of heavy metals on the mat surface, whereas, sorption experiments showed that neither microbial mats were completely saturated with heavy metals present in the mine waters, indicating that they have a large potential to absorb significant quantities of metal. The metagenomic analysis revealed that Methylococcaceae and Methylophilaceae families were the most abundant in both communities, moreover, it strongly suggest that backbones of both mats were formed by filamentous bacteria, such as Leptothrix, Thiothrix, and Beggiatoa. The Kowary bacterial community was enriched with the Helicobacteraceae family, whereas the Zloty Stok community consist mainly of Sphingomonadaceae, Rhodobacteraceae, and Caulobacteraceae families. Functional (culture-based) and metagenome (sequence-based) analyses showed that bacteria involved in immobilization of heavy metals, rather than those engaged in mobilization, were the main driving force within the analyzed communities. In turn, a comparison of functional genes revealed that the biofilm formation and heavy metal resistance (HMR) functions are more desirable in microorganisms engaged in water purification than the ability to utilize heavy metals in the respiratory process (oxidation-reduction). These findings provide insight on the activity of bacteria leading, from biofilm formation to self-purification, of mine waters contaminated with heavy metals. PMID:27559332

Practicing Dentists’ Self-Efficacy and Associated Factors in Managing the Treatment of Adults with Mental and Physical Disabilities: An Exploratory Cross-Sectional Study in Riyadh, Saudi Arabia

PubMed Central

AlQahtani, Sakher; Zakaria Murshid, Ebtissam; Kassim, Saba

2017-01-01

Background: Provision of oral healthcare to adults with mental and physical disabilities (AMPD) remains a challenging area across various healthcare systems. The present study aimed to assess self-reported efficacy and investigate factors associated with self-efficacy in the management of AMPD among practicing dentists in Saudi Arabia. Methods: A pilot-tested, self-administered questionnaire was distributed to a convenience sample of 1000 dentists. Descriptive and inferential analyses were performed on the collected responses. Results: Among the respondents (54%), 43% were males. Only 14% described their self-efficacy in managing AMPD as “High”. Multivariable regression analyses revealed significant associations between “High” self-efficacy and male gender (Odd ratio (OR) = 2.39, 95% CI = 1.16–4.89), experience practicing dentistry for 11 years or more (OR = 2.19, 95% CI = 1.04–4.47), specialization in pediatric dentistry (OR = 3.98, 95% CI = 1.31–12.07), previous experience in managing AMPD (OR = 4.23, 95% CI = 1.59–11.22), and awareness of regulations for managing AMPD (OR = 2.62, 95% CI = 1.42–4.38). The interaction of gender x age was significantly associated (p = 0.028) with “High” self-efficacy. Gender-stratified analyses revealed a significant association between age and “High” self-efficacy among male dentists only. Conclusions: The findings of the present study highlight that a large percentage of dentists reported “Low/Moderate” self-efficacy in managing AMPD, particularly among female dentists. However, further studies are required to verify the factors associated with self-efficacy in the present study, and to identify other factors that may influence self-efficacy in managing AMPD. PMID:29232884

Practicing Dentists' Self-Efficacy and Associated Factors in Managing the Treatment of Adults with Mental and Physical Disabilities: An Exploratory Cross-Sectional Study in Riyadh, Saudi Arabia.

PubMed

AlQahtani, Sakher; Murshid, Ebtissam Zakaria; Fadel, Hani Talal; Kassim, Saba

2017-12-11

Background: Provision of oral healthcare to adults with mental and physical disabilities (AMPD) remains a challenging area across various healthcare systems. The present study aimed to assess self-reported efficacy and investigate factors associated with self-efficacy in the management of AMPD among practicing dentists in Saudi Arabia. Methods: A pilot-tested, self-administered questionnaire was distributed to a convenience sample of 1000 dentists. Descriptive and inferential analyses were performed on the collected responses. Results: Among the respondents (54%), 43% were males. Only 14% described their self-efficacy in managing AMPD as "High". Multivariable regression analyses revealed significant associations between "High" self-efficacy and male gender (Odd ratio (OR) = 2.39, 95% CI = 1.16-4.89), experience practicing dentistry for 11 years or more (OR = 2.19, 95% CI = 1.04-4.47), specialization in pediatric dentistry (OR = 3.98, 95% CI = 1.31-12.07), previous experience in managing AMPD (OR = 4.23, 95% CI = 1.59-11.22), and awareness of regulations for managing AMPD (OR = 2.62, 95% CI = 1.42-4.38). The interaction of gender x age was significantly associated ( p = 0.028) with "High" self-efficacy. Gender-stratified analyses revealed a significant association between age and "High" self-efficacy among male dentists only. Conclusions: The findings of the present study highlight that a large percentage of dentists reported "Low/Moderate" self-efficacy in managing AMPD, particularly among female dentists. However, further studies are required to verify the factors associated with self-efficacy in the present study, and to identify other factors that may influence self-efficacy in managing AMPD.

Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar

PubMed Central

2014-01-01

Background Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. Results Our aim was to search for genetic footprints of Myanmar’s geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. Conclusion Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia. PMID:24467713

Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in “Real-World” Settings

PubMed Central

Brenner, Bluma G.; Ibanescu, Ruxandra-Ilinca; Hardy, Isabelle; Roger, Michel

2017-01-01

HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings. PMID:29283390

Sex chromosome abnormalities and sterility in river buffalo.

PubMed

Di Meo, G P; Perucatti, A; Di Palo, R; Iannuzzi, A; Ciotola, F; Peretti, V; Neglia, G; Campanile, G; Zicarelli, L; Iannuzzi, L

2008-01-01

Thirteen male river buffaloes, 119 females with reproductive problems (which had reached reproductive age but had failed to become pregnant in the presence of bulls) and two male co-twins underwent both clinical and cytogenetic investigation. Clinical analyses performed by veterinary practitioners revealed normal body conformation and external genitalia for most females. However, some subjects showed some slight male traits such as large base horn circumference, prominent withers and tight pelvis. Rectal palpation revealed damage to internal sex adducts varying between atrophy of Mullerian ducts to complete lack of internal sex adducts (with closed vagina). All bulls had normal karyotypes at high resolution banding, while 25 animals (23 females and 2 male co-twins) (20.7%) with reproductive problems were found to carry the following sex chromosome abnormalities: X monosomy (2 females); X trisomy (1 female); sex reversal syndrome (2 females); and free-martinism (18 females and 2 males). All female carriers were sterile. Copyright 2008 S. Karger AG, Basel.

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

Kimelman, Aya; Levy, Asaf; Sberro, Hila

In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of smallmore » non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator dnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.« less

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

PubMed Central

Dephoure, Noah; Hwang, Sunyoung; O'Sullivan, Ciara; Dodgson, Stacie E; Gygi, Steven P; Amon, Angelika; Torres, Eduardo M

2014-01-01

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms. DOI: http://dx.doi.org/10.7554/eLife.03023.001 PMID:25073701

Discourse of women on Unesa’s magazine

NASA Astrophysics Data System (ADS)

Jatiningsih, O.; Habibah, S. M.

2018-01-01

This research aims to reveal the discourse of women in Unesa as mentioned in Unesa’s magazine that is Media of Information and Communication. The data are collected by using documentation technique. The objects of the study are archives, some articles of women published in the Unesa’s magazine. Since 2009, there are three editions of the magazines talked about women. The research used discourse analyses of Foucault. The results reveal that women have been holding large chance to work and having their success, but they must commit themselves to do their role as a wife and a mother. The dominant savoir is domestication of career women. Moreover, the savoir are (1) Women as the first and principal educators of their children; (2) the sacrifice of a wife is an expression of her devotion to her husband. The women’s main sphere is domestics and public is only as an additional sphere. This reflects that patriarchy gender ideology as dominant discourse placing women on their traditional role has been strongly running.

Trophic segregation of a fish assemblage along lateral depth gradients in a subtropical coastal lagoon revealed by stable isotope analyses.

PubMed

Mont'Alverne, R; Pereyra, P E R; Garcia, A M

2016-07-01

Stable isotopes were used to evaluate the hypothesis that fish assemblages occurring in shallow and deep areas of a large coastal lagoon are structured in partially segregated trophic modules with consumers showing contrasting reliance on benthic or pelagic food sources. The results revealed that fishes in deep areas were mainly dependent on particulate organic matter in the sediment (SOM), whereas emergent macrophytes were as important as SOM to fish consumers in shallow areas. Conceptual trophic diagrams depicting relationships among basal food sources and consumers in different regions of the lagoon highlighted the greater use of multiple basal food sources by more feeding mode functional guilds in shallow water compared with the use of predominantly benthic resources (SOM) in deep areas. The findings appear to corroborate the initial hypothesis and offer complementary perspectives in understanding the role of spatial ecology in structuring coastal ecosystem function and productivity. © 2016 The Fisheries Society of the British Isles.

An mRNA-Derived Noncoding RNA Targets and Regulates the Ribosome

PubMed Central

Pircher, Andreas; Bakowska-Zywicka, Kamilla; Schneider, Lukas; Zywicki, Marek; Polacek, Norbert

2014-01-01

Summary The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells and organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome. This 18-mer ncRNA binds to polysomes upon salt stress and is crucial for efficient growth under hyperosmotic conditions. Although the 18-mer RNA originates from the TRM10 locus, which encodes a tRNA methyltransferase, genetic analyses revealed the 18-mer RNA nucleotide sequence, rather than the mRNA-encoded enzyme, as the translation regulator. Our data reveal the ribosome as a target for a small regulatory ncRNA and demonstrate the existence of a yet unkown mechanism of translation regulation. Ribosome-targeted small ncRNAs are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules. PMID:24685157

Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

PubMed Central

Beaudet, Denis; Chen, Eric C H; Mathieu, Stephanie; Yildirir, Gokalp; Ndikumana, Steve; Dalpé, Yolande; Séguin, Sylvie; Farinelli, Laurent; Stajich, Jason E; Corradi, Nicolas

2018-01-01

Abstract Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material. PMID:29211832

The fate of b-ions in the two worlds of collision-induced dissociation.

PubMed

Waldera-Lupa, Daniel M; Stefanski, Anja; Meyer, Helmut E; Stühler, Kai

2013-12-01

Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss. © 2013.

Physical Mechanisms Controlling Upper Tropospheric Water Vapor as Revealed by MLS Data from UARS

NASA Technical Reports Server (NTRS)

Newell, Reginald E.

1998-01-01

The seasonal changes of the upper tropospheric humidity are studied with the water vapor data from the Microwave Limb Sounder on the NASA Upper Atmosphere Research Satellite, and the winds and vertical velocity data obtained from the European Centre for Medium-Range Weather Forecasts. Using the same algorithm for vertical transport as that used for horizontal transport (Zhu and Newell, 1998), we find that the moisture in the tropical upper troposphere may be increased mainly by intensified local convection in a small portion, less than 10%, of the whole area between 40 deg S to 40 deg N. The contribution of large scale background circulations and divergence of horizontal transport is relatively small in these regions. These dynamic processes cannot be revealed by the traditional analyses of moisture fluxes. The negative feedback suggested by Lindzen (1990) also exists, if enhanced convection is concentrated in the tropics, but is apparently not the dominant process in the moisture budget.

Discopersicus n. gen., a New Member of the Family Tylenchidae Örley, 1880 with Detailed SEM Study on Two Known Species of the Genus Discotylenchus Siddiqi, 1980 (Nematoda; Tylenchidae) from Iran.

PubMed

Yaghoubi, Ali; Pourjam, Ebrahim; Álvarez-Ortega, Sergio; Liébanas, Gracia; Atighi, Mohammad Reza; Pedram, Majid

2016-09-01

Discopersicus iranicus n. gen., n. comb., previously described from Iran as a new species under the genus Discotylenchus , is illustrated using light microscope and scanning electron microscope (SEM) observations and further studied using molecular characters. SEM studies revealed the newly proposed genus has oblique amphidial apertures on the lateral sides of the lip region. SEM images are also provided for two species of Discotylenchus , namely D. discretus and D. brevicaudatus , as the first SEM study of the genus . These results confirmed longitudinal amphidial aperture type on lateral sides of the lip region in genus Discotylenchus , as noted by Siddiqi while erecting the genus with D. discretus as the type species . Molecular phylogenetic analyses using partial small subunit (SSU) and large subunit (LSU) rDNA sequences revealed the affinity of the genus Discopersicus n. gen. with members of the subfamily Boleodorinae, as supported by morphological characters (mainly, the oblique amphidial opening).

Structural variations in prefrontal cortex mediate the relationship between early childhood stress and spatial working memory

PubMed Central

Hanson, Jamie L.; Chung, Moo K.; Avants, Brian B.; Rudolph, Karen D.; Shirtcliff, Elizabeth A.; Gee, James C.; Davidson, Richard J.; Pollak, Seth D.

2012-01-01

A large corpus of research indicates exposure to stress impairs cognitive abilities, specifically executive functioning dependent on the prefrontal cortex (PFC). We collected structural MRI scans (n=61), well-validated assessments of executive functioning, and detailed interviews assessing stress exposure in humans, to examine whether cumulative life stress affected brain morphometry and one type of executive functioning, spatial working memory, during adolescence—a critical time of brain development and reorganization. Analysis of variations in brain structure revealed that cumulative life stress and spatial working memory were related to smaller volumes in the PFC, specifically prefrontal gray and white matter between the anterior cingulate and the frontal poles. Mediation analyses revealed that individual differences in prefrontal volumes accounted for the association between cumulative life stress and spatial working memory. These results suggest that structural changes in the PFC may serve as a mediating mechanism through which greater cumulative life stress engenders decrements in cognitive functioning. PMID:22674267

Determinants of National Fire Plan Fuels Treatment Expenditures: A Revealed Preference Analysis for Northern New Mexico

NASA Astrophysics Data System (ADS)

Shepherd, Curt; Grimsrud, Kristine; Berrens, Robert P.

2009-10-01

The accumulation of fire fuels in forests throughout the world contributes significantly to the severity of wildfires. To combat the threat of wildfire, especially in the wildland-urban interface (WUI), US federal land management agencies have implemented a number of forest restoration and wildfire risk reduction programs. In the spirit of revealed preference analyses, the objective of this study is to investigate the pattern and determinants of National Fire Plan (NFP) expenditures for fuel reduction treatments in northern New Mexico (USA). Estimation results from a set of Generalized Estimating Equations models are mixed with respect to risk reduction hypotheses, and also raise issues regarding how risk reduction should be defined for a region characterized by both pockets of urban sprawl into the WUI and large areas of chronic rural poverty. Program preferences for project funding under the federal Collaborative Forest Restoration Program in New Mexico are shown to be distinctly different (e.g., exhibiting greater concern for social equity) than for other NFP-funded projects.

Novel insights into the interplay between ventral neck muscles in individuals with whiplash-associated disorders.

PubMed

Peterson, Gunnel; Nilsson, David; Trygg, Johan; Falla, Deborah; Dedering, Åsa; Wallman, Thorne; Peolsson, Anneli

2015-10-16

Chronic whiplash-associated disorder (WAD) is common after whiplash injury, with considerable personal, social, and economic burden. Despite decades of research, factors responsible for continuing pain and disability are largely unknown, and diagnostic tools are lacking. Here, we report a novel model of mechanical ventral neck muscle function recorded from non-invasive, real-time, ultrasound measurements. We calculated the deformation area and deformation rate in 23 individuals with persistent WAD and compared them to 23 sex- and age-matched controls. Multivariate statistics were used to analyse interactions between ventral neck muscles, revealing different interplay between muscles in individuals with WAD and healthy controls. Although the cause and effect relation cannot be established from this data, for the first time, we reveal a novel method capable of detecting different neck muscle interplay in people with WAD. This non-invasive method stands to make a major breakthrough in the assessment and diagnosis of people following a whiplash trauma.

The influence of discrete emotions on judgement and decision-making: a meta-analytic review.

PubMed

Angie, Amanda D; Connelly, Shane; Waples, Ethan P; Kligyte, Vykinta

2011-12-01

During the past three decades, researchers interested in emotions and cognition have attempted to understand the relationship that affect and emotions have with cognitive outcomes such as judgement and decision-making. Recent research has revealed the importance of examining more discrete emotions, showing that same-valence emotions (e.g., anger and fear) differentially impact judgement and decision-making outcomes. Narrative reviews of the literature (Lerner & Tiedens, 2006 ; Pham, 2007 ) have identified some under-researched topics, but provide a limited synthesis of findings. The purpose of this study was to review the research examining the influence of discrete emotions on judgement and decision-making outcomes and provide an assessment of the observed effects using a meta-analytic approach. Results, overall, show that discrete emotions have moderate to large effects on judgement and decision-making outcomes. However, moderator analyses revealed differential effects for study-design characteristics and emotion-manipulation characteristics by emotion type. Implications are discussed.

OSPAR standard method and software for statistical analysis of beach litter data.

PubMed

Schulz, Marcus; van Loon, Willem; Fleet, David M; Baggelaar, Paul; van der Meulen, Eit

2017-09-15

The aim of this study is to develop standard statistical methods and software for the analysis of beach litter data. The optimal ensemble of statistical methods comprises the Mann-Kendall trend test, the Theil-Sen slope estimation, the Wilcoxon step trend test and basic descriptive statistics. The application of Litter Analyst, a tailor-made software for analysing the results of beach litter surveys, to OSPAR beach litter data from seven beaches bordering on the south-eastern North Sea, revealed 23 significant trends in the abundances of beach litter types for the period 2009-2014. Litter Analyst revealed a large variation in the abundance of litter types between beaches. To reduce the effects of spatial variation, trend analysis of beach litter data can most effectively be performed at the beach or national level. Spatial aggregation of beach litter data within a region is possible, but resulted in a considerable reduction in the number of significant trends. Copyright © 2017 Elsevier Ltd. All rights reserved.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

PubMed

Dudas, Gytis; Carvalho, Luiz Max; Bedford, Trevor; Tatem, Andrew J; Baele, Guy; Faria, Nuno R; Park, Daniel J; Ladner, Jason T; Arias, Armando; Asogun, Danny; Bielejec, Filip; Caddy, Sarah L; Cotten, Matthew; D'Ambrozio, Jonathan; Dellicour, Simon; Di Caro, Antonino; Diclaro, Joseph W; Duraffour, Sophie; Elmore, Michael J; Fakoli, Lawrence S; Faye, Ousmane; Gilbert, Merle L; Gevao, Sahr M; Gire, Stephen; Gladden-Young, Adrianne; Gnirke, Andreas; Goba, Augustine; Grant, Donald S; Haagmans, Bart L; Hiscox, Julian A; Jah, Umaru; Kugelman, Jeffrey R; Liu, Di; Lu, Jia; Malboeuf, Christine M; Mate, Suzanne; Matthews, David A; Matranga, Christian B; Meredith, Luke W; Qu, James; Quick, Joshua; Pas, Suzan D; Phan, My V T; Pollakis, Georgios; Reusken, Chantal B; Sanchez-Lockhart, Mariano; Schaffner, Stephen F; Schieffelin, John S; Sealfon, Rachel S; Simon-Loriere, Etienne; Smits, Saskia L; Stoecker, Kilian; Thorne, Lucy; Tobin, Ekaete Alice; Vandi, Mohamed A; Watson, Simon J; West, Kendra; Whitmer, Shannon; Wiley, Michael R; Winnicki, Sarah M; Wohl, Shirlee; Wölfel, Roman; Yozwiak, Nathan L; Andersen, Kristian G; Blyden, Sylvia O; Bolay, Fatorma; Carroll, Miles W; Dahn, Bernice; Diallo, Boubacar; Formenty, Pierre; Fraser, Christophe; Gao, George F; Garry, Robert F; Goodfellow, Ian; Günther, Stephan; Happi, Christian T; Holmes, Edward C; Kargbo, Brima; Keïta, Sakoba; Kellam, Paul; Koopmans, Marion P G; Kuhn, Jens H; Loman, Nicholas J; Magassouba, N'Faly; Naidoo, Dhamari; Nichol, Stuart T; Nyenswah, Tolbert; Palacios, Gustavo; Pybus, Oliver G; Sabeti, Pardis C; Sall, Amadou; Ströher, Ute; Wurie, Isatta; Suchard, Marc A; Lemey, Philippe; Rambaut, Andrew

2017-04-20

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Novel gene function revealed by mouse mutagenesis screens for models of age-related disease.

PubMed

Potter, Paul K; Bowl, Michael R; Jeyarajan, Prashanthini; Wisby, Laura; Blease, Andrew; Goldsworthy, Michelle E; Simon, Michelle M; Greenaway, Simon; Michel, Vincent; Barnard, Alun; Aguilar, Carlos; Agnew, Thomas; Banks, Gareth; Blake, Andrew; Chessum, Lauren; Dorning, Joanne; Falcone, Sara; Goosey, Laurence; Harris, Shelley; Haynes, Andy; Heise, Ines; Hillier, Rosie; Hough, Tertius; Hoslin, Angela; Hutchison, Marie; King, Ruairidh; Kumar, Saumya; Lad, Heena V; Law, Gemma; MacLaren, Robert E; Morse, Susan; Nicol, Thomas; Parker, Andrew; Pickford, Karen; Sethi, Siddharth; Starbuck, Becky; Stelma, Femke; Cheeseman, Michael; Cross, Sally H; Foster, Russell G; Jackson, Ian J; Peirson, Stuart N; Thakker, Rajesh V; Vincent, Tonia; Scudamore, Cheryl; Wells, Sara; El-Amraoui, Aziz; Petit, Christine; Acevedo-Arozena, Abraham; Nolan, Patrick M; Cox, Roger; Mallon, Anne-Marie; Brown, Steve D M

2016-08-18

Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss.

Novel gene function revealed by mouse mutagenesis screens for models of age-related disease

PubMed Central

Potter, Paul K.; Bowl, Michael R.; Jeyarajan, Prashanthini; Wisby, Laura; Blease, Andrew; Goldsworthy, Michelle E.; Simon, Michelle M.; Greenaway, Simon; Michel, Vincent; Barnard, Alun; Aguilar, Carlos; Agnew, Thomas; Banks, Gareth; Blake, Andrew; Chessum, Lauren; Dorning, Joanne; Falcone, Sara; Goosey, Laurence; Harris, Shelley; Haynes, Andy; Heise, Ines; Hillier, Rosie; Hough, Tertius; Hoslin, Angela; Hutchison, Marie; King, Ruairidh; Kumar, Saumya; Lad, Heena V.; Law, Gemma; MacLaren, Robert E.; Morse, Susan; Nicol, Thomas; Parker, Andrew; Pickford, Karen; Sethi, Siddharth; Starbuck, Becky; Stelma, Femke; Cheeseman, Michael; Cross, Sally H.; Foster, Russell G.; Jackson, Ian J.; Peirson, Stuart N.; Thakker, Rajesh V.; Vincent, Tonia; Scudamore, Cheryl; Wells, Sara; El-Amraoui, Aziz; Petit, Christine; Acevedo-Arozena, Abraham; Nolan, Patrick M.; Cox, Roger; Mallon, Anne-Marie; Brown, Steve D. M.

2016-01-01

Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss. PMID:27534441

Effects of Hydrological Parameters on Palm Oil Fresh Fruit Bunch Yield)

NASA Astrophysics Data System (ADS)

Nda, M.; Adnan, M. S.; Suhadak, M. A.; Zakaria, M. S.; Lopa, R. T.

2018-04-01

Climate change effects and variability have been studied by many researchers in diverse geophysical fields. Malaysia produces large volume of palm oil, the effects of climate change on hydrological parameters (rainfall and precipitation) could have adverse effects on palm oil fresh fruit bunch (FFB) production with implications at both local and international market. It is important to understand the effects of climate change on crop yield to adopt new cultivation techniques and guaranteeing food security globally. Based on this background, the paper’s objective is to investigate the effects of rainfall and temperature pattern on crop yield (FFB) within five years period (2013 - 2017) at Batu Pahat District. The Man - Kendall rank technique (trend test) and statistical analyses (correlation and regression) were applied to the dataset used for the study. The results reveal that there are variabilities in rainfall and temperature from one month to the other and the statistical analysis reveals that the hydrological parameters have an insignificant effect on crop yield.

Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells.

PubMed

Sun, Rui; Fu, Ling; Liu, Keke; Tian, Caiping; Yang, Yong; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C; Yang, Jing

2017-10-01

4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adduct to cysteine. ONE-derived adducts co-localize and exhibit crosstalk with many histone marks and redox sensitive sites. All four types of modifications derived from ONE can be reversed site-specifically in cells. Taken together, our study provides much-needed mechanistic insights into the cellular signaling and potential toxicities associated with this important lipid derived electrophile. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

SCFSAP controls organ size by targeting PPD proteins for degradation in Arabidopsis thaliana

PubMed Central

Wang, Zhibiao; Li, Na; Jiang, Shan; Gonzalez, Nathalie; Huang, Xiahe; Wang, Yingchun; Inzé, Dirk; Li, Yunhai

2016-01-01

Control of organ size by cell proliferation and growth is a fundamental process, but the mechanisms that determine the final size of organs are largely elusive in plants. We have previously revealed that the ubiquitin receptor DA1 regulates organ size by repressing cell proliferation in Arabidopsis. Here we report that a mutant allele of STERILE APETALA (SAP) suppresses the da1-1 mutant phenotype. We show that SAP is an F-box protein that forms part of a SKP1/Cullin/F-box E3 ubiquitin ligase complex and controls organ size by promoting the proliferation of meristemoid cells. Genetic analyses suggest that SAP may act in the same pathway with PEAPOD1 and PEAPOD2, which are negative regulators of meristemoid proliferation, to control organ size, but does so independently of DA1. Further results reveal that SAP physically associates with PEAPOD1 and PEAPOD2, and targets them for degradation. These findings define a molecular mechanism by which SAP and PEAPOD control organ size. PMID:27048938

SCF(SAP) controls organ size by targeting PPD proteins for degradation in Arabidopsis thaliana.

PubMed

Wang, Zhibiao; Li, Na; Jiang, Shan; Gonzalez, Nathalie; Huang, Xiahe; Wang, Yingchun; Inzé, Dirk; Li, Yunhai

2016-04-06

Control of organ size by cell proliferation and growth is a fundamental process, but the mechanisms that determine the final size of organs are largely elusive in plants. We have previously revealed that the ubiquitin receptor DA1 regulates organ size by repressing cell proliferation in Arabidopsis. Here we report that a mutant allele of STERILE APETALA (SAP) suppresses the da1-1 mutant phenotype. We show that SAP is an F-box protein that forms part of a SKP1/Cullin/F-box E3 ubiquitin ligase complex and controls organ size by promoting the proliferation of meristemoid cells. Genetic analyses suggest that SAP may act in the same pathway with PEAPOD1 and PEAPOD2, which are negative regulators of meristemoid proliferation, to control organ size, but does so independently of DA1. Further results reveal that SAP physically associates with PEAPOD1 and PEAPOD2, and targets them for degradation. These findings define a molecular mechanism by which SAP and PEAPOD control organ size.

Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions.

PubMed

Goard, Michael J; Pho, Gerald N; Woodson, Jonathan; Sur, Mriganka

2016-08-04

Mapping specific sensory features to future motor actions is a crucial capability of mammalian nervous systems. We investigated the role of visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices for sensorimotor mapping in mice during performance of a memory-guided visual discrimination task. Large-scale calcium imaging revealed that V1, PPC, and fMC neurons exhibited heterogeneous responses spanning all task epochs (stimulus, delay, response). Population analyses demonstrated unique encoding of stimulus identity and behavioral choice information across regions, with V1 encoding stimulus, fMC encoding choice even early in the trial, and PPC multiplexing the two variables. Optogenetic inhibition during behavior revealed that all regions were necessary during the stimulus epoch, but only fMC was required during the delay and response epochs. Stimulus identity can thus be rapidly transformed into behavioral choice, requiring V1, PPC, and fMC during the transformation period, but only fMC for maintaining the choice in memory prior to execution.

Differential Relations of Depression and Social Anxiety Symptoms to the Facets of Extraversion/Positive Emotionality

PubMed Central

Naragon-Gainey, Kristin; Watson, David; Markon, Kristian E.

2009-01-01

Previous research has shown that depression and social anxiety—two “facets” of internalizing psychopathology— both are characterized by low levels of extraversion/positive emotionality (E/PE). However, little is known about the relations of the facets of E/PE with symptoms of depression and social anxiety. This study utilized multiple measures of each facet of E/PE, as well as depression and social anxiety symptoms. Self-report data were collected from large samples of college students and psychiatric outpatients. Separate factor analyses in each sample revealed a four-factor structure of E/PE, consisting of Sociability, Positive Emotionality, Ascendance, and Fun-Seeking. Structural equation modeling revealed that, after controlling for the higher-order internalizing factor and the overlap among the E/PE facets, social anxiety was broadly related to all four facets of E/PE, whereas depression was strongly related only to low positive emotionality. Implications for hierarchical models of personality and psychopathology, assessment and treatment, and etiological models are discussed. PMID:19413405

Sunken wood habitat for thiotrophic symbiosis in mangrove swamps.

PubMed

Laurent, Mélina C Z; Gros, Olivier; Brulport, Jean-Pierre; Gaill, Françoise; Bris, Nadine Le

2009-03-01

Large organic falls to the benthic environment, such as dead wood or whale bones, harbour organisms relying on sulfide-oxidizing symbionts. Nothing is known however, concerning sulfide enrichment at the wood surface and its relation to wood colonization by sulfide-oxidizing symbiotic organisms. In this study we combined in situ hydrogen sulfide and pH measurements on sunken wood, with associated fauna microscopy analyses in a tropical mangrove swamp. This shallow environment is known to harbour thiotrophic symbioses and is also abundantly supplied with sunken wood. A significant sulfide enrichment at the wood surface was revealed. A 72h sequence of measurements emphasized the wide fluctuation of sulfide levels (0.1->100muM) over time with both a tidal influence and rapid fluctuations. Protozoans observed on the wood surface were similar to Zoothamnium niveum and to vorticellids. Our SEM observations revealed their association with ectosymbiotic bacteria, which are likely to be sulfide-oxidizers. These results support the idea that sunken wood surfaces constitute an environment suitable for sulfide-oxidizing symbioses.

Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity

PubMed Central

Sakamoto, Manabu; Ruta, Marcello

2012-01-01

Background Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation. PMID:22792186

Plastidic Phosphoglucose Isomerase Is an Important Determinant of Starch Accumulation in Mesophyll Cells, Growth, Photosynthetic Capacity, and Biosynthesis of Plastidic Cytokinins in Arabidopsis

PubMed Central

De Diego, Nuria; Muñoz, Francisco J.; Baroja-Fernández, Edurne; Li, Jun; Ricarte-Bermejo, Adriana; Baslam, Marouane; Aranjuelo, Iker; Almagro, Goizeder; Humplík, Jan F.; Novák, Ondřej; Spíchal, Lukáš; Doležal, Karel; Pozueta-Romero, Javier

2015-01-01

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization of glucose-6-phosphate and fructose-6-phosphate. It is involved in glycolysis and in the regeneration of glucose-6-P molecules in the oxidative pentose phosphate pathway (OPPP). In chloroplasts of illuminated mesophyll cells PGI also connects the Calvin-Benson cycle with the starch biosynthetic pathway. In this work we isolated pgi1-3, a mutant totally lacking pPGI activity as a consequence of aberrant intron splicing of the pPGI encoding gene, PGI1. Starch content in pgi1-3 source leaves was ca. 10-15% of that of wild type (WT) leaves, which was similar to that of leaves of pgi1-2, a T-DNA insertion pPGI null mutant. Starch deficiency of pgi1 leaves could be reverted by the introduction of a sex1 null mutation impeding β-amylolytic starch breakdown. Although previous studies showed that starch granules of pgi1-2 leaves are restricted to both bundle sheath cells adjacent to the mesophyll and stomata guard cells, microscopy analyses carried out in this work revealed the presence of starch granules in the chloroplasts of pgi1-2 and pgi1-3 mesophyll cells. RT-PCR analyses showed high expression levels of plastidic and extra-plastidic β-amylase encoding genes in pgi1 leaves, which was accompanied by increased β-amylase activity. Both pgi1-2 and pgi1-3 mutants displayed slow growth and reduced photosynthetic capacity phenotypes even under continuous light conditions. Metabolic analyses revealed that the adenylate energy charge and the NAD(P)H/NAD(P) ratios in pgi1 leaves were lower than those of WT leaves. These analyses also revealed that the content of plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway derived cytokinins (CKs) in pgi1 leaves were exceedingly lower than in WT leaves. Noteworthy, exogenous application of CKs largely reverted the low starch content phenotype of pgi1 leaves. The overall data show that pPGI is an important determinant of photosynthesis, energy status, growth and starch accumulation in mesophyll cells likely as a consequence of its involvement in the production of OPPP/glycolysis intermediates necessary for the synthesis of plastidic MEP-pathway derived hormones such as CKs. PMID:25811607

Lower catecholamine activity is associated with greater levels of anger in adults.

PubMed

Schwartz, Joseph A; Portnoy, Jill

2017-10-01

Previous research has revealed a consistent association between heart rate at rest and during stress and behavioral problems, potentially implicating autonomic nervous system (ANS) functioning in the etiological development of antisocial behavior. A complementary line of research has focused on the potential independent and interactive role of the two subsystems that comprise the ANS, the parasympathetic nervous system (PNS) and the sympathetic nervous system (SNS), on behavioral problems. The current study aims to contribute to the existing literature by examining the influence of heart rate (HR) reactivity, high-frequency heart rate variability (HF-HRV) reactivity, and catecholamine activity on a comprehensive measure of anger in a large, nationally-representative sample of adults from the United States. Results from a series of structural equation models (SEMs) revealed that catecholamine activity was most consistently linked to anger, while associations involving HR and HF-HRV reactivity were nonsignificant. Additional analyses revealed that HF-HRV did not significantly moderate the association between catecholamine activity and anger. These findings highlight the importance of SNS activity in the development of more reactive forms of aggression such as anger. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of Panglial Gap Junction Networks in the Thalamus, Neocortex, and Hippocampus Reveals a Unique Population of Glial Cells

PubMed Central

Griemsmann, Stephanie; Höft, Simon P.; Bedner, Peter; Zhang, Jiong; von Staden, Elena; Beinhauer, Anna; Degen, Joachim; Dublin, Pavel; Cope, David W.; Richter, Nadine; Crunelli, Vincenzo; Jabs, Ronald; Willecke, Klaus; Theis, Martin; Seifert, Gerald; Kettenmann, Helmut; Steinhäuser, Christian

2015-01-01

The thalamus plays important roles as a relay station for sensory information in the central nervous system (CNS). Although thalamic glial cells participate in this activity, little is known about their properties. In this study, we characterized the formation of coupled networks between astrocytes and oligodendrocytes in the murine ventrobasal thalamus and compared these properties with those in the hippocampus and cortex. Biocytin filling of individual astrocytes or oligodendrocytes revealed large panglial networks in all 3 gray matter regions. Combined analyses of mice with cell type-specific deletion of connexins (Cxs), semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and western blotting showed that Cx30 is the dominant astrocytic Cx in the thalamus. Many thalamic astrocytes even lack expression of Cx43, while in the hippocampus astrocytic coupling is dominated by Cx43. Deletion of Cx30 and Cx47 led to complete loss of panglial coupling, which was restored when one allele of either Cxs was present. Immunohistochemistry revealed a unique antigen profile of thalamic glia and identified an intermediate cell type expressing both Olig2 and Cx43. Our findings further the emerging concept of glial heterogeneity across brain regions. PMID:25037920

Investigation of Structure and Property of Indian Cocos nucifera L. Fibre

NASA Astrophysics Data System (ADS)

Basu, Gautam; Mishra, Leena; Samanta, Ashis Kumar

2017-12-01

Structure and physico-mechanical properties of Cocos nucifera L. fibre from a specific agro-climatic region of India, was thoroughly studied. Fine structure of the fibre was examined by Fourier Transform Infra-Red (FTIR) spectroscopy, Thermo-Gravimetric Analysis (TGA), X-Ray Diffraction (XRD), component analysis, Scanning Electron Microscope (SEM) and optical microscope. SEM shows prominent longitudinal cracks and micro-pores on the surface. XRD shows a low degree of crystallinity (45%), bigger crystallite size, and even the presence of appreciable amount of non-cellulose matter. FTIR reveals presence of large quantities of hydroxyl, phenolic and aldehyde groups. Component and thermal analyses indicates presence of cellulose and lignin as major components. Physical parameters reveal that, fibres are highly variable in length (range 44-305 mm), and diameter (range 100-795 µm). Mechanical properties of the fibre viz. breaking tenacity, breaking extensibility, specific work of rupture, and coefficient of friction were measured. Microbial decomposition test under soil reveals excellent durability of coconut fibre which makes it appropriate for the application in geotextiles. Mass specific electrical resistance of 4 Ω-kg/m2 indicates its enhanced insulation as compared to the jute.

Circadian analysis of large human populations: inferences from the power grid.

PubMed

Stowie, Adam C; Amicarelli, Mario J; Crosier, Caitlin J; Mymko, Ryan; Glass, J David

2015-03-01

Few, if any studies have focused on the daily rhythmic nature of modern industrialized populations. The present study utilized real-time load data from the U.S. Pacific Northwest electrical power grid as a reflection of human operative household activity. This approach involved actigraphic analyses of continuously streaming internet data (provided in 5 min bins) from a human subject pool of approximately 43 million primarily residential users. Rhythm analyses reveal striking seasonal and intra-week differences in human activity patterns, largely devoid of manufacturing and automated load interference. Length of the diurnal activity period (alpha) is longer during the spring than the summer (16.64 h versus 15.98 h, respectively; p < 0.01). As expected, significantly more activity occurs in the solar dark phase during the winter than during the summer (6.29 h versus 2.03 h, respectively; p < 0.01). Interestingly, throughout the year a "weekend effect" is evident, where morning activity onset occurs approximately 1 h later than during the work week (5:54 am versus 6:52 am, respectively; p < 0.01). This indicates a general phase-delaying response to the absence of job-related or other weekday morning arousal cues, substantiating a preference or need to sleep longer on weekends. Finally, a shift in onset time can be seen during the transition to Day Light Saving Time, but not the transition back to Standard Time. The use of grid power load as a means for human actimetry assessment thus offers new insights into the collective diurnal activity patterns of large human populations.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses.

PubMed

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore's space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species' space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species' space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses

PubMed Central

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore’s space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species’ space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species’ space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes. PMID:26630393

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

PubMed

Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

2014-01-01

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

Genome size diversity in orchids: consequences and evolution

PubMed Central

Leitch, I. J.; Kahandawala, I.; Suda, J.; Hanson, L.; Ingrouille, M. J.; Chase, M. W.; Fay, M. F.

2009-01-01

Background The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae. Scope A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0·33–55·4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity. Conclusions Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study. PMID:19168860

21 CFR 814.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., reports of adverse events, or new analyses of previously submitted data (e.g., meta-analyses) if the studies, events or analyses reveal risks of a different type or greater severity or frequency than... per year. (o) Newly acquired information means data, analyses, or other information not previously...

Phylogenomic and functional analyses of salmon lice aquaporins uncover the molecular diversity of the superfamily in Arthropoda.

PubMed

Stavang, Jon Anders; Chauvigné, Francois; Kongshaug, Heidi; Cerdà, Joan; Nilsen, Frank; Finn, Roderick Nigel

2015-08-19

An emerging field in biomedical research is focusing on the roles of aquaporin water channels in parasites that cause debilitating or lethal diseases to their vertebrate hosts. The primary vectorial agents are hematophagous arthropods, including mosquitoes, flies, ticks and lice, however very little is known concerning the functional diversity of aquaporins in non-insect members of the Arthropoda. Here we conducted phylogenomic and functional analyses of aquaporins in the salmon louse, a marine ectoparasitic copepod that feeds on the skin and body fluids of salmonids, and used the primary structures of the isolated channels to uncover the genomic repertoires in Arthropoda. Genomic screening identified 7 aquaporin paralogs in the louse in contrast to 42 in its host the Atlantic salmon. Phylogenetic inference of the louse nucleotides and proteins in relation to orthologs identified in Chelicerata, Myriapoda, Crustacea and Hexapoda revealed that the arthropod aquaporin superfamily can be classified into three major grades (1) classical aquaporins including Big brain (Bib) and Prip-like (PripL) channels (2) aquaglyceroporins (Glp) and (3) unorthodox aquaporins (Aqp12-like). In Hexapoda, two additional subfamilies exist as Drip and a recently classified entomoglyceroporin (Eglp) group. Cloning and remapping the louse cDNAs to the genomic DNA revealed that they are encoded by 1-7 exons, with two of the Glps being expressed as N-terminal splice variants (Glp1_v1, -1_v2, -3_v1, -3_v2). Heterologous expression of the cRNAs in amphibian oocytes demonstrated that PripL transports water and urea, while Bib does not. Glp1_v1, -2, -3_v1 and -3_v2 each transport water, glycerol and urea, while Glp1_v2 and the Aqp12-like channels were retained intracellularly. Transcript abundance analyses revealed expression of each louse paralog at all developmental stages, except for glp1_v1, which is specific to preadult and adult males. Our data suggest that the aquaporin repertoires of extant arthropods have expanded independently in the different lineages, but can be phylogenetically classified into three major grades as opposed to four present in deuterostome animals. While the aquaporin repertoire of Atlantic salmon represents a 6-fold redundancy compared to the louse, the functional assays reveal that the permeation properties of the different crustacean grades of aquaporin are largely conserved to the vertebrate counterparts.

The paradox of HBV evolution as revealed from a 16th century mummy

PubMed Central

Duggan, Ana T.; Poinar, Debi; Poinar, Hendrik N.

2018-01-01

Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen. PMID:29300782

Layered Crustal and Mantle Structure and Anisotropy beneath the Afar Depression and Malawi Rift Zone

NASA Astrophysics Data System (ADS)

Reed, Cory Alexander

Although a wealth of geophysical data sets have been acquired within the vicinity of continental rift zones, the mechanisms responsible for the breakup of stable continental lithosphere are ambiguous. Eastern Africa is host to the largest contemporary rift zone on Earth, and is thus the most prominent site with which to investigate the processes which govern the rupture of continental lithosphere. The studies herein represent teleseismic analyses of the velocity and thermomechanical structure of the crust and mantle beneath the Afar Depression and Malawi Rift Zone (MRZ) of the East African Rift System. Within the Afar Depression, the first densely-spaced receiver function investigation of crustal thickness and inferred velocity attenuation across the Tendaho Graben is conducted, and the largest to-date study of the topography of the mantle transition zone (MTZ) beneath NE Africa is provided, which reveals low upper-mantle velocities beneath the Afar concordant with a probable mantle plume traversing the MTZ beneath the western Ethiopian Plateau. In the vicinity of the MRZ, a data set comprised of 35 seismic stations is employed that was deployed over a two year period from mid-2012 to mid-2014, belonging to the SAFARI (Seismic Arrays For African Rift Initiation) experiment. Accordingly, the first MTZ topography and shear wave splitting analyses were conducted in the region. The latter reveals largely plate motion-parallel anisotropy that is locally modulated by lithospheric thickness abnormalities adjacent to the MRZ, while the former reveals normal MTZ thicknesses and shallow discontinuities that support the presence of a thick lithospheric keel within the MRZ region. These evidences strongly argue for the evolution of the MRZ via passive rifting mechanisms absent lower-mantle influences.

Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains

PubMed Central

Davidson, Rebecca M.; Hasan, Nabeeh A.; de Moura, Vinicius Calado Nogueira; Duarte, Rafael Silva; Jackson, Mary; Strong, Michael

2013-01-01

Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents. PMID:24055961

Women and Men Together in Recruit Training.

PubMed

Orme, Geoffrey J; Kehoe, E James

2018-05-01

Although men and women recruits to the Australian Army have trained in mixed-gender platoons since 1995, restrictions on women joining the combat arms were only removed in 2016. As part of a longitudinal study starting with recruit training, this article examined recruit records collected before 2016 with the aims of delineating (1) the relative performance of women versus men in mixed-gender platoons and (2) the relative performance of men in mixed-gender platoons versus all-male platoons. De-identified instructor ratings for 630 females and 4,505 males who completed training between 2011 and 2015 were obtained. Recruits were distributed across 128 platoons (averaging 41.6 members, SD = 8.3) of which 75% contained females, in proportions from 5% to 45%. These analyses were conducted under defense ethics approval DPR-LREP 069-15. Factor analyses revealed that instructor ratings generally loaded onto a single factor, accounting 77.2% of the variance. Consequently, a composite recruit performance score (range 1-5) was computed for 16 of 19 competencies. Analyses of the scores revealed that the distributions of the scores for females and males overlapped considerably. Observed effects were negligible to small in size. The distributions were all centered between 3.0 and 3.5. In mixed-gender platoons, 51% of the females and 52% of the males fell in this band, and 44% of recruits in all-male platoons had scores in this band. The lower three bands (1.0-3.0) contained a slightly greater proportion of females (18%) than males in either mixed-gender platoons (12%) or all-male platoons (12%). Conversely, the upper three bands (3.5-5.0) contained a slightly smaller percentage of females (31%) than males in either mixed-gender platoons (36%) or all-male platoons (44%). Although scores for females were reliably lower than those of males in mixed-gender platoons, χ2 (4) = 16.01, p < 0.01, the effect size (V = 0.07) did not reach the criterion for even a small effect (0.10). For male recruits, those in mixed-gender platoons had scores that were reliably lower than in all-male platoons, χ2 (4) = 48.38, p < 0.001; its effect size (V = 0.11) just exceeded the criterion for a small effect (0.10). Further analyses revealed that male scores had a near-zero correlation (r = -0.033) with the proportion of females in platoons (0-45%). This large-scale secondary analysis of instructor ratings of female and male recruits provides a platform for monitoring the integration of women into the combat arms. The analyses revealed nearly complete overlap in the performance of female versus male recruits. The detected gender-related differences were negligible to small in size. These small differences must be viewed with considerable caution. They may be artifacts of rater bias or other uncontrolled features of the rating system, which was designed for reporting individual recruit performance rather than aggregate analyses. Even with these limitations, this baseline snapshot of recruit performance suggests that, at recruit training, women and men are already working well together, which bodes well for their subsequent integration into the combat arms.

What Would I Know About Mercy? Faith and Optimistic Expectancies Among African Americans

PubMed Central

Mattis, Jacqueline S.; Powell, Wizdom; Grayman, Nyasha A.; Murray, Yohance; Cole-Lewis, Yasmin C.; Goodwill, Janelle R.

2017-01-01

A small body of research has begun to explore the association between faith and optimism among African Americans. However, missing from the extant work is an examination of the extent to which traditional indices of religious commitment work together with beliefs about God to shape optimism. The present study examines the utility of indices of social location, religious commitment (i.e., early and current religious service attendance, subjective religiosity), belief about the quality of one’s relationship with God (i.e., a belief that one is connected to a loving God), and beliefs about being the recipient of divine forgiveness for predicting dispositional optimism among a sample of community residing African American adults (N = 241). Age, subjective religiosity, and organizational religiosity were positively related to optimism in bivariate analyses. Hierarchical regression analyses demonstrated a significant association between age, subjective religiosity, and optimism; however, those associations were eliminated once relationship with God and belief in one’s forgiveness by God were entered into the model. Only belief in God’s love predicted optimism in multivariate analyses. Serial mediation analyses revealed that beliefs about the quality of one’s relationship with God and belief in divine forgiveness fully mediated the relationship between subjective religiosity and optimism, but that the relationship is driven largely by relationship with God. Implications of these findings are discussed. PMID:29057016

Analyses from Near (Meteorites) and Far (Spacecraft): Complementary Approaches to Planetary Geochemistry

NASA Astrophysics Data System (ADS)

McSween, H. Y.

2013-12-01

Spacecraft missions have transformed planets from astronomical objects into geologic worlds, but geochemical remote sensing has limits. Considerably greater geologic insights are possible for a few bodies to which we can confidently assign meteorite samples. Mars and asteroid 4 Vesta demonstrate the advances provided by coupling spacecraft remote sensing data and laboratory analyses of meteorites. Martian meteorites sample at least 7 as-yet unidentified sites but are strongly biased towards young crystallization ages compared to Martian surface ages. Geochemical comparison with generally older rocks analyzed by Mars rovers APXS reveals evolutionary differences [1] that might be explained by water or redox state. Trace elements and radiogenic isotopes, readily measured in Martian meteorites but not yet possible by remote sensing, constrain the planet's volatile inventory, the chronology of magmatism, and the compositions of mantle source regions and the bulk planet [2]. The origin and geochemical cycling of water that orbiters indicate once sculpted Mars' geomorphology and now resides in the Martian subsurface is revealed by measurements of stable isotopes and of apatite OH in meteorites. Although sedimentary rocks are nearly absent from the Martian meteorite collection, determining the processes that produced the regolith and the nature and source of organic matter on Mars are facilitated by comparing rover analyses of soils with meteorite data. In a similar way, analyses of Vesta by the Dawn orbiting spacecraft [3] are leveraged by laboratory analyses of the howardite, eucrite, diogenite (HED) meteorites [4]. Visible/near-infrared spectra of HEDs provide the calibration necessary for lithologic mapping of Vesta's surface, revealing an ancient eucrite crust, diogenite excavated from a huge crater, and a pervasive regolith of howardite. Gamma-ray and neutron data from Vesta are similarly interpreted by comparison with meteorite elemental abundances. The unexpected discovery of hydrogen in low-albedo regions on Vesta is explained by incorporation of carbonaceous chondrite impactor debris, as seen in clasts within howardites. An estimate of Vesta's bulk composition based on HEDs is consistent with the measured bulk density and the calculated mass of the core. The meteorites provide information on igneous and impact chronology and constrain models for Vesta's magmatic differentiation, which can be tested with spacecraft remote sensing observations. Meteorite analyses are limited by lack of geologic context, and spacecraft data are hampered by incomplete geochemical measurements, but taken together they offer great synergy. Mars and Vesta (and, of course, the Moon) illustrate that planets, large and small, can be rigorously deciphered by geochemical analyses, from near and far. [1] McSween, H. Y. et al. (2009) Science, 324, 736-739, [2] McSween, H. Y. and McLennan, S. M. (2013) Treatise in Geochemistry, 2nd ed., in press, [3] Russell C. T., et al. (2012) Science, 336, 684-686, [4] McSween, H. Y. et al. (2012) Space Sci. Rev., 163-174.

Comparative immunogenomics of molluscs.

PubMed

Schultz, Jonathan H; Adema, Coen M

2017-10-01

Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity. Initial studies showed that the Mollusca (second largest animal phylum), and invertebrates in general, possess innate defenses but lack the lymphocytic immune system that characterizes vertebrate immunology. Recognizing the reality of both common and taxon-specific immune features, and applying up-to-date cell and molecular research capabilities, in-depth studies of a select number of bivalve and gastropod species continue to reveal novel aspects of molluscan immunity. The genomics era heralded a new stage of comparative immunology; large-scale efforts yielded an initial set of full molluscan genome sequences that is available for analyses of full complements of immune genes and regulatory sequences. Next-generation sequencing (NGS), due to lower cost and effort required, allows individual researchers to generate large sequence datasets for growing numbers of molluscs. RNAseq provides expression profiles that enable discovery of immune genes and genome sequences reveal distribution and diversity of immune factors across molluscan phylogeny. Although computational de novo sequence assembly will benefit from continued development and automated annotation may require some experimental validation, NGS is a powerful tool for comparative immunology, especially increasing coverage of the extensive molluscan diversity. To date, immunogenomics revealed new levels of complexity of molluscan defense by indicating sequence heterogeneity in individual snails and bivalves, and members of expanded immune gene families are expressed differentially to generate pathogen-specific defense responses. Copyright © 2017 Elsevier Ltd. All rights reserved.

An Evaluation of a Theoretical Model Predicting Dieting Behaviors: Tests of Measurement and Structural Invariance across Ethnicity and Gender

ERIC Educational Resources Information Center

Boie, Ioana; Lopez, Anna L.; Sass, Daniel A.

2013-01-01

This study evaluated a model linking internalization and dieting behaviors in a sample ("n" = 499) of Latina/o and White college students. Analyses revealed that the scales were invariant across ethnic and gender groups and generally supported the invariance of the proposed model across these groups. Analyses also revealed no ethnic mean…

Utilization of Large Scale Surface Models for Detailed Visibility Analyses

NASA Astrophysics Data System (ADS)

Caha, J.; Kačmařík, M.

2017-11-01

This article demonstrates utilization of large scale surface models with small spatial resolution and high accuracy, acquired from Unmanned Aerial Vehicle scanning, for visibility analyses. The importance of large scale data for visibility analyses on the local scale, where the detail of the surface model is the most defining factor, is described. The focus is not only the classic Boolean visibility, that is usually determined within GIS, but also on so called extended viewsheds that aims to provide more information about visibility. The case study with examples of visibility analyses was performed on river Opava, near the Ostrava city (Czech Republic). The multiple Boolean viewshed analysis and global horizon viewshed were calculated to determine most prominent features and visibility barriers of the surface. Besides that, the extended viewshed showing angle difference above the local horizon, which describes angular height of the target area above the barrier, is shown. The case study proved that large scale models are appropriate data source for visibility analyses on local level. The discussion summarizes possible future applications and further development directions of visibility analyses.

Seafood prices reveal impacts of a major ecological disturbance

PubMed Central

Smith, Martin D.; Oglend, Atle; Kirkpatrick, A. Justin; Asche, Frank; Bennear, Lori S.; Craig, J. Kevin; Nance, James M.

2017-01-01

Coastal hypoxia (dissolved oxygen ≤ 2 mg/L) is a growing problem worldwide that threatens marine ecosystem services, but little is known about economic effects on fisheries. Here, we provide evidence that hypoxia causes economic impacts on a major fishery. Ecological studies of hypoxia and marine fauna suggest multiple mechanisms through which hypoxia can skew a population’s size distribution toward smaller individuals. These mechanisms produce sharp predictions about changes in seafood markets. Hypoxia is hypothesized to decrease the quantity of large shrimp relative to small shrimp and increase the price of large shrimp relative to small shrimp. We test these hypotheses using time series of size-based prices. Naive quantity-based models using treatment/control comparisons in hypoxic and nonhypoxic areas produce null results, but we find strong evidence of the hypothesized effects in the relative prices: Hypoxia increases the relative price of large shrimp compared with small shrimp. The effects of fuel prices provide supporting evidence. Empirical models of fishing effort and bioeconomic simulations explain why quantifying effects of hypoxia on fisheries using quantity data has been inconclusive. Specifically, spatial-dynamic feedbacks across the natural system (the fish stock) and human system (the mobile fishing fleet) confound “treated” and “control” areas. Consequently, analyses of price data, which rely on a market counterfactual, are able to reveal effects of the ecological disturbance that are obscured in quantity data. Our results are an important step toward quantifying the economic value of reduced upstream nutrient loading in the Mississippi Basin and are broadly applicable to other coupled human-natural systems. PMID:28137850

Structure-Function Analysis of a Broad Specificity Populus trichocarpa Endo-β-glucanase Reveals an Evolutionary Link between Bacterial Licheninases and Plant XTH Gene Products*

PubMed Central

Eklöf, Jens M.; Shojania, Shaheen; Okon, Mark; McIntosh, Lawrence P.; Brumer, Harry

2013-01-01

The large xyloglucan endotransglycosylase/hydrolase (XTH) gene family continues to be the focus of much attention in studies of plant cell wall morphogenesis due to the unique catalytic functions of the enzymes it encodes. The XTH gene products compose a subfamily of glycoside hydrolase family 16 (GH16), which also comprises a broad range of microbial endoglucanases and endogalactanases, as well as yeast cell wall chitin/β-glucan transglycosylases. Previous whole-family phylogenetic analyses have suggested that the closest relatives to the XTH gene products are the bacterial licheninases (EC 3.2.1.73), which specifically hydrolyze linear mixed linkage β(1→3)/β(1→4)-glucans. In addition to their specificity for the highly branched xyloglucan polysaccharide, XTH gene products are distinguished from the licheninases and other GH16 enzyme subfamilies by significant active site loop alterations and a large C-terminal extension. Given these differences, the molecular evolution of the XTH gene products in GH16 has remained enigmatic. Here, we present the biochemical and structural analysis of a unique, mixed function endoglucanase from black cottonwood (Populus trichocarpa), which reveals a small, newly recognized subfamily of GH16 members intermediate between the bacterial licheninases and plant XTH gene products. We postulate that this clade comprises an important link in the evolution of the large plant XTH gene families from a putative microbial ancestor. As such, this analysis provides new insights into the diversification of GH16 and further unites the apparently disparate members of this important family of proteins. PMID:23572521

Magnetic fields at uranus.

PubMed

Ness, N F; Acuña, M H; Behannon, K W; Burlaga, L F; Connerney, J E; Lepping, R P; Neubauer, F M

1986-07-04

The magnetic field experiment on the Voyager 2 spacecraft revealed a strong planetary magnetic field of Uranus and an associated magnetosphere and fully developed bipolar masnetic tail. The detached bow shock wave in the solar wind supersonic flow was observed upstream at 23.7 Uranus radii (1 R(U) = 25,600 km) and the magnetopause boundary at 18.0 R(U), near the planet-sun line. A miaximum magnetic field of 413 nanotesla was observed at 4.19 R(U ), just before closest approach. Initial analyses reveal that the planetary magnetic field is well represented by that of a dipole offset from the center of the planet by 0.3 R(U). The angle between Uranus' angular momentum vector and the dipole moment vector has the surprisingly large value of 60 degrees. Thus, in an astrophysical context, the field of Uranus may be described as that of an oblique rotator. The dipole moment of 0.23 gauss R(3)(U), combined with the large spatial offset, leads to minimum and maximum magnetic fields on the surface of the planet of approximately 0.1 and 1.1 gauss, respectively. The rotation period of the magnetic field and hence that of the interior of the planet is estimated to be 17.29+/- 0.10 hours; the magnetotail rotates about the planet-sun line with the same period. Thelarge offset and tilt lead to auroral zones far from the planetary rotation axis poles. The rings and the moons are embedded deep within the magnetosphere, and, because of the large dipole tilt, they will have a profound and diurnally varying influence as absorbers of the trapped radiation belt particles.

Seafood prices reveal impacts of a major ecological disturbance.

PubMed

Smith, Martin D; Oglend, Atle; Kirkpatrick, A Justin; Asche, Frank; Bennear, Lori S; Craig, J Kevin; Nance, James M

2017-02-14

Coastal hypoxia (dissolved oxygen ≤ 2 mg/L) is a growing problem worldwide that threatens marine ecosystem services, but little is known about economic effects on fisheries. Here, we provide evidence that hypoxia causes economic impacts on a major fishery. Ecological studies of hypoxia and marine fauna suggest multiple mechanisms through which hypoxia can skew a population's size distribution toward smaller individuals. These mechanisms produce sharp predictions about changes in seafood markets. Hypoxia is hypothesized to decrease the quantity of large shrimp relative to small shrimp and increase the price of large shrimp relative to small shrimp. We test these hypotheses using time series of size-based prices. Naive quantity-based models using treatment/control comparisons in hypoxic and nonhypoxic areas produce null results, but we find strong evidence of the hypothesized effects in the relative prices: Hypoxia increases the relative price of large shrimp compared with small shrimp. The effects of fuel prices provide supporting evidence. Empirical models of fishing effort and bioeconomic simulations explain why quantifying effects of hypoxia on fisheries using quantity data has been inconclusive. Specifically, spatial-dynamic feedbacks across the natural system (the fish stock) and human system (the mobile fishing fleet) confound "treated" and "control" areas. Consequently, analyses of price data, which rely on a market counterfactual, are able to reveal effects of the ecological disturbance that are obscured in quantity data. Our results are an important step toward quantifying the economic value of reduced upstream nutrient loading in the Mississippi Basin and are broadly applicable to other coupled human-natural systems.

Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion.

PubMed

Ni, ZhouXian; Ye, YouJu; Bai, Tiandao; Xu, Meng; Xu, Li-An

2017-09-11

The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between "IRa" and "IRb". The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.

DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders.

PubMed

Ryan, Niamh M; Lihm, Jayon; Kramer, Melissa; McCarthy, Shane; Morris, Stewart W; Arnau-Soler, Aleix; Davies, Gail; Duff, Barbara; Ghiban, Elena; Hayward, Caroline; Deary, Ian J; Blackwood, Douglas H R; Lawrie, Stephen M; McIntosh, Andrew M; Evans, Kathryn L; Porteous, David J; McCombie, W Richard; Thomson, Pippa A

2018-06-07

Psychiatric disorders are a group of genetically related diseases with highly polygenic architectures. Genome-wide association analyses have made substantial progress towards understanding the genetic architecture of these disorders. More recently, exome- and whole-genome sequencing of cases and families have identified rare, high penetrant variants that provide direct functional insight. There remains, however, a gap in the heritability explained by these complementary approaches. To understand how multiple genetic variants combine to modify both severity and penetrance of a highly penetrant variant, we sequenced 48 whole genomes from a family with a high loading of psychiatric disorder linked to a balanced chromosomal translocation. The (1;11)(q42;q14.3) translocation directly disrupts three genes: DISC1, DISC2, DISC1FP and has been linked to multiple brain imaging and neurocognitive outcomes in the family. Using DNA sequence-level linkage analysis, functional annotation and population-based association, we identified common and rare variants in GRM5 (minor allele frequency (MAF) > 0.05), PDE4D (MAF > 0.2) and CNTN5 (MAF < 0.01) that may help explain the individual differences in phenotypic expression in the family. We suggest that whole-genome sequencing in large families will improve the understanding of the combined effects of the rare and common sequence variation underlying psychiatric phenotypes.

Host plant development, water level and water parameters shape Phragmites australis-associated oomycete communities and determine reed pathogen dynamics in a large lake.

PubMed

Wielgoss, Anna; Nechwatal, Jan; Bogs, Carolin; Mendgen, Kurt

2009-08-01

In a 3-year-study, we analysed the population dynamics of the reed pathogen Pythium phragmitis and other reed-associated oomycetes colonizing fresh and dried reed leaves in the littoral zone of a large lake. Oomycete communities derived from internal transcribed spacer clone libraries were clearly differentiated according to substrate and seasonal influences. In fresh leaves, diverse communities consisting of P. phragmitis and other reed-associated pathogens were generally dominant. Pythium phragmitis populations peaked in spring with the emergence of young reed shoots, and in autumn after extreme flooding events. In summer it decreased with falling water levels, changing water chemistry and rising temperatures. Another Pythium species was also highly abundant in fresh leaves throughout the year and might represent a new, as-yet uncultured reed pathogen. In dried leaves, reed pathogens were rarely detected, whereas saprophytic species occurred abundantly during all seasons. Saprophyte communities were less diverse, less temperature sensitive and independent of reed development. In general, our results provide evidence for the occurrence of highly specialized sets of reed-associated oomycetes in a natural reed ecosystem. Quantitative analyses (clone abundances and quantitative real-time PCR) revealed that the reed pathogen P. phragmitis is particularly affected by changing water levels, water chemistry and the stage of reed development.

Holocene climate variability revealed by oxygen isotope analysis of Sphagnum cellulose from Walton Moss, northern England

NASA Astrophysics Data System (ADS)

Daley, T. J.; Barber, K. E.; Street-Perrott, F. A.; Loader, N. J.; Marshall, J. D.; Crowley, S. F.; Fisher, E. H.

2010-07-01

Stable isotope analyses of Sphagnum alpha-cellulose, precipitation and bog water from three sites across northwestern Europe (Raheenmore, Ireland, Walton Moss, northern England and Dosenmoor, northern Germany) over a total period of 26 months were used to investigate the nature of the climatic signal recorded by Sphagnum moss. The δ18O values of modern alpha-cellulose tracked precipitation more closely than bog water, with a mean isotopic fractionation factor αcellulose-precipitation of 1.0274 ± 0.001 (1 σ) (≈27‰). Sub-samples of isolated Sphagnum alpha-cellulose were subsequently analysed from core WLM22, Walton Moss, northern England yielding a Sphagnum-specific isotope record spanning the last 4300 years. The palaeo-record, calibrated using the modern data, provides evidence for large amplitude variations in the estimated oxygen isotope composition of precipitation during the mid- to late Holocene. Estimates of palaeotemperature change derived from statistical relationships between modern surface air temperatures and δ18O precipitation values for the British Isles give unrealistically large variation in comparison to proxies from other archives. We conclude that use of such relationships to calibrate mid-latitude palaeo-data must be undertaken with caution. The δ18O record from Sphagnum cellulose was highly correlated with a palaeoecologically-derived index of bog surface wetness (BSW), suggesting a common climatic driver.

Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research

PubMed Central

2012-01-01

Background As a human replacement, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a significant obstacle for its broader use. Results Here, we sequenced the transcriptome of 16 tissues originated from two individuals of crab-eating macaque (male and female), and identified genes to resolve the main obstacles for understanding the biological response of the crab-eating macaque. From 4 million reads with 1.4 billion base sequences, 31,786 isotigs containing genes similar to those of humans, 12,672 novel isotigs, and 348,160 singletons were identified using the GS FLX sequencing method. Approximately 86% of human genes were represented among the genes sequenced in this study. Additionally, 175 tissue-specific transcripts were identified, 81 of which were experimentally validated. In total, 4,314 alternative splicing (AS) events were identified and analyzed. Intriguingly, 10.4% of AS events were associated with transposable element (TE) insertions. Finally, investigation of TE exonization events and evolutionary analysis were conducted, revealing interesting phenomena of human-specific amplified trends in TE exonization events. Conclusions This report represents the first large-scale transcriptome sequencing and genetic analyses of M. fascicularis and could contribute to its utility for biomedical research and basic biology. PMID:22554259

Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents

PubMed Central

Maghuly, Fatemeh; Jankowicz-Cieslak, Joanna; Pabinger, Stephan; Till, Bradley J; Laimer, Margit

2015-01-01

Increasing economic interest in Jatropha curcas requires a major research focus on the genetic background and geographic origin of this non-edible biofuel crop. To determine the worldwide genetic structure of this species, amplified fragment length polymorphisms, inter simple sequence repeats, and novel single nucleotide polymorphisms (SNPs) were employed for a large collection of 907 J. curcas accessions and related species (RS) from three continents, 15 countries and 53 regions. PCoA, phenogram, and cophenetic analyses separated RS from two J. curcas groups. Accessions from Mexico, Bolivia, Paraguay, Kenya, and Ethiopia with unknown origins were found in both groups. In general, there was a considerable overlap between individuals from different regions and countries. The Bayesian approach using structure demonstrated two groups with a low genetic variation. Analysis of molecular varience revealed significant variation among individuals within populations. SNPs found by in silico analyses of Δ12 fatty acid desaturase indicated possible changes in gene expression and thus in fatty acid profiles. SNP variation was higher in the curcin gene compared to genes involved in oil production. Novel SNPs allowed separating toxic, non-toxic, and Mexican accessions. The present study confirms that human activities had a major influence on the genetic diversity of J. curcas, not only because of domestication, but also because of biased selection. PMID:25511658

A novel method for visualising and quantifying through-plane skin layer deformations.

PubMed

Gerhardt, L-C; Schmidt, J; Sanz-Herrera, J A; Baaijens, F P T; Ansari, T; Peters, G W M; Oomens, C W J

2012-10-01

Skin is a multilayer composite and exhibits highly non-linear, viscoelastic, anisotropic material properties. In many consumer product and medical applications (e.g. during shaving, needle insertion, patient re-positioning), large tissue displacements and deformations are involved; consequently large local strains in the skin tissue can occur. Here, we present a novel imaging-based method to study skin deformations and the mechanics of interacting skin layers of full-thickness skin. Shear experiments and real-time video recording were combined with digital image correlation and strain field analysis to visualise and quantify skin layer deformations during dynamic mechanical testing. A global shear strain of 10% was applied to airbrush-patterned porcine skin (thickness: 1.2-1.6mm) using a rotational rheometer. The recordings were analysed with ARAMIS image correlation software, and local skin displacement, strain and stiffness profiles through the skin layers determined. The results of this pilot study revealed inhomogeneous skin deformation, characterised by a gradual transition from a low (2.0-5.0%; epidermis) to high (10-22%; dermis) shear strain regime. Shear moduli ranged from 20 to 130kPa. The herein presented method will be used for more extended studies on viable human skin, and is considered a valuable foundation for further development of constitutive models which can be used in advanced finite element analyses of skin. Copyright © 2012 Elsevier Ltd. All rights reserved.

Long-term accumulation and transport of anthropogenic phosphorus in world river basins

NASA Astrophysics Data System (ADS)

Powers, S. M.

2015-12-01

Global food production crucially depends on phosphorus (P). In agricultural and urban landscapes, much P is anthropogenic, entering via trade, and then can be transported by a combination of fluvial and human processes. To date there have been few long-term, large-scale analyses combining both fluvial and human modes of P transport. Here we present reconstructed historical records of anthropogenic P entering and leaving soils and aquatic systems via a combination of trade, infrastructure, food waste, and fluvial fluxes. We then report the net annual P inputs, and the mass of P that has accumulated over the long-term, for entire river basins. Our analyses reveal rapid historical P accumulation for two mixed agricultural-urban landscapes (Thames Basin, UK, Yangtze Basin, China), and one rural agricultural landscape (Maumee Basin, USA). We also show that the human P fluxes massively dominate over the fluvial fluxes in these large basins. For Thames and Maumee Basins, recently there has been modest P depletion/drawdown of the massive P pool accumulated in prior decades, whereas the Yangtze Basin has consistently and rapidly accumulated P since 1980. These first estimates of the magnitude of historical P accumulation in contrasting settings illustrate the scope of management challenges surrounding the storage, fate, exploitation, and reactivation of legacy P that is currently present in the Earth's critical zone.

Analyses of Sox-B and Sox-E Family Genes in the Cephalopod Sepia officinalis: Revealing the Conserved and the Unusual

PubMed Central

Focareta, Laura; Cole, Alison G.

2016-01-01

Cephalopods provide an unprecedented opportunity for comparative studies of the developmental genetics of organ systems that are convergent with analogous vertebrate structures. The Sox-family of transcription factors is an important class of DNA-binding proteins that are known to be involved in many aspects of differentiation, but have been largely unstudied in lophotrochozoan systems. Using a degenerate primer strategy we have isolated coding sequence for three members of the Sox family of transcription factors from a cephalopod mollusk, the European cuttlefish Sepia officinalis: Sof-SoxE, Sof-SoxB1, and Sof-SoxB2. Analyses of their expression patterns during organogenesis reveals distinct spatial and temporal expression domains. Sof-SoxB1 shows early ectodermal expression throughout the developing epithelium, which is gradually restricted to presumptive sensory epithelia. Expression within the nervous system appears by mid-embryogenesis. Sof-SoxB2 expression is similar to Sof-SoxB1 within the developing epithelia in early embryogenesis, however appears in largely non-overlapping expression domains within the central nervous system and is not expressed in the maturing sensory epithelium. In contrast, Sof-SoxE is expressed throughout the presumptive mesodermal territories at the onset of organogenesis. As development proceeds, Sof-SoxE expression is elevated throughout the developing peripheral circulatory system. This expression disappears as the circulatory system matures, but expression is maintained within undifferentiated connective tissues throughout the animal, and appears within the nervous system near the end of embryogenesis. SoxB proteins are widely known for their role in neural specification in numerous phylogenetic lineages. Our data suggests that Sof-SoxB genes play similar roles in cephalopods. In contrast, Sof-SoxE appears to be involved in the early stages of vasculogenesis of the cephalopod closed circulatory system, a novel role for a member of this gene family. PMID:27331398

Ocean acidification impacts bacteria-phytoplankton coupling at low-nutrient conditions

NASA Astrophysics Data System (ADS)

Hornick, Thomas; Bach, Lennart T.; Crawfurd, Katharine J.; Spilling, Kristian; Achterberg, Eric P.; Woodhouse, Jason N.; Schulz, Kai G.; Brussaard, Corina P. D.; Riebesell, Ulf; Grossart, Hans-Peter

2017-01-01

The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm ( ˜ 55 m3) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO2) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO2-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO2 treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO2 as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO2 impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of the four fCO2-treated mesocosms from both control mesocosms, indicating that complex trophic interactions might be altered in a future acidified ocean. Possible consequences for nutrient cycling and carbon export are still largely unknown, in particular in a nutrient-limited ocean.

A New Mouse Allele of Glutamate Receptor Delta 2 with Cerebellar Atrophy and Progressive Ataxia

PubMed Central

Miyoshi, Yuka; Yoshioka, Yoshichika; Suzuki, Kinuko; Miyazaki, Taisuke; Koura, Minako; Saigoh, Kazumasa; Kajimura, Naoko; Monobe, Yoko; Kusunoki, Susumu; Matsuda, Junichiro; Watanabe, Masahiko; Hayasaka, Naoto

2014-01-01

Spinocerebellar degenerations (SCDs) are a large class of sporadic or hereditary neurodegenerative disorders characterized by progressive motion defects and degenerative changes in the cerebellum and other parts of the CNS. Here we report the identification and establishment from a C57BL/6J mouse colony of a novel mouse line developing spontaneous progressive ataxia, which we refer to as ts3. Frequency of the phenotypic expression was consistent with an autosomal recessive Mendelian trait of inheritance, suggesting that a single gene mutation is responsible for the ataxic phenotype of this line. The onset of ataxia was observed at about three weeks of age, which slowly progressed until the hind limbs became entirely paralyzed in many cases. Micro-MRI study revealed significant cerebellar atrophy in all the ataxic mice, although individual variations were observed. Detailed histological analyses demonstrated significant atrophy of the anterior folia with reduced granule cells (GC) and abnormal morphology of cerebellar Purkinje cells (PC). Study by ultra-high voltage electron microscopy (UHVEM) further indicated aberrant morphology of PC dendrites and their spines, suggesting both morphological and functional abnormalities of the PC in the mutants. Immunohistochemical studies also revealed defects in parallel fiber (PF)–PC synapse formation and abnormal distal extension of climbing fibers (CF). Based on the phenotypic similarities of the ts3 mutant with other known ataxic mutants, we performed immunohistological analyses and found that expression levels of two genes and their products, glutamate receptor delta2 (grid2) and its ligand, cerebellin1 (Cbln1), are significantly reduced or undetectable. Finally, we sequenced the candidate genes and detected a large deletion in the coding region of the grid2 gene. Our present study suggests that ts3 is a new allele of the grid2 gene, which causes similar but different phenotypes as compared to other grid2 mutants. PMID:25250835

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).

PubMed

Molano, Eddy Patricia Lopez; Cabrera, Odalys García; Jose, Juliana; do Nascimento, Leandro Costa; Carazzolle, Marcelo Falsarella; Teixeira, Paulo José Pereira Lima; Alvarez, Javier Correa; Tiburcio, Ricardo Augusto; Tokimatu Filho, Paulo Massanari; de Lima, Gustavo Machado Alvares; Guido, Rafael Victório Carvalho; Corrêa, Thamy Lívia Ribeiro; Leme, Adriana Franco Paes; Mieczkowski, Piotr; Pereira, Gonçalo Amarante Guimarães

2018-01-17

The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity.

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development.

PubMed

Parker, Heidi G; Dreger, Dayna L; Rimbault, Maud; Davis, Brian W; Mullen, Alexandra B; Carpintero-Ramirez, Gretchen; Ostrander, Elaine A

2017-04-25

There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Converging flow and anisotropy cause large-scale folding in Greenland's ice sheet

PubMed Central

Bons, Paul D.; Jansen, Daniela; Mundel, Felicitas; Bauer, Catherine C.; Binder, Tobias; Eisen, Olaf; Jessell, Mark W.; Llorens, Maria-Gema; Steinbach, Florian; Steinhage, Daniel; Weikusat, Ilka

2016-01-01

The increasing catalogue of high-quality ice-penetrating radar data provides a unique insight in the internal layering architecture of the Greenland ice sheet. The stratigraphy, an indicator of past deformation, highlights irregularities in ice flow and reveals large perturbations without obvious links to bedrock shape. In this work, to establish a new conceptual model for the formation process, we analysed the radar data at the onset of the Petermann Glacier, North Greenland, and created a three-dimensional model of several distinct stratigraphic layers. We demonstrate that the dominant structures are cylindrical folds sub-parallel to the ice flow. By numerical modelling, we show that these folds can be formed by lateral compression of mechanically anisotropic ice, while a general viscosity contrast between layers would not lead to folding for the same boundary conditions. We conclude that the folds primarily form by converging flow as the mechanically anisotropic ice is channelled towards the glacier. PMID:27126274

Eavesdropping on the Arctic: Automated bioacoustics reveal dynamics in songbird breeding phenology

PubMed Central

Ellis, Daniel P. W.; Pérez, Jonathan H.; Wingfield, John C.; Boelman, Natalie T.

2018-01-01

Bioacoustic networks could vastly expand the coverage of wildlife monitoring to complement satellite observations of climate and vegetation. This approach would enable global-scale understanding of how climate change influences phenomena such as migratory timing of avian species. The enormous data sets that autonomous recorders typically generate demand automated analyses that remain largely undeveloped. We devised automated signal processing and machine learning approaches to estimate dates on which songbird communities arrived at arctic breeding grounds. Acoustically estimated dates agreed well with those determined via traditional surveys and were strongly related to the landscape’s snow-free dates. We found that environmental conditions heavily influenced daily variation in songbird vocal activity, especially before egg laying. Our novel approaches demonstrate that variation in avian migratory arrival can be detected autonomously. Large-scale deployment of this innovation in wildlife monitoring would enable the coverage necessary to assess and forecast changes in bird migration in the face of climate change. PMID:29938220

Text mixing shapes the anatomy of rank-frequency distributions

NASA Astrophysics Data System (ADS)

Williams, Jake Ryland; Bagrow, James P.; Danforth, Christopher M.; Dodds, Peter Sheridan

2015-05-01

Natural languages are full of rules and exceptions. One of the most famous quantitative rules is Zipf's law, which states that the frequency of occurrence of a word is approximately inversely proportional to its rank. Though this "law" of ranks has been found to hold across disparate texts and forms of data, analyses of increasingly large corpora since the late 1990s have revealed the existence of two scaling regimes. These regimes have thus far been explained by a hypothesis suggesting a separability of languages into core and noncore lexica. Here we present and defend an alternative hypothesis that the two scaling regimes result from the act of aggregating texts. We observe that text mixing leads to an effective decay of word introduction, which we show provides accurate predictions of the location and severity of breaks in scaling. Upon examining large corpora from 10 languages in the Project Gutenberg eBooks collection, we find emphatic empirical support for the universality of our claim.

Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

PubMed

Tani, Hidenori

2017-03-22

Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 < 4 h) include known regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

Influence maximization in complex networks through optimal percolation

NASA Astrophysics Data System (ADS)

Morone, Flaviano; Makse, Hernan; CUNY Collaboration; CUNY Collaboration

The whole frame of interconnections in complex networks hinges on a specific set of structural nodes, much smaller than the total size, which, if activated, would cause the spread of information to the whole network, or, if immunized, would prevent the diffusion of a large scale epidemic. Localizing this optimal, that is, minimal, set of structural nodes, called influencers, is one of the most important problems in network science. Here we map the problem onto optimal percolation in random networks to identify the minimal set of influencers, which arises by minimizing the energy of a many-body system, where the form of the interactions is fixed by the non-backtracking matrix of the network. Big data analyses reveal that the set of optimal influencers is much smaller than the one predicted by previous heuristic centralities. Remarkably, a large number of previously neglected weakly connected nodes emerges among the optimal influencers. Reference: F. Morone, H. A. Makse, Nature 524,65-68 (2015)

First bone-cracking dog coprolites provide new insight into bone consumption in Borophagus and their unique ecological niche

PubMed Central

White, Stuart C; Balisi, Mairin; Biewer, Jacob; Sankey, Julia; Garber, Dennis; Tseng, Z Jack

2018-01-01

Borophagine canids have long been hypothesized to be North American ecological ‘avatars’ of living hyenas in Africa and Asia, but direct fossil evidence of hyena-like bone consumption is hitherto unknown. We report rare coprolites (fossilized feces) of Borophagus parvus from the late Miocene of California and, for the first time, describe unambiguous evidence that these predatory canids ingested large amounts of bone. Surface morphology, micro-CT analyses, and contextual information reveal (1) droppings in concentrations signifying scent-marking behavior, similar to latrines used by living social carnivorans; (2) routine consumption of skeletons; (3) undissolved bones inside coprolites indicating gastrointestinal similarity to modern striped and brown hyenas; (4) B. parvus body weight of ~24 kg, reaching sizes of obligatory large-prey hunters; and (5) prey size ranging ~35–100 kg. This combination of traits suggests that bone-crushing Borophagus potentially hunted in collaborative social groups and occupied a niche no longer present in North American ecosystems. PMID:29785931

Morphologic, cytometric and functional characterization of the common octopus (Octopus vulgaris) hemocytes.

PubMed

Castellanos-Martínez, S; Prado-Alvarez, M; Lobo-da-Cunha, A; Azevedo, C; Gestal, C

2014-05-01

The hemocytes of Octopus vulgaris were morphologically and functionally characterized. Light and electron microscopy (TEM and SEM), and flow cytometry analyses revealed the existence of two hemocyte populations. Large granulocytes showed U-shaped nucleus, a mean of 11.6 μm±1.2 in diameter with basophilic granules, polysaccharide and lysosomic deposits in the cytoplasm. Small granulocytes measured a mean of 8.1 μm±0.7 in diameter, and have a round nucleus occupying almost the entire cell and few or not granules in the cytoplasm. Flow cytometry analysis showed that large granulocytes are the principal cells that develop phagocytosis of latex beads (rising up to 56%) and ROS after zymosan stimulation. Zymosan induced the highest production of both ROS and NO. This study is the first tread towards understanding the O. vulgaris immune system by applying new tools to provide a most comprehensive morpho-functional study of their hemocytes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ice stream motion facilitated by a shallow-deforming and accreting bed

PubMed Central

Spagnolo, Matteo; Phillips, Emrys; Piotrowski, Jan A.; Rea, Brice R.; Clark, Chris D.; Stokes, Chris R.; Carr, Simon J.; Ely, Jeremy C.; Ribolini, Adriano; Wysota, Wojciech; Szuman, Izabela

2016-01-01

Ice streams drain large portions of ice sheets and play a fundamental role in governing their response to atmospheric and oceanic forcing, with implications for sea-level change. The mechanisms that generate ice stream flow remain elusive. Basal sliding and/or bed deformation have been hypothesized, but ice stream beds are largely inaccessible. Here we present a comprehensive, multi-scale study of the internal structure of mega-scale glacial lineations (MSGLs) formed at the bed of a palaeo ice stream. Analyses were undertaken at macro- and microscales, using multiple techniques including X-ray tomography, thin sections and ground penetrating radar (GPR) acquisitions. Results reveal homogeneity in stratigraphy, kinematics, granulometry and petrography. The consistency of the physical and geological properties demonstrates a continuously accreting, shallow-deforming, bed and invariant basal conditions. This implies that ice stream basal motion on soft sediment beds during MSGL formation is accommodated by plastic deformation, facilitated by continuous sediment supply and an inefficient drainage system. PMID:26898399

Novel divergent nidovirus in a python with pneumonia.

PubMed

Bodewes, Rogier; Lempp, Charlotte; Schürch, Anita C; Habierski, Andre; Hahn, Kerstin; Lamers, Mart; von Dörnberg, Katja; Wohlsein, Peter; Drexler, Jan Felix; Haagmans, Bart L; Smits, Saskia L; Baumgärtner, Wolfgang; Osterhaus, Albert D M E

2014-11-01

The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales. © 2014 The Authors.

Associations between motor timing, music practice, and intelligence studied in a large sample of twins.

PubMed

Ullén, Fredrik; Mosing, Miriam A; Madison, Guy

2015-03-01

Music performance depends critically on precise processing of time. A common model behavior in studies of motor timing is isochronous serial interval production (ISIP), that is, hand/finger movements with a regular beat. ISIP accuracy is related to both music practice and intelligence. Here we present a study of these associations in a large twin cohort, demonstrating that the effects of music practice and intelligence on motor timing are additive, with no significant multiplicative (interaction) effect. Furthermore, the association between music practice and motor timing was analyzed with the use of a co-twin control design using intrapair differences. These analyses revealed that the phenotypic association disappeared when all genetic and common environmental factors were controlled. This suggests that the observed association may not reflect a causal effect of music practice on ISIP performance but rather reflect common influences (e.g., genetic effects) on both outcomes. The relevance of these findings for models of practice and expert performance is discussed. © 2014 New York Academy of Sciences.

Clonal dynamics of native haematopoiesis

PubMed Central

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B.; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D.

2015-01-01

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease. PMID:25296256

Clonal dynamics of native haematopoiesis.

PubMed

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D

2014-10-16

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease.

ELUCIDATING BRAIN CONNECTIVITY NETWORKS IN MAJOR DEPRESSIVE DISORDER USING CLASSIFICATION-BASED SCORING.

PubMed

Sacchet, Matthew D; Prasad, Gautam; Foland-Ross, Lara C; Thompson, Paul M; Gotlib, Ian H

2014-04-01

Graph theory is increasingly used in the field of neuroscience to understand the large-scale network structure of the human brain. There is also considerable interest in applying machine learning techniques in clinical settings, for example, to make diagnoses or predict treatment outcomes. Here we used support-vector machines (SVMs), in conjunction with whole-brain tractography, to identify graph metrics that best differentiate individuals with Major Depressive Disorder (MDD) from nondepressed controls. To do this, we applied a novel feature-scoring procedure that incorporates iterative classifier performance to assess feature robustness. We found that small-worldness , a measure of the balance between global integration and local specialization, most reliably differentiated MDD from nondepressed individuals. Post-hoc regional analyses suggested that heightened connectivity of the subcallosal cingulate gyrus (SCG) in MDDs contributes to these differences. The current study provides a novel way to assess the robustness of classification features and reveals anomalies in large-scale neural networks in MDD.

Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells.

PubMed

Boo, Kyungjin; Bhin, Jinhyuk; Jeon, Yoon; Kim, Joomyung; Shin, Hi-Jai R; Park, Jong-Eun; Kim, Kyeongkyu; Kim, Chang Rok; Jang, Hyonchol; Kim, In-Hoo; Kim, V Narry; Hwang, Daehee; Lee, Ho; Baek, Sung Hee

2015-04-10

The actions of transcription factors, chromatin modifiers and noncoding RNAs are crucial for the programming of cell states. Although the importance of various epigenetic machineries for controlling pluripotency of embryonic stem (ES) cells has been previously studied, how chromatin modifiers cooperate with specific transcription factors still remains largely elusive. Here, we find that Pontin chromatin remodelling factor plays an essential role as a coactivator for Oct4 for maintenance of pluripotency in mouse ES cells. Genome-wide analyses reveal that Pontin and Oct4 share a substantial set of target genes involved in ES cell maintenance. Intriguingly, we find that the Oct4-dependent coactivator function of Pontin extends to the transcription of large intergenic noncoding RNAs (lincRNAs) and in particular linc1253, a lineage programme repressing lincRNA, is a Pontin-dependent Oct4 target lincRNA. Together, our findings demonstrate that the Oct4-Pontin module plays critical roles in the regulation of genes involved in ES cell fate determination.

Facile hydrothermal synthesis of mesoporous In2O3 nanoparticles with superior formaldehyde-sensing properties

NASA Astrophysics Data System (ADS)

Zhang, Su; Song, Peng; Yang, Zhongxi; Wang, Qi

2018-03-01

Mesoporous In2O3 nanoparticles were successfully synthesized via a facile, template free, and low-cost hydrothermal method. Their morphology and structure were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), differential thermal and thermogravimetry analysis (DSC-TG), and N2 adsorption-desorption analyses. The results reveal that mesoporous In2O3 nanoparticles with a size range of 40-60 nm, possess plenty of pores, and average pore size is about 5 nm. Importantly, the mesoporous structure, large specific surface area, and small size endow the mesoporous In2O3 nanoparticles with highly sensing performance for formaldehyde detection. The response value to 10 ppm HCHO is 20 at an operating temperature of 280 °C, and the response and recovery time are 4 and 8 s, respectively. It is expected that the mesoporous In2O3 nanoparticles with large specific surface area and excellent sensing properties will become a promising functional material in monitoring and detecting formaldehyde.

Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment.

PubMed

Eyboulet, Fanny; Cibot, Camille; Eychenne, Thomas; Neil, Helen; Alibert, Olivier; Werner, Michel; Soutourina, Julie

2013-12-01

Mediator is a large multiprotein complex conserved in all eukaryotes. The crucial function of Mediator in transcription is now largely established. However, we found that this complex also plays an important role by connecting transcription with DNA repair. We identified a functional contact between the Med17 Mediator subunit and Rad2/XPG, the 3' endonuclease involved in nucleotide excision DNA repair. Genome-wide location analyses revealed that Rad2 is associated with RNA polymerase II (Pol II)- and Pol III-transcribed genes and telomeric regions in the absence of exogenous genotoxic stress. Rad2 occupancy of Pol II-transcribed genes is transcription-dependent. Genome-wide Rad2 occupancy of class II gene promoters is well correlated with that of Mediator. Furthermore, UV sensitivity of med17 mutants is correlated with reduced Rad2 occupancy of class II genes and concomitant decrease of Mediator interaction with Rad2 protein. Our results suggest that Mediator is involved in DNA repair by facilitating Rad2 recruitment to transcribed genes.

Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment

PubMed Central

Eyboulet, Fanny; Cibot, Camille; Eychenne, Thomas; Neil, Helen; Alibert, Olivier; Werner, Michel; Soutourina, Julie

2013-01-01

Mediator is a large multiprotein complex conserved in all eukaryotes. The crucial function of Mediator in transcription is now largely established. However, we found that this complex also plays an important role by connecting transcription with DNA repair. We identified a functional contact between the Med17 Mediator subunit and Rad2/XPG, the 3′ endonuclease involved in nucleotide excision DNA repair. Genome-wide location analyses revealed that Rad2 is associated with RNA polymerase II (Pol II)- and Pol III-transcribed genes and telomeric regions in the absence of exogenous genotoxic stress. Rad2 occupancy of Pol II-transcribed genes is transcription-dependent. Genome-wide Rad2 occupancy of class II gene promoters is well correlated with that of Mediator. Furthermore, UV sensitivity of med17 mutants is correlated with reduced Rad2 occupancy of class II genes and concomitant decrease of Mediator interaction with Rad2 protein. Our results suggest that Mediator is involved in DNA repair by facilitating Rad2 recruitment to transcribed genes. PMID:24298055

The microbiological conditions of carcasses from large game animals in Italy.

PubMed

Avagnina, A; Nucera, D; Grassi, M A; Ferroglio, E; Dalmasso, A; Civera, T

2012-07-01

This study investigates the microbiological conditions of large game animal carcasses following evisceration. Carcasses of animals (N=291) hunted in the Upper Susa Valley (Italian Alps) were analysed for pH, Aerobic Viable Count (AVC), Enterobacteriaceae, Yersinia spp., Listeria monocytogenes and Salmonella spp. After shooting, evisceration occurred within 60 min in 90.7% of animals and sampling within 90 min in 88.3% of animals. Mean pH values (5.97: ruminants; 5.77: wild boar) were similar to those of regularly slaughtered domestic species. AVC values were highest in animals shot in the abdomen. Within species, AVC and Enterobacteriaceae values did not differ across different shooting-evisceration/sampling times. However, these counts exceeded 5 and 2.5 log, respectively, in 18% of wild boar and 39% of ruminants; the highest values were detected in wild boar. No pathogens were detected in any species. These results reveal inadequate hygiene in game meat handling/harvesting, implicating the need for improved practices. Copyright © 2012 Elsevier Ltd. All rights reserved.

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin

PubMed Central

Williams, Samuel M.; Otway, Nicholas M.; Nielsen, Einar E.; Maher, Safia L.; Bennett, Mike B.; Ovenden, Jennifer R.

2017-01-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier. PMID:28791159

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin.

PubMed

Holmes, Bonnie J; Williams, Samuel M; Otway, Nicholas M; Nielsen, Einar E; Maher, Safia L; Bennett, Mike B; Ovenden, Jennifer R

2017-07-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST  > 0.14, p  < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .

Text mixing shapes the anatomy of rank-frequency distributions.

PubMed

Williams, Jake Ryland; Bagrow, James P; Danforth, Christopher M; Dodds, Peter Sheridan

2015-05-01

Natural languages are full of rules and exceptions. One of the most famous quantitative rules is Zipf's law, which states that the frequency of occurrence of a word is approximately inversely proportional to its rank. Though this "law" of ranks has been found to hold across disparate texts and forms of data, analyses of increasingly large corpora since the late 1990s have revealed the existence of two scaling regimes. These regimes have thus far been explained by a hypothesis suggesting a separability of languages into core and noncore lexica. Here we present and defend an alternative hypothesis that the two scaling regimes result from the act of aggregating texts. We observe that text mixing leads to an effective decay of word introduction, which we show provides accurate predictions of the location and severity of breaks in scaling. Upon examining large corpora from 10 languages in the Project Gutenberg eBooks collection, we find emphatic empirical support for the universality of our claim.

Complementary codes for odor identity and intensity in olfactory cortex

PubMed Central

Bolding, Kevin A; Franks, Kevin M

2017-01-01

The ability to represent both stimulus identity and intensity is fundamental for perception. Using large-scale population recordings in awake mice, we find distinct coding strategies facilitate non-interfering representations of odor identity and intensity in piriform cortex. Simply knowing which neurons were activated is sufficient to accurately represent odor identity, with no additional information about identity provided by spike time or spike count. Decoding analyses indicate that cortical odor representations are not sparse. Odorant concentration had no systematic effect on spike counts, indicating that rate cannot encode intensity. Instead, odor intensity can be encoded by temporal features of the population response. We found a subpopulation of rapid, largely concentration-invariant responses was followed by another population of responses whose latencies systematically decreased at higher concentrations. Cortical inhibition transforms olfactory bulb output to sharpen these dynamics. Our data therefore reveal complementary coding strategies that can selectively represent distinct features of a stimulus. DOI: http://dx.doi.org/10.7554/eLife.22630.001 PMID:28379135

The PHF21B gene is associated with major depression and modulates the stress response.

PubMed

Wong, M-L; Arcos-Burgos, M; Liu, S; Vélez, J I; Yu, C; Baune, B T; Jawahar, M C; Arolt, V; Dannlowski, U; Chuah, A; Huttley, G A; Fogarty, R; Lewis, M D; Bornstein, S R; Licinio, J

2017-07-01

Major depressive disorder (MDD) affects around 350 million people worldwide; however, the underlying genetic basis remains largely unknown. In this study, we took into account that MDD is a gene-environment disorder, in which stress is a critical component, and used whole-genome screening of functional variants to investigate the 'missing heritability' in MDD. Genome-wide association studies (GWAS) using single- and multi-locus linear mixed-effect models were performed in a Los Angeles Mexican-American cohort (196 controls, 203 MDD) and in a replication European-ancestry cohort (499 controls, 473 MDD). Our analyses took into consideration the stress levels in the control populations. The Mexican-American controls, comprised primarily of recent immigrants, had high levels of stress due to acculturation issues and the European-ancestry controls with high stress levels were given higher weights in our analysis. We identified 44 common and rare functional variants associated with mild to moderate MDD in the Mexican-American cohort (genome-wide false discovery rate, FDR, <0.05), and their pathway analysis revealed that the three top overrepresented Gene Ontology (GO) processes were innate immune response, glutamate receptor signaling and detection of chemical stimulus in smell sensory perception. Rare variant analysis replicated the association of the PHF21B gene in the ethnically unrelated European-ancestry cohort. The TRPM2 gene, previously implicated in mood disorders, may also be considered replicated by our analyses. Whole-genome sequencing analyses of a subset of the cohorts revealed that European-ancestry individuals have a significantly reduced (50%) number of single nucleotide variants compared with Mexican-American individuals, and for this reason the role of rare variants may vary across populations. PHF21b variants contribute significantly to differences in the levels of expression of this gene in several brain areas, including the hippocampus. Furthermore, using an animal model of stress, we found that Phf21b hippocampal gene expression is significantly decreased in animals resilient to chronic restraint stress when compared with non-chronically stressed animals. Together, our results reveal that including stress level data enables the identification of novel rare functional variants associated with MDD.

Large-Scale Comparative Phenotypic and Genomic Analyses Reveal Ecological Preferences of Shewanella Species and Identify Metabolic Pathways Conserved at the Genus Level ▿ †

PubMed Central

Rodrigues, Jorge L. M.; Serres, Margrethe H.; Tiedje, James M.

2011-01-01

The use of comparative genomics for the study of different microbiological species has increased substantially as sequence technologies become more affordable. However, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at a time. In this study, we provided a high-throughput alternative to this limiting step by coupling comparative genomics to the use of phenotype arrays for five sequenced Shewanella strains. Positive phenotypes were obtained for 441 nutrients (C, N, P, and S sources), with N-based compounds being the most utilized for all strains. Many genes and pathways predicted by genome analyses were confirmed with the comparative phenotype assay, and three degradation pathways believed to be missing in Shewanella were confirmed as missing. A number of previously unknown gene products were predicted to be parts of pathways or to have a function, expanding the number of gene targets for future genetic analyses. Ecologically, the comparative high-throughput phenotype analysis provided insights into niche specialization among the five different strains. For example, Shewanella amazonensis strain SB2B, isolated from the Amazon River delta, was capable of utilizing 60 C compounds, whereas Shewanella sp. strain W3-18-1, isolated from deep marine sediment, utilized only 25 of them. In spite of the large number of nutrient sources yielding positive results, our study indicated that except for the N sources, they were not sufficiently informative to predict growth phenotypes from increasing evolutionary distances. Our results indicate the importance of phenotypic evaluation for confirming genome predictions. This strategy will accelerate the functional discovery of genes and provide an ecological framework for microbial genome sequencing projects. PMID:21642407