Gaze behavior predicts memory bias for angry facial expressions in stable dysphoria.

PubMed

Wells, Tony T; Beevers, Christopher G; Robison, Adrienne E; Ellis, Alissa J

2010-12-01

Interpersonal theories suggest that depressed individuals are sensitive to signs of interpersonal rejection, such as angry facial expressions. The present study examined memory bias for happy, sad, angry, and neutral facial expressions in stably dysphoric and stably nondysphoric young adults. Participants' gaze behavior (i.e., fixation duration, number of fixations, and distance between fixations) while viewing these facial expressions was also assessed. Using signal detection analyses, the dysphoric group had better accuracy on a surprise recognition task for angry faces than the nondysphoric group. Further, mediation analyses indicated that greater breadth of attentional focus (i.e., distance between fixations) accounted for enhanced recall of angry faces among the dysphoric group. There were no differences between dysphoria groups in gaze behavior or memory for sad, happy, or neutral facial expressions. Findings from this study identify a specific cognitive mechanism (i.e., breadth of attentional focus) that accounts for biased recall of angry facial expressions in dysphoria. This work also highlights the potential for integrating cognitive and interpersonal theories of depression.

Herbivore-induced plant volatiles accurately predict history of coexistence, diet breadth, and feeding mode of herbivores

USDA-ARS?s Scientific Manuscript database

Herbivore induced plant volatiles (HIPVs) serve as specific cues to higher trophic levels. Novel, exotic herbivores entering foodwebs with a common co-existence history may disrupt the native infochemical network due to changes in HIPV profiles. Here we analyzed HIPV blends of native Brassica rapa p...

How the First Amendment Applies to Offensive Expression on the Campuses of Public Colleges and Universities.

ERIC Educational Resources Information Center

Tatel, David S.; And Others

The pamphlet addresses the application of the United States Constitution's First Amendment to offensive expression and expressive conduct, particularly by students, at public colleges and universities. Sections 1 through 4 summarize applicable First Amendment principles including the breadth of the First Amendment; exceptions to content-based…

Anthropometric and craniofacial patterns in mentally retarded males with emphasis on the fragile X syndrome.

PubMed

Butler, M G; Pratesi, R; Watson, M S; Breg, W R; Singh, D N

1993-09-01

Anthropometric and craniofacial profile patterns indicating the percent difference from the overall mean were developed on 34 physical parameters with 31 white, mentally retarded males (23 adults and 8 children) with the fra(X) syndrome matched for age with 31 white, mentally retarded males without a known cause of their retardation. The fra(X) syndrome males consistently showed larger dimensions for all anthropometric variables, with significant differences for height, sitting height, arm span, hand length, middle finger length, hand breadth, foot length, foot breadth, and testicular volume. A craniofacial pattern did emerge between the two groups of mentally retarded males, but with overlap of several variables. Significant differences were noted for head circumference, head breadth, lower face height, bizygomatic diameter, inner canthal distance, ear length and ear width, with the fra(X) syndrome males having larger head dimensions (head circumference, head breadth, head length, face height and lower face height), but smaller measurements for minimal frontal diameter, bizygomatic diameter, bigonial diameter, and inner canthal distance. Several significant correlations were found with the variables for both mentally retarded males with and without the fra(X) syndrome. In a combined anthropometric and craniofacial profile of 19 variables comparing 26 white fra(X) syndrome males (13 with high expression (> 30%) and 13 with low expression (< 30%), but matched for age), a relatively flat profile was observed with no significant differences for any of the variables. Generally, fra(X) syndrome males with increased fragile X chromosome expression have larger amplifications of the CGG trinucleotide repeat of the FMR-1 gene. No physical differences were detectable in our study between fra(X) males with high expression and apparently larger amplifications of the CGG trinucleotide repeats compared with those patients with low expression. Our research illustrates the use of anthropometry in identifying differences between mentally retarded males with or without the fra(X) syndrome and offers a comprehensive approach for screening males for the fra(X) syndrome and selecting those individuals for cytogenetic and/or molecular genetic testing.

Anthropometric and craniofacial patterns in mentally retarded males with emphasis on the fragile X syndrome

PubMed Central

Butler, Merlin G.; Pratesi, Riccardo; Watson, Michael S.; Breg, W. Roy; Singh, Dharmdeo N.

2017-01-01

Anthropometric and craniofacial profile patterns indicating the percent difference from the overall mean were developed on 34 physical parameters with 31 white, mentally retarded males (23 adults and 8 children) with the fra(X) syndrome matched for age with 31 white, mentally retarded males without a known cause of their retardation. The fra(X) syndrome males consistently showed larger dimensions for all anthropometric variables, with significant differences for height, sitting height, arm span, hand length, middle finger length, hand breadth, foot length, foot breadth, and testicular volume. A craniofacial pattern did emerge between the two groups of mentally retarded males, but with overlap of several variables. Significant differences were noted for head circumference, head breadth, lower face height, bizygomatic diameter, inner canthal distance, ear length and ear width, with the fra(X) syndrome males having larger head dimensions (head circumference, head breadth, head length, face height and lower face height), but smaller measurements for minimal frontal diameter, bizygomatic diameter, bigonial diameter, and inner canthal distance. Several significant correlations were found with the variables for both mentally retarded males with and without the fra(X) syndrome. In a combined anthropometric and craniofacial profile of 19 variables comparing 26 white fra(X) syndrome males (13 with high expression (>30%) and 13 with low expression (< 30%), but matched for age), a relatively flat profile was observed with no significant differences for any of the variables. Generally, fra(X) syndrome males with increased fragile X chromosome expression have larger amplifications of the CGG trinucleotide repeat of the FMR-1 gene. No physical differences were detectable in our study between fra(X) males with high expression and apparently larger amplifications of the CGG trinucleotide repeats compared with those patients with low expression. Our research illustrates the use of anthropometry in identifying differences between mentally retarded males with or without the fra(X) syndrome and offers a comprehensive approach for screening males for the fra(X) syndrome and selecting those individuals for cytogenetic and/or molecular genetic testing. PMID:8275570

Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity.

PubMed

Birnbaum, Stephanie S L; Rinker, David C; Gerardo, Nicole M; Abbot, Patrick

2017-12-01

Interactions between plants and herbivorous insects have been models for theories of specialization and co-evolution for over a century. Phytochemicals govern many aspects of these interactions and have fostered the evolution of adaptations by insects to tolerate or even specialize on plant defensive chemistry. While genomic approaches are providing new insights into the genes and mechanisms insect specialists employ to tolerate plant secondary metabolites, open questions remain about the evolution and conservation of insect counterdefences, how insects respond to the diversity defences mounted by their host plants, and the costs and benefits of resistance and tolerance to plant defences in natural ecological communities. Using a milkweed-specialist aphid (Aphis nerii) model, we test the effects of host plant species with increased toxicity, likely driven primarily by increased secondary metabolites, on aphid life history traits and whole-body gene expression. We show that more toxic plant species have a negative effect on aphid development and lifetime fecundity. When feeding on more toxic host plants with higher levels of secondary metabolites, aphids regulate a narrow, targeted set of genes, including those involved in canonical detoxification processes (e.g., cytochrome P450s, hydrolases, UDP-glucuronosyltransferases and ABC transporters). These results indicate that A. nerii marshal a variety of metabolic detoxification mechanisms to circumvent milkweed toxicity and facilitate host plant specialization, yet, despite these detoxification mechanisms, aphids experience reduced fitness when feeding on more toxic host plants. Disentangling how specialist insects respond to challenging host plants is a pivotal step in understanding the evolution of specialized diet breadths. © 2017 John Wiley & Sons Ltd.

The Many Dimensions of Diet Breadth: Phytochemical, Genetic, Behavioral, and Physiological Perspectives on the Interaction between a Native Herbivore and an Exotic Host

PubMed Central

Harrison, Joshua G.; Gompert, Zachariah; Fordyce, James A.; Buerkle, C. Alex; Grinstead, Rachel; Jahner, Joshua P.; Mikel, Scott; Nice, Christopher C.; Santamaria, Aldrin; Forister, Matthew L.

2016-01-01

From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization by L. melissa; specifically, we examined variation in phytochemistry, foliar protein, and plant population genetic structure, as well as responses of caterpillars and adult butterflies to foliage from the same populations. Regional patterns of alfalfa colonization by L. melissa were well predicted by phytochemical variation, and colonized patches of alfalfa showed a similar level of inter-individual phytochemical diversity. However, phytochemical variation was a poor predictor of larval performance, despite the fact that survival and weight gain differed dramatically among caterpillars reared on plants from different alfalfa populations. Moreover, we observed a mismatch between alfalfa supporting the best larval performance and alfalfa favored by ovipositing females. Thus, the axes of plant variation that mediate interactions with L. melissa depend upon herbivore life history stage, which raises important issues for our understanding of adaptation to novel resources by an organism with a complex life history. PMID:26836490

Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys.

PubMed

Barouch, Dan H; O'Brien, Kara L; Simmons, Nathaniel L; King, Sharon L; Abbink, Peter; Maxfield, Lori F; Sun, Ying-Hua; La Porte, Annalena; Riggs, Ambryice M; Lynch, Diana M; Clark, Sarah L; Backus, Katherine; Perry, James R; Seaman, Michael S; Carville, Angela; Mansfield, Keith G; Szinger, James J; Fischer, Will; Muldoon, Mark; Korber, Bette

2010-03-01

The worldwide diversity of HIV-1 presents an unprecedented challenge for vaccine development. Antigens derived from natural HIV-1 sequences have elicited only a limited breadth of cellular immune responses in nonhuman primate studies and clinical trials to date. Polyvalent 'mosaic' antigens, in contrast, are designed to optimize cellular immunologic coverage of global HIV-1 sequence diversity. Here we show that mosaic HIV-1 Gag, Pol and Env antigens expressed by recombinant, replication-incompetent adenovirus serotype 26 vectors markedly augmented both the breadth and depth without compromising the magnitude of antigen-specific T lymphocyte responses as compared with consensus or natural sequence HIV-1 antigens in rhesus monkeys. Polyvalent mosaic antigens therefore represent a promising strategy to expand cellular immunologic vaccine coverage for genetically diverse pathogens such as HIV-1.

The transcriptional landscape of αβ T cell differentiation

PubMed Central

Mingueneau, Michael; Kreslavsky, Taras; Gray, Daniel; Heng, Tracy; Cruse, Richard; Ericson, Jeffrey; Bendall, Sean; Spitzer, Matt; Nolan, Garry; Kobayashi, Koichi; von Boehmer, Harald; Mathis, Diane; Benoist, Christophe

2013-01-01

αβT cell differentiation from thymic precursors is a complex process, explored here with the breadth of ImmGen expression datasets, analyzing how differentiation of thymic precursors gives rise to transcriptomes. After surprisingly gradual changes though early T commitment, transit through the CD4+CD8+ stage involves a shutdown or rare breadth, and correlating tightly with MYC. MHC-driven selection promotes a large-scale transcriptional reactivation. We identify distinct signatures that mark cells destined for positive selection versus apoptotic deletion. Differential expression of surprisingly few genes accompany CD4 or CD8 commitment, a similarity that carries through to peripheral T cells and their activation, revealed by mass cytometry phosphoproteomics. The novel transcripts identified as candidate mediators of key transitions help define the “known unknown” of thymocyte differentiation. PMID:23644507

Global pattern of plant utilization across different organisms: Does plant apparency or plant phylogeny matter?

PubMed

Dai, Xiaohua; Zhang, Wei; Xu, Jiasheng; Duffy, Kevin J; Guo, Qingyun

2017-04-01

The present study is the first to consider human and nonhuman consumers together to reveal several general patterns of plant utilization. We provide evidence that at a global scale, plant apparency and phylogenetic isolation can be important predictors of plant utilization and consumer diversity. Using the number of species or genera or the distribution area of each plant family as the island "area" and the minimum phylogenetic distance to common plant families as the island "distance", we fitted presence-area relationships and presence-distance relationships with a binomial GLM (generalized linear model) with a logit link. The presence-absence of consumers among each plant family strongly depended on plant apparency (family size and distribution area); the diversity of consumers increased with plant apparency but decreased with phylogenetic isolation. When consumers extended their host breadth, unapparent plants became more likely to be used. Common uses occurred more often on common plants and their relatives, showing higher host phylogenetic clustering than uncommon uses. On the contrary, highly specialized uses might be related to the rarity of plant chemicals and were therefore very species-specific. In summary, our results provide a global illustration of plant-consumer combinations and reveal several general patterns of plant utilization across humans, insects and microbes. First, plant apparency and plant phylogenetic isolation generally govern plant utilization value, with uncommon and isolated plants suffering fewer parasites. Second, extension of the breadth of utilized hosts helps explain the presence of consumers on unapparent plants. Finally, the phylogenetic clustering structure of host plants is different between common uses and uncommon uses. The strength of such consistent plant utilization patterns across a diverse set of usage types suggests that the persistence and accumulation of consumer diversity and use value for plant species are determined by similar ecological and evolutionary processes.

From filaments to function: The role of the plant actin cytoskeleton in pathogen perception, signaling and immunity.

PubMed

Porter, Katie; Day, Brad

2016-04-01

The eukaryotic actin cytoskeleton is required for numerous cellular processes, including cell shape, development and movement, gene expression and signal transduction, and response to biotic and abiotic stress. In recent years, research in both plants and animal systems have described a function for actin as the ideal surveillance platform, linking the function and activity of primary physiological processes to the immune system. In this review, we will highlight recent advances that have defined the regulation and breadth of function of the actin cytoskeleton as a network required for defense signaling following pathogen infection. Coupled with an overview of recent work demonstrating specific targeting of the plant actin cytoskeleton by a diversity of pathogens, including bacteria, fungi and viruses, we will highlight the importance of actin as a key signaling hub in plants, one that mediates surveillance of cellular homeostasis and the activation of specific signaling responses following pathogen perception. Based on the studies highlighted herein, we propose a working model that posits changes in actin filament organization is in and of itself a highly specific signal, which induces, regulates and physically directs stimulus-specific signaling processes, most importantly, those associated with response to pathogens. © 2015 Institute of Botany, Chinese Academy of Sciences.

7 CFR 29.1085 - Width.

Code of Federal Regulations, 2010 CFR

2010-01-01

....) Elements Degrees Maturity Immature Unripe Mature Ripe Mellow. Leaf structure Tight Close Firm Open Body... Type 92) § 29.1085 Width. The relative breadth of a tobacco leaf expressed in relation to its length...

7 CFR 29.1085 - Width.

Code of Federal Regulations, 2013 CFR

2013-01-01

....) Elements Degrees Maturity Immature Unripe Mature Ripe Mellow. Leaf structure Tight Close Firm Open Body... Type 92) § 29.1085 Width. The relative breadth of a tobacco leaf expressed in relation to its length...

7 CFR 29.1085 - Width.

Code of Federal Regulations, 2011 CFR

2011-01-01

....) Elements Degrees Maturity Immature Unripe Mature Ripe Mellow. Leaf structure Tight Close Firm Open Body... Type 92) § 29.1085 Width. The relative breadth of a tobacco leaf expressed in relation to its length...

7 CFR 29.1085 - Width.

Code of Federal Regulations, 2014 CFR

2014-01-01

....) Elements Degrees Maturity Immature Unripe Mature Ripe Mellow. Leaf structure Tight Close Firm Open Body... Type 92) § 29.1085 Width. The relative breadth of a tobacco leaf expressed in relation to its length...

7 CFR 29.1085 - Width.

Code of Federal Regulations, 2012 CFR

2012-01-01

....) Elements Degrees Maturity Immature Unripe Mature Ripe Mellow. Leaf structure Tight Close Firm Open Body... Type 92) § 29.1085 Width. The relative breadth of a tobacco leaf expressed in relation to its length...

Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

PubMed

Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

2016-04-01

This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Tri-Trophic Interactions Hypothesis: Interactive Effects of Host Plant Quality, Diet Breadth and Natural Enemies on Herbivores

PubMed Central

Mooney, Kailen A.; Pratt, Riley T.; Singer, Michael S.

2012-01-01

Several influential hypotheses in plant-herbivore and herbivore-predator interactions consider the interactive effects of plant quality, herbivore diet breadth, and predation on herbivore performance. Yet individually and collectively, these hypotheses fail to address the simultaneous influence of all three factors. Here we review existing hypotheses, and propose the tri-trophic interactions (TTI) hypothesis to consolidate and integrate their predictions. The TTI hypothesis predicts that dietary specialist herbivores (as compared to generalists) should escape predators and be competitively dominant due to faster growth rates, and that such differences should be greater on low quality (as compared to high quality) host plants. To provide a preliminary test of these predictions, we conducted an empirical study comparing the effects of plant (Baccharis salicifolia) quality and predators between a specialist (Uroleucon macolai) and a generalist (Aphis gossypii) aphid herbivore. Consistent with predictions, these three factors interactively determine herbivore performance in ways not addressed by existing hypotheses. Compared to the specialist, the generalist was less fecund, competitively inferior, and more sensitive to low plant quality. Correspondingly, predator effects were contingent upon plant quality only for the generalist. Contrary to predictions, predator effects were weaker for the generalist and on low-quality plants, likely due to density-dependent benefits provided to the generalist by mutualist ants. Because the TTI hypothesis predicts the superior performance of specialists, mutualist ants may be critical to A. gossypii persistence under competition from U. macolai. In summary, the integrative nature of the TTI hypothesis offers novel insight into the determinants of plant-herbivore and herbivore-predator interactions and the coexistence of specialist and generalist herbivores. PMID:22509298

46 CFR 69.207 - Measurements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... dimensions must be expressed in feet and inches to the nearest half inch or in feet and tenths of a foot to..., breadth, and depth. (c) The Coast Guard may verify dimensions of vessels measured under this subpart. ...

46 CFR 69.207 - Measurements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... dimensions must be expressed in feet and inches to the nearest half inch or in feet and tenths of a foot to..., breadth, and depth. (c) The Coast Guard may verify dimensions of vessels measured under this subpart. ...

46 CFR 69.207 - Measurements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... dimensions must be expressed in feet and inches to the nearest half inch or in feet and tenths of a foot to..., breadth, and depth. (c) The Coast Guard may verify dimensions of vessels measured under this subpart. ...

Expressions of Emotion as Mediated by Context

ERIC Educational Resources Information Center

Altarriba, Jeanette

2008-01-01

In her thoughtful work regarding various aspects of emotion and emotion related words, Pavlenko explores a variety of perspectives on how we might characterize and conceptualize expressions of emotion. It is a work that is quite rich in breadth--one that leads to a variety of different thoughts on this topic, many of which are amenable to…

Trait responses of invasive aquatic macrophyte congeners: colonizing diploid outperforms polyploid

USDA-ARS?s Scientific Manuscript database

Understanding traits underlying colonization and niche breadth of invasive plants is key to developing sustainable management solutions to curtail invasions at the establishment phase, when efforts are often most effective. The aim of this study was to evaluate how two invasive congeners differing i...

Fast and robust curve skeletonization for real-world elongated objects

USDA-ARS?s Scientific Manuscript database

We consider the problem of extracting curve skeletons of three-dimensional, elongated objects given a noisy surface, which has applications in agricultural contexts such as extracting the branching structure of plants. We describe an efficient and robust method based on breadth-first search that ca...

[Species composition and spatial structure of plants in urban parks of Beijing].

PubMed

Zhao, Juan-Juan; Ouyang, Zhi-Yun; Zheng, Hua; Xu, Wei-Hua; Wang, Xiao-Ke

2009-02-01

By the method of stratified random sampling, the species composition and spatial structure of the plants in 53 parks in Beijing urban area were investigated, aimed to provide basic information for the protection of plant diversity in the parks and the management of the parks. A total of 492 plant species belong to 96 families and 283 genera were recorded. Based on the data of 21 investigation items about the trees, shrubs, and grasses in the study area and related statistical analyses, the plant structural patterns commonly seen in the green space of the parks of Beijing urban area were introduced. Among the plants in the parks, native species occupied 53.86% of the total. The chorological composition of the genera embraced broad kinds of geographical elements in China, and the predominance of dominant plants was remarkable. In most green patches of the parks, herbaceous species were more abundant and had higher coverage, shrubs had relatively low coverage and were less beneath tree canopy, and trees and shrubs had lower species richness and density. The canopy breadth and the diameter of breast height of trees as well as the breadth of shrubs and the heights of trees and shrubs were basically at the second grade, but the canopy structure of the trees were better, with good conditions of sunlight and growth. The crown missing of the shrubs was relatively low. It was suggested from correlation analyses and document survey of Beijing parks construction history that park landscape design, alien species introduction; and cultivation management were the main factors affecting the species composition and spatial structure of the plants in Beijing urban parks.

Interactive Effects of Nutrient and Mechanical Stresses on Plant Morphology

PubMed Central

Puijalon, Sara; Lena, Jean-Paul; Bornette, Gudrun

2007-01-01

Background and Aims Plant species frequently encounter multiple stresses under natural conditions, and the way they cope with these stresses is a major determinant of their ecological breadth. The way mechanical (e.g. wind, current) and resource stresses act simultaneously on plant morphological traits has been poorly addressed, even if both stresses often interact. This paper aims to assess whether hydraulic stress affects plant morphology in the same way at different nutrient levels. Methods An examination was made of morphological variations of an aquatic plant species growing under four hydraulic stress (flow velocity) gradients located in four habitats distributed along a nutrient gradient. Morphological traits covering plant size, dry mass allocation, organ water content and foliage architecture were measured. Key Results Significant interactive effects of flow velocity and nutrient level were observed for all morphological traits. In particular, increased flow velocity resulted in size reductions under low nutrient conditions, suggesting an adaptive response to flow stress (escape strategy). On the other hand, moderate increases in flow velocity resulted in increased size under high nutrient conditions, possibly related to an inevitable growth response to a higher nutrient supply induced by water renewal at the plant surface. For some traits (e.g. dry mass allocation), a consistent sense of variation as a result of increasing flow velocity was observed, but the amount of variation was either reduced or amplified under nutrient-rich compared with nutrient-poor conditions, depending on the traits considered. Conclusions These results suggest that, for a given species, a stress factor may result, in contrasting patterns and hence strategies, depending on a second stress factor. Such results emphasize the relevance of studies on plant responses to multiple stresses for understanding the actual ecological breadth of species. PMID:17913725

Functionally specialised birds respond flexibly to seasonal changes in fruit availability.

PubMed

Bender, Irene M A; Kissling, W Daniel; Böhning-Gaese, Katrin; Hensen, Isabell; Kühn, Ingolf; Wiegand, Thorsten; Dehling, D Matthias; Schleuning, Matthias

2017-07-01

Interactions between resource and consumer species result in complex ecological networks. The overall structure of these networks is often stable in space and time, but little is known about the temporal stability of the functional roles of consumer species in these networks. We used a trait-based approach to investigate whether consumers (frugivorous birds) show similar degrees of functional specialisation on resources (plants) in ecological networks across seasons. We additionally tested whether closely related bird species have similar degrees of functional specialisation and whether birds that are functionally specialised on specific resource types within a season are flexible in switching to other resource types in other seasons. We analysed four seasonal replicates of two species-rich plant-frugivore networks from the tropical Andes. To quantify fruit preferences of frugivorous birds, we projected their interactions with plants into a multidimensional plant trait space. To measure functional specialisation of birds, we calculated a species' functional niche breadth (the extent of seasonal plant trait space utilised by a particular bird) and functional originality (the extent to which a bird species' fruit preference functionally differs from those of other species in a seasonal network). We additionally calculated functional flexibility, i.e. the ability of bird species to change their fruit preference across seasons in response to variation in plant resources. Functional specialisation of bird species varied more among species than across seasons, and phylogenetically similar bird species showed similar degrees of functional niche breadth (phylogenetic signal λ = 0·81) and functional originality (λ = 0·89). Additionally, we found that birds with high functional flexibility across seasons had narrow functional niche breadth and high functional originality per season, suggesting that birds that are seasonally specialised on particular resources are most flexible in switching to other fruit resources across seasons. The high flexibility of functionally specialised bird species to switch seasonally to other resources challenges the view that consumer species rely on functionally similar resources throughout the year. This flexibility of consumer species may be an important, but widely neglected mechanism that could potentially stabilise consumer-resource networks in response to human disturbance and environmental change. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

PubMed

Trotta, Edoardo

2016-05-17

The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana.

PubMed

Vaneechoutte, Dries; Estrada, April R; Lin, Ying-Chen; Loraine, Ann E; Vandepoele, Klaas

2017-12-01

Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of differential transcript usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes, and have been linked to development and stress response. However, neither the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates, and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths and functions show large differences in the frequency at which they undergo DTU, and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Vaccinia-based influenza vaccine overcomes previously induced immunodominance hierarchy for heterosubtypic protection.

PubMed

Kwon, Ji-Sun; Yoon, Jungsoon; Kim, Yeon-Jung; Kang, Kyuho; Woo, Sunje; Jung, Dea-Im; Song, Man Ki; Kim, Eun-Ha; Kwon, Hyeok-Il; Choi, Young Ki; Kim, Jihye; Lee, Jeewon; Yoon, Yeup; Shin, Eui-Cheol; Youn, Jin-Won

2014-08-01

Growing concerns about unpredictable influenza pandemics require a broadly protective vaccine against diverse influenza strains. One of the promising approaches was a T cell-based vaccine, but the narrow breadth of T-cell immunity due to the immunodominance hierarchy established by previous influenza infection and efficacy against only mild challenge condition are important hurdles to overcome. To model T-cell immunodominance hierarchy in humans in an experimental setting, influenza-primed C57BL/6 mice were chosen and boosted with a mixture of vaccinia recombinants, individually expressing consensus sequences from avian, swine, and human isolates of influenza internal proteins. As determined by IFN-γ ELISPOT and polyfunctional cytokine secretion, the vaccinia recombinants of influenza expanded the breadth of T-cell responses to include subdominant and even minor epitopes. Vaccine groups were successfully protected against 100 LD50 challenges with PR/8/34 and highly pathogenic avian influenza H5N1, which contained the identical dominant NP366 epitope. Interestingly, in challenge with pandemic A/Cal/04/2009 containing mutations in the dominant epitope, only the group vaccinated with rVV-NP + PA showed improved protection. Taken together, a vaccinia-based influenza vaccine expressing conserved internal proteins improved the breadth of influenza-specific T-cell immunity and provided heterosubtypic protection against immunologically close as well as distant influenza strains. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Missing Dimensions of Mathematics Instruction.

ERIC Educational Resources Information Center

Meyer, Walter

1995-01-01

Emphasizes how to express the breadth of mathematics itself. Addresses other missing dimensions which make mathematics attractive to a larger number of students by making it appear less isolated and more tied to thoughts and experiences that students find familiar and congenial. (ASK)

Vaccine Targeting of Subdominant CD8+ T Cell Epitopes Increases the Breadth of the T Cell Response upon Viral Challenge, but May Impair Immediate Virus Control.

PubMed

Steffensen, Maria A; Pedersen, Louise H; Jahn, Marie L; Nielsen, Karen N; Christensen, Jan P; Thomsen, Allan R

2016-03-15

As a result of the difficulties in making efficient vaccines against genetically unstable viruses such as HIV, it has been suggested that future vaccines should preferentially target subdominant epitopes, the idea being that this should allow a greater breadth of the induced T cell response and, hence, a greater efficiency in controlling escape variants. However, to our knowledge the evidence supporting this concept is limited at best. To improve upon this, we used the murine lymphocytic choriomeningitis virus model and adenoviral vectors to compare a vaccine expressing unmodified Ag to a vaccine expressing the same Ag without its immunodominant epitope. We found that removal of the dominant epitope allowed the induction of CD8(+) T cell responses targeting at least two otherwise subdominant epitopes. Importantly, the overall magnitude of the induced T cell responses was similar, allowing us to directly compare the efficiency of these vaccines. Doing this, we observed that mice vaccinated with the vaccine expressing unmodified Ag more efficiently controlled an acute viral challenge. In the course of a more chronic viral infection, mice vaccinated using the vaccine targeting subdominant epitopes caught up with the conventionally vaccinated mice, and analysis of the breadth of the CD8(+) T cell response revealed that this was notably greater in the former mice. However, under the conditions of our studies, we never saw any functional advantage of this. This may represent a limitation of our model, but clearly our findings underscore the importance of carefully weighing the pros and cons of changes in epitope targeting before any implementation. Copyright © 2016 by The American Association of Immunologists, Inc.

Physiological Basis and Transcriptional Profiling of Three Salt-Tolerant Mutant Lines of Rice

PubMed Central

Domingo, Concha; Lalanne, Eric; Catalá, María M.; Pla, Eva; Reig-Valiente, Juan L.; Talón, Manuel

2016-01-01

Salinity is a complex trait that affects growth and productivity in many crops, including rice. Mutation induction, a useful tool to generate salt tolerant plants, enables the analysis of plants with similar genetic background, facilitating the understanding of the salt tolerance mechanisms. In this work, we generated three salt tolerant mutant lines by irradiation of a salt-sensitive cultivar plants and screened M2 plants at seedling stage in the presence of high salinity. These three lines, SaT20, SaS62, and SaT58, showed different responses to salinity, but exhibited similar phenotype to wild type plants, except SaT20 that displayed shorter height when grown in the absence of salt. Under salt conditions, all three mutants and the parental line showed similar reduction in yield, although relevant differences in other physiological parameters, such as Na+ accumulation in healthy leaves of SaT20, were registered. Microarray analyses of gene expression profiles in roots revealed the occurrence of common and specific responses in the mutants. The three mutants showed up-regulation of responsive genes, the activation of oxido-reduction process and the inhibition of ion transport. The participation of jasmonate in the plant response to salt was evident by down-regulation of a gene coding for a jasmonate O-methyltransferase. Genes dealing with lipid transport and metabolism were, in general, up-regulated except in SaS62, that also exhibited down-regulation of genes involved in ion transport and Ca2+ signal transduction. The two most tolerant varieties, SaS62 and SaT20, displayed lower levels of transcripts involved in K+ uptake. The physiological study and the description of the expression analysis evidenced that the three lines showed different responses to salt: SaT20 showed a high Na+ content in leaves, SaS62 presented an inhibition of lipid metabolism and ion transport and SaT58 differs in both features in the response to salinity. The analysis of these salt tolerant mutants illustrates the complexity of this trait evidencing the breadth of the plant responses to salinity including simultaneous cooperation of alternative or complementary mechanisms. PMID:27733859

Niche analysis and conservation of the orchids of east Macedonia (NE Greece)

NASA Astrophysics Data System (ADS)

Tsiftsis, Spyros; Tsiripidis, Ioannis; Karagiannakidou, Vassiliki; Alifragis, Dimitrios

2008-01-01

The orchid family is one of the largest in the flowering plant kingdom and includes a lot of rare, threatened or endangered species. The determination of plant species niche is considered fundamental for their conservation. Two parameters closely related with species niche are niche marginality and breadth. The first parameter is a measure of how typical or atypical a species niche is within an area, while the second is a measure of species tolerance. This study deals with niche analysis of the orchids of east Macedonia (NE Greece). Factors that are known to determine species distribution on a regional scale, such as altitude, aspect, habitat type, bedrock type and soil properties (acidity, organic matter, and phosphorus content) were used as explanatory variables. Geographical coordinates were also employed in order to explore spatial patterns in orchid distribution. Niche analysis was carried out using the Outlying Mean Index (OMI) analysis. Out of the total data of 55 taxa that were analyzed, 41 had a significant marginal niche compared with the average niche of the study area. Altitude, soil acidity and certain habitat types were found to be the most important factors in determining orchid distribution. Five different species groups were distinguished on the basis of their ecological preferences and niche breadth. Species niche marginality and breadth, the amplitude of their geographical distribution, the size of their populations and the rareness and conservation status of their habitats were taken into account in order to set conservation priorities for the orchids in the study area. The above characteristics combined with intuitive criteria (e.g. geographical distribution, endemicity) for the species with a small number of occurrences could form a sound basis for setting conservation priorities.

Measuring Preschool Cognitive Growth while It's Still Happening: The Learning Express

ERIC Educational Resources Information Center

McDermott, Paul A.; Fantuzzo, John W.; Waterman, Clare; Angelo, Lauren E.; Warley, Heather P.; Gadsden, Vivian L.; Zhang, Xiuyuan

2009-01-01

Educators need accurate assessments of preschool cognitive growth to guide curriculum design, evaluation, and timely modification of their instructional programs. But available tests do not provide content breadth or growth sensitivity over brief intervals. This article details evidence for a multiform, multiscale test criterion-referenced to…

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

PubMed

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

2015-02-10

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

Nonadaptive radiation: Pervasive diet specialization by drift in scale insects?

PubMed

Hardy, Nate B; Peterson, Daniel A; Normark, Benjamin B

2016-10-01

At least half of metazoan species are herbivorous insects. Why are they so diverse? Most herbivorous insects feed on few plant species, and adaptive host specialization is often invoked to explain their diversification. Nevertheless, it is possible that the narrow host ranges of many herbivorous insects are nonadaptive. Here, we test predictions of this hypothesis with comparative phylogenetic analyses of scale insects, a group for which there appear to be few host-use trade-offs that would select against polyphagy, and for which passive wind-dispersal should make host specificity costly. We infer a strong positive relationship between host range and diversification rate, and a marked asymmetry in cladogenetic changes in diet breadth. These results are consonant with a system of pervasive nonadaptive host specialization in which small, drift- and extinction-prone populations are frequently isolated from persistent and polyphagous source populations. They also contrast with the negative relationship between diet breadth and taxonomic diversification that has been estimated in butterflies, a disparity that likely stems from differences in the average costs and benefits of host specificity and generalism in scale insects versus butterflies. Our results indicate the potential for nonadaptive processes to be important to diet-breadth evolution and taxonomic diversification across herbivorous insects. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

eVoc Strategies: 10 Ways to Use Technology to Build Vocabulary

ERIC Educational Resources Information Center

Dalton, Bridget; Grisham, Dana L.

2011-01-01

Vocabulary knowledge is key to comprehension and expression. For students in the intermediate grades, the need for breadth and depth of vocabulary accelerates as they encounter more challenging academic texts in print and on the Internet. Drawing on research-based principles of vocabulary instruction and multimedia learning, this article presents…

46 CFR 69.207 - Measurements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... dimensions must be expressed in feet and inches to the nearest half inch or in feet and tenths of a foot to the nearest .05 of a foot. (b) For a multi-hull vessel, each hull must be measured separately for..., breadth, and depth. (c) The Coast Guard may verify dimensions of vessels measured under this subpart. ...

46 CFR 69.207 - Measurements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... dimensions must be expressed in feet and inches to the nearest half inch or in feet and tenths of a foot to the nearest .05 of a foot. (b) For a multi-hull vessel, each hull must be measured separately for..., breadth, and depth. (c) The Coast Guard may verify dimensions of vessels measured under this subpart. ...

Comparing the Lexical Features of EAP Students' Essays by Prompt and Rating

ERIC Educational Resources Information Center

Lavallée, Maxime; McDonough, Kim

2015-01-01

Previous research has shown that high frequency lexical items, such as AWL words and formulaic expressions, may differentiate between texts written by expert and novice writers (Chen & Baker, 2010; Hancioglu, 2009), and that lexical features related to breadth, depth, and accessibility differentiate among texts from L2 writers of different…

Immune Interventions to Eliminate the HIV Reservoir.

PubMed

Hsu, Denise C; Ananworanich, Jintanat

2017-10-26

Inducing HIV remission is a monumental challenge. A potential strategy is the "kick and kill" approach where latently infected cells are first activated to express viral proteins and then eliminated through cytopathic effects of HIV or immune-mediated killing. However, pre-existing immune responses to HIV cannot eradicate HIV infection due to the presence of escape variants, inadequate magnitude, and breadth of responses as well as immune exhaustion. The two major approaches to boost immune-mediated elimination of infected cells include enhancing cytotoxic T lymphocyte mediated killing and harnessing antibodies to eliminate HIV. Specific strategies include increasing the magnitude and breadth of T cell responses through therapeutic vaccinations, reversing the effects of T cell exhaustion using immune checkpoint inhibition, employing bispecific T cell targeting immunomodulatory proteins or dual-affinity re-targeting molecules to direct cytotoxic T lymphocytes to virus-expressing cells and broadly neutralizing antibody infusions. Methods to steer immune responses to tissue sites where latently infected cells are located need to be further explored. Ultimately, strategies to induce HIV remission must be tolerable, safe, and scalable in order to make a global impact.

Plant Molecular Biology 2008 Gordon Research Conference - July 13-18, 2008

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

Richard M. Amasino

The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2008 conference will continue in that tradition. There will be sessions on metabolism; new methods to study genomes, proteomes and metabolomes; plant-microbe interactions; plant hormones; epigenetics. A new topic for the conference this year will be bioenergy. Thus this conference will bring together a range of disciplines to foster the exchange ideas and to permit the participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additionalmore » speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner.« less

To what extent does sexual dimorphism exist in competitive powerlifters?

PubMed

Keogh, Justin W L; Hume, Patria A; Pearson, Simon N; Mellow, Peter

2008-03-01

We examined sexual dimorphism in the anthropometry of 68 Australasian and Pacific powerlifters (14 females, 54 males) who were competing in one of two national or international powerlifting competitions held in New Zealand. All powerlifters were assessed for 37 anthropometric dimensions by ISAK (International Society for the Advancement of Kinanthropometry) Level II and III accredited anthropometrists. While the powerlifters were highly mesomorphic and possessed large girths and bone breadths, both in absolute terms and when expressed as Z(p)-scores compared through the Phantom (Ross & Wilson, 1974), these characteristics were often more pronounced in male than female lifters. No significant inter-gender differences in any of the measures of adiposity were observed. When normalized through the Phantom, the female and male powerlifters had relatively similar segment lengths and bone breadths, indicating that regardless of gender, competitive powerlifters possess comparable skeletal proportions. These results indicate that although competitive powerlifters exhibit sexual dimorphism for many absolute anthropometric measures, little dimorphism is found for measures of adiposity and for proportional segment lengths and bone breadths. These results further support the importance of anthropometric profiling for powerlifting, and suggest that successful male and female powerlifters will possess similar proportional characteristics.

Ecological networks are more sensitive to plant than to animal extinction under climate change

PubMed Central

Schleuning, Matthias; Fründ, Jochen; Schweiger, Oliver; Welk, Erik; Albrecht, Jörg; Albrecht, Matthias; Beil, Marion; Benadi, Gita; Blüthgen, Nico; Bruelheide, Helge; Böhning-Gaese, Katrin; Dehling, D. Matthias; Dormann, Carsten F.; Exeler, Nina; Farwig, Nina; Harpke, Alexander; Hickler, Thomas; Kratochwil, Anselm; Kuhlmann, Michael; Kühn, Ingolf; Michez, Denis; Mudri-Stojnić, Sonja; Plein, Michaela; Rasmont, Pierre; Schwabe, Angelika; Settele, Josef; Vujić, Ante; Weiner, Christiane N.; Wiemers, Martin; Hof, Christian

2016-01-01

Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on >700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks. PMID:28008919

Ecological networks are more sensitive to plant than to animal extinction under climate change.

PubMed

Schleuning, Matthias; Fründ, Jochen; Schweiger, Oliver; Welk, Erik; Albrecht, Jörg; Albrecht, Matthias; Beil, Marion; Benadi, Gita; Blüthgen, Nico; Bruelheide, Helge; Böhning-Gaese, Katrin; Dehling, D Matthias; Dormann, Carsten F; Exeler, Nina; Farwig, Nina; Harpke, Alexander; Hickler, Thomas; Kratochwil, Anselm; Kuhlmann, Michael; Kühn, Ingolf; Michez, Denis; Mudri-Stojnić, Sonja; Plein, Michaela; Rasmont, Pierre; Schwabe, Angelika; Settele, Josef; Vujić, Ante; Weiner, Christiane N; Wiemers, Martin; Hof, Christian

2016-12-23

Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on >700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks.

The History and Implications of Technology on School Counseling in North Carolina School Districts

ERIC Educational Resources Information Center

Chancy, Eric Joseph

2015-01-01

The world has changed as technology has been invented, created for mass distribution and implemented. The ways in which people interact, communicate, tell jokes, express dismay or displeasure, and find information and entertainment have changed tremendously in both scope and breadth, and school counselors have a choice to make: They can fight…

Medicinal history of North American Veratrum

PubMed Central

Chandler, Christopher M.

2014-01-01

Plants belonging to the genus Veratrum have been used throughout history for their medicinal properties. During the nineteenth and twentieth centuries, phytochemical investigations revealed a host of steroidal alkaloids in Veratrum species, some of which are potent bioactives. This review discusses Veratrum species that grow in North America with a focus on the medicinal history of these plants and the steroidal alkaloids they contain. While significant reviews have been devoted to singularly describing the plant species within the genus Veratrum (botany), the staggering breadth of alkaloids isolated from these and related plants (phytochemistry), and the intricacies of how the various alkaloids act on their biological targets (physiology and biochemistry), this review will straddle the margins of the aforementioned disciplines in an attempt to provide a unified, coherent picture of the Veratrum plants of North America and the medicinal uses of their bioactive steroidal alkaloids. PMID:25379034

Exploring older and younger adults' preferences for health information and participation in decision making using the Health Information Wants Questionnaire (HIWQ).

PubMed

Xie, Bo; Wang, Mo; Feldman, Robert; Zhou, Le

2014-12-01

Existing measurements of patient preferences cover only a limited range of health information and participation in decision making. A broader approach is necessary to understand the breadth and variations in patient preferences. To explore the breadth and variances in patient preferences for health information and participation in decision making and to understand the relationship between age and each type of preference. The Health Information Wants Questionnaire (HIWQ) was administered during May-December 2010 to gather data about the information and corresponding decision-making autonomy participants would want in seven areas: diagnosis, treatment, laboratory tests, self-care, complementary and alternative medicine (CAM), psychosocial factors and health-care providers. A large state university, public libraries and senior centres in Maryland, USA. A convenience sample of 438 individuals, including 226 undergraduates (mean age = 20; SD = 2.15) and 212 community-dwelling older adults (mean age = 72; SD = 9.00). Ratings on the information and decision-making items of the HIWQ. Participants expressed higher levels of preference for information than for participation in decision making on six of seven subscales. On the psychosocial subscale, they expressed stronger desire for participation in decision making than for information. Age had no predictive effect on the overall preferences or specific preferences for information and participation in decision making about standard treatments and CAM. The predictive effect of age on the other types of preferences varied significantly. Physicians should take into account the breadth and variations in patient preferences. The predictive effect of age on patient preferences varied depending on the specific area of preferences. © 2012 John Wiley & Sons Ltd.

A matter of scale: apparent niche differentiation of diploid and tetraploid plants may depend on extent and grain of analysis.

PubMed

Kirchheimer, Bernhard; Schinkel, Christoph C F; Dellinger, Agnes S; Klatt, Simone; Moser, Dietmar; Winkler, Manuela; Lenoir, Jonathan; Caccianiga, Marco; Guisan, Antoine; Nieto-Lugilde, Diego; Svenning, Jens-Christian; Thuiller, Wilfried; Vittoz, Pascal; Willner, Wolfgang; Zimmermann, Niklaus E; Hörandl, Elvira; Dullinger, Stefan

2016-03-22

Emerging polyploids may depend on environmental niche shifts for successful establishment. Using the alpine plant Ranunculus kuepferi as a model system, we explore the niche shift hypothesis at different spatial resolutions and in contrasting parts of the species range. European Alps. We sampled 12 individuals from each of 102 populations of R. kuepferi across the Alps, determined their ploidy levels, derived coarse-grain (100 × 100 m) environmental descriptors for all sampling sites by downscaling WorldClim maps, and calculated fine-scale environmental descriptors (2 × 2 m) from indicator values of the vegetation accompanying the sampled individuals. Both coarse and fine-scale variables were further computed for 8239 vegetation plots from across the Alps. Subsequently, we compared niche optima and breadths of diploid and tetraploid cytotypes by combining principal components analysis and kernel smoothing procedures. Comparisons were done separately for coarse and fine-grain data sets and for sympatric, allopatric and the total set of populations. All comparisons indicate that the niches of the two cytotypes differ in optima and/or breadths, but results vary in important details. The whole-range analysis suggests differentiation along the temperature gradient to be most important. However, sympatric comparisons indicate that this climatic shift was not a direct response to competition with diploid ancestors. Moreover, fine-grained analyses demonstrate niche contraction of tetraploids, especially in the sympatric range, that goes undetected with coarse-grained data. Although the niche optima of the two cytotypes differ, separation along ecological gradients was probably less decisive for polyploid establishment than a shift towards facultative apomixis, a particularly effective strategy to avoid minority cytotype exclusion. In addition, our results suggest that coarse-grained analyses overestimate niche breadths of widely distributed taxa. Niche comparison analyses should hence be conducted at environmental data resolutions appropriate for the organism and question under study.

Anthropometric dimensions of male powerlifters of varying body mass.

PubMed

Keogh, Justin W L; Hume, Patria A; Pearson, Simon N; Mellow, Peter

2007-10-01

In this study, we examined the anthropometric dimensions of powerlifters across various body mass (competitive bodyweight) categories. Fifty-four male Oceania competitive powerlifters (9 lightweight, 30 middleweight, and 15 heavyweight) were recruited from one international and two national powerlifting competitions held in New Zealand. Powerlifters were assessed for 37 anthropometric dimensions by ISAK (International Society for the Advancement of Kinanthropometry) level II and III accredited anthropometrists. The powerlifters were highly mesomorphic and had large girths and bony breadths, both in absolute units and when expressed as Z(p)-scores compared through the Phantom (Ross & Wilson, 1974). These anthropometric characteristics were more pronounced in heavyweights, who were significantly heavier, had greater muscle and fat mass, were more endo-mesomorphic, and had larger girths and bony breadths than the lighter lifters. Although middleweight and heavyweight lifters typically had longer segment lengths than the lightweights, all three groups had similar Zp-scores for the segment lengths, indicating similar segment length proportions. While population comparisons would be required to identify any connection between specific anthropometric dimensions that confer a competitive advantage to the expression of maximal strength, anthropometric profiling may prove useful for talent identification and for the assessment of training progression in powerlifting.

Germination niche breadth varies inconsistently among three Asclepias congeners along a latitudinal gradient.

PubMed

Finch, Jessamine; Walck, Jeffrey L; Hidayati, Siti N; Kramer, Andrea T; Lason, Victoria; Havens, Kayri

2018-05-20

Species responses to climate change will be primarily driven by their environmental tolerance range, or niche breadth, with the expectation that broad niches will increase resilience. Niche breadth is expected to be greater in more heterogeneous environments and moderated by life history. Niche breadth also varies across life stage. Therefore, the life stage with the narrowest niche may serve as the best predictor of climatic vulnerability. To investigate the relationship between niche breadth, climate, and life stage we identify germination niche breadth for dormant and nondormant seeds in multiple populations of three milkweed (Asclepias) species. Complementary trials evaluated germination under conditions simulating historic and predicted future climate by varying cold-moist stratification temperature, length, and incubation temperature. Germination niche breadth was derived from germination evenness across treatments (Levins B n ), with stratified seeds considered less dormant than non-stratified seeds. Germination response varies significantly among species, populations, and treatments. Cold-moist stratification ≥ 4 weeks (1-3°C) followed by incubation at 25/15°C+ achieves peak germination for most populations. Germination niche breadth significantly expands following stratification and interacts significantly with latitude of origin. Interestingly, two species display a positive relationship between niche breadth and latitude, while the third presents a concave quadratic relationship. Germination niche breadth significantly varies by species, latitude, and population, suggesting an interaction between source climate, life history, and site-specific factors. Results contribute to our understanding of inter- and intraspecific variation in germination, underscore the role of dormancy in germination niche breadth, and have implications for prioritizing and conserving species under climate change. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Mosaic vaccines elicit CD8+ T cell responses in monkeys that confer immune coverage of diverse HIV strains

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

Fischer, Will; Korber, Bette

2009-01-01

Creation of a successful HIV vaccine will require the development of a strategy to generate cellular immunity with sufficient cross-clade breadth to deal with the extreme genetic diversity of the virus. Polyvalent mosaic immunogens derived from in silica recombination of natural strains of HIV are designed to induce cellular immune responses that maximally cover the sequence diversity of circulating virus isolates. Immunization of rhesus monkeys with plasmid DNA and recombinant vaccinia virus vaccine constructs expressing either consensus immunogens or polyvalent mosaic immunogens elicited a CD4+ T lymphocyte-biased response with comparably broad epitope-specific total T lymphocyte specificities. However, immunization with themore » mosaic immunogens induced HIV-specific CD8+ T lymphocyte responses with markedly greater depth and breadth. Therefore, the use of polyvalent mosaic immunogens is a promising strategy for a global vaccine for HIV.« less

Average niche breadths of species in lake macrophyte communities respond to ecological gradients variably in four regions on two continents.

PubMed

Alahuhta, Janne; Virtala, Antti; Hjort, Jan; Ecke, Frauke; Johnson, Lucinda B; Sass, Laura; Heino, Jani

2017-05-01

Different species' niche breadths in relation to ecological gradients are infrequently examined within the same study and, moreover, species niche breadths have rarely been averaged to account for variation in entire ecological communities. We investigated how average environmental niche breadths (climate, water quality and climate-water quality niches) in aquatic macrophyte communities are related to ecological gradients (latitude, longitude, altitude, species richness and lake area) among four distinct regions (Finland, Sweden and US states of Minnesota and Wisconsin) on two continents. We found that correlations between the three different measures of average niche breadths and ecological gradients varied considerably among the study regions, with average climate and average water quality niche breadth models often showing opposite trends. However, consistent patterns were also found, such as widening of average climate niche breadths and narrowing of average water quality niche breadths of aquatic macrophytes along increasing latitudinal and altitudinal gradients. This result suggests that macrophyte species are generalists in relation to temperature variations at higher latitudes and altitudes, whereas species in southern, lowland lakes are more specialised. In contrast, aquatic macrophytes growing in more southern nutrient-rich lakes were generalists in relation to water quality, while specialist species are adapted to low-productivity conditions and are found in highland lakes. Our results emphasise that species niche breadths should not be studied using only coarse-scale data of species distributions and corresponding environmental conditions, but that investigations on different kinds of niche breadths (e.g., climate vs. local niches) also require finer resolution data at broad spatial extents.

How is the rate of climatic-niche evolution related to climatic-niche breadth?

PubMed

Fisher-Reid, M Caitlin; Kozak, Kenneth H; Wiens, John J

2012-12-01

The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Preliminary shape analysis of the outline of the baropodometric foot: patterns of covariation, allometry, sex and age differences, and loading variations.

PubMed

Bruner, E; Mantini, S; Guerrini, V; Ciccarelli, A; Giombini, A; Borrione, P; Pigozzi, F; Ripani, M

2009-09-01

Baropodometrical digital techniques map the pressures exerted on the foot plant during both static and dynamic loadings. The study of the distribution of such pressures makes it possible to evaluate the postural and locomotory biomechanics together with its pathological variations. This paper is aimed at evaluating the integration between baropodometric analysis (pressure distribution) and geometrical models (shape of the footprints), investigating the pattern of variation associated with normal plantar morphology. The sample includes 91 individuals (47 males, 44 females), ranging from 5 to 85 years of age (mean and standard deviation = 40 + or - 24).The first component of variation is largely associated with the breadth of the isthmus, along a continuous gradient of increasing/decreasing flattening of the foot plant. This character being dominant upon the whole set of morphological components even in a non-pathological sample, such multivariate computation may represent a good diagnostic tool to quantify its degree of expression in individual subject or group samples. Sexual differences are not significant, and allometric variations associated with increasing plantar surface or stature are not quantitatively relevant. There are some differences between adult and young individuals, associated in the latter with a widening of the medial and posterior areas. These results provide a geometrical framework of baropodometrical analysis, suggesting possible future applications in diagnosis and basic research.

What Does Stock Ownership Breadth Measure?*

PubMed Central

Choi, James J.; Jin, Li; Yan, Hongjun

2013-01-01

Using holdings data on a representative sample of all Shanghai Stock Exchange investors, we show that increases in ownership breadth (the fraction of market participants who own a stock) predict low returns: highest change quintile stocks underperform lowest quintile stocks by 23% per year. Small retail investors drive this result. Retail ownership breadth increases appear to be correlated with overpricing. Among institutional investors, however, the opposite holds: Stocks in the top decile of wealth-weighted institutional breadth change outperform the bottom decile by 8% per year, consistent with prior work that interprets breadth as a measure of short-sales constraints. PMID:24764801

Psicolinguistica, psicologia del linguaggio e "Analisi elettroacustica del linguaggio" di P. Agostino Gemelli (Psycholinguistics, Psychology of Language and P. Agostino Gemelli's "Electric-Acoustical Analysis of Language").

ERIC Educational Resources Information Center

Titone, Renzo

1987-01-01

Discusses the contribution of the little-known linguist Gemelli who favors a holistic approach to human language emphasizing the human personality as an essential factor in the expression of speech. Gemelli makes clear the breadth of the field of language psychology in contrast with the narrowness of psycholinguistics. (CFM)

An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)

PubMed Central

Shaffer, Justin P.; U'Ren, Jana M.; Gallery, Rachel E.; Baltrus, David A.; Arnold, A. Elizabeth

2017-01-01

Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions. PMID:28382021

[Spatial and temporal variation in diet composition of invertivore fishes in a tropical stream, Venezuela].

PubMed

Ortaz, Mario; Martín, Ricardo; López-Ordaz, Adriana

2011-09-01

Invertivores fishes are an important component of neotropical streams and they represent a link between aquatic invertebrates and piscivorous species. This study evaluated the breadth diet and interspecific food overlap of nine invertivores fish species during three consecutive hydrological phases: falling (December/07, January/08, February/08 and March/08), low (April/08) and rising waters (June/08), in two sections of a Venezuelan neotropical stream, which were located at different elevation, high watershed (HW) and low watershed (LW). The fishes were collected with a beach seine (5mm mesh) between 8:00 and 11:00 hours. The diet of each species was evaluated using an index of relative importance (IRI), which includes as variables the number, weight and occurrence frequency of food items consumed. The Levin' index (B ) and Morisita (IM) were used to estimate the breadth diet and interspecific food overlap, respectively. All estimations were made using the numeric proportion of preys. Nine fish species were captured, eight Characiformes, of which three were captured in HW (Knodus deuteronoides, Creagrutus bolivari and C. melasma) and five in LW (Thoracocharax stellatus, Moenkhausia lepidura, Cheirodon pulcher, Ctenobrycon spilurus and Aphyocharax alburnus), and one Cyprinodontiformes (Poecilia reticulata), which was also found in HW. In HW aquatic insects were the main resource consumed by fishes while plant material and terrestrial arthropods were secondary resources. In LW the fishes ingested all of these items in addition to zooplankton (Copepoda, Cladocera and larval stages of Decapoda). However, there was a temporal replacement with a predominance of zooplankton in falling and low water. In general, the breadth diet decreased during the falling water in both sections and increased in rising water. However, the average breadth diet was higher in HW. The interspecific food overlap was high in HW while low values were more frequent in LW and its temporal variation was opposed in both sections during almost all the sampling period.

Increased frequencies of CD8+CD57+ T cells are associated with antibody neutralization breadth against HIV in viraemic controllers

PubMed Central

Palmer, Christine D; Romero-Tejeda, Marisol; Scully, Eileen P; Lockhart, Ainsley; Seaman, Michael S; Goldenthal, Ariel; Piechocka-Trocha, Alicja; Walker, Bruce D; Chibnik, Lori B; Jost, Stephanie; Porichis, Filippos

2016-01-01

Introduction An effective prophylactic vaccine against HIV will need to elicit antibody responses capable of recognizing and neutralizing rapidly evolving antigenic regions. The immunologic milieu associated with development of neutralizing antibody breadth remains to be fully defined. In this study, we sought to identify immunological signatures associated with neutralization breadth in HIV controllers. We applied an immune monitoring approach to analyze markers of T cell and myeloid cell activation by flow cytometry, comparing broad neutralizers with low- and non-neutralizers using multivariate and univariate analyses. Methods Antibody neutralization breadth was determined, and cryopreserved peripheral blood mononuclear cells were stained for T cell and myeloid cell activation markers. Subjects were grouped according to neutralization breadth, and T cell and myeloid cell activation was analyzed by partial least squares discriminant analysis to determine immune signatures associated with high neutralization breadth. Results We show that neutralization breadth in HIV viraemic controllers (VC) was strongly associated with increased frequencies of CD8+CD57+ T cells and that this association was independent of viral load, CD4 count and time since HIV diagnosis. Conclusions Our data show elevated frequencies of CD8+CD57+ T cells in VC who develop neutralization breadth against HIV. This immune signature could serve as a potential biomarker of neutralization breadth and should be further investigated in other HIV-positive cohorts and in HIV vaccine trials. PMID:27938646

Predatory birds and ants partition caterpillar prey by body size and diet breadth.

PubMed

Singer, Michael S; Clark, Robert E; Lichter-Marck, Issac H; Johnson, Emily R; Mooney, Kailen A

2017-10-01

The effects of predator assemblages on herbivores are predicted to depend critically on predator-predator interactions and the extent to which predators partition prey resources. The role of prey heterogeneity in generating such multiple predator effects has received limited attention. Vertebrate and arthropod insectivores constitute two co-dominant predatory taxa in many ecosystems, and the emergent properties of their joint effects on insect herbivores inform theory on multiple predator effects as well as biological control of insect herbivores. Here we use a large-scale factorial manipulation to assess the extent to which birds and ants engage in antagonistic predator-predator interactions and the consequences of heterogeneity in herbivore body size and diet breadth (i.e. the diversity of host plants used) for prey partitioning. We excluded birds and reduced ant density (by 60%) in the canopies of eight northeastern USA deciduous tree species during two consecutive years and measured the community composition and traits of lepidopteran larvae (caterpillars). Birds did not affect ant density, implying limited intraguild predation between these taxa in this system. Birds preyed selectively upon large-bodied caterpillars (reducing mean caterpillar length by 12%) and ants preyed selectively upon small-bodied caterpillars (increasing mean caterpillar length by 6%). Birds and ants also partitioned caterpillar prey by diet breadth. Birds reduced the frequency dietary generalist caterpillars by 24%, while ants had no effect. In contrast, ants reduced the frequency of dietary specialists by 20%, while birds had no effect, but these effects were non-additive; under bird exclusion, ants had no detectable effect, while in the presence of birds, they reduced the frequency of specialists by 40%. As a likely result of prey partitioning by body size and diet breadth, the combined effects of birds and ants on total caterpillar density were additive, with birds and ants reducing caterpillar density by 44% and 20% respectively. These results show evidence for the role of prey heterogeneity in driving functional complementarity among predators and enhanced top-down control. Heterogeneity in herbivore body size and diet breadth, as well as other prey traits, may represent key predictors of the strength of top-down control from predator communities. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Seasonal Alterations in Host Range and Fidelity in the Polyphagous Mirid Bug, Apolygus lucorum (Heteroptera: Miridae)

PubMed Central

Pan, Hongsheng; Liu, Bing; Lu, Yanhui; Wyckhuys, Kris A. G.

2015-01-01

In herbivorous insects, host plant switching is commonly observed and plays an important role in their annual life cycle. However, much remains to be learned about seasonal host switching of various pestiferous arthropods under natural conditions. From 2006 until 2012, we assessed Apolygus lucorum (Meyer-Dür) host plant use in successive spring, summer and winter seasons at one single location (Langfang, China). Data were used to quantify changes in host plant breadth and host fidelity between seasons. Host fidelity of A. lucorum differed between seasons, with 87.9% of spring hosts also used in the summer and 36.1% of summer hosts used in winter. In contrast, as little as 25.6% host plant species were shared between winter and spring. Annual herbaceous plants are most often used for overwintering, while perennial woody plants are relatively important for initial population build-up in the spring. Our study contributes to an improved understanding of evolutionary interactions between A. lucorum and its host plants and lays the groundwork for the design of population management strategies for this important pest in myriad crops. PMID:25692969

2010 Plant Molecular Biology Gordon Research Conference

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

Michael Sussman

The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides anmore » excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.« less

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

Hart, William E.; Siirola, John Daniel

We describe new capabilities for modeling MPEC problems within the Pyomo modeling software. These capabilities include new modeling components that represent complementar- ity conditions, modeling transformations for re-expressing models with complementarity con- ditions in other forms, and meta-solvers that apply transformations and numeric optimization solvers to optimize MPEC problems. We illustrate the breadth of Pyomo's modeling capabil- ities for MPEC problems, and we describe how Pyomo's meta-solvers can perform local and global optimization of MPEC problems.

Enhancing the Breadth of Efficacy of Therapeutic Vaccines for Breast Cancer

DTIC Science & Technology

2014-10-01

4b. Generate specific tumor antigen lysates from recombinant baculovirus- infected insect cells. *Currently expressing antigens in C1R cells since... Immunology Conference, Breckenridge CO (invited by Jim Hagman). Sept 20, 2014, Analysis of the T cell repertoire in breast cancer using emulsion...by Jonathan Bramson).   13 Nov 11, 2014 (anticipated), Elimination of the bottlenecks in T cell receptor antigen discovery, Immunology Forum

Different personal propensities among scientists relate to deeper vs. broader knowledge contributions

PubMed Central

Bateman, Thomas S.; Hess, Andrew M.

2015-01-01

Scientific journal publications, and their contributions to knowledge, can be described by their depth (specialized, domain-specific knowledge extensions) and breadth (topical scope, including spanning multiple knowledge domains). Toward generating hypotheses about how scientists’ personal dispositions would uniquely predict deeper vs. broader contributions to the literature, we assumed that conducting broader studies is generally viewed as less attractive (e.g., riskier) than conducting deeper studies. Study 1 then supported our assumptions: the scientists surveyed considered a hypothetical broader study, compared with an otherwise-comparable deeper study, to be riskier, a less-significant opportunity, and of lower potential importance; they further reported being less likely to pursue it and, in a forced choice, most chose to work on the deeper study. In Study 2, questionnaire measures of medical researchers’ personal dispositions and 10 y of PubMed data indicating their publications’ topical coverage revealed how dispositions differentially predict depth vs. breadth. Competitiveness predicted depth positively, whereas conscientiousness predicted breadth negatively. Performance goal orientation predicted depth but not breadth, and learning goal orientation contrastingly predicted breadth but not depth. Openness to experience positively predicted both depth and breadth. Exploratory work behavior (the converse of applying and exploiting one’s current knowledge) predicted breadth positively and depth negatively. Thus, this research distinguishes depth and breadth of published knowledge contributions, and provides new insights into how scientists’ personal dispositions influence research processes and products. PMID:25733900

Different personal propensities among scientists relate to deeper vs. broader knowledge contributions.

PubMed

Bateman, Thomas S; Hess, Andrew M

2015-03-24

Scientific journal publications, and their contributions to knowledge, can be described by their depth (specialized, domain-specific knowledge extensions) and breadth (topical scope, including spanning multiple knowledge domains). Toward generating hypotheses about how scientists' personal dispositions would uniquely predict deeper vs. broader contributions to the literature, we assumed that conducting broader studies is generally viewed as less attractive (e.g., riskier) than conducting deeper studies. Study 1 then supported our assumptions: the scientists surveyed considered a hypothetical broader study, compared with an otherwise-comparable deeper study, to be riskier, a less-significant opportunity, and of lower potential importance; they further reported being less likely to pursue it and, in a forced choice, most chose to work on the deeper study. In Study 2, questionnaire measures of medical researchers' personal dispositions and 10 y of PubMed data indicating their publications' topical coverage revealed how dispositions differentially predict depth vs. breadth. Competitiveness predicted depth positively, whereas conscientiousness predicted breadth negatively. Performance goal orientation predicted depth but not breadth, and learning goal orientation contrastingly predicted breadth but not depth. Openness to experience positively predicted both depth and breadth. Exploratory work behavior (the converse of applying and exploiting one's current knowledge) predicted breadth positively and depth negatively. Thus, this research distinguishes depth and breadth of published knowledge contributions, and provides new insights into how scientists' personal dispositions influence research processes and products.

Dietary breadth of grizzly bears in the Greater Yellowstone Ecosystem

USGS Publications Warehouse

Gunther, Kerry A.; Shoemaker, Rebecca; Frey, Kevin L.; Haroldson, Mark A.; Cain, Steven L.; van Manen, Frank T.; Fortin, Jennifer K.

2014-01-01

Grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem (GYE) are opportunistic omnivores that eat a great diversity of plant and animal species. Changes in climate may affect regional vegetation, hydrology, insects, and fire regimes, likely influencing the abundance, range, and elevational distribution of the plants and animals consumed by GYE grizzly bears. Determining the dietary breadth of grizzly bears is important to document future changes in food resources and how those changes may affect the nutritional ecology of grizzlies. However, no synthesis exists of all foods consumed by grizzly bears in the GYE. We conducted a review of available literature and compiled a list of species consumed by grizzly bears in the GYE. We documented >266 species within 200 genera from 4 kingdoms, including 175 plant, 37 invertebrate, 34 mammal, 7 fungi, 7 bird, 4 fish, 1 amphibian, and 1 algae species as well as 1 soil type consumed by grizzly bears. The average energy values of the ungulates (6.8 kcal/g), trout (Oncorhynchus spp., 6.1 kcal/g), and small mammals (4.5 kcal/g) eaten by grizzlies were higher than those of the plants (3.0 kcal/g) and invertebrates (2.7 kcal/g) they consumed. The most frequently detected diet items were graminoids, ants (Formicidae), whitebark pine seeds (Pinus albicaulis), clover (Trifolium spp.), and dandelion (Taraxacum spp.). The most consistently used foods on a temporal basis were graminoids, ants, whitebark pine seeds, clover, elk (Cervus elaphus), thistle (Cirsium spp.), and horsetail (Equisetum spp.). Historically, garbage was a significant diet item for grizzlies until refuse dumps were closed. Use of forbs increased after garbage was no longer readily available. The list of foods we compiled will help managers of grizzly bears and their habitat document future changes in grizzly bear food habits and how bears respond to changing food resources.

Trait differences between naturalized and invasive plant species independent of residence time and phylogeny.

PubMed

Gallagher, R V; Randall, R P; Leishman, M R

2015-04-01

The ability to predict which alien plants will transition from naturalized to invasive prior to their introduction to novel regions is a key goal for conservation and has the potential to increase the efficacy of weed risk assessment (WRA). However, multiple factors contribute to plant invasion success (e.g., functional traits, range characteristics, residence time, phylogeny), and they all must be taken into account simultaneously in order to identify meaningful correlates of invasion success. We compiled 146 pairs of phylogenetically paired (congeneric) naturalized and invasive plant species in Australia with similar minimum residence times (i.e., time since introduction in years). These pairs were used to test for differences in 5 functional traits (flowering duration, leaf size, maximum height, specific leaf area [SLA], seed mass) and 3 characteristics of species' native ranges (biome occupancy, mean annual temperature, and rainfall breadth) between naturalized and invasive species. Invasive species, on average, had larger SLA, longer flowering periods, and were taller than their congeneric naturalized relatives. Invaders also exhibited greater tolerance for different environmental conditions in the native range, where they occupied more biomes and a wider breadth of rainfall and temperature conditions than naturalized congeners. However, neither seed mass nor leaf size differed between pairs of naturalized and invasive species. A key finding was the role of SLA in distinguishing between naturalized and invasive pairs. Species with high SLA values were typically associated with faster growth rates, more rapid turnover of leaf material, and shorter lifespans than those species with low SLA. This suite of characteristics may contribute to the ability of a species to transition from naturalized to invasive across a wide range of environmental contexts and disturbance regimes. Our findings will help in the refinement of WRA protocols, and we advocate the inclusion of quantitative traits, in particular SLA, into the WRA schemes. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Niches of dominant fish in the waters surrounding the Taishan Islands, China

NASA Astrophysics Data System (ADS)

Yang, Lu; Chen, Jie; Yang, Shengyun; Zhong, Huiqi; Ju, Peilong; Yang, Shunliang; Sun, Qinqin; Chen, Mingru

2016-07-01

An index of relative importance (IRI) was employed to screen for dominant fish in the waters surrounding the Taishan Islands, China, using data from four seasonal trawl surveys undertaken between 2012 and 2013. Niche breadth and niche overlap were measured using the Feinsinger and Morisita-Horn indices, respectively, and the characteristics and seasonal variations in the niches of dominant fish were assessed via non-metric multidimensional scaling (NMDS) and cluster analysis. A total of 80 fish species, including 16 dominant species, were recorded. Only Amblychaeturichthys hexanema was dominant in all seasons. According to niche breadth values and NMDS, the 16 dominant species were grouped into the following three types: (1) wide niche breadth species, including Cynoglossus macrolepidotus, A. hexanema, and Trypauchen vagina, among others; (2) medium niche breadth species, including Setipinna taty and Johnius belangerii; and (3) narrow niche breadth species, including Atrobucca nibe and Coilia mystus. Most species with a wider niche breadth were demersal fish with a lower swimming capability and even distribution. The niche breadth of migrating fish was narrower than that of settled fish. At a given spatial scale, fish with stronger swimming capabilities had a narrower niche breadth. Niche overlap, which is associated with niche specialization, ranged from 0.000 to 0.886 and had an annual mean value of 0.314. In summer and autumn, niche overlap was relatively high within species of the Sciaenidae family and within species of the Gobiidae in autumn. Differences in thermophily, feeding habits, food organism abundance/distribution and predator-prey relationships affected the niche overlap of fish in this area. Cluster analysis revealed that species with the narrowest niche breadth and lowest niche overlap values usually displayed lower aggregation and greater distribution differences compared with other species.

Abyssal Sequestration of Nuclear Waste in Earth's Crust

NASA Astrophysics Data System (ADS)

Germanovich, L. N.; Garagash, D.; Murdoch, L. C.; Robinowitz, M.

2013-12-01

This work outlines a new method for disposing of hazardous (e.g., nuclear) waste. The technique is called Abyssal Sequestration, and it involves placing the waste at extreme depths in Earth's crust where it could achieve the geologically-long period of isolation. Abyssal Sequestration involves storing the waste in hydraulic fractures driven by gravity, a process we term gravity fracturing. In short, we suggest creating a dense fluid (slurry) containing waste, introducing the fluid into a fracture, and extending the fracture downward until it becomes long enough to propagate independently. The fracture will continue to propagate downward to great depth, permanently isolating the waste. Storing solid wastes by mixing them with fluids and injecting them into hydraulic fractures is a well-known technology. The essence of our idea differs from conventional hydraulic fracturing techniques only slightly in that it uses fracturing fluid heavier than the surrounding rock. This difference is fundamental, however, because it allows hydraulic fractures to propagate downward and carry wastes by gravity instead of or in addition to being injected by pumping. An example of similar gravity-driven fractures with positive buoyancy is given by magmatic dikes that may serve as an analog of Abyssal Sequestration occurring in nature. Mechanics of fracture propagation in conditions of positive (diking) and negative (heavy waste slurry) buoyancy is similar and considered in this work for both cases. Analog experiments in gelatin show that fracture breadth (horizontal dimension) remains nearly stationary when fracturing process in the fracture 'head' (where breadth is 'created') is dominated by solid toughness, as opposed to the viscous fluid dissipation dominant in the fracture tail. We model propagation of the resulting 'buoyant' or 'sinking' finger-like fracture of stationary breadth with slowly varying opening along the crack length. The elastic response of the crack to fluid loading in a horizontal cross-section is local and can be treated similar to the classical Perkins-Kern-Nordgren (PKN) model of hydraulic fracturing. The propagation condition for a finger-like crack is based on balancing the global energy release rate due to unit crack extension and the rock fracture toughness. It allows to relate the net fluid pressure at the tip to the fracture breadth and rock toughness. Unlike the PKN fracture, which breadth is known a priori, the final breadth of a finger-like fracture is a result of the fracturing process in the fracture head. To resolve the breadth, we relax the local elasticity assumption in the fracture head by neglecting viscous pressure drop there. The resulting fracture head model is a 3D analog of the Weertman's hydrostatic pulse, and yields expressions for the terminal breadth, b = 0.34 (K / Delta rho g))^(2/3), and for the head volume, V = 10.4 K b^(5/2) / E'. We then combine the finger crack solution for the viscous tail with the 3-D pulse solution for the fracture head. The obtained closed-form solution is compared to numerical simulations. Based on this solution, we analyzed the gravity fracture propagation in conditions of either continuous injection or finite volume release for sets of parameters representative of the heavy waste injection technique and low viscosity magma diking.

Metal species involved in long distance metal transport in plants

PubMed Central

Álvarez-Fernández, Ana; Díaz-Benito, Pablo; Abadía, Anunciación; López-Millán, Ana-Flor; Abadía, Javier

2014-01-01

The mechanisms plants use to transport metals from roots to shoots are not completely understood. It has long been proposed that organic molecules participate in metal translocation within the plant. However, until recently the identity of the complexes involved in the long-distance transport of metals could only be inferred by using indirect methods, such as analyzing separately the concentrations of metals and putative ligands and then using in silico chemical speciation software to predict metal species. Molecular biology approaches also have provided a breadth of information about putative metal ligands and metal complexes occurring in plant fluids. The new advances in analytical techniques based on mass spectrometry and the increased use of synchrotron X-ray spectroscopy have allowed for the identification of some metal-ligand species in plant fluids such as the xylem and phloem saps. Also, some proteins present in plant fluids can bind metals and a few studies have explored this possibility. This study reviews the analytical challenges researchers have to face to understand long-distance metal transport in plants as well as the recent advances in the identification of the ligand and metal-ligand complexes in plant fluids. PMID:24723928

The importance of job autonomy, cognitive ability, and job-related skill for predicting role breadth and job performance.

PubMed

Morgeson, Frederick P; Delaney-Klinger, Kelly; Hemingway, Monica A

2005-03-01

Role theory suggests and empirical research has found that there is considerable variation in how broadly individuals define their jobs. We investigated the theoretically meaningful yet infrequently studied relationships between incumbent job autonomy, cognitive ability, job-related skill, role breadth, and job performance. Using multiple data sources and multiple measurement occasions in a field setting, we found that job autonomy, cognitive ability, and job-related skill were positively related to role breadth, accounting for 23% of the variance in role breadth. In addition, role breadth was positively related to job performance and was found to mediate the relationship between job autonomy, cognitive ability, job-related skill, and job performance. These results add to our understanding of the factors that predict role breadth, as well as having implications for how job aspects and individual characteristics are translated into performance outcomes and the treatment of variability in incumbent reports of job tasks.

Deficiency of gustatory sensitivity to some deterrent compounds in "polyphagous" mutant strains of the silkworm, Bombyx mori.

PubMed

Asaoka, K

2000-11-01

Sawa-J, CSJ02 and N601 x C601 are selected mutant strains of Bombyx mori, which grow on various artificial diets or temporarily ingest various plant leaves. To examine the mechanisms mediating diet breadth of caterpillars, gustatory spike responses of the silkworms, called 'polyphagous" strains, were compared with normal strains, N137 x C146 and C02. There were notable differences in their feeding habits and in their sensitivity to salicin in deterrent cells in the maxillary medial styloconic sensilla and the epipharyngeal sensilla. By contrast, the deterrent cells of all strains responded similarly to strychnine nitrate in a dose-dependent manner. In additional comparisons of Sawa-J and N137 x C146, Sawa-J maxillary deterrent cells were significantly less sensitive to phloridzin, amygdalin and arbutin, but responded to some alkaloids and 20-hydroxyecdysone with similar or even higher firing rate. These results suggest that the deficiency of the sensitivity to some deterrent compounds on the deterrent cell of the polyphagous strains may be caused by mutant genes and affects the diet breadth of caterpillars.

Scalability of the muscular action in a parametric 3D model of the index finger.

PubMed

Sancho-Bru, Joaquín L; Vergara, Margarita; Rodríguez-Cervantes, Pablo-Jesús; Giurintano, David J; Pérez-González, Antonio

2008-01-01

A method for scaling the muscle action is proposed and used to achieve a 3D inverse dynamic model of the human finger with all its components scalable. This method is based on scaling the physiological cross-sectional area (PCSA) in a Hill muscle model. Different anthropometric parameters and maximal grip force data have been measured and their correlations have been analyzed and used for scaling the PCSA of each muscle. A linear relationship between the normalized PCSA and the product of the length and breadth of the hand has been finally used for scaling, with a slope of 0.01315 cm(-2), with the length and breadth of the hand expressed in centimeters. The parametric muscle model has been included in a parametric finger model previously developed by the authors, and it has been validated reproducing the results of an experiment in which subjects from different population groups exerted maximal voluntary forces with their index finger in a controlled posture.

MASC: Multiprocessor Architecture for Symbolic Processing

DTIC Science & Technology

1989-08-01

accomplish the ultimate goal of reducing the time to develop the 5- 12 correct parse. 5.6.5 Effect of’ Sentence Length Figure 5-6 shows the relationship...later; this effectively restricts the breadth of study rather severely. 6.1.2. Objective The tools described here have been developed in response to...either expressed or implied, of the Defense Advanced Research Projects Agency or the U.S. Government. ROME AIR DEVELOPMENT CENTER Air Force Systems

Enhancing the Breadth and Efficacy of Therapeutic Vaccines for Breast Cancer

DTIC Science & Technology

2015-10-01

including antigens preferentially expressed by breast cancer stem cells. We will identify both MHC-I- and MHC-II- restricted antigens driving both CD8...even two of them were exclusively targeted by T cells in chronic lymphocytic leukemia ( CLL ) patients (3). This analysis demonstrated both that...lymphocytic leukemia ( CLL ) 7 positive CLLs (23%) 3 Table 1. Immunogenic peptides that have been eluted from the cell surface of breast carcinoma cells

Translations on Eastern Europe. Political, Sociologiclal and Military Affairs, Number 1419

DTIC Science & Technology

1977-07-19

works have been created that express truly and movingly the basic processes and problems in life, penetrate deeper and deeper in the rich spirit of...They took prominent place in the national, cultural treasure and si- multaneously showed how many rich and diversified possibilities exist in the...culture in all its breadth and richness . As is known, Lenin devoted great care to the development of artistic cre- ativity and gave exceptional importance

Organization, Breadth of Categorization and Free-Recall Learning in Children.

ERIC Educational Resources Information Center

Strassberg-Rosenberg, Barbara; Shuell, Thomas J.

The primary objective of this study was to determine the existence of a relationship between free-recall learning and breadth of categorization, an independent measure of conceptual organization. The relationship between breadth of categorization and more conventional measures of organization was also investigated. Two free-recall tasks…

A multistressor, multitrait approach to assessing the effects of wind and dust on Eucalyptus tereticornis.

PubMed

Leonard, Ryan J; McArthur, Clare; Hochuli, Dieter F

2016-08-01

Plants are routinely subjected to multiple environmental stressors, and the ability to respond to these stressors determines species survival and ecological breadth. Despite stressors such as wind and dust significantly influencing plant development, morphology, and chemistry, the combined influence of these factors is yet to be investigated. We used a manipulative glasshouse approach to compare the morphological, physiological, and biomechanical responses of Eucalyptus tereticornis to the independent and combined effects of wind and dust. Wind decreased both E. tereticornis height and stem flexural stiffness. Additionally, wind had no effect on leaf physiology, nor did dust have any significant effect on any of the traits measured. Our results suggest that wind and dust in combination may have an additive effect on several plant traits and provide new insight into the effects and importance of studying wind, dust, and different stress combinations. © 2016 Botanical Society of America.

Understanding phototropism: from Darwin to today.

PubMed

Holland, Jennifer J; Roberts, Diana; Liscum, Emmanuel

2009-01-01

Few individuals have had the lasting impact on such a breadth of science as Charles Darwin. While his writings about time aboard the HMS Beagle, his study of the Galapagos islands (geology, fauna, and flora), and his theories on evolution are well known, less appreciated are his studies on plant growth responses to a variety of environmental stimuli. In fact, Darwin, together with the help of his botanist son Francis, left us an entire book, 'The power of movements in plants', describing his many, varied, and insightful observations on this topic. Darwin's findings have provided an impetus for an entire field of study, the study of plant tropic responses, or differential growth (curvature) of plant organs in response to directional stimuli. One tropic response that has received a great deal of attention is the phototropic response, or curvature response to directional light. This review summarizes many of the most significant advancements that have been made in our understanding of this response and place these recent findings in the context of Darwin's initial observations.

Expanded breadth of the T-cell response to mosaic HIV-1 envelope DNA vaccination

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

Korber, Bette; Fischer, William; Wallstrom, Timothy

2009-01-01

An effective AIDS vaccine must control highly diverse circulating strains of HIV-1. Among HIV -I gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV -I Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential Tcell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining (ICS) in inbred mice with a standardized panel of highlymore » conserved 15-mer PTE peptides. I, 2 and 3 mosaic sets were developed that increased theoretical epitope coverage. The breadth and magnitude ofT-cell immunity stimulated by these vaccines were compared to natural strain Env's; additional comparisons were performed on mutant Env's, including gpl60 or gpl45 with or without V regions and gp41 deletions. Among them, the 2 or 3 mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the 3 mosaic set elicited responses to an average of 8 peptide pools compared to 2 pools for a set of3 natural Env's. Synthetic mosaic HIV -I antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T -cell-based HIV -1 vaccines.« less

Characterization and Implementation of a Diverse Simian Immunodeficiency Virus SIVsm Envelope Panel in the Assessment of Neutralizing Antibody Breadth Elicited in Rhesus Macaques by Multimodal Vaccines Expressing the SIVmac239 Envelope

PubMed Central

Kilgore, Katie M.; Murphy, Megan K.; Burton, Samantha L.; Wetzel, Katherine S.; Smith, S. Abigail; Xiao, Peng; Reddy, Sharmila; Francella, Nicholas; Sodora, Donald L.; Silvestri, Guido; Cole, Kelly S.; Villinger, Francois; Robinson, James E.; Pulendran, Bali; Hunter, Eric; Collman, Ronald G.; Amara, Rama R.

2015-01-01

ABSTRACT Antibodies that can neutralize diverse viral strains are likely to be an important component of a protective human immunodeficiency virus type 1 (HIV-1) vaccine. To this end, preclinical simian immunodeficiency virus (SIV)-based nonhuman primate immunization regimens have been designed to evaluate and enhance antibody-mediated protection. However, these trials often rely on a limited selection of SIV strains with extreme neutralization phenotypes to assess vaccine-elicited antibody activity. To mirror the viral panels used to assess HIV-1 antibody breadth, we created and characterized a novel panel of 14 genetically and phenotypically diverse SIVsm envelope (Env) glycoproteins. To assess the utility of this panel, we characterized the neutralizing activity elicited by four SIVmac239 envelope-expressing DNA/modified vaccinia virus Ankara vector- and protein-based vaccination regimens that included the immunomodulatory adjuvants granulocyte-macrophage colony-stimulating factor, Toll-like receptor (TLR) ligands, and CD40 ligand. The SIVsm Env panel exhibited a spectrum of neutralization sensitivity to SIV-infected plasma pools and monoclonal antibodies, allowing categorization into three tiers. Pooled sera from 91 rhesus macaques immunized in the four trials consistently neutralized only the highly sensitive tier 1a SIVsm Envs, regardless of the immunization regimen. The inability of vaccine-mediated antibodies to neutralize the moderately resistant tier 1b and tier 2 SIVsm Envs defined here suggests that those antibodies were directed toward epitopes that are not accessible on most SIVsm Envs. To achieve a broader and more effective neutralization profile in preclinical vaccine studies that is relevant to known features of HIV-1 neutralization, more emphasis should be placed on optimizing the Env immunogen, as the neutralization profile achieved by the addition of adjuvants does not appear to supersede the neutralizing antibody profile determined by the immunogen. IMPORTANCE Many in the HIV/AIDS vaccine field believe that the ability to elicit broadly neutralizing antibodies capable of blocking genetically diverse HIV-1 variants is a critical component of a protective vaccine. Various SIV-based nonhuman primate vaccine studies have investigated ways to improve antibody-mediated protection against a heterologous SIV challenge, including administering adjuvants that might stimulate a greater neutralization breadth. Using a novel SIV neutralization panel and samples from four rhesus macaque vaccine trials designed for cross comparison, we show that different regimens expressing the same SIV envelope immunogen consistently elicit antibodies that neutralize only the very sensitive tier 1a SIV variants. The results argue that the neutralizing antibody profile elicited by a vaccine is primarily determined by the envelope immunogen and is not substantially broadened by including adjuvants, resulting in the conclusion that the envelope immunogen itself should be the primary consideration in efforts to elicit antibodies with greater neutralization breadth. PMID:26018167

The Importance of Construct Breadth when Examining Interrole Conflict

ERIC Educational Resources Information Center

Huffman, Ann H.; Youngcourt, Satoris S.; Payne, Stephanie C.; Castro, Carl A.

2008-01-01

Research examining the influence of nonwork issues on work-related outcomes has flourished. Often, however, the breadth of the interrole conflict construct varies widely between studies. To determine if the breadth of the interrole conflict measure makes a difference, the current study compares the criterion-related validity of scores yielded by a…

Habitat niche breadth predicts invasiveness in solitary ascidians.

PubMed

Granot, Itai; Shenkar, Noa; Belmaker, Jonathan

2017-10-01

A major focus of invasion biology is understanding the traits associated with introduction success. Most studies assess these traits in the invaded region, while only few compare nonindigenous species to the pool of potential invaders in their native region. We focused on the niche breadth hypothesis , commonly evoked but seldom tested, which states that generalist species are more likely to become introduced as they are capable of thriving under a wide set of conditions. Based on the massive introduction of tropical species into the Mediterranean via the Suez Canal (Lessepsian migration), we defined ascidians in the Red Sea as the pool of potential invaders. We constructed unique settlement plates, each representing six different niches, to assess ascidian niche breadth, and deployed them in similar habitats in the native and invaded regions. For each species found on plates, we evaluated its abundance, relative abundance across successional stages, and niche breadth, and then compared (1) species in the Red Sea known to have been introduced into the Mediterranean (Lessepsian species) and those not known from the Mediterranean (non-Lessepsian); and (2) nonindigenous and indigenous species in the Mediterranean. Lessepsian species identified on plates in the Red Sea demonstrated wider niche breadth than non-Lessepsian species, supporting the niche breadth hypothesis within the native region. No differences were found between Lessepsian and non-Lessepsian species in species abundance and successional stages. In the Mediterranean, nonindigenous species numerically dominated the settlement plates. This precluded robust comparisons of niche breadth between nonindigenous and indigenous species in the invaded region. In conclusion, using Red Sea ascidians as the pool of potential invaders, we found clear evidence supporting the niche breadth hypothesis in the native region. We suggest that such patterns may often be obscured when conducting trait-based studies in the invaded regions alone. Our findings indicate that quantifying the niche breadth of species in their native regions will improve estimates of invasiveness potential.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

PubMed

Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

2015-12-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

PubMed Central

Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

2015-01-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution. PMID:26685068

Multiple regression analysis of anthropometric measurements influencing the cephalic index of male Japanese university students.

PubMed

Hossain, Md Golam; Saw, Aik; Alam, Rashidul; Ohtsuki, Fumio; Kamarul, Tunku

2013-09-01

Cephalic index (CI), the ratio of head breadth to head length, is widely used to categorise human populations. The aim of this study was to access the impact of anthropometric measurements on the CI of male Japanese university students. This study included 1,215 male university students from Tokyo and Kyoto, selected using convenient sampling. Multiple regression analysis was used to determine the effect of anthropometric measurements on CI. The variance inflation factor (VIF) showed no evidence of a multicollinearity problem among independent variables. The coefficients of the regression line demonstrated a significant positive relationship between CI and minimum frontal breadth (p < 0.01), bizygomatic breadth (p < 0.01) and head height (p < 0.05), and a negative relationship between CI and morphological facial height (p < 0.01) and head circumference (p < 0.01). Moreover, the coefficient and odds ratio of logistic regression analysis showed a greater likelihood for minimum frontal breadth (p < 0.01) and bizygomatic breadth (p < 0.01) to predict round-headedness, and morphological facial height (p < 0.05) and head circumference (p < 0.01) to predict long-headedness. Stepwise regression analysis revealed bizygomatic breadth, head circumference, minimum frontal breadth, head height and morphological facial height to be the best predictor craniofacial measurements with respect to CI. The results suggest that most of the variables considered in this study appear to influence the CI of adult male Japanese students.

Enhancing the Breadth of Efficacy of Therapeutic Vaccines for Breast Cancer

DTIC Science & Technology

2015-10-01

from recombinant baculovirus- infected insect cells . *Currently expressing antigens in C1R cells since these cells can also be used as antigen...co-transfect SF9 insect cells . Co-transfection of SF9 cells is initially assesed by survival of the cells compared to un-infected controls. The...Clones with higher TCR production are amplified again and used to infect Hi5 insect cells for protein production. 17 Figure 10. ELISA used to

Disentangling Intensity from Breadth of Science Interest: What Predicts Learning Behaviors?

ERIC Educational Resources Information Center

Bathgate, Meghan; Schunn, Christian

2016-01-01

Overall interest in science has been argued to drive learner participation and engagement. However, there are other important aspects of interest such as breadth of interest within a science domain (e.g., biology, earth science). We demonstrate that intensity of science interest is separable from topic breadth using surveys from a sample of 600…

Visual attention and goal pursuit: deliberative and implemental mindsets affect breadth of attention.

PubMed

Büttner, Oliver B; Wieber, Frank; Schulz, Anna Maria; Bayer, Ute C; Florack, Arnd; Gollwitzer, Peter M

2014-10-01

Mindset theory suggests that a deliberative mindset entails openness to information in one's environment, whereas an implemental mindset entails filtering of information. We hypothesized that this open- versus closed-mindedness influences individuals' breadth of visual attention. In Studies 1 and 2, we induced an implemental or deliberative mindset, and measured breadth of attention using participants' length estimates of x-winged Müller-Lyer figures. Both studies demonstrate a narrower breadth of attention in the implemental mindset than in the deliberative mindset. In Study 3, we manipulated participants' mindsets and measured the breadth of attention by tracking eye movements during scene perception. Implemental mindset participants focused on foreground objects, whereas deliberative mindset participants attended more evenly to the entire scene. Our findings imply that deliberative versus implemental mindsets already operate at the level of visual attention. © 2014 by the Society for Personality and Social Psychology, Inc.

Breadth and Depth of Vocabulary Knowledge and Their Effects on L2 Vocabulary Profiles

ERIC Educational Resources Information Center

Bardakçi, Mehmet

2016-01-01

Breadth and depth of vocabulary knowledge have been studied from many different perspectives, but the related literature lacks serious studies dealing with their effects on vocabulary profiles of EFL learners. In this paper, with an aim to fill this gap, the relative effects of breadth and depth of vocabulary knowledge on L2 vocabulary profiles…

Sex determination from hand and foot dimensions in a North Indian population.

PubMed

Krishan, Kewal; Kanchan, Tanuj; Sharma, Abhilasha

2011-03-01

Hands and feet are often recovered from the site of natural as well as man-made disasters because of bomb blasts, train accidents, plane crashes, or mass homicides. This study is intended to establish standards for determination of sex from the dimensions of hands and feet in a North Indian population. The data for this study comprise 123 men and 123 women aged between 17 and 20 years from the "Rajput" population of Himachal Pradesh in North India. Four anthropometric measurements viz. hand length, hand breadth, foot length, and foot breadth have been taken on both sides of each subject following international anthropometric standards. The hand index (hand breadth/hand length × 100) and the foot index (foot breadth/foot length × 100) were calculated. Sectioning points and regression models are derived for the hand and foot dimensions and the derived indices. The hand and foot dimensions show a higher accuracy in sex determination by sectioning point analysis when compared to hand and foot index. Of the hand and the foot dimensions, hand breadth and foot breadth showed better accuracy in sex determination. Hand index and foot index remain poor sex discriminators in the study. © 2011 American Academy of Forensic Sciences.

Evidence of Niche Partitioning under Ontogenetic Influences among Three Morphologically Similar Siluriformes in Small Subtropical Streams

PubMed Central

Bonato, Karine Orlandi; Fialho, Clarice Bernhardt

2014-01-01

Ontogenetic influences in patterns of niche breadth and feeding overlap were investigated in three species of Siluriformes (Heptapterus sp., Rhamdia quelen and Trichomycterus poikilos) aiming at understanding the species coexistence. Samplings were conducted bimonthly by electrofishing technique from June/2012 to June/2013 in ten streams of the northwestern state of Rio Grande do Sul, Brazil. The stomach contents of 1,948 individuals were analyzed by volumetric method, with 59 food items identified. In general Heptapterus sp. consumed a high proportion of Aegla sp., terrestrial plant remains and Megaloptera; R. quelen consumed fish, and Oligochaeta, followed by Aegla sp.; while the diet of T. poikilos was based on Simuliidae, Ephemeroptera and Trichoptera. Specie segregation was observed in the NMDS. Through PERMANOVA analysis feeding differences among species, and between a combination of species plus size classes were observed. IndVal showed which items were indicators of these differences. Niche breadth values were high for all species. The niche breadth values were low only for the larger size of R. quelen and Heptapterus sp. while T. poikilos values were more similar. Overall the species were a low feeding overlap values. The higher frequency of high feeding overlap was observed for interaction between Heptapterus sp. and T. poikilos. The null model confirmed the niche partitioning between the species. The higher frequency of high and intermediate feeding overlap values were reported to smaller size classes. The null model showed resource sharing between the species/size class. Therefore, overall species showed a resource partitioning because of the use of occasional items. However, these species share resources mainly in the early ontogenetic stages until the emphasized change of morphological characteristics leading to trophic niche expansion and the apparent segregation observed. PMID:25340614

Immune defence strategies of generalist and specialist insect herbivores

PubMed Central

Barthel, Andrea; Kopka, Isabell; Vogel, Heiko; Zipfel, Peter; Heckel, David G.; Groot, Astrid T.

2014-01-01

Ecological immunology examines the adaptive responses of animals to pathogens in relation to other environmental factors and explores the consequences of trade-offs between investment in immune function and other life-history traits. Among species of herbivorous insects, diet breadth may vary greatly, with generalists consuming a wide variety of plant families and specialists restricted to a few species. Generalists may thus be exposed to a wider range of pathogens exerting stronger selection on the innate immune system. To examine whether this produces an increase in the robustness of the immune response, we compared larvae of the generalist herbivore Heliothis virescens and the specialist Heliothis subflexa challenged by entomopathogenic and non-pathogenic bacteria. Heliothis virescens larvae showed lower mortality, a lower number of recoverable bacteria, lower proliferation of haemocytes and higher phagocytic activity. These results indicate a higher tolerance to entomopathogenic bacteria by the generalist, which is associated with a more efficient cell-mediated immune response by mechanisms that differ between these closely related species. Our findings provide novel insights into the consequences of diet breadth and related environmental factors, which may be significant in further studies to understand the ecological forces and investment trade-offs that shape the evolution of innate immunity. PMID:24943370

Dietary breadth is positively correlated with venom complexity in cone snails.

PubMed

Phuong, Mark A; Mahardika, Gusti N; Alfaro, Michael E

2016-05-26

Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.

GenomicusPlants: a web resource to study genome evolution in flowering plants.

PubMed

Louis, Alexandra; Murat, Florent; Salse, Jérôme; Crollius, Hugues Roest

2015-01-01

Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces ('views') are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes 'painted' with colours of another genome of interest. All four views are interconnected and benefit from many customizable features. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Morphological adaptation to climate in modern Homo sapiens crania: the importance of basicranial breadth.

PubMed

Nowaczewska, Wioletta; Dabrowski, Paweł; Kuźmiński, Łukasz

2011-09-01

The aim of this study is to investigate whether the variation in breadth of the cranial base among modern human populations that inhabit different regions of the world is linked with climatic adaptation. This work provides an examination of two hypotheses. The first hypothesis is that the correlation between basicranial breadth and ambient temperature is stronger than the correlation between temperature and other neurocranial variables, such as maximum cranial breadth, maximum neurocranial length, and the endocranial volume. The second hypothesis is that the correlation between the breadth of the cranial base and the ambient temperature is significant even when other neurocranial features used in this study (including the size of the neurocranium) are constant. For the sake of this research, the necessary neurocranial variables for fourteen human populations living in diverse environments were obtained from Howells' data (except for endocranial volume which was obtained by means of estimation). The ambient temperature (more precisely, the mean yearly temperature) of the environments inhabited by these populations was used as a major climatic factor. Data were analysed using Pearson correlation coefficients, linear regression and partial correlation analyses. The results supported the two hypotheses, thus suggesting that ambient temperature may contribute to the observed differences in the breadth of the cranial base in the studied modern humans.

Isotopic niches support the resource breadth hypothesis

USGS Publications Warehouse

Rader, Jonathan A.; Newsome, Seth D.; Sabat, Pablo; Chesser, R. Terry; Dillon, Michael E.; Martinez del Rio, Carlos

2017-01-01

Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges.We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology.We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology.Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.

Discriminant functions for sex estimation of modern Japanese skulls.

PubMed

Ogawa, Yoshinori; Imaizumi, Kazuhiko; Miyasaka, Sachio; Yoshino, Mineo

2013-05-01

The purpose of this study is to generate a set of discriminant functions in order to estimate the sex of modern Japanese skulls. To conduct the analysis, the anthropological measurement data of 113 individuals (73 males and 40 females) were collected from recent forensic anthropological test records at the National Research Institute of Police Science, Japan. Birth years of the individuals ranged from 1926 to 1979, and age at death was over 19 years for all individuals. A total of 10 anthropological measurements were used in the discriminant function analysis: maximum cranial length, cranial base length, maximum cranial breadth, maximum frontal breadth, basion-bregmatic height, upper facial breadth, bizygomatic breadth, bicondylar breadth, bigonial breadth, and ramal height. As a result, nine discriminant functions were established. The classification accuracy ranged from 79.0 to 89.9% when the measurements of the 113 individuals were substituted into the established functions, from 77.8 to 88.1% when a leave-one-out cross-validation procedure was applied to the data, and from 86.7 to 93.0% when the measurements of 50 new individuals (25 males and 25 females), unrelated to the establishment of the discriminant functions, were used. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Children with Developmental Language Impairment Have Vocabulary Deficits Characterized by Limited Breadth and Depth

PubMed Central

McGregor, Karla K.; Oleson, Jacob; Bahnsen, Alison; Duff, Dawna

2012-01-01

Background Deficient vocabulary is a frequently reported symptom of developmental language impairment but the nature of the deficit and its developmental course are not well documented. Aims We aimed to describe the nature of the deficit in terms of breadth and depth of vocabulary knowledge and to determine whether the nature and the extent of the deficit change over the school years. Methods A total of 25,681 oral definitions produced by 177 children with developmental language impairment (LI) and 325 grade-mates with normally developing language (ND) in grades 2, 4, 8, and 10 were taken from an existing longitudinal database. We analyzed these for breadth by counting the number of words defined correctly and for depth by determining the amount of information in each correct definition. Via a linear mixed model, we determined whether breadth and depth varied with language diagnosis independent of nonverbal IQ, mothers’ education level, race, gender, income and (for depth only) word. Results Children with LI scored significantly lower than children with ND on breadth and depth of vocabulary knowledge in all grades. The extent of the deficit did not vary significantly across grades. Language diagnosis was an independent predictor of breadth and depth and as strong a predictor as maternal education. For the LI group, growth in depth relative to breadth was slower than for the ND group. Conclusions Compared to their grade-mates, children with LI have fewer words in their vocabularies and they have shallower knowledge of the words that are in their vocabularies. This deficit persists over developmental time. PMID:23650887

Soil nutrients influence spatial distributions of tropical trees species

USGS Publications Warehouse

John, R.; Dalling, J.W.; Harms, K.E.; Yavitt, J.B.; Stallard, R.F.; Mirabello, M.; Hubbell, S.P.; Valencia, R.; Navarrete, H.; Vallejo, M.; Foster, R.B.

2007-01-01

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. ?? 2007 by The National Academy of Sciences of the USA.

Telling plant species apart with DNA: from barcodes to genomes

PubMed Central

Li, De-Zhu; van der Bank, Michelle

2016-01-01

Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481790

Incorporating population-level variation in thermal performance into predictions of geographic range shifts.

PubMed

Angert, Amy L; Sheth, Seema N; Paul, John R

2011-11-01

Determining how species' geographic ranges are governed by current climates and how they will respond to rapid climatic change poses a major biological challenge. Geographic ranges are often spatially fragmented and composed of genetically differentiated populations that are locally adapted to different thermal regimes. Tradeoffs between different aspects of thermal performance, such as between tolerance to high temperature and tolerance to low temperature or between maximal performance and breadth of performance, suggest that the performance of a given population will be a subset of that of the species. Therefore, species-level projections of distribution might overestimate the species' ability to persist at any given location. However, current approaches to modeling distributions often do not consider variation among populations. Here, we estimated genetically-based differences in thermal performance curves for growth among 12 populations of the scarlet monkeyflower, Mimulus cardinalis, a perennial herb of western North America. We inferred the maximum relative growth rate (RGR(max)), temperature optimum (T(opt)), and temperature breadth (T(breadth)) for each population. We used these data to test for tradeoffs in thermal performance, generate mechanistic population-level projections of distribution under current and future climates, and examine how variation in aspects of thermal performance influences forecasts of range shifts. Populations differed significantly in RGR(max) and had variable, but overlapping, estimates of T(opt) and T(breadth). T(opt) declined with latitude and increased with temperature of origin, consistent with tradeoffs between performances at low temperatures versus those at high temperatures. Further, T(breadth) was negatively related to RGR(max), as expected for a specialist-generalist tradeoff. Parameters of the thermal performance curve influenced properties of projected distributions. For both current and future climates, T(opt) was negatively related to latitudinal position, while T(breadth) was positively related to projected range size. The magnitude and direction of range shifts also varied with T(opt) and T(breadth), but sometimes in unexpected ways. For example, the fraction of habitat remaining suitable increased with T(opt) but decreased with T(breadth). Northern limits of all populations were projected to shift north, but the magnitude of shift decreased with T(opt) and increased with T(breadth). Median latitude was projected to shift north for populations with high T(breadth) and low T(opt), but south for populations with low T(breadth) and high T(opt). Distributions inferred by integrating population-level projections did not differ from a species-level projection that ignored variation among populations. However, the species-level approach masked the potential array of divergent responses by populations that might lead to genotypic sorting within the species' range. Thermal performance tradeoffs among populations within the species' range had important, but sometimes counterintuitive, effects on projected responses to climatic change. © The Author 2011. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.

Isotopic niches support the resource breadth hypothesis.

PubMed

Rader, Jonathan A; Newsome, Seth D; Sabat, Pablo; Chesser, R Terry; Dillon, Michael E; Martínez Del Rio, Carlos

2017-03-01

Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Dietary niche variation and its relationship to lizard population density.

PubMed

Novosolov, Maria; Rodda, Gordon H; Gainsbury, Alison M; Meiri, Shai

2018-01-01

Insular species are predicted to broaden their niches, in response to having fewer competitors. They can thus exploit a greater proportion of the resource spectrum. In turn, broader niches are hypothesized to facilitate (or be a consequence of) increased population densities. We tested whether insular lizards have broader dietary niches than mainland species, how it relates to competitor and predator richness, and the nature of the relationship between population density and dietary niche breadth. We collected population density and dietary niche breadth data for 36 insular and 59 mainland lizard species, and estimated competitor and predator richness at the localities where diet data were collected. We estimated dietary niche shift by comparing island species to their mainland relatives. We controlled for phylogenetic relatedness, body mass and the size of the plots over which densities were estimated. We found that island and mainland species had similar niche breadths. Dietary niche breadth was unrelated to competitor and predator richness, on both islands and the mainland. Population density was unrelated to dietary niche breadth across island and mainland populations. Our results indicate that dietary generalism is not an effective way of increasing population density nor is it result of lower competitive pressure. A lower variety of resources on islands may prevent insular animals from increasing their niche breadths even in the face of few competitors. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Botanicals With Dermatologic Properties Derived From First Nations Healing: Part 2-Plants and Algae.

PubMed

Colantonio, Sophia; Rivers, Jason K

Plants and algae have played a central role in the treatment of skin conditions in both traditional First Nations healing and in modern dermatology. The objective of this study was to examine the evidence supporting the dermatological use of seaweed, witch hazel, bearberry, and mayapple. Four plants and algae used in traditional First Nations treatments of skin disease were selected based on expert recommendations. Several databases were searched to identify relevant citations without language restrictions. Seaweed has potential clinical use in the treatment of acne and wrinkles and may be incorporated into biofunctional textiles. Witch hazel is an effective and well-tolerated treatment of inflammation and diaper dermatitis. Bearberry leaves contain arbutin, a skin-lightening agent that is an alternative for the treatment of hyperpigmentation. Mayapple contains podophyllotoxin, a treatment for condyloma accuminata, molluscum contagiosum, and recalcitrant palmoplantar warts. Common plants and algae are replete with bioactive agents that may have beneficial effects on the skin. Further research will open the door to new and innovative products in the future. Limitations of this study include that the scope of our study is limited to 4 plants and algae, a small sample of the breadth of plants used by First Nations for dermatological treatments.

Interaction of vascular plants and vesicular-arbuscular mycorrhizal fungi across a soil moisture-nutrient gradient.

PubMed

Anderson, R C; Liberta, A E; Dickman, L A

1984-09-01

Abundance and distribution of vascular plants and vesicular-arbuscular mycorrhizal (VAM) fungi across a soil moisture-nutrient gradient were studied at a single site. Vegetation on the site varied from a dry mesic paririe dominated by little bluestem (Schizachyrium scoparium) to emergent aquatic vegetation dominated by cattail (Typha latifolia) and water smartweed (Polygonum hydropiperoides). Plant cover, VAM spore abundance, plant species richness, and number of VAM fungi represented as spores, had significant positive correlations with each other and with percent organic matter. The plant and VAM spore variables had significant negative correlations with soil pH and available Ca, Mg, P and gravimetric soil moisture. Using stepwise multiple regression, Ca was found to be the best predictor of spore abundance. Test for association between plant species and VAM fungal spores indicated that the spores of Glomus caledonium are associated with plants from dry, nutrient poor sites and spores of gigaspora gigantea are positively associated with plants occurring on the wet, relatively nutrient rich sites. Glomus fasciculatum was the most abundant and widely distributed VAM fungus and it had more positive associations with endophyte hosts than the other VAM fungi. We found no relationship between beta niche breadth of plant species and the presence or absence of mycorrhizal infection. However, our data suggest that some plant species may vary with respect to their infection status depending upon soil moisture conditions that may fluctuate seasonally or annually to favor or hinder VAM associations.

High Levels of Antibodies to Multiple Domains and Strains of VAR2CSA Correlate with the Absence of Placental Malaria in Cameroonian Women Living in an Area of High Plasmodium falciparum Transmission

PubMed Central

Tutterrow, Yeung L.; Avril, Marion; Singh, Kavita; Long, Carole A.; Leke, Robert J.; Sama, Grace; Salanti, Ali; Smith, Joseph D.; Leke, Rose G. F.

2012-01-01

Placental malaria, caused by sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, is associated with increased risk of maternal morbidity and poor birth outcomes. The parasite antigen VAR2CSA (variant surface antigen 2-chondroitin sulfate A) is expressed on infected erythrocytes and mediates binding to chondroitin sulfate A, initiating inflammation and disrupting homeostasis at the maternal-fetal interface. Although antibodies can prevent sequestration, it is unclear whether parasite clearance is due to antibodies to a single Duffy binding-like (DBL) domain or to an extensive repertoire of antibodies to multiple DBL domains and allelic variants. Accordingly, plasma samples collected longitudinally from pregnant women were screened for naturally acquired antibodies against an extensive panel of VAR2CSA proteins, including 2 to 3 allelic variants for each of 5 different DBL domains. Analyses were performed on plasma samples collected from 3 to 9 months of pregnancy from women living in areas in Cameroon with high and low malaria transmission. The results demonstrate that high antibody levels to multiple VAR2CSA domains, rather than a single domain, were associated with the absence of placental malaria when antibodies were present from early in the second trimester until term. Absence of placental malaria was associated with increasing antibody breadth to different DBL domains and allelic variants in multigravid women. Furthermore, the antibody responses of women in the lower-transmission site had both lower magnitude and lesser breadth than those in the high-transmission site. These data suggest that immunity to placental malaria results from high antibody levels to multiple VAR2CSA domains and allelic variants and that antibody breadth is influenced by malaria transmission intensity. PMID:22331427

Gravity-Driven Hydraulic Fractures

NASA Astrophysics Data System (ADS)

Germanovich, L. N.; Garagash, D.; Murdoch, L. C.; Robinowitz, M.

2014-12-01

This study is motived by a new method for disposing of nuclear waste by injecting it as a dense slurry into a hydraulic fracture that grows downward to great enough depth to permanently isolate the waste. Disposing of nuclear waste using gravity-driven hydraulic fractures is mechanically similar to the upward growth of dikes filled with low density magma. A fundamental question in both applications is how the injected fluid controls the propagation dynamics and fracture geometry (depth and breadth) in three dimensions. Analog experiments in gelatin [e.g., Heimpel and Olson, 1994; Taisne and Tait, 2009] show that fracture breadth (the short horizontal dimension) remains nearly stationary when the process in the fracture "head" (where breadth is controlled) is dominated by solid toughness, whereas viscous fluid dissipation is dominant in the fracture tail. We model propagation of the resulting gravity-driven (buoyant or sinking), finger-like fracture of stationary breadth with slowly varying opening along the crack length. The elastic response to fluid loading in a horizontal cross-section is local and can be treated similar to the classical Perkins-Kern-Nordgren (PKN) model of hydraulic fracturing. The propagation condition for a finger-like crack is based on balancing the global energy release rate due to a unit crack extension with the rock fracture toughness. It allows us to relate the net fluid pressure at the tip to the fracture breadth and rock toughness. Unlike the PKN fracture, where breadth is known a priori, the final breadth of a finger-like fracture is a result of processes in the fracture head. Because the head is much more open than the tail, viscous pressure drop in the head can be neglected leading to a 3D analog of Weertman's hydrostatic pulse. This requires relaxing the local elasticity assumption of the PKN model in the fracture head. As a result, we resolve the breadth, and then match the viscosity-dominated tail with the 3-D, toughness-dominated head to obtain a complete closed-form solution. We then analyze the gravity fracture propagation in conditions of either continuous injection or finite volume release for sets of parameters representative of dense waste injection technique and low viscosity magma diking.

Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding

PubMed Central

Chappell, Paul E; Meziane, El Kahina; Harrison, Michael; Magiera, Łukasz; Hermann, Clemens; Mears, Laura; Wrobel, Antoni G; Durant, Charlotte; Nielsen, Lise Lotte; Buus, Søren; Ternette, Nicola; Mwangi, William; Butter, Colin; Nair, Venugopal; Ahyee, Trudy; Duggleby, Richard; Madrigal, Alejandro; Roversi, Pietro; Lea, Susan M; Kaufman, Jim

2015-01-01

Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation. DOI: http://dx.doi.org/10.7554/eLife.05345.001 PMID:25860507

Let physics substantiate music and music enhance physics- give principle to the other disciplines.

NASA Astrophysics Data System (ADS)

Chang, Hui-Yiing

2006-03-01

A conventional practice in K-12 education is to synchronize the arts and the sciences. Physics, traditionally been considered the mother of the sciences, and music, the mother of the arts, are interdependent and help to establishing a complete understanding of the other disciplines. Intense musical expression is attained when progression aims towards infinity. Motions are made in curves across time, imitating physical phenomena. The meaning of each element is enhanced according to the relative duration and dynamics of its context. Complete musical expression considers the three dimensions of space- length, breadth and height- and the three dimensions of time- past, present and future when balancing the instrumental parts and developing the structural elements. Overall, equilibrium is sought for like gravitational forces as expressed in equations. In learning processes, sensing precedes reasoning. Music attunes one to sensitive reactions towards the environment while physics substantiates the concepts by imposing a hierarchical order, the highest form of which is elegantly beautiful and most effectively expressed in music.

Atmospheric carbon dioxide: a driver of photosynthetic eukaryote evolution for over a billion years?

PubMed Central

Beerling, David J.

2012-01-01

Exciting evidence from diverse fields, including physiology, evolutionary biology, palaeontology, geosciences and molecular genetics, is providing an increasingly secure basis for robustly formulating and evaluating hypotheses concerning the role of atmospheric carbon dioxide (CO2) in the evolution of photosynthetic eukaryotes. Such studies span over a billion years of evolutionary change, from the origins of eukaryotic algae through to the evolution of our present-day terrestrial floras, and have relevance for plant and ecosystem responses to future global CO2 increases. The papers in this issue reflect the breadth and depth of approaches being adopted to address this issue. They reveal new discoveries pointing to deep evidence for the role of CO2 in shaping evolutionary changes in plants and ecosystems, and establish an exciting cross-disciplinary research agenda for uncovering new insights into feedbacks between biology and the Earth system. PMID:22232760

Atmospheric carbon dioxide: a driver of photosynthetic eukaryote evolution for over a billion years?

PubMed

Beerling, David J

2012-02-19

Exciting evidence from diverse fields, including physiology, evolutionary biology, palaeontology, geosciences and molecular genetics, is providing an increasingly secure basis for robustly formulating and evaluating hypotheses concerning the role of atmospheric carbon dioxide (CO(2)) in the evolution of photosynthetic eukaryotes. Such studies span over a billion years of evolutionary change, from the origins of eukaryotic algae through to the evolution of our present-day terrestrial floras, and have relevance for plant and ecosystem responses to future global CO(2) increases. The papers in this issue reflect the breadth and depth of approaches being adopted to address this issue. They reveal new discoveries pointing to deep evidence for the role of CO(2) in shaping evolutionary changes in plants and ecosystems, and establish an exciting cross-disciplinary research agenda for uncovering new insights into feedbacks between biology and the Earth system.

Regulation of Plant Cellular and Organismal Development by SUMO.

PubMed

Elrouby, Nabil

2017-01-01

This chapter clearly demonstrates the breadth and spectrum of the processes that SUMO regulates during plant development. The gross phenotypes observed in mutants of the SUMO conjugation and deconjugation enzymes reflect these essential roles, and detailed analyses of these mutants under different growth conditions revealed roles in biotic and abiotic stress responses, phosphate starvation, nitrate and sulphur metabolism, freezing and drought tolerance and response to excess copper. SUMO functions also intersect with those regulated by several hormones such as salicylic acid , abscisic acid , gibberellins and auxin, and detailed studies provide mechanistic clues of how sumoylation may regulate these processes. The regulation of COP1 and PhyB functions by sumoylation provides very strong evidence that SUMO is heavily involved in the regulation of light signaling in plants. At the cellular and subcellular levels, SUMO regulates meristem architecture, the switch from the mitotic cycle into the endocycle, meiosis, centromere decondensation and exit from mitosis, transcriptional control, and release from transcriptional silencing. Most of these advances in our understanding of SUMO functions during plant development emerged over the past 6-7 years, and they may only predict a prominent rise of SUMO as a major regulator of eukaryotic cellular and organismal growth and development.

Xylocopa bees in tropical coastal sand dunes: use of resources and their floral syndromes.

PubMed

Figueiredo, N; Gimenes, M; de Miranda, M D; Oliveira-Rebouças, P

2013-06-01

Large bees such as species from Xylocopa Latreille are usually associated with pollination in tropical sand dune areas, which frequently present shrubby herbaceous vegetation adapted to conditions of high salinity, high solar radiation and strong winds. We report on the diversity of Xylocopa and the plants they visited to collect nectar and pollen, focusing on the floral syndromes they present in these plants and on the breadth of the trophic niche in a tropical sand dune fragment over the year. The field work was carried out monthly in Baixio (Bahia, Brazil; Northern Coast Environmental Protection Area) from April 2008 to March 2009, over two consecutive days, from 06:30 AM to 05:00 PM. The medium-large body sized Xylocopa (Neoxylocopa) cearensis Ducke and Xylocopa (Schonnherria) subcyanea Pérez were noticeable for their frequency, constancy on the flowers and sharing of plant species. Xylocopa spp. visited plants with flowers of different shapes, colors, inflorescence arrangement and syndromes. However, their resource collections were mainly concentrated on Cuphea brachiata, Waltheria cinerascens, Croton sellowii and Chamaecrista ramosa, which may be considered key species for Xylocopa spp. maintenance in coastal sand dune and restinga environments in Northeast Brazil.

Working-memory performance is related to spatial breadth of attention.

PubMed

Kreitz, Carina; Furley, Philip; Memmert, Daniel; Simons, Daniel J

2015-11-01

Working memory and attention are closely related constructs. Models of working memory often incorporate an attention component, and some even equate working memory and attentional control. Although some attention-related processes, including inhibitory control of response conflict and interference resolution, are strongly associated with working memory, for other aspects of attention the link is less clear. We examined the association between working-memory performance and attentional breadth, the ability to spread attention spatially. If the link between attention and working memory is broader than inhibitory and interference resolution processes, then working-memory performance might also be associated with other attentional abilities, including attentional breadth. We tested 123 participants on a variety of working-memory and attentional-breadth measures, finding a strong correlation between performances on these two types of tasks. This finding demonstrates that the link between working memory and attention extends beyond inhibitory processes.

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance.

PubMed

Sémon, Marie; Mouchiroud, Dominique; Duret, Laurent

2005-02-01

Mammalian chromosomes are characterized by large-scale variations of DNA base composition (the so-called isochores). In contradiction with previous studies, Lercher et al. (Hum. Mol. Genet., 12, 2411, 2003) recently reported a strong correlation between gene expression breadth and GC-content, suggesting that there might be a selective pressure favoring the concentration of housekeeping genes in GC-rich isochores. We reassessed this issue by examining in human and mouse the correlation between gene expression and GC-content, using different measures of gene expression (EST, SAGE and microarray) and different measures of GC-content. We show that correlations between GC-content and expression are very weak, and may vary according to the method used to measure expression. Such weak correlations have a very low predictive value. The strong correlations reported by Lercher et al. (2003) are because of the fact that they measured variables over neighboring genes windows. We show here that using gene windows artificially enhances the correlation. The assertion that the expression of a given gene depends on the GC-content of the region where it is located is therefore not supported by the data.

Human body mass estimation: a comparison of "morphometric" and "mechanical" methods.

PubMed

Auerbach, Benjamin M; Ruff, Christopher B

2004-12-01

In the past, body mass was reconstructed from hominin skeletal remains using both "mechanical" methods which rely on the support of body mass by weight-bearing skeletal elements, and "morphometric" methods which reconstruct body mass through direct assessment of body size and shape. A previous comparison of two such techniques, using femoral head breadth (mechanical) and stature and bi-iliac breadth (morphometric), indicated a good general correspondence between them (Ruff et al. [1997] Nature 387:173-176). However, the two techniques were never systematically compared across a large group of modern humans of diverse body form. This study incorporates skeletal measures taken from 1,173 Holocene adult individuals, representing diverse geographic origins, body sizes, and body shapes. Femoral head breadth, bi-iliac breadth (after pelvic rearticulation), and long bone lengths were measured on each individual. Statures were estimated from long bone lengths using appropriate reference samples. Body masses were calculated using three available femoral head breadth (FH) formulae and the stature/bi-iliac breadth (STBIB) formula, and compared. All methods yielded similar results. Correlations between FH estimates and STBIB estimates are 0.74-0.81. Slight differences in results between the three FH estimates can be attributed to sampling differences in the original reference samples, and in particular, the body-size ranges included in those samples. There is no evidence for systematic differences in results due to differences in body proportions. Since the STBIB method was validated on other samples, and the FH methods produced similar estimates, this argues that either may be applied to skeletal remains with some confidence. 2004 Wiley-Liss, Inc.

Breadth and depth involvement: Understanding Internet gambling involvement and its relationship to gambling problems.

PubMed

LaPlante, Debi A; Nelson, Sarah E; Gray, Heather M

2014-06-01

The "involvement effect" refers to the finding that controlling for gambling involvement often reduces or eliminates frequently observed game-specific associations with problem gambling. In other words, broader patterns of gambling behavior, particularly the number of types of games played over a defined period, contribute more to problem gambling than playing specific games (e.g., lottery, casino, Internet gambling). This study extends this burgeoning area of inquiry in three primary ways. First, it tests independently and simultaneously the predictive power of two gambling patterns: breadth involvement (i.e., the number of games an individual plays) and depth involvement (i.e., the number of days an individual plays). Second, it includes the first involvement analyses of actual betting activity records that are associated with clinical screening information. Third, it evaluates and compares the linearity of breadth and depth effects. We conducted analyses of the actual gambling activity of 1,440 subscribers to the bwin.party gambling service who completed an online gambling disorder screen. In all, 11 of the 16 games we examined had a significant univariate association with a positive screen for gambling disorder. However, after controlling for breadth involvement, only Live Action Internet sports betting retained a significant relationship with potential gambling-related problems. Depth involvement, though significantly related to potential problems, did not impact game-based gambling disorder associations as much as breadth involvement. Finally, breadth effects appeared steeply linear, with a slight quadratic component manifesting beyond four games played, but depth effects appeared to have a strong linear component and a slight cubic component.

Breadth versus volume: Neurology outpatient clinic cases in medical education.

PubMed

Albert, Dara V; Blood, Angela D; Park, Yoon Soo; Brorson, James R; Lukas, Rimas V

2016-06-01

This study examined how volume in certain patient case types and breadth across patient case types in the outpatient clinic setting are related to Neurology Clerkship student performance. Case logs from the outpatient clinic experience of 486 students from The University of Chicago Pritzker School of Medicine, USA, participating in the 4week Neurology Clerkship from July 2008 to June 2013 were reviewed. A total of 12,381 patient encounters were logged and then classified into 13 diagnostic categories. How volume of cases within categories and the breadth of cases across categories relate to the National Board of Medical Examiners Clinical Subject Examination for Neurology and a Neurology Clerkship Objective Structured Clinical Examination was analyzed. Volume of cases was significantly correlated with the National Board of Medical Examiners Clinical Subject Examination for Neurology (r=.290, p<.001), the Objective Structured Clinical Examination physical examination (r=.236, p=.011), and the Objective Structured Clinical Examination patient note (r=.238, p=.010). Breadth of cases was significantly correlated with the National Board of Medical Examiners Clinical Subject Examination for Neurology (r=.231, p=.017), however was not significantly correlated with any component of the Objective Structured Clinical Examination. Volume of cases correlated with higher performance on measures of specialty knowledge and clinical skill. Fewer relationships emerged correlating breadth of cases and performance on the same measures. This study provides guidance to educators who must decide how much emphasis to place on volume versus breadth of cases in outpatient clinic learning experiences. Copyright © 2016 Elsevier Ltd. All rights reserved.

46 CFR 69.113 - Superstructure tonnage.

Code of Federal Regulations, 2011 CFR

2011-10-01

... is one-half the nearest breadth. If an end is in the form of an arc or curve having a decided flat...-third of the interval between the points at which the breadths are taken. The product is the square foot...

46 CFR 69.113 - Superstructure tonnage.

Code of Federal Regulations, 2010 CFR

2010-10-01

... is one-half the nearest breadth. If an end is in the form of an arc or curve having a decided flat...-third of the interval between the points at which the breadths are taken. The product is the square foot...

Biochemical and Ultrastructural Changes in Sida cordifolia L. and Catharanthus roseus L. to Auto Pollution.

PubMed

Verma, Vijeta; Chandra, Neelam

2014-01-01

Auto pollution is the by-product of our mechanized mobility, which adversely affects both plant and human life. However, plants growing in the urban locations provide a great respite to us from the brunt of auto pollution by absorbing the pollutants at their foliar surface. Foliar surface configuration and biochemical changes in plant species, namely, Sida cordifolia L. and Catharanthus roseus L. grown at roadside (polluted site 1, Talkatora; polluted site 2, Charbagh) in Lucknow city and in the garden of the university campus, which has been taken as reference site, were investigated. It was observed that air pollution caused by auto exhaust showed marked alterations in photosynthetic pigments (chlorophyll, carotenoid, and phaeophytin), and relative water content was reduced while antioxidative enzymes like catalase and peroxidase were found to be enhanced. The changes in the foliar configuration reveal marked alteration in epidermal traits, with decreased number of stomata, stomatal indices, and epidermal cells per unit area, while length and breadth of stomata and epidermal cells were found to be increased in leaves samples wich can be used as biomarkers of auto pollution.

Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria.

PubMed

Raaijmakers, Jos M; Mazzola, Mark

2012-01-01

Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.

Biochemical and Ultrastructural Changes in Sida cordifolia L. and Catharanthus roseus L. to Auto Pollution

PubMed Central

Verma, Vijeta; Chandra, Neelam

2014-01-01

Auto pollution is the by-product of our mechanized mobility, which adversely affects both plant and human life. However, plants growing in the urban locations provide a great respite to us from the brunt of auto pollution by absorbing the pollutants at their foliar surface. Foliar surface configuration and biochemical changes in plant species, namely, Sida cordifolia L. and Catharanthus roseus L. grown at roadside (polluted site 1, Talkatora; polluted site 2, Charbagh) in Lucknow city and in the garden of the university campus, which has been taken as reference site, were investigated. It was observed that air pollution caused by auto exhaust showed marked alterations in photosynthetic pigments (chlorophyll, carotenoid, and phaeophytin), and relative water content was reduced while antioxidative enzymes like catalase and peroxidase were found to be enhanced. The changes in the foliar configuration reveal marked alteration in epidermal traits, with decreased number of stomata, stomatal indices, and epidermal cells per unit area, while length and breadth of stomata and epidermal cells were found to be increased in leaves samples wich can be used as biomarkers of auto pollution. PMID:27355010

Determinants of host species range in plant viruses.

PubMed

Moury, Benoît; Fabre, Frédéric; Hébrard, Eugénie; Froissart, Rémy

2017-04-01

Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant-virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.

Phytochemical diversity drives plant–insect community diversity

PubMed Central

Richards, Lora A.; Dyer, Lee A.; Forister, Matthew L.; Smilanich, Angela M.; Dodson, Craig D.; Leonard, Michael D.; Jeffrey, Christopher S.

2015-01-01

What are the ecological causes and consequences of variation in phytochemical diversity within and between plant taxa? Despite decades of natural products discovery by organic chemists and research by chemical ecologists, our understanding of phytochemically mediated ecological processes in natural communities has been restricted to studies of either broad classes of compounds or a small number of well-characterized molecules. Until now, no studies have assessed the ecological causes or consequences of rigorously quantified phytochemical diversity across taxa in natural systems. Consequently, hypotheses that attempt to explain variation in phytochemical diversity among plants remain largely untested. We use spectral data from crude plant extracts to characterize phytochemical diversity in a suite of co-occurring plants in the tropical genus Piper (Piperaceae). In combination with 20 years of data focused on Piper-associated insects, we find that phytochemical diversity has a direct and positive effect on the diversity of herbivores but also reduces overall herbivore damage. Elevated chemical diversity is associated with more specialized assemblages of herbivores, and the cascading positive effect of phytochemistry on herbivore enemies is stronger as herbivore diet breadth narrows. These results are consistent with traditional hypotheses that predict positive associations between plant chemical diversity, insect herbivore diversity, and trophic specialization. It is clear from these results that high phytochemical diversity not only enhances the diversity of plant-associated insects but also contributes to the ecological predominance of specialized insect herbivores. PMID:26283384

Anthropometric Survey of US Army Personnel (1988): Correlation Coefficients and Regression Equations. Part 5. Stepwise and Standard Multiple Regression Tables

DTIC Science & Technology

1990-05-01

0.759 0.744 0.768 0.753 106 (THUMBBR) THUMB BREADTH -0.652 -0.673 -0.539 -0.663 217 (LIPLGTHH) LIP LENGTH HEADBOARD 0.017 0.019 0.020 51 (FTBRHOR) FOOT...DEPENDENT VARIABLE: (106) THUMB BREADTH (THUBBR) MODEL INDEPENDENT VARIABLE 1 2 3 4 5 INTERCEPT 6.621 5.016 6.267 5.697 4.528 59 (HANDCIRC) HAND...95 (SLLSPEL) SLEEVE LENGTH: SPINE-ELBOW -0.020 -0.019 -C.018 9 (BLFTCIRC) BALL OF FOOT CIRCUMFERENCE -0.032 -0.039 106 (THUMBBR) THUMB BREADTH 0.228

[Application of niche theory in evaluation of main tourism scenic areas in Zhangjiajie City].

PubMed

Xiang, Yan-ping; Xiang, Chang-guo; Chen, You-lian

2010-05-01

Five tourism scenic areas in Zhangjiajie City were selected as research objects, and fifty kinds of resource conditions affecting the development of tourism scenic area were taken as evaluation indices. Through disposing and consolidating the indices level by level, an analysis was made on the niche breadth and niche overlap of the five tourism scenic areas at three levels (I, II, and III). In the five scenic areas, index level had significant effects on the niche breadth (F = 10.278, P = 0.006), but less effects on the relative niche breadth, suggesting that in the evaluation of the development potential of tourism scenic area, relative niche breadth was more reasonable than absolute niche breadth. From level III to level I, the niche overlap of the five scenic areas was increasing, indicating that level choice would affect the evaluation of the actual niche overlap of the scenic areas. With the progressive refinement of the indices to certain level, and when the difference between observed and Monte Carlo-simulated Pianka indices achieved to significant level, this index level could be used as the minimum standard of the refinement, and the simulated niche overlap could be taken as an important reference in the competition evaluation of tourism scenic area.

Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers.

PubMed

Ibanez, Sébastien; Manneville, Olivier; Miquel, Christian; Taberlet, Pierre; Valentini, Alice; Aubert, Serge; Coissac, Eric; Colace, Marie-Pascale; Duparc, Quentin; Lavorel, Sandra; Moretti, Marco

2013-12-01

Food preferences and food availability are two major determinants of the diet of generalist herbivores and of their spatial distribution. How do these factors interact and eventually lead to diet differentiation in co-occurring herbivores? We quantified the diet of four grasshopper species co-occurring in subalpine grasslands using DNA barcoding of the plants contained in the faeces of individuals sampled in the field. The food preferences of each grasshopper species were assessed by a choice (cafeteria) experiment from among 24 plant species common in five grassland plots, in which the four grasshoppers were collected, while the habitat was described by the relative abundance of plant species in the grassland plots. Plant species were characterised by their leaf economics spectrum (LES), quantifying their nutrient vs. structural tissue content. The grasshoppers' diet, described by the mean LES of the plants eaten, could be explained by their plant preferences but not by the available plants in their habitat. The diet differed significantly across four grasshopper species pairs out of six, which validates food preferences assessed in standardised conditions as indicators for diet partitioning in nature. In contrast, variation of the functional diversity (FD) for LES in the diet was mostly correlated to the FD of the available plants in the habitat, suggesting that diet mixing depends on the environment and is not an intrinsic property of the grasshopper species. This study sheds light on the mechanisms determining the feeding niche of herbivores, showing that food preferences influence niche position whereas habitat diversity affects niche breadth.

Assessment of sex in a modern Turkish population using cranial anthropometric parameters.

PubMed

Ekizoglu, Oguzhan; Hocaoglu, Elif; Inci, Ercan; Can, Ismail Ozgur; Solmaz, Dilek; Aksoy, Sema; Buran, Cudi Ferat; Sayin, Ibrahim

2016-07-01

The utilization of radiological imaging methods in anthropometric studies is being expanded by the application of modern imaging methods, leading to a decrease in costs, a decrease in the time required for analysis and the ability to create three-dimensional images. This retrospective study investigated 400 patients within the 18-45-years age group (mean age: 30.7±11.2years) using cranial computed tomography images. We measured 14 anthropometric parameters (basion-bregma height, basion-prosthion length, maximum cranial length and cranial base lengths, maximum cranial breadth, bizygomatic diameter, upper facial breadth, bimastoid diameter, orbital breadth, orbital length, biorbital breadth, interorbital breadth, foramen magnum breadth and foramen magnum length) of cranial measurements. The intra- and inter-observer repeatability and consistency were good. From the results of logistic regression analysis using morphometric measurements, the most conspicuous measurements in terms of dimorphism were maximum cranial length, bizygomatic diameter, basion-bregma height, and cranial base length. The most dimorphic structure was the bizygomatic diameter with an accuracy rate of 83% in females and 77% in males. In this study, 87.5% of females and 87.0% of males were classified accurately by this model including four parameters with a sensitivity of 91.5% and specificity of 85.0%. In conclusion, CT cranial morphometric analysis may be reliable for the assessment of sex in the Turkish population and is recommended for comparison of data of modern populations with those of former populations. Additionally, cranial morphometric data that we obtained from modern Turkish population may reveal population specific data, which may help current criminal investigations and identification of disaster victims. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Longitudinal analysis of high-technology medical services and hospital financial performance.

PubMed

Zengul, Ferhat D; Weech-Maldonado, Robert; Ozaydin, Bunyamin; Patrician, Patricia A; OʼConnor, Stephen J

U.S. hospitals have been investing in high-technology medical services as a strategy to improve financial performance. Despite the interest in high-tech medical services, there is not much information available about the impact of high-tech services on financial performance. The aim of this study was to examine the impact of high-tech medical services on financial performance of U.S. hospitals by using the resource-based view of the firm as a conceptual framework. Fixed-effects regressions with 2 years lagged independent variables using a longitudinal panel sample of 3,268 hospitals (2005-2010). It was hypothesized that hospitals with rare or large numbers (breadth) of high-tech medical services will experience better financial performance. Fixed effects regression results supported the link between a larger breadth of high-tech services and total margin, but only among not-for-profit hospitals. Both breadth and rareness of high-tech services were associated with high total margin among not-for-profit hospitals. Neither breadth nor rareness of high-tech services was associated with operating margin. Although breadth and rareness of high-tech services resulted in lower expenses per inpatient day among not-for-profit hospitals, these lower costs were offset by lower revenues per inpatient day. Enhancing the breadth of high-tech services may be a legitimate organizational strategy to improve financial performance, especially among not-for-profit hospitals. Hospitals may experience increased productivity and efficiency, and therefore lower inpatient operating costs, as a result of newer technologies. However, the negative impact on operating revenue should caution hospital administrators about revenue reducing features of these technologies, which may be related to the payer mix that these technologies may attract. Therefore, managers should consider both the cost and revenue implications of these technologies.

Breadth of Extracurricular Participation and Adolescent Adjustment Among African-American and European-American Youth

PubMed Central

Fredricks, Jennifer A.; Eccles, Jacquelynne S.

2012-01-01

We examined the linear and nonlinear relations between breadth of extracurricular participation in 11th grade and developmental outcomes at 11th grade and 1 year after high school in an economically diverse sample of African-American and European-American youth. In general, controlling for demographic factors, children's motivation, and the dependent variable measured 3 years earlier, breadth was positively associated with indicators of academic adjustment at 11th grade and at 1 year after high school. In addition, for the three academic outcomes (i.e., grades, educational expectations, and educational status) the nonlinear function was significant; at high levels of involvement the well-being of youth leveled off or declined slightly. In addition, breadth of participation at 11th grade predicted lower internalizing behavior, externalizing behavior, alcohol use, and marijuana use at 11th grade. Finally, the total number of extracurricular activities at 11th grade was associated with civic engagement 2 years later. PMID:22837637

Sexual dimorphism in finger ridge breadth measurements: a tool for sex estimation from fingerprints.

PubMed

Mundorff, Amy Z; Bartelink, Eric J; Murad, Turhon A

2014-07-01

Previous research has demonstrated significant sexual dimorphism in friction ridge skin characteristics. This study uses a novel method for measuring sexual dimorphism in finger ridge breadths to evaluate its utility as a sex estimation method from an unknown fingerprint. Beginning and ending in a valley, the width of ten parallel ridges with no obstructions or minutia was measured in a sample of 250 males and females (N = 500). The results demonstrate statistically significant differences in ridge breadth between males and females (p < 0.001), with classification accuracy for each digit varying from 83.2% to 89.3%. Classification accuracy for the pooled finger samples was 83.9% for the right hand and 86.2% for the left hand, which is applicable for cases where the digit number cannot be determined. Weight, stature, and to a lesser degree body mass index also significantly correlate with ridge breadth and account for the degree of overlap between males and females. © 2014 American Academy of Forensic Sciences.

Breadth of Extracurricular Participation and Adolescent Adjustment Among African-American and European-American Youth.

PubMed

Fredricks, Jennifer A; Eccles, Jacquelynne S

2010-06-01

We examined the linear and nonlinear relations between breadth of extracurricular participation in 11th grade and developmental outcomes at 11th grade and 1 year after high school in an economically diverse sample of African-American and European-American youth. In general, controlling for demographic factors, children's motivation, and the dependent variable measured 3 years earlier, breadth was positively associated with indicators of academic adjustment at 11th grade and at 1 year after high school. In addition, for the three academic outcomes (i.e., grades, educational expectations, and educational status) the nonlinear function was significant; at high levels of involvement the well-being of youth leveled off or declined slightly. In addition, breadth of participation at 11th grade predicted lower internalizing behavior, externalizing behavior, alcohol use, and marijuana use at 11th grade. Finally, the total number of extracurricular activities at 11th grade was associated with civic engagement 2 years later.

Ecological niche differentiation of polyploidization is not supported by environmental differences among species in a cosmopolitan grass genus.

PubMed

Visser, Vernon; Molofsky, Jane

2015-01-01

• Polyploidization frequently results in the creation of new plant species, the establishment of which is thought to often be facilitated by ecological niche differentiation from the diploid species. We tested this hypothesis using the cosmopolitan grass genus Phalaris (Poaceae), consisting of 19 species that range from diploid to tetraploid to hexaploid. Specifically, we tested whether (1) polyploids occupy more extreme environments and/or (2) have broader niche breadths and/or (3) whether the polyploid species' distributions indicate a niche shift from diploid species.• We employed a bootstrapping approach using distribution data for each species and eight environmental variables to investigate differences between species in the means, extremes, and breadths of each environmental variable. We used a kernel smoothing technique to quantify niche overlap between species.• Although we found some support for the three hypotheses for a few diploid-polyploid pairs and for specific environmental variables, none of these hypotheses were generally supported.• Our results suggest that these commonly held hypotheses about the effects of polyploidization on ecological distributions are not universally applicable. Correlative biogeographic studies like ours provide a necessary first step for suggesting specific hypotheses that require experimental verification. A combination of genetic, physiological, and ecological studies will be required to achieve a better understanding of the role of polyploidization in niche evolution. © 2015 Botanical Society of America, Inc.

The influence of relative body breadth on the diaphyseal morphology of the human lower limb.

PubMed

Davies, Thomas G; Stock, Jay T

2014-01-01

Variation in relative body breadth between individuals is potentially a significant influence on the biomechanical loading placed upon the lower limb. This study investigates the influence of relative body breadth on the periosteal geometry of the diaphyses of the limb bones among individuals from a broad range of human populations. This study applies a 3D laser scanning approach to the extraction and analysis of periosteal cross-sectional properties throughout the diaphyses of the femur and tibia to test for influences of body shape on diaphyseal morphology throughout the lower limb. Analyses are based on data collected from seven populations, encompassing a broad range of modern human variation in body shape. Hypertrophy of the proximal end of the femur diaphysis in wider bodied individuals is observed and appears to extend at least as far as the femur midshaft, while the mid diaphyseal region of the tibia is the least influenced by body shape. However correlations with relative body breadth were also observed towards the distal end of the femur diaphysis and towards both ends of the tibial diaphysis, especially among females. Relative body breadth is correlated with the periosteal geometry of the lower limb bones, particularly towards the proximal end of the femur diaphysis, but correlations in other regions also suggest integration of the diaphyseal geometry with epiphyseal dimensions. © 2014 Wiley Periodicals, Inc.

Intensity and breadth of participation in organized activities during the adolescent years: multiple associations with youth outcomes.

PubMed

Denault, Anne-Sophie; Poulin, François

2009-10-01

The goal of this study was to examine initial levels and rates of change in the intensity and breadth of participation in organized activities during the adolescent years, and how these participation practices were related to youth outcomes in later adolescence. The main objectives were (a) to examine growth curves of intensity and breadth of participation from Grades 7 through 11 and their interrelations, and (b) to test the associations between these dimensions of participation and academic orientation, risky behaviors, internalizing problems, and civic development in Grade 11. A homogenous sample of 299 youth (mean age = 13.37, SD = .41; 62% girls) were surveyed annually using questionnaires and phone interviews. The main results revealed that (a) even though both intensity and breadth of participation decreased over time, intensity of participation showed steeper declines by later grades, and (b) initial levels of participation were better predictors of later outcomes than rates of change over time. Regardless of the levels of change taking place over time, results revealed that youth with high initial levels of participation (both intensity and breadth) were more committed to school and developed more positive values towards society by Grade 11 than those who participated less. This might suggest that a high level of participation during early-to-mid-adolescence is particularly important when it comes to later outcomes.

Impacts of Experiential Learning Depth and Breadth on Student Outcomes

ERIC Educational Resources Information Center

Coker, Jeffrey Scott; Heiser, Evan; Taylor, Laura; Book, Connie

2017-01-01

This 5-year study of graduating seniors at Elon University (n = 2,058) evaluates the impacts of experiential learning depth (amount of time commitment) and breadth (number of different types of experiences) on student outcomes. Data on study abroad, undergraduate research, internships, service, and leadership experiences were pulled from…

Eco-evolutionary factors drive induced plant volatiles: a meta-analysis.

PubMed

Rowen, Elizabeth; Kaplan, Ian

2016-04-01

Herbivore-induced plant volatiles (HIPVs) mediate critical ecological functions, but no studies have quantitatively synthesized data published on HIPVs to evaluate broad patterns. We tested three hypotheses that use eco-evolutionary theory to predict volatile induction: feeding guild (chewing arthropods > sap feeders), diet breadth (specialist herbivores > generalists), and selection history (domesticated plants < wild species). To test these hypotheses, we extracted data from 236 experiments that report volatiles produced by herbivore-damaged and undamaged plants. These data were subjected to meta-analysis, including effects on total volatiles and major biochemical classes. Overall, we found that chewers induced more volatiles than sap feeders, for both total volatiles and most volatile classes (e.g. green leaf volatiles, monoterpenes). Although specialist herbivores induced more total volatiles than generalists, this was inconsistent across chemical classes. Contrary to our expectation, domesticated species induced stronger volatile responses than wild species, even when controlling for plant taxonomy. Surprisingly, this is the first quantitative synthesis of published studies on HIPVs. Our analysis provides support for perceptions in the published literature (chewers > sap feeders), while challenging other commonly held notions (wild > crop). Despite the large number of experiments, we identified several gaps in the existing literature that should guide future investigations. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations.

PubMed

Geib, Jennifer C; Galen, Candace

2012-07-01

Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline.

Root structural and functional dynamics in terrestrial biosphere models--evaluation and recommendations.

PubMed

Warren, Jeffrey M; Hanson, Paul J; Iversen, Colleen M; Kumar, Jitendra; Walker, Anthony P; Wullschleger, Stan D

2015-01-01

There is wide breadth of root function within ecosystems that should be considered when modeling the terrestrial biosphere. Root structure and function are closely associated with control of plant water and nutrient uptake from the soil, plant carbon (C) assimilation, partitioning and release to the soils, and control of biogeochemical cycles through interactions within the rhizosphere. Root function is extremely dynamic and dependent on internal plant signals, root traits and morphology, and the physical, chemical and biotic soil environment. While plant roots have significant structural and functional plasticity to changing environmental conditions, their dynamics are noticeably absent from the land component of process-based Earth system models used to simulate global biogeochemical cycling. Their dynamic representation in large-scale models should improve model veracity. Here, we describe current root inclusion in models across scales, ranging from mechanistic processes of single roots to parameterized root processes operating at the landscape scale. With this foundation we discuss how existing and future root functional knowledge, new data compilation efforts, and novel modeling platforms can be leveraged to enhance root functionality in large-scale terrestrial biosphere models by improving parameterization within models, and introducing new components such as dynamic root distribution and root functional traits linked to resource extraction. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

Breadth of Perspective--An Important Concept for Public Relations.

ERIC Educational Resources Information Center

Culbertson, Hugh M.

"Breadth of perspective" is a significant concept for definition of public goals, especially in line with the two-way symmetric model of public relations practice. The concept involves four components: (1) awareness that more than one definition, stand, or conclusion is possible and is probably accepted as valid by significant persons or…

Predicting extinctions as a result of climate change

Treesearch

Mark W. Schwartz; Louis R. Iverson; Anantha M. Prasad; Stephen N. Matthews; Raymond J. O' Connor; Raymond J. O' Connor

2006-01-01

Widespread extinction is a predicted ecological consequence of global warming. Extinction risk under climate change scenarios is a function of distribution breadth. Focusing on trees and birds of the eastern United States, we used joint climate and environment models to examine fit and climate change vulnerability as a function of distribution breadth. We found that...

33 CFR 157.03 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... port of final cargo discharge. Breadth or B means the maximum molded breadth of a vessel in meters... lightweight displacement and the total displacement of a vessel measured in water of specific gravity 1.025 at... of each is more than 1/15 of the total depth of the tank. Length or L means the distance in meters...

33 CFR 157.03 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... port of final cargo discharge. Breadth or B means the maximum molded breadth of a vessel in meters... lightweight displacement and the total displacement of a vessel measured in water of specific gravity 1.025 at... of each is more than 1/15 of the total depth of the tank. Length or L means the distance in meters...

33 CFR 157.03 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... port of final cargo discharge. Breadth or B means the maximum molded breadth of a vessel in meters... lightweight displacement and the total displacement of a vessel measured in water of specific gravity 1.025 at... of each is more than 1/15 of the total depth of the tank. Length or L means the distance in meters...

The Mediational Role of Adolescents' Friends in Relations between Activity Breadth and Adjustment

ERIC Educational Resources Information Center

Simpkins, Sandra D.; Eccles, Jacquelynne S.; Becnel, Jennifer N.

2008-01-01

This investigation addresses the mediational role of friends' characteristics between adolescents' activity breadth (i.e., variety in activity participation) and their later adjustment. Data were drawn from 2 longitudinal studies: the Childhood and Beyond (CAB; N = 925) study and the Maryland Adolescent Development in Context Study (MADICS; N =…

Impact of Depth and Breadth of Student Involvement on Academic Achievement

ERIC Educational Resources Information Center

Ivanova, Albena; Moretti, Anthony

2018-01-01

We investigate the direct and interaction effects of breadth and depth of student involvement in campus activities on student grade point average. Using data from the Student Engagement Transcripts on 475 students and ordinary least squares regression, we provide evidence for both direct and interaction effects. A more detailed analysis of the…

Secular trends in Cherokee cranial morphology: Eastern vs Western bands.

PubMed

Sutphin, Rebecca; Ross, Ann H; Jantz, Richard L

2014-01-01

The research objective was to examine if secular trends can be identified for cranial data commissioned by Boas in 1892, specifically for cranial breadth and cranial length of the Eastern and Western band Cherokee who experienced environmental hardships. Multiple regression analysis was used to test the degree of relationship between each of the cranial measures: cranial length, cranial breadth and cephalic index, along with predictor variables (year-of-birth, location, sex, admixture); the model revealed a significant difference for all craniometric variables. Additional regression analysis was performed with smoothing Loess plots to observe cranial length and cranial breadth change over time (year-of-birth) separately for Eastern and Western Cherokee band females and males born between 1783-1874. This revealed the Western and Eastern bands show a decrease in cranial length over time. Eastern band individuals maintain a relatively constant head breadth, while Western Band individuals show a sharp decline beginning around 1860. These findings support negative secular trend occurring for both Cherokee bands where the environment made a detrimental impact; this is especially marked with the Western Cherokee band.

An evaluation of the influence of modifications of selected face elements on the reliability of composite drawings.

PubMed

Lewandowski, Z

2004-01-01

The modification of various face elements in a composite drawing influences its reliability in relation to the corresponding photograph. Changes in various face elements are the cause of this decrease in similarity, when examined by both sexes. The results of an initial test suggest: regardless of the observing subject's sex, the highest rated picture (regarded as the most similar one) was the original picture. The face with a shortened nose height (n-sn) was recognised as the least similar to the original. In the second test, this picture obtained the lowest number of points, irrespective of the examining subjects' sex. In the examining group of females, the picture with changed bigonial breadth (go-go) was rated low. In the group of males the picture with a shortened interocular breadth (en-en) appeared poorly reliable. In the case of females, the likeness of the composite drawing to the photograph is least affected by shortening of mouth breadth (ch-ch), whereas in males, by the decrease in nose breadth (al-al).

[Melissopalynology and trophic niche of Apis cerana ceraca and Apis mellifera ligustica in Yunnan Province of Southwest China].

PubMed

Liu, Yu-Jia; Zhao, Tian-Rui; Zhao, Feng-Yun

2013-01-01

In 2010 and 2011, the honey samples of Apis cerana cerana and A. mellifera ligustica were collected from Kunming and Mengzi of Yunnan Province, respectively, aimed to analyze the melissopalynology and tropic niche of the two bee species. The absolute pollen concentration of the honey of A. cerana cerana was 1.55 x 10(4) ind x g(-1), being significantly higher than that (1.01 x 10(4) ind x g(-1)) of A. mellifera ligustica, and the number of nectar plant species collected by A. cerana cerana was 12.9, also significantly higher than that (7.7) collected by A. mellifera ligustica, indicating that A. cerana cerana could utilize more nectar plants, while A. mellifera ligustica had stronger selectivity to the nectar plants. The trophic niche breadth of A. cerana cerana was 0.35, which was significantly higher than that (0.23) of A. mellifera ligustica. The trophic niche overlap index between the two bee species was 0.71, and the interspecific competition index was 0.93, suggesting that the food competition between A. cerana cerana and A. mellifera ligustica was fierce.

Leaf maximum photosynthetic rate and venation are linked by hydraulics.

PubMed

Brodribb, Tim J; Feild, Taylor S; Jordan, Gregory J

2007-08-01

Leaf veins are almost ubiquitous across the range of terrestrial plant diversity, yet their influence on leaf photosynthetic performance remains uncertain. We show here that specific physical attributes of the vascular plumbing network are key limiters of the hydraulic and photosynthetic proficiency of any leaf. Following the logic that leaf veins evolved to bypass inefficient water transport through living mesophyll tissue, we examined the hydraulic pathway beyond the distal ends of the vein system as a possible limiter of water transport in leaves. We tested a mechanistic hypothesis that the length of this final traverse, as water moves from veins across the mesophyll to where it evaporates from the leaf, governs the hydraulic efficiency and photosynthetic carbon assimilation of any leaf. Sampling 43 species across the breadth of plant diversity from mosses to flowering plants, we found that the post-vein traverse as determined by characters such as vein density, leaf thickness, and cell shape, was strongly correlated with the hydraulic conductivity and maximum photosynthetic rate of foliage. The shape of this correlation provided clear support for the a priori hypothesis that vein positioning limits photosynthesis via its influence on leaf hydraulic efficiency.

Niche shifts and energetic condition of songbirds in response to phenology of food-resource availability in a high-elevation sagebrush ecosystem

USGS Publications Warehouse

Cutting, Kyle A.; Anderson, Michelle L.; Beever, Erik; Schroff, Sean; Korb, Nathan; Klaphake, Eric; McWilliams, Scott R.

2016-01-01

Seasonal fluctuations in food availability can affect diets of consumers, which in turn may influence the physiological state of individuals and shape intra- and inter-specific patterns of resource use. High-elevation ecosystems often exhibit a pronounced seasonal “pulse” in productivity, although few studies document how resource use and energetic condition by avian consumers change in relation to food-resource availability in these ecosystems. We tested the hypothesis that seasonal increases (pulses) in food resources in high-elevation sagebrush ecosystems result in 2 changes after the pulse, relative to the before-pulse period: (1) reduced diet breadth of, and overlap between, 2 sympatric sparrow species; and (2) enhanced energetic condition in both species. We tracked breeding-season diets using stable isotopes and energetic condition using plasma metabolites of Brewer's Sparrows (Spizella breweri), Vesper Sparrows (Pooecetes gramineus), and their food resources during 2011, and of only Brewer's Sparrows and their food resources during 2013. We quantify diet breadth and overlap between both species, along with coincident physiological consequences of temporal changes in resource use. After invertebrate biomass increased following periods of rainfall in 2011, dietary breadth decreased by 35% in Brewer's Sparrows and by 48% in Vesper Sparrows, while dietary overlap decreased by 88%. Energetic condition of both species increased when dietary overlap was lower and diet breadth decreased, after the rapid rise of food-resource availability. However, energetic condition of Brewer's Sparrows remained constant in 2013, a year with low precipitation and lack of a strong pulse in food resources, even though the species' dietary breadth again decreased that year. Our results indicate that diet breadth and overlap in these sparrow species inhabiting sagebrush ecosystems generally varied as predicted in relation to intra- and interannual changes in food resources, and this difference in diet was associated with improved energetic condition of sparrows at least in one year.

Museum specimens reveal loss of pollen host plants as key factor driving wild bee decline in The Netherlands.

PubMed

Scheper, Jeroen; Reemer, Menno; van Kats, Ruud; Ozinga, Wim A; van der Linden, Giel T J; Schaminée, Joop H J; Siepel, Henk; Kleijn, David

2014-12-09

Evidence for declining populations of both wild and managed bees has raised concern about a potential global pollination crisis. Strategies to mitigate bee loss generally aim to enhance floral resources. However, we do not really know whether loss of preferred floral resources is the key driver of bee decline because accurate assessment of host plant preferences is difficult, particularly for species that have become rare. Here we examine whether population trends of wild bees in The Netherlands can be explained by trends in host plants, and how this relates to other factors such as climate change. We determined host plant preference of bee species using pollen loads on specimens in entomological collections that were collected before the onset of their decline, and used atlas data to quantify population trends of bee species and their host plants. We show that decline of preferred host plant species was one of two main factors associated with bee decline. Bee body size, the other main factor, was negatively related to population trend, which, because larger bee species have larger pollen requirements than smaller species, may also point toward food limitation as a key factor driving wild bee loss. Diet breadth and other potential factors such as length of flight period or climate change sensitivity were not important in explaining twentieth century bee population trends. These results highlight the species-specific nature of wild bee decline and indicate that mitigation strategies will only be effective if they target the specific host plants of declining species.

Museum specimens reveal loss of pollen host plants as key factor driving wild bee decline in The Netherlands

PubMed Central

Scheper, Jeroen; Reemer, Menno; van Kats, Ruud; Ozinga, Wim A.; van der Linden, Giel T. J.; Schaminée, Joop H. J.; Siepel, Henk; Kleijn, David

2014-01-01

Evidence for declining populations of both wild and managed bees has raised concern about a potential global pollination crisis. Strategies to mitigate bee loss generally aim to enhance floral resources. However, we do not really know whether loss of preferred floral resources is the key driver of bee decline because accurate assessment of host plant preferences is difficult, particularly for species that have become rare. Here we examine whether population trends of wild bees in The Netherlands can be explained by trends in host plants, and how this relates to other factors such as climate change. We determined host plant preference of bee species using pollen loads on specimens in entomological collections that were collected before the onset of their decline, and used atlas data to quantify population trends of bee species and their host plants. We show that decline of preferred host plant species was one of two main factors associated with bee decline. Bee body size, the other main factor, was negatively related to population trend, which, because larger bee species have larger pollen requirements than smaller species, may also point toward food limitation as a key factor driving wild bee loss. Diet breadth and other potential factors such as length of flight period or climate change sensitivity were not important in explaining twentieth century bee population trends. These results highlight the species-specific nature of wild bee decline and indicate that mitigation strategies will only be effective if they target the specific host plants of declining species. PMID:25422416

A Generic Multiple Reaction Monitoring Based Approach for Plant Flavonoids Profiling Using a Triple Quadrupole Linear Ion Trap Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yan, Zhixiang; Lin, Ge; Ye, Yang; Wang, Yitao; Yan, Ru

2014-06-01

Flavonoids are one of the largest classes of plant secondary metabolites serving a variety of functions in plants and associating with a number of health benefits for humans. Typically, they are co-identified with many other secondary metabolites using untargeted metabolomics. The limited data quality of untargeted workflow calls for a shift from the breadth-first to the depth-first screening strategy when a specific biosynthetic pathway is focused on. Here we introduce a generic multiple reaction monitoring (MRM)-based approach for flavonoids profiling in plants using a hybrid triple quadrupole linear ion trap (QTrap) mass spectrometer. The approach includes four steps: (1) preliminary profiling of major aglycones by multiple ion monitoring triggered enhanced product ion scan (MIM-EPI); (2) glycones profiling by precursor ion triggered EPI scan (PI-EPI) of major aglycones; (3) comprehensive aglycones profiling by combining MIM-EPI and neutral loss triggered EPI scan (NL-EPI) of major glycone; (4) in-depth flavonoids profiling by MRM-EPI with elaborated MRM transitions. Particularly, incorporation of the NH3 loss and sugar elimination proved to be very informative and confirmative for flavonoids screening. This approach was applied for profiling flavonoids in Astragali radix ( Huangqi), a famous herb widely used for medicinal and nutritional purposes in China. In total, 421 flavonoids were tentatively characterized, among which less than 40 have been previously reported in this medicinal plant. This MRM-based approach provides versatility and sensitivity that required for flavonoids profiling in plants and serves as a useful tool for plant metabolomics.

Sorting It Out: Cultural Competency and Healthcare Literacy in the World Today.

PubMed

Karnick, Paula M

2016-04-01

Healthcare literacy and cultural competence are necessary components in keeping patients informed. Nurses are the foundation of healthcare and pivotal in creating trusting relationships with patients by sharing information. Respect is key in developing a tailored approach to individuals' healthcare literacy and nurses' cultural competence. In practice, the consequence of understanding healthcare literacy and being culturally competent should not be understated. Whether on a mission trip to another country or working in a clinic in the United States, diverse cultures abound. While a person from a particular culture may have some of the same beliefs of others in a culture, the breadth of expression of culture, personal beliefs, and worldview may be vastly different. Humans express themselves in unique ways even within cultures. Seeking ways to understand one another is vital not only in healthcare but in all aspects of life. © The Author(s) 2016.

"Over the Edge of the Wild": Lessons of Discovery through Developing Transdisciplinary (Breadth) Units in Blended Courses

ERIC Educational Resources Information Center

Osborne, Jo; Dibben, Mark

2017-01-01

Universities are increasingly recognising the need to broaden the experience and understanding of their students beyond a single disciplinary approach, to produce graduates more capable of solving the problems of a multidisciplinary world. At the University of Tasmania, a "breadth unit" programme is underway with the dual purpose of…

The Breadth of Coarticulatory Units in Children and Adults

ERIC Educational Resources Information Center

Goffman, Lisa; Smith, Anne; Heisler, Lori; Ho, Michael

2008-01-01

Purpose: To assess, in children and adults, the breadth of coarticulatory movements associated with a single rounded vowel. Method: Upper and lower lip movements were recorded from 8 young adults and 8 children (aged 4-5 years). A single rounded versus unrounded vowel was embedded in the medial position of pairs of 7-word/7-syllable sentences.…

Breadth of Extracurricular Participation and Adolescent Adjustment among African-American and European-American Youth

ERIC Educational Resources Information Center

Fredricks, Jennifer A.; Eccles, Jacquelynne S.

2010-01-01

We examined the linear and nonlinear relations between breadth of extracurricular participation in 11th grade and developmental outcomes at 11th grade and 1 year after high school in an economically diverse sample of African-American and European-American youth. In general, controlling for demographic factors, children's motivation, and the…

The Relationship between Vocabulary Learning Strategies and Breadth and Depth of Vocabulary Knowledge

ERIC Educational Resources Information Center

Zhang, Xian; Lu, Xiaofei

2015-01-01

This study investigated the relationship between vocabulary learning strategies and vocabulary breadth and depth knowledge. One hundred and fifty first-year university students in China took the Vocabulary Levels Test, a meaning recall task, and the Depth of Vocabulary Knowledge Test. The first two tests were used to elicit two types of vocabulary…

Beyond Breadth: The Contributions of Vocabulary Depth to Reading Comprehension among Skilled Readers

ERIC Educational Resources Information Center

Binder, Katherine S.; Cote, Nicole Gilbert; Lee, Cheryl; Bessette, Emily; Vu, Huong

2017-01-01

This study investigated the relationships among vocabulary breadth, vocabulary depth, reading comprehension, and reading rate among college-aged students. While the relationships of some of these variables have been explored in previous research, the current study's focus on the role of vocabulary depth on the literacy measures within a sample of…

The Medical School Learning Environment Survey: An Examination of Its Factor Structure and Relationship to Student Performance and Satisfaction

ERIC Educational Resources Information Center

Rusticus, Shayna; Worthington, Anne; Wilson, Derek; Joughin, Karen

2014-01-01

The Medical School Learning Environment Survey (MSLES) was used with a sample of 311 undergraduate medical students in British Columbia, Canada, to assess the seven scales of Medical Breadth of Interest, Personal Breadth of Interest, Emotional Climate, Flexibility, Meaningful Learning Experience, Organization, Nurturance and Student-Student…

Sustainability of Breadth and Depth of Vocabulary after Implicit versus Explicit Instruction in Kindergarten

ERIC Educational Resources Information Center

Damhuis, Carmen M. P.; Segers, Eliane; Verhoeven, Ludo

2014-01-01

We investigated the sustained effects of explicit versus implicit instruction on the breadth and depth of children's vocabularies, while taking their general vocabulary and verbal short-term memory into account. Two experimental groups with 12 and 15 kindergarten children respectively learned two sets of 17 words counterbalanced to be taught first…

Assessing the Depth and Breadth of Vocabulary Knowledge with Listening Comprehension

ERIC Educational Resources Information Center

Teng, Feng

2014-01-01

This study was inspired by Qian (1999) and Staehr (2009) and researched 88 Chinese learners who had already passed the College English Test 4 (CET). These learners volunteered to participate in the study regarding the depth and breadth of vocabulary knowledge and its relationship with listening comprehension, which was assessed by analyzing the…

Ancient origin and recent innovations of RNA polymerase IV and V

DOE PAGES

Huang, Yi; Kendall, Timmy; Forsythe, Evan S.; ...

2015-03-12

Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highlymore » in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Finally, evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.« less

Ancient origin and recent innovations of RNA polymerase IV and V

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

Huang, Yi; Kendall, Timmy; Forsythe, Evan S.

Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highlymore » in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Finally, evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.« less

Methods of expressing and detecting activity of expansin in plant cells

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

Hood, Elizabeth E.; Yoon, Sangwoong

A method of expressing heterologous expansin in a plant cell is provided where a nucleic acid molecule encoding expansin is introduced into the plant cell and in an embodiment is operably linked to a promoter preferentially expressing in the seed tissue of the plant, and in another embodiment is linked to a promoter preferentially expressing in the embryo tissue of the seed. An embodiment provides the nucleic acid molecule is operably linked to a second nucleic acid molecule that directs expression to the endoplasmic reticulum, vacuole or cell wall. Plants and plant parts expressing expansin are provided. An assay formore » detection of expansin activity is also provided.« less

Children with Developmental Language Impairment Have Vocabulary Deficits Characterized by Limited Breadth and Depth

ERIC Educational Resources Information Center

McGregor, Karla K.; Oleson, Jacob; Bahnsen, Alison; Duff, Dawna

2013-01-01

Background: Deficient vocabulary is a frequently reported symptom of developmental language impairment, but the nature of the deficit and its developmental course are not well documented. Aims: To describe the nature of the deficit in terms of breadth and depth of vocabulary knowledge and to determine whether the nature and the extent of the…

Depth versus Breadth of Lexical Repertoire: Assessing Their Roles in EFL Students' Incidental Vocabulary Acquisition

ERIC Educational Resources Information Center

Ehsanzadeh, Seyed Jafar

2012-01-01

This study explores the roles of depth and breadth of lexical repertoire in L2 lexical inferencing success and incidental vocabulary acquisition through reading. Students read a graded reader containing 13 pseudo-words and attempted to infer the meanings of underlined target words. The Word Associates Test (WAT, Read, 2004) and the Vocabulary…

Coping with School Violence through the Lens of Teachers' Role Breadth: The Impact of Participative Management and Job Autonomy

ERIC Educational Resources Information Center

Somech, Anit; Oplatka, Izhar

2009-01-01

Purpose: The current literature's call for a more ecological approach to violence theory, research, and practice stimulated the current study. This model postulates that teachers' willingness to engage in behaviors intended to tackle violence in school as part of their in-role duties (role breadth) will affect school violence. Specifically, the…

Effect of Mood States on the Breadth of Spatial Attentional Focus: An Event-Related Potential Study

ERIC Educational Resources Information Center

Moriya, Hiroki; Nittono, Hiroshi

2011-01-01

In order to determine the processing stage that is responsible for the effect of mood states on the breadth of attentional focus, we recorded event-related potentials from 18 students who performed a flanker task involving adjacent letters. To induce a specific mood state, positive, neutral, or negative affective pictures were presented repeatedly…

Individual Differences in Very Young Chinese Children's English Vocabulary Breadth and Semantic Depth: Internal and External Factors

ERIC Educational Resources Information Center

Sun, He; Steinkrauss, Rasmus; Wieling, Martijn; de Bot, Kees

2018-01-01

This study examines the English vocabulary development of 43 very young child English as a foreign language (FL) learners (age 3.2-6.2) in China. They were tested twice for vocabulary breadth (reception and production) and semantic depth (paradigmatic and syntagmatic vocabulary knowledge). The development of the English vocabulary knowledge…

Breadth of Productive Vocabulary Knowledge of Pre-Service Teachers: Basis for the Proposed Intervention Strategies in Vocabulary Enhancement

ERIC Educational Resources Information Center

Calub, Cecilia L.; Calub, Francelle L.

2017-01-01

This research sought to determine the level of productive vocabulary knowledge of the students grouped according to type of school and curriculum year level; performance of the students in the vocabulary test categorized according to frequency levels; their breadth of productive vocabulary knowledge related to type of school enrolled in,…

Repressor-mediated tissue-specific gene expression in plants

DOEpatents

Meagher, Richard B [Athens, GA; Balish, Rebecca S [Oxford, OH; Tehryung, Kim [Athens, GA; McKinney, Elizabeth C [Athens, GA

2009-02-17

Plant tissue specific gene expression by way of repressor-operator complexes, has enabled outcomes including, without limitation, male sterility and engineered plants having root-specific gene expression of relevant proteins to clean environmental pollutants from soil and water. A mercury hyperaccumulation strategy requires that mercuric ion reductase coding sequence is strongly expressed. The actin promoter vector, A2pot, engineered to contain bacterial lac operator sequences, directed strong expression in all plant vegetative organs and tissues. In contrast, the expression from the A2pot construct was restricted primarily to root tissues when a modified bacterial repressor (LacIn) was coexpressed from the light-regulated rubisco small subunit promoter in above-ground tissues. Also provided are analogous repressor operator complexes for selective expression in other plant tissues, for example, to produce male sterile plants.

Kinanthropometric comparison between young elite kayakers and canoeists.

PubMed

Alacid, Fernando; Marfell-Jones, Michael; Muyor, José Maria; López-Miñarro, Pedro Angel; Martínez, Ignacio

2015-03-01

The aims of this study were to describe and compare kinanthropometric characteristics of elite young kayakers and canoeists and to compare their proportionality with Olympic paddlers. One hundred and twenty young elite sprint paddlers (66 kayakers and 58 canoeists), aged 13- and 14-years-old, were assessed using a battery of 32 anthropometric dimensions. Somatotypes, Phantom Z-scores and corrected girths were calculated. Comparison between kayakers and canoeists showed that kayakers had greater height, body weight, sitting height, arm span and upper body lengths, breadths and girths than canoeists. Higher proportional humerus breadth and arm girths were also found in kayakers. However, canoeists had higher Z-scores in femur breadth. Olympic paddlers had higher proportional dimensions in upper body girths, and biacromial breadth in both disciplines. Mean somatotypes of kayakers were best described as balanced mesomorphs, while canoeists were ecto-mesomorphs. Differences between kayak and canoe paddlers may be explained by the continual need for physical development in kayakers, in order to remain competitive, compared to the young canoeists' need to place much greater emphasis on the development of their technical ability. The data provided in this study could be used as a guideline for talent identification in sprint canoeing and kayaking.

Expressed var gene repertoire and variant surface antigen diversity in a shrinking Plasmodium falciparum population.

PubMed

Carlos, Bianca C; Fotoran, Wesley L; Menezes, Maria J; Cabral, Fernanda J; Bastos, Marcele F; Costa, Fabio T M; Sousa-Neto, Jayme A; Ribolla, Paulo E M; Wunderlich, Gerhard; Ferreira, Marcelo U

2016-11-01

The var gene-encoded erythrocyte membrane protein-1 of Plasmodium falciparum (PfEMP-1) is the main variant surface antigen (VSA) expressed on infected erythrocytes. The rate at which antibody responses to VSA expressed by circulating parasites are acquired depends on the size of the local VSA repertoire and the frequency of exposure to new VSA. Because parasites from areas with declining malaria endemicity, such as the Amazon, typically express a restricted PfEMP-1 repertoire, we hypothesized that Amazonians would rapidly acquire antibodies to most locally circulating VSA. Consistent with our expectations, the analysis of 5878 sequence tags expressed by 10 local P. falciparum samples revealed little PfEMP-1 DBL1α domain diversity. Among the most commonly expressed DBL1α types, 45% were shared by two or more independent parasite lines. Nevertheless, Amazonians displayed major gaps in their repertoire of anti-VSA antibodies, although the breadth of anti-VSA antibody responses correlated positively with their cumulative exposure to malaria. We found little antibody cross-reactivity even when testing VSA from related parasites expressing the same dominant DBL1α types. We conclude that variant-specific immunity to P. falciparum VSAs develops slowly despite the relatively restricted PfEMP-1 repertoire found in low-endemicity settings. Copyright © 2016 Elsevier Inc. All rights reserved.

Regulated Expression of a Calmodulin Isoform Alters Growth and Development in Potato

NASA Technical Reports Server (NTRS)

Poovaiah, B. W.; Takezawa, D.; An, G.; Han, T.-J.

1996-01-01

A transgene approach was taken to study the consequences of altered expression of a calmodutin iso-form on plant growth and development. Eight genomic clones of potato calmodulin (PCM 1 to 8) have been isolated and characterized. Among the potato calmodulin isoforms studied, PCM 1 differs from the other isoforms because of its unique amino acid substitutions. Transgenic potato plants were produced carrying sense construct of PCM 1 fused to the CAMV 35S promoter. Transgenic plants showing a moderate increase in PCM 1 MRNA exhibited strong apical dominance, produced elongated tubers, and were taller than the controls. Interestingly, the plants expressing the highest level of PCM 1 MRNA did not form underground tubers. Instead, these transgenic plants produced aerial tubers when allowed to grow for longer periods. The expression of different calmodulin isoforms (PCM 1, 5, 6, and 8) was studied in transgenic plants. Among the four potato calmodulin isoforms, only the expression of PCM 1 MRNA was altered in transgenic plants, while the expression of other isoforms was not significantly altered. Western analysis revealed increased PCM 1 protein in transgenic plants, indicating that the expression of both MRNA and protein are altered in transgenic plants. These results suggest that increasing the expression of PCM 1 alters growth and development in potato plants.

Real time expression of ACC oxidase and PR-protein genes mediated by Methylobacterium spp. in tomato plants challenged with Xanthomonas campestris pv. vesicatoria.

PubMed

Yim, W J; Kim, K Y; Lee, Y W; Sundaram, S P; Lee, Y; Sa, T M

2014-07-15

Biotic stress like pathogenic infection increases ethylene biosynthesis in plants and ethylene inhibitors are known to alleviate the severity of plant disease incidence. This study aimed to reduce the bacterial spot disease incidence in tomato plants caused by Xanthomonas campestris pv. vesicatoria (XCV) by modulating stress ethylene with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity of Methylobacterium strains. Under greenhouse condition, Methylobacterium strains inoculated and pathogen challenged tomato plants had low ethylene emission compared to pathogen infected ones. ACC accumulation and ACC oxidase (ACO) activity with ACO related gene expression increased in XCV infected tomato plants over Methylobacterium strains inoculated plants. Among the Methylobacterium spp., CBMB12 resulted lowest ACO related gene expression (1.46 Normalized Fold Expression), whereas CBMB20 had high gene expression (3.42 Normalized Fold Expression) in pathogen challenged tomato. But a significant increase in ACO gene expression (7.09 Normalized Fold Expression) was observed in the bacterial pathogen infected plants. In contrast, Methylobacterium strains enhanced β-1,3-glucanase and phenylalanine ammonia-lyase (PAL) enzyme activities in pathogen challenged tomato plants. The respective increase in β-1,3-glucanase related gene expressions due to CBMB12, CBMB15, and CBMB20 strains were 66.3, 25.5 and 10.4% higher over pathogen infected plants. Similarly, PAL gene expression was high with 0.67 and 0.30 Normalized Fold Expression, in pathogen challenged tomato plants inoculated with CBMB12 and CBMB15 strains. The results suggest that ethylene is a crucial factor in bacterial spot disease incidence and that methylobacteria with ACC deaminase activity can reduce the disease severity with ultimate pathogenesis-related protein increase in tomato. Copyright © 2014 Elsevier GmbH. All rights reserved.

Distinct contributions of replication and transcription to mutation rate variation of human genomes.

PubMed

Cui, Peng; Ding, Feng; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun

2012-02-01

Here, we evaluate the contribution of two major biological processes--DNA replication and transcription--to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes. Copyright © 2012 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

PubMed Central

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes

PubMed Central

García-Robledo, Carlos; Erickson, David L.; Staines, Charles L.; Erwin, Terry L.; Kress, W. John

2013-01-01

Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt’s sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions. PMID:23308128

Occupational Therapy: Meeting the Needs of Families of People With Autism Spectrum Disorder.

PubMed

Kuhaneck, Heather Miller; Watling, Renee

2015-01-01

Occupational therapy has much to offer to families of people with autism spectrum disorder (ASD). However, people outside the profession may be unaware of occupational therapy's breadth and scope. It is our responsibility and our duty to express the full range of occupational therapy services through research, clinical practice, advocacy, and consumer education. This special issue of the American Journal of Occupational Therapy, with its focus on autism, embarks on this endeavor by highlighting research and theoretical articles that address the various aspects of occupational therapy practice that can help to fully meet the needs of people with ASD and their families. Copyright © 2015 by the American Occupational Therapy Association, Inc.

Forecasting Effects of MISO Actions: An ABM Methodology

DTIC Science & Technology

2013-12-01

process of opinion change for polio vaccination in Ut- tar Pradesh, India. His analysis combines word-of-mouth and mass media broadcasting for agent...this abstraction is an appropriate comparison between treatments , rather than actual forecasting of specific levels of rebellion or anti-government...effect of breadth upon griev- ance. There is insufficient evidence to show that this effect differs between treatments . Breadth and campaign type

Too Much of a Good Thing? How Breadth of Extracurricular Participation Relates to School-Related Affect and Academic Outcomes during Adolescence

ERIC Educational Resources Information Center

Knifsend, Casey A.; Graham, Sandra

2012-01-01

Although adolescents often participate in multiple extracurricular activities, little research has examined how the breadth of activities in which an adolescent is involved relates to school-related affect and academic performance. Relying on a large, multi-ethnic sample (N = 864; 55.9% female), the current study investigated linear and non-linear…

Reliable Predictors of Reduced Redundancy Test Performance: The Interaction between Lexical Bonds and Test Takers' Depth and Breadth of Vocabulary Knowledge

ERIC Educational Resources Information Center

Janebi Enayat, Mostafa; Babaii, Esmat

2018-01-01

The present study intended to investigate whether test takers' breadth and depth of vocabulary knowledge can contribute to their efficient use of lexical bonds while restoring damaged texts in reduced redundancy tests. Moreover, the moderating role of general language proficiency was investigated in this interaction. In so doing, Vocabulary Levels…

PLEXdb: Gene expression resources for plants and plant pathogens

USDA-ARS?s Scientific Manuscript database

PLEXdb (Plant Expression Database), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facili...

MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system

PubMed Central

Kapsimali, Marika; Kloosterman, Wigard P; de Bruijn, Ewart; Rosa, Frederic; Plasterk, Ronald HA; Wilson, Stephen W

2007-01-01

Background MicroRNA (miRNA) encoding genes are abundant in vertebrate genomes but very few have been studied in any detail. Bioinformatic tools allow prediction of miRNA targets and this information coupled with knowledge of miRNA expression profiles facilitates formulation of hypotheses of miRNA function. Although the central nervous system (CNS) is a prominent site of miRNA expression, virtually nothing is known about the spatial and temporal expression profiles of miRNAs in the brain. To provide an overview of the breadth of miRNA expression in the CNS, we performed a comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain. Results Our results show miRNAs have a wide variety of different expression profiles in neural cells, including: expression in neuronal precursors and stem cells (for example, miR-92b); expression associated with transition from proliferation to differentiation (for example, miR-124); constitutive expression in mature neurons (miR-124 again); expression in both proliferative cells and their differentiated progeny (for example, miR-9); regionally restricted expression (for example, miR-222 in telencephalon); and cell-type specific expression (for example, miR-218a in motor neurons). Conclusion The data we present facilitate prediction of likely modes of miRNA function in the CNS and many miRNA expression profiles are consistent with the mutual exclusion mode of function in which there is spatial or temporal exclusion of miRNAs and their targets. However, some miRNAs, such as those with cell-type specific expression, are more likely to be co-expressed with their targets. Our data provide an important resource for future functional studies of miRNAs in the CNS. PMID:17711588

Regulated expression of a calmodulin isoform alters growth and development in potato.

PubMed

Poovaiah, B W; Takezawa, D; An, G; Han, T J

1996-01-01

A transgene approach was taken to study the consequences of altered expression of a calmodulin isoform on plant growth and development. Eight genomic clones of potato calmodulin (PCM1 to 8) have been isolated and characterized (Takezawa et al., 1995). Among the potato calmodulin isoforms studied, PCM1 differs from the other isoforms because of its unique amino acid substitutions. Transgenic potato plants were produced carrying sense construct of PCM1 fused to the CaMV 35S promoter. Transgenic plants showing a moderate increase in PCM1 mRNA exhibited strong apical dominance, produced elongated tubers, and were taller than the controls. Interestingly, the plants expressing the highest level of PCM1 mRNA did not form underground tubers. Instead, these transgenic plants produced aerial tubers when allowed to grow for longer periods. The expression of different calmodulin isoforms (PCM1, 5, 6, and 8) was studied in transgenic plants. Among the four potato calmodulin isoforms, only the expression of PCM1 mRNA was altered in transgenic plants, while the expression of other isoforms was not significantly altered. Western analysis revealed increased PCM1 protein in transgenic plants, indicating that the expression of both mRNA and protein are altered in transgenic plants. These results suggest that increasing the expression of PCM1 alters growth and development in potato plants.

Controlled expression of pectic enzymes in Arabidopsis thaliana enhances biomass conversion without adverse effects on growth.

PubMed

Tomassetti, Susanna; Pontiggia, Daniela; Verrascina, Ilaria; Reca, Ida Barbara; Francocci, Fedra; Salvi, Gianni; Cervone, Felice; Ferrari, Simone

2015-04-01

Lignocellulosic biomass from agriculture wastes is a potential source of biofuel, but its use is currently limited by the recalcitrance of the plant cell wall to enzymatic digestion. Modification of the wall structural components can be a viable strategy to overcome this bottleneck. We have previously shown that the expression of a fungal polygalacturonase (pga2 from Aspergillus niger) in Arabidopsis and tobacco plants reduces the levels of de-esterified homogalacturonan in the cell wall and significantly increases saccharification efficiency. However, plants expressing pga2 show stunted growth and reduced biomass production, likely as a consequence of an extensive loss of pectin integrity during the whole plant life cycle. We report here that the expression in Arabidopsis of another pectic enzyme, the pectate lyase 1 (PL1) of Pectobacterium carotovorum, under the control of a chemically inducible promoter, results, after induction of the transgene, in a saccharification efficiency similar to that of plants expressing pga2. However, lines with high levels of transgene induction show reduced growth even in the absence of the inducer. To overcome the problem of plant fitness, we have generated Arabidopsis plants that express pga2 under the control of the promoter of SAG12, a gene expressed only during senescence. These plants expressed pga2 only at late stages of development, and their growth was comparable to that of WT plants. Notably, leaves and stems of transgenic plants were more easily digested by cellulase, compared to WT plants, only during senescence. Expression of cell wall-degrading enzymes at the end of the plant life cycle may be therefore a useful strategy to engineer crops unimpaired in biomass yield but improved for bioconversion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome.

PubMed

Nicholson, Matthew J; Theodorou, Michael K; Brookman, Jayne L

2005-01-01

The anaerobic gut fungi occupy a unique niche in the intestinal tract of large herbivorous animals and are thought to act as primary colonizers of plant material during digestion. They are the only known obligately anaerobic fungi but molecular analysis of this group has been hampered by difficulties in their culture and manipulation, and by their extremely high A+T nucleotide content. This study begins to answer some of the fundamental questions about the structure and organization of the anaerobic gut fungal genome. Directed plasmid libraries using genomic DNA digested with highly or moderately rich AT-specific restriction enzymes (VspI and EcoRI) were prepared from a polycentric Orpinomyces isolate. Clones were sequenced from these libraries and the breadth of genomic inserts, both genic and intergenic, was characterized. Genes encoding numerous functions not previously characterized for these fungi were identified, including cytoskeletal, secretory pathway and transporter genes. A peptidase gene with no introns and having sequence similarity to a gene encoding a bacterial peptidase was also identified, extending the range of metabolic enzymes resulting from apparent trans-kingdom transfer from bacteria to fungi, as previously characterized largely for genes encoding plant-degrading enzymes. This paper presents the first thorough analysis of the genic, intergenic and rDNA regions of a variety of genomic segments from an anaerobic gut fungus and provides observations on rules governing intron boundaries, the codon biases observed with different types of genes, and the sequence of only the second anaerobic gut fungal promoter reported. Large numbers of retrotransposon sequences of different types were found and the authors speculate on the possible consequences of any such transposon activity in the genome. The coding sequences identified included several orphan gene sequences, including one with regions strongly suggestive of structural proteins such as collagens and lampirin. This gene was present as a single copy in Orpinomyces, was expressed during vegetative growth and was also detected in genomes from another gut fungal genus, Neocallimastix.

Production of recombinant allergens in plants.

PubMed

Schmidt, Georg; Gadermaier, Gabriele; Pertl, Heidi; Siegert, Marc; Oksman-Caldentey, Kirsi-Marja; Ritala, Anneli; Himly, Martin; Obermeyer, Gerhard; Ferreira, Fatima

2008-10-01

A large percentage of allergenic proteins are of plant origin. Hence, plant-based expression systems are considered ideal for the recombinant production of certain allergens. First attempts to establish production of plant-derived allergens in plants focused on transient expression in Nicotiana benthamiana infected with recombinant viral vectors. Accordingly, allergens from birch and mugwort pollen, as well as from apple have been expressed in plants. Production of house dust mite allergens has been achieved by Agrobacterium-mediated transformation of tobacco plants. Beside the use of plants as production systems, other approaches have focused on the development of edible vaccines expressing allergens or epitopes thereof, which bypasses the need of allergen purification. The potential of this approach has been convincingly demonstrated for transgenic rice seeds expressing seven dominant human T cell epitopes derived from Japanese cedar pollen allergens. Parallel to efforts in developing recombinant-based diagnostic and therapeutic reagents, different gene-silencing approaches have been used to decrease the expression of allergenic proteins in allergen sources. In this way hypoallergenic ryegrass, soybean, rice, apple, and tomato were developed.

Antibody specificities associated with neutralization breadth in plasma from human immunodeficiency virus type 1 subtype C-infected blood donors.

PubMed

Gray, Elin S; Taylor, Natasha; Wycuff, Diane; Moore, Penny L; Tomaras, Georgia D; Wibmer, Constantinos Kurt; Puren, Adrian; DeCamp, Allan; Gilbert, Peter B; Wood, Blake; Montefiori, David C; Binley, James M; Shaw, George M; Haynes, Barton F; Mascola, John R; Morris, Lynn

2009-09-01

Defining the specificities of the anti-human immunodeficiency virus type 1 (HIV-1) envelope antibodies able to mediate broad heterologous neutralization will assist in identifying targets for an HIV-1 vaccine. We screened 70 plasmas from chronically HIV-1-infected individuals for neutralization breadth. Of these, 16 (23%) were found to neutralize 80% or more of the viruses tested. Anti-CD4 binding site (CD4bs) antibodies were found in almost all plasmas independent of their neutralization breadth, but they mainly mediated neutralization of the laboratory strain HxB2 with little effect on the primary virus, Du151. Adsorption with Du151 monomeric gp120 reduced neutralizing activity to some extent in most plasma samples when tested against the matched virus, although these antibodies did not always confer cross-neutralization. For one plasma, this activity was mapped to a site overlapping the CD4-induced (CD4i) epitope and CD4bs. Anti-membrane-proximal external region (MPER) (r = 0.69; P < 0.001) and anti-CD4i (r = 0.49; P < 0.001) antibody titers were found to be correlated with the neutralization breadth. These anti-MPER antibodies were not 4E10- or 2F5-like but spanned the 4E10 epitope. Furthermore, we found that anti-cardiolipin antibodies were correlated with the neutralization breadth (r = 0.67; P < 0.001) and anti-MPER antibodies (r = 0.6; P < 0.001). Our study suggests that more than one epitope on the envelope glycoprotein is involved in the cross-reactive neutralization elicited during natural HIV-1 infection, many of which are yet to be determined, and that polyreactive antibodies are possibly involved in this phenomenon.

Antibody Specificities Associated with Neutralization Breadth in Plasma from Human Immunodeficiency Virus Type 1 Subtype C-Infected Blood Donors▿ †

PubMed Central

Gray, Elin S.; Taylor, Natasha; Wycuff, Diane; Moore, Penny L.; Tomaras, Georgia D.; Wibmer, Constantinos Kurt; Puren, Adrian; DeCamp, Allan; Gilbert, Peter B.; Wood, Blake; Montefiori, David C.; Binley, James M.; Shaw, George M.; Haynes, Barton F.; Mascola, John R.; Morris, Lynn

2009-01-01

Defining the specificities of the anti-human immunodeficiency virus type 1 (HIV-1) envelope antibodies able to mediate broad heterologous neutralization will assist in identifying targets for an HIV-1 vaccine. We screened 70 plasmas from chronically HIV-1-infected individuals for neutralization breadth. Of these, 16 (23%) were found to neutralize 80% or more of the viruses tested. Anti-CD4 binding site (CD4bs) antibodies were found in almost all plasmas independent of their neutralization breadth, but they mainly mediated neutralization of the laboratory strain HxB2 with little effect on the primary virus, Du151. Adsorption with Du151 monomeric gp120 reduced neutralizing activity to some extent in most plasma samples when tested against the matched virus, although these antibodies did not always confer cross-neutralization. For one plasma, this activity was mapped to a site overlapping the CD4-induced (CD4i) epitope and CD4bs. Anti-membrane-proximal external region (MPER) (r = 0.69; P < 0.001) and anti-CD4i (r = 0.49; P < 0.001) antibody titers were found to be correlated with the neutralization breadth. These anti-MPER antibodies were not 4E10- or 2F5-like but spanned the 4E10 epitope. Furthermore, we found that anti-cardiolipin antibodies were correlated with the neutralization breadth (r = 0.67; P < 0.001) and anti-MPER antibodies (r = 0.6; P < 0.001). Our study suggests that more than one epitope on the envelope glycoprotein is involved in the cross-reactive neutralization elicited during natural HIV-1 infection, many of which are yet to be determined, and that polyreactive antibodies are possibly involved in this phenomenon. PMID:19553335

Technical note: comparability of Hrdlička's Catalog of Crania data based on measurement landmark definitions.

PubMed

Stojanowski, Christopher M; Euber, Julie K

2011-09-01

Archival sources of data are critical anthropological resources that inform inferences about human biology and evolutionary history. Craniometric data are one of the most widely available sources of information on human population history because craniometrics were critical in early 20th century debates about race and biological variation. As such, extensive databases of raw craniometric data were published at the same time that the field was working to standardize measurement protocol. Hrdlička published between 10 and 16 raw craniometric variables for over 8,000 individuals in a series of seven catalogs throughout his career. With a New World emphasis, Hrdlička's data complement those of Howells (1973, 1989) and the two databases have been combined in the past. In this note we verify the consistency of Hrdlička's measurement protocol throughout the Catalog series and compare these definitions to those used by Howells. We conclude that 12 measurements are comparable throughout the Catalogs, with five of these equivalent to Howells' measurements: maximum cranial breadth (XCB), basion-bregma height (BBH), maximum bizygomatic breadth (ZYB), nasal breadth (NLB), and breadth of the upper alveolar arch (MAB). Most of Hrdlička's measurements are not strictly comparable to those of Howells, thus limiting the utility of combined datasets for multivariate analysis. Four measurements are inconsistently defined by Hrdlička and we recommend not using these data: nasal height, orbit breadth, orbit height, and menton-nasion height. This note promotes Hrdlička's tireless efforts at data collection and re-emphasizes observer error as a legitimate concern in craniometry as the field shifts to morphometric digital data acquisition. 2011 Wiley-Liss, Inc.

Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader?

USGS Publications Warehouse

Redman, R.S.; Dunigan, D.D.; Rodriguez, R.J.

2001-01-01

Plant symbiotic fungi are generally thought to express a single lifestyle that might increase (mutualism), decrease (parasitism), or have no influence (commensalism) on host fitness. However, data are presented here demonstrating that plant pathogenic Colletotrichum species are able to asymptomatically colonize plants and express nonpathogenic lifestyles. Experiments were conducted in growth chambers and plant colonization was assessed by emergence of fungi from surface sterilized plant tissues. Expression of symbiotic lifestyles was assessed by monitoring the ability of fungi to confer disease resistance, drought tolerance and growth enhancement. Several pathogenic Colletotrichum species expressed either mutualistic or commensal lifestyles in plants not known to be hosts. Mutualists conferred disease resistance, drought tolerance, and/or growth enhancement to host plants. Lifestyle-altered mutants expressing nonpathogenic lifestyles had greater host ranges than the parental wildtype isolate. Successive colonization studies indicated that the ability of a symbiont to colonize a plant was dependent on previous colonization events and the lifestyles expressed by the initial colonizing fungus. The results indicate that the outcome of symbiosis is controlled by the plant's physiology. ?? New Phytologist.

Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research.

PubMed

Bennett, Bradley C; Balick, Michael J

2014-03-28

Medical research on plant-derived compounds requires a breadth of expertise from field to laboratory and clinical skills. Too often basic botanical skills are evidently lacking, especially with respect to plant taxonomy and botanical nomenclature. Binomial and familial names, synonyms and author citations are often misconstrued. The correct botanical name, linked to a vouchered specimen, is the sine qua non of phytomedical research. Without the unique identifier of a proper binomial, research cannot accurately be linked to the existing literature. Perhaps more significant, is the ambiguity of species determinations that ensues of from poor taxonomic practices. This uncertainty, not surprisingly, obstructs reproducibility of results-the cornerstone of science. Based on our combined six decades of experience with medicinal plants, we discuss the problems of inaccurate taxonomy and botanical nomenclature in biomedical research. This problems appear all too frequently in manuscripts and grant applications that we review and they extend to the published literature. We also review the literature on the importance of taxonomy in other disciplines that relate to medicinal plant research. In most cases, questions regarding orthography, synonymy, author citations, and current family designations of most plant binomials can be resolved using widely-available online databases and other electronic resources. Some complex problems require consultation with a professional plant taxonomist, which also is important for accurate identification of voucher specimens. Researchers should provide the currently accepted binomial and complete author citation, provide relevant synonyms, and employ the Angiosperm Phylogeny Group III family name. Taxonomy is a vital adjunct not only to plant-medicine research but to virtually every field of science. Medicinal plant researchers can increase the precision and utility of their investigations by following sound practices with respect to botanical nomenclature. Correct spellings, accepted binomials, author citations, synonyms, and current family designations can readily be found on reliable online databases. When questions arise, researcher should consult plant taxonomists. © 2013 Published by Elsevier Ireland Ltd.

Insect-Flower Interaction Network Structure Is Resilient to a Temporary Pulse of Floral Resources from Invasive Rhododendron ponticum

PubMed Central

Tiedeken, Erin Jo; Stout, Jane C.

2015-01-01

Invasive alien plants can compete with native plants for resources, and may ultimately decrease native plant diversity and/or abundance in invaded sites. This could have consequences for native mutualistic interactions, such as pollination. Although invasive plants often become highly connected in plant-pollinator interaction networks, in temperate climates they usually only flower for part of the season. Unless sufficient alternative plants flower outside this period, whole-season floral resources may be reduced by invasion. We hypothesized that the cessation of flowering of a dominant invasive plant would lead to dramatic, seasonal compositional changes in plant-pollinator communities, and subsequent changes in network structure. We investigated variation in floral resources, flower-visiting insect communities, and interaction networks during and after the flowering of invasive Rhododendron ponticum in four invaded Irish woodland sites. Floral resources decreased significantly after R. ponticum flowering, but the magnitude of the decrease varied among sites. Neither insect abundance nor richness varied between the two periods (during and after R. ponticum flowering), yet insect community composition was distinct, mostly due to a significant reduction in Bombus abundance after flowering. During flowering R. ponticum was frequently visited by Bombus; after flowering, these highly mobile pollinators presumably left to find alternative floral resources. Despite compositional changes, however, network structural properties remained stable after R. ponticum flowering ceased: generality increased, but quantitative connectance, interaction evenness, vulnerability, H’2 and network size did not change. This is likely because after R. ponticum flowering, two to three alternative plant species became prominent in networks and insects increased their diet breadth, as indicated by the increase in network-level generality. We conclude that network structure is robust to seasonal changes in floral abundance at sites invaded by alien, mass-flowering plant species, as long as alternative floral resources remain throughout the season to support the flower-visiting community. PMID:25764085

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

PubMed Central

Horn, Sebastian; Caruso, Tancredi; Verbruggen, Erik; Rillig, Matthias C; Hempel, Stefan

2014-01-01

Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota. PMID:24824667

Induced polyploidization in Brassica campestris L. (Brassicaceae).

PubMed

Kumar, G; Dwivedi, K

2014-01-01

Present experimental design has been made up to obtain crop with higher ploidy level via synthetic polyploidization. Since ploidy manipulation is generally associated with the obtainment of some increased enviable traits of the crop and also provides them greater adaptability to unfavorable or harsh circumstances as compared to its diploids counterparts. Thus, herein present research autotetraploids of Brassica campestris L. have been lucratively achieved by the application of colchicine. Two methods of treatment were utilized i.e. seed treatment and seedling treatment. No polyploidy could be obtained through seed treatment while seedling treatment responded well towards polyploidy. However, the status of autotetraploidy has been confirmed by cytomorphological investigations of treated plants as against its diploids counterparts. For the purpose, morphological parameters such as increased stomata size, pollen diameter, flower size, reproductive organs whereas reduction in plant height, leaf length, leaf breadth, stomata frequency, number of flowers/inflorescence etc. were appraised. Further, cytological observations were made that had clearly revealed the doubling of genome in the autotetraploids as compared to diploids. Meanwhile, pollen fertility and size of pollen grains were evaluated as well.

Overexpression of LOV KELCH protein 2 confers dehydration tolerance and is associated with enhanced expression of dehydration-inducible genes in Arabidopsis thaliana.

PubMed

Miyazaki, Yuji; Abe, Hiroshi; Takase, Tomoyuki; Kobayashi, Masatomo; Kiyosue, Tomohiro

2015-05-01

The overexpression of LKP2 confers dehydration tolerance in Arabidopsis thaliana ; this is likely due to enhanced expression of dehydration-inducible genes and reduced stomatal opening. LOV KELCH protein 2 (LKP2) modulates the circadian rhythm and flowering time in plants. In this study, we observed that LKP2 overexpression enhanced dehydration tolerance in Arabidopsis. Microarray analysis demonstrated that expression of water deprivation-responsive genes was higher in the absence of dehydration stress in transgenic Arabidopsis plants expressing green fluorescent protein-tagged LKP2 (GFP-LKP2) than in control transgenic plants expressing GFP. After dehydration followed by rehydration, GFP-LKP2 plants developed more leaves and roots and exhibited higher survival rates than control plants. In the absence of dehydration stress, four dehydration-inducible genes, namely DREB1A, DREB1B, DREB1C, and RD29A, were expressed in GFP-LKP2 plants, whereas they were not expressed or were expressed at low levels in control plants. Under dehydration stress, the expression of DREB2B and RD29A peaked faster in the GFP-LKP2 plants than in control plants. The stomatal aperture of GFP-LKP2 plants was smaller than that of control plants. These results suggest that the dehydration tolerance of GFP-LKP2 plants is caused by upregulation of DREB1A-C/CBF1-3 and their downstream targets; restricted stomatal opening in the absence of dehydration stress also appears to contribute to the phenotype. The rapid and high expression of DREB2B and its downstream target genes also likely accounts for some features of the GFP-LKP2 phenotype. Our results suggest that LKP2 can be used for biotechnological applications not only to adjust the flowering time control but also to enhance dehydration tolerance.

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum[OPEN

PubMed Central

Hardigan, Michael A.; Crisovan, Emily; Hamilton, John P.; Laimbeer, Parker; Leisner, Courtney P.; Manrique-Carpintero, Norma C.; Newton, Linsey; Pham, Gina M.; Vaillancourt, Brieanne; Zeng, Zixian; Jiang, Jiming

2016-01-01

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways. PMID:26772996

Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera.

PubMed

Skeels, Alexander; Cardillo, Marcel

2017-03-01

The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of "hotspot niche conservatism" whereby the accumulation of plant diversity in Mediterranean-type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The Relationship between Intensity and Breadth of After-School Program Participation and Academic Achievement: Evidence from a Short-Term Longitudinal Study

ERIC Educational Resources Information Center

Springer, Ken; Diffily, Deborah

2012-01-01

We explored the extent to which intensity and breadth of participation in an after-school program (ASP) predicted academic achievement, as measured by changes in grades and attendance. The sample comprised 719 2nd-grade through 8th-grade Boys and Girls Clubs of Greater Dallas members during the 2009-2010 academic year. With respect to intensity,…

Measurer’s Handbook: US Army and Marine Corps Anthropometric Surveys, 2010-2011

DTIC Science & Technology

2011-08-01

Circumference Ankle Circumference Heel Ankle Circumference Ball of Foot Circumference Bimalleolar Breadth Heel Breadth Lateral Malleolus Height...will be asked to put on a stocking from ankle to knee to compress the hair to prevent scan distortion. For all participants, sanitary protective...malleolus (outside ankle bone). Knee point, anterior - the most protruding point of the right kneecap of a seated participant. Medial malleolus - the

Faster-X Evolution of Gene Expression in Drosophila

PubMed Central

Meisel, Richard P.; Malone, John H.; Clark, Andrew G.

2012-01-01

DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA–seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the “faster-X” effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals. PMID:23071459

Narrow Networks On The Health Insurance Marketplaces: Prevalence, Pricing, And The Cost Of Network Breadth.

PubMed

Dafny, Leemore S; Hendel, Igal; Marone, Victoria; Ody, Christopher

2017-09-01

Anecdotal reports and systematic research highlight the prevalence of narrow-network plans on the Affordable Care Act's health insurance Marketplaces. At the same time, Marketplace premiums in the period 2014-16 were much lower than projected by the Congressional Budget Office in 2009. Using detailed data on the breadth of both hospital and physician networks, we studied the prevalence of narrow networks and quantified the association between network breadth and premiums. Controlling for many potentially confounding factors, we found that a plan with narrow physician and hospital networks was 16 percent cheaper than a plan with broad networks for both, and that narrowing the breadth of just one type of network was associated with a 6-9 percent decrease in premiums. Narrow-network plans also have a sizable impact on federal outlays, as they depress the premium of the second-lowest-price silver plan, to which subsidy amounts are linked. Holding all else constant, we estimate that federal subsidies would have been 10.8 percent higher in 2014 had Marketplaces required all plans to offer broad provider networks. Narrow networks are a promising source of potential savings for other segments of the commercial insurance market. Project HOPE—The People-to-People Health Foundation, Inc.

Thermal tolerance breadths among groundwater crustaceans living in a thermally constant environment.

PubMed

Mermillod-Blondin, F; Lefour, C; Lalouette, L; Renault, D; Malard, F; Simon, L; Douady, C J

2013-05-01

The climate variability hypothesis assumes that the thermal tolerance breadth of a species is primarily determined by temperature variations experienced in its environment. If so, aquatic invertebrates living in thermally buffered environments would be expected to exhibit narrow thermal tolerance breadths (stenothermy). We tested this prediction by studying the thermal physiology of three isopods (Asellidae, Proasellus) colonizing groundwater habitats characterized by an annual temperature amplitude of less than 1°C. The species responses to temperature variation were assessed in the laboratory using five physiological variables: survival, locomotor activity, aerobic respiration, immune defense and concentrations of total free amino acids and sugars. The three species exhibited contrasted thermal physiologies, although all variables were not equally informative. In accordance with the climate variability hypothesis, two species were extremely sensitive even to moderate changes in temperature (2°C) below and above their habitat temperature. In contrast, the third species exhibited a surprisingly high thermal tolerance breadth (11°C). Differences in response to temperature variation among Proasellus species indicated that their thermal physiology was not solely shaped by the current temperature seasonality in their natural habitats. More particularly, recent gene flow among populations living in thermally constant yet contrasted habitats might explain the occurrence of eurytherm species in thermally buffered environments.

The Perils of Picky Eating: Dietary Breadth Is Related to Extinction Risk in Insectivorous Bats

PubMed Central

Boyles, Justin G.; Storm, Jonathan J.

2007-01-01

Several recent papers evaluate the relationship between ecological characteristics and extinction risk in bats. These studies report that extinction risk is negatively related to geographic range size and positively related to habitat specialization. Here, we evaluate the hypothesis that extinction risk is also related to dietary specialization in insectivorous vespertilionid bats using both traditional and phylogenetically-controlled analysis of variance. We collected dietary data and The World Conservation Union (IUCN) rankings for 44 Australian, European, and North American bat species. Our results indicate that species of conservation concern (IUCN ranking near threatened or above) are more likely to have a specialized diet than are species of least concern. Additional analyses show that dietary breadth is not correlated to geographic range size or wing morphology, characteristics previously found to correlate with extinction risk. Therefore, there is likely a direct relationship between dietary specialization and extinction risk; however, the large variation in dietary breadth within species of least concern suggests that diet alone cannot explain extinction risk. Our results may have important implications for the development of predictive models of extinction risk and for the assignment of extinction risk to insectivorous bat species. Similar analyses should be conducted on additional bat families to assess the generality of this relationship between niche breadth and extinction risk. PMID:17653286

The breadth and titer of maternal HIV-1-specific heterologous neutralizing antibodies are not associated with a lower rate of mother-to-child transmission of HIV-1.

PubMed

Chaillon, Antoine; Wack, Thierry; Braibant, Martine; Mandelbrot, Laurent; Blanche, Stéphane; Warszawski, Josiane; Barin, Francis

2012-10-01

It has been hypothesized that neutralizing antibodies (NAbs) should have broad specificity to be effective in protection against diverse HIV-1 variants. The mother-to-child transmission model of HIV-1 provides the opportunity to examine whether the breadth of maternal NAbs is associated with protection of infants from infection. Samples were obtained at delivery from 57 transmitting mothers (T) matched with 57 nontransmitting mothers (NT) enrolled in the multicenter French perinatal cohort (ANRS EPF CO1) between 1990 and 1996. Sixty-eight (59.6%) and 46 (40.4%) women were infected by B and non-B viruses, respectively. Neutralization assays were carried out with TZM-bl cells, using a panel of 10 primary isolates of 6 clades (A, B, C, F, CRF01_AE, and CRF02_AG), selected for their moderate or low sensitivity to neutralization. Neutralization breadths were not statistically different between T and NT mothers. However, a few statistically significant differences were observed, with higher frequencies or titers of NAbs toward several individual strains for NT mothers when the clade B-infected or non-clade B-infected mothers were analyzed separately. Our study confirms that the breadth of maternal NAbs is not associated with protection of infants from infection.

Specific CD8+ T Cell Responses Correlate with Control of Simian Immunodeficiency Virus Replication in Mauritian Cynomolgus Macaques

PubMed Central

Budde, Melisa L.; Greene, Justin M.; Chin, Emily N.; Ericsen, Adam J.; Scarlotta, Matthew; Cain, Brian T.; Pham, Ngoc H.; Becker, Ericka A.; Harris, Max; Weinfurter, Jason T.; O'Connor, Shelby L.; Piatak, Michael; Lifson, Jeffrey D.; Gostick, Emma; Price, David A.; Friedrich, Thomas C.

2012-01-01

Specific major histocompatibility complex (MHC) class I alleles are associated with an increased frequency of spontaneous control of human and simian immunodeficiency viruses (HIV and SIV). The mechanism of control is thought to involve MHC class I-restricted CD8+ T cells, but it is not clear whether particular CD8+ T cell responses or a broad repertoire of epitope-specific CD8+ T cell populations (termed T cell breadth) are principally responsible for mediating immunologic control. To test the hypothesis that heterozygous macaques control SIV replication as a function of superior T cell breadth, we infected MHC-homozygous and MHC-heterozygous cynomolgus macaques with the pathogenic virus SIVmac239. As measured by a gamma interferon enzyme-linked immunosorbent spot assay (IFN-γ ELISPOT) using blood, T cell breadth did not differ significantly between homozygotes and heterozygotes. Surprisingly, macaques that controlled SIV replication, regardless of their MHC zygosity, shared durable T cell responses against similar regions of Nef. While the limited genetic variability in these animals prevents us from making generalizations about the importance of Nef-specific T cell responses in controlling HIV, these results suggest that the T cell-mediated control of virus replication that we observed is more likely the consequence of targeting specificity rather than T cell breadth. PMID:22573864

Methods and compositions for regulating gene expression in plant cells

NASA Technical Reports Server (NTRS)

Dai, Shunhong (Inventor); Beachy, Roger N. (Inventor); Luis, Maria Isabel Ordiz (Inventor)

2010-01-01

Novel chimeric plant promoter sequences are provided, together with plant gene expression cassettes comprising such sequences. In certain preferred embodiments, the chimeric plant promoters comprise the BoxII cis element and/or derivatives thereof. In addition, novel transcription factors are provided, together with nucleic acid sequences encoding such transcription factors and plant gene expression cassettes comprising such nucleic acid sequences. In certain preferred embodiments, the novel transcription factors comprise the acidic domain, or fragments thereof, of the RF2a transcription factor. Methods for using the chimeric plant promoter sequences and novel transcription factors in regulating the expression of at least one gene of interest are provided, together with transgenic plants comprising such chimeric plant promoter sequences and novel transcription factors.

Methods and compositions for altering lignin composition in plants

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

Srivastava, Avinash C.; Tang, Yuhong; Blancaflor, Elison

The invention provides methods for decreasing lignin content in plants by reducing expression of a folylpolyglutamate synthetase 1 (FPGS1) coding sequence in the plant. Also provided are methods for reducing lignin content in a plant by down-regulation of FPGS1 expression in the plant. Nucleic acid molecules for modulation of FPGS1 expression and transgenic plants the same are also provided. Plants described herein may be used, for example, as improved biofuel feedstock and as highly digestible forage crops. Methods for processing plant tissue and for producing biofuels by utilizing such plants are also provided.

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory.

PubMed

Tanigaki, Yusuke; Higashi, Takanobu; Takayama, Kotaro; Nagano, Atsushi J; Honjo, Mie N; Fukuda, Hirokazu

2015-01-01

In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions.

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory

PubMed Central

Tanigaki, Yusuke; Higashi, Takanobu; Takayama, Kotaro; Nagano, Atsushi J.; Honjo, Mie N.; Fukuda, Hirokazu

2015-01-01

In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions. PMID:26624004

Effect of external and internal factors on the expression of reporter genes driven by the N resistance gene promoter.

PubMed

Kathiria, Palak; Sidler, Corinne; Woycicki, Rafal; Yao, Youli; Kovalchuk, Igor

2013-07-01

The role of resistance (R) genes in plant pathogen interaction has been studied extensively due to its economical impact on agriculture. Interaction between tobacco mosaic virus (TMV) and the N protein from tobacco is one of the most widely used models to understand various aspects of pathogen resistance. The transcription activity governed by N gene promoter is one of the least understood elements of the model. In this study, the N gene promoter was cloned and fused with two different reporter genes, one encoding β-glucuronidase (N::GUS) and another, luciferase (N::LUC). Tobacco plants transformed with the N::GUS or N::LUC reporter constructs were screened for homozygosity and stable expression. Histochemical analysis of N::GUS tobacco plants revealed that the expression is organ specific and developmentally regulated. Whereas two week old plants expressed GUS in midveins only, 6-wk-old plants also expressed GUS in leaf lamella. Roots did not show GUS expression at any time during development. Experiments to address effects of external stress were performed using N::LUC tobacco plants. These experiments showed that N gene promoter expression was suppressed when plants were exposed to high but not low temperatures. Expression was also upregulated in response to TMV, but no changes were observed in plants treated with SA.

Transgenic plants expressing the AaIT/GNA fusion protein show increased resistance and toxicity to both chewing and sucking pests.

PubMed

Liu, Shu-Min; Li, Jie; Zhu, Jin-Qi; Wang, Xiao-Wei; Wang, Cheng-Shu; Liu, Shu-Sheng; Chen, Xue-Xin; Li, Sheng

2016-04-01

The adoption of pest-resistant transgenic plants to reduce yield losses and decrease pesticide use has been successful. To achieve the goal of controlling both chewing and sucking pests in a given transgenic plant, we generated transgenic tobacco, Arabidopsis, and rice plants expressing the fusion protein, AaIT/GNA, in which an insecticidal scorpion venom neurotoxin (Androctonus australis toxin, AaIT) is fused to snowdrop lectin (Galanthus nivalis agglutinin, GNA). Compared with transgenic tobacco and Arabidopsis plants expressing AaIT or GNA, transgenic plants expressing AaIT/GNA exhibited increased resistance and toxicity to one chewing pest, the cotton bollworm, Helicoverpa armigera. Transgenic tobacco and rice plants expressing AaIT/GNA showed increased resistance and toxicity to two sucking pests, the whitefly, Bemisia tabaci, and the rice brown planthopper, Nilaparvata lugens, respectively. Moreover, in the field, transgenic rice plants expressing AaIT/GNA exhibited a significant improvement in grain yield when infested with N. lugens. This study shows that expressing the AaIT/GNA fusion protein in transgenic plants can be a useful approach for controlling pests, particularly sucking pests which are not susceptible to the toxin in Bt crops. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Co-expression of NCED and ALO improves vitamin C level and tolerance to drought and chilling in transgenic tobacco and stylo plants.

PubMed

Bao, Gegen; Zhuo, Chunliu; Qian, Chunmei; Xiao, Ting; Guo, Zhenfei; Lu, Shaoyun

2016-01-01

Abscisic acid (ABA) regulates plant adaptive responses to various environmental stresses, while L-ascorbic acid (AsA) that is also named vitamin C is an important antioxidant and involves in plant stress tolerance and the immune system in domestic animals. Transgenic tobacco (Nicotiana tabacum L.) and stylo [Stylosanthes guianensis (Aublet) Swartz], a forage legume, plants co-expressing stylo 9-cis-epoxycarotenoid dioxygenase (SgNCED1) and yeast D-arabinono-1,4-lactone oxidase (ALO) genes were generated in this study, and tolerance to drought and chilling was analysed in comparison with transgenic tobacco overexpressing SgNCED1 or ALO and the wild-type plants. Compared to the SgNCED1 or ALO transgenic plants, in which only ABA or AsA levels were increased, both ABA and AsA levels were increased in transgenic tobacco and stylo plants co-expressing SgNCED1 and ALO genes. Compared to the wild type, an enhanced drought tolerance was observed in SgNCED1 transgenic tobacco plants with induced expression of drought-responsive genes, but not in ALO plants, while an enhanced chilling tolerance was observed in ALO transgenic tobaccos with induced expression of cold-responsive genes, but not in SgNCED1 plants. Co-expression of SgNCED1 and ALO genes resulted in elevated tolerance to both drought and chilling in transgenic tobacco and stylo plants with induced expression of both drought and cold-responsive genes. Our result suggests that co-expression of SgNCED1 and ALO genes is an effective way for use in forage plant improvement for increased tolerance to drought and chilling and nutrition quality. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Hyperactive mutant of a wheat plasma membrane Na+/H+ antiporter improves the growth and salt tolerance of transgenic tobacco.

PubMed

Zhou, Yang; Lai, Zesen; Yin, Xiaochang; Yu, Shan; Xu, Yuanyuan; Wang, Xiaoxiao; Cong, Xinli; Luo, Yuehua; Xu, Haixia; Jiang, Xingyu

2016-12-01

Wheat SOS1 (TaSOS1) activity could be relieved upon deletion of the C-terminal 168 residues (the auto-inhibitory domain). This truncated form of wheat SOS1 (TaSOS1-974) was shown to increase compensation (compared to wild-type TaSOS1) for the salt sensitivity of a yeast mutant strain, AXT3K, via increased Na + transportation out of cells during salinity stress. Expression of the plasma membrane proteins TaSOS1-974 or TaSOS1 improved the growth of transgenic tobacco plants compared with wild-type plants under normal conditions. However, plants expressing TaSOS1-974 grew better than TaSOS1-transformed plants. Upon salinity stress, Na + efflux and K + influx rates in the roots of transgenic plants expressing TaSOS1-974 or TaSOS1 were greater than those of wild-type plants. Furthermore, compared to TaSOS1-transgenic plants, TaSOS1-974-expressing roots showed faster Na + efflux and K + influx, resulting in less Na + and more K + accumulation in TaSOS1-974-transgenic plants compared to TaSOS1-transgenic and wild-type plants. TaSOS1-974-expressing plants had the lowest MDA content and electrolyte leakage among all tested plants, indicating that TaSOS1-974 might protect the plasma membrane against oxidative damage generated by salt stress. Overall, TaSOS1-974 conferred higher salt tolerance in transgenic plants compared to TaSOS1. Consistent with this result, transgenic plants expressing TaSOS1-974 showed a better growth performance than TaSOS1-expressing and wild-type plants under saline conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Production of recombinant allergens in plants

PubMed Central

2010-01-01

A large percentage of allergenic proteins are of plant origin. Hence, plant-based expression systems are considered ideal for the recombinant production of certain allergens. First attempts to establish production of plant-derived allergens in plants focused on transient expression in Nicotiana benthamiana infected with recombinant viral vectors. Accordingly, allergens from birch and mugwort pollen, as well as from apple have been expressed in plants. Production of house dust mite allergens has been achieved by Agrobacterium-mediated transformation of tobacco plants. Beside the use of plants as production systems, other approaches have focused on the development of edible vaccines expressing allergens or epitopes thereof, which bypasses the need of allergen purification. The potential of this approach has been convincingly demonstrated for transgenic rice seeds expressing seven dominant human T cell epitopes derived from Japanese cedar pollen allergens. Parallel to efforts in developing recombinant-based diagnostic and therapeutic reagents, different gene-silencing approaches have been used to decrease the expression of allergenic proteins in allergen sources. In this way hypoallergenic ryegrass, soybean, rice, apple, and tomato were developed. PMID:21258627

An exploration of the potential mechanisms and translational potential of five medicinal plants for applications in Alzheimer’s disease

PubMed Central

Shakir, Taner; Coulibaly, Ahmed Y; Kehoe, Patrick G

2013-01-01

Alzheimer’s disease (AD) is the most common type of dementia, and represents a vast worldwide socio-economic burden, and in the absence of a current cure, effective therapeutic strategies are still needed. Cholinergic and cerebral blood flow deficits, excessive levels of oxidative stress, neuroinflammation and glutamate excitatory mechanisms are all believed to contribute to the development and progression of the disease. Scoparia dulcis, Catharanthus roseus, Sesamum indicum, Erythrina senegalensis and Vigna unguiculata represent five plants that have been used as traditional medicines for the treatment of AD in certain cultures. Review of the scientific literature was conducted to explore the properties of these plants that might be beneficial and explain what would be perceived by many to be largely anecdotal evidence of their benefit. All plants were found to possess varying levels of anti-oxidant capability. Scoparia dulcis was also found to potentiate nerve growth factor-like effects upon cell lines. Catharanthus roseus appears to inhibit acetylcholinesterase with relatively high potency, while Sesamum indicum demonstrated the strongest antioxidant ability. Comparisons with currently used plant derived therapeutics illustrate how these plants may be likely to have some therapeutic benefits in AD. The evidence presented also highlights how appropriate dietary supplementation with some of these plants in various cultural settings might have effects analogous or complementary to the so-called protective Mediterranean diet. However, prior to embarking on making any formal recommendations to this end, further rigorous evaluation is needed to better elucidate the breadth and potential toxicological aspects of medicinal properties harboured by these plants. This would be vital to ensuring a more informed and safe delivery of preparations of these plants if they were to be considered as a form of dietary supplementation and where appropriate, how these might interact with more formally established therapies in relation to AD. PMID:23844333

An exploration of the potential mechanisms and translational potential of five medicinal plants for applications in Alzheimer's disease.

PubMed

Shakir, Taner; Coulibaly, Ahmed Y; Kehoe, Patrick G

2013-01-01

Alzheimer's disease (AD) is the most common type of dementia, and represents a vast worldwide socio-economic burden, and in the absence of a current cure, effective therapeutic strategies are still needed. Cholinergic and cerebral blood flow deficits, excessive levels of oxidative stress, neuroinflammation and glutamate excitatory mechanisms are all believed to contribute to the development and progression of the disease. Scoparia dulcis, Catharanthus roseus, Sesamum indicum, Erythrina senegalensis and Vigna unguiculata represent five plants that have been used as traditional medicines for the treatment of AD in certain cultures. Review of the scientific literature was conducted to explore the properties of these plants that might be beneficial and explain what would be perceived by many to be largely anecdotal evidence of their benefit. All plants were found to possess varying levels of anti-oxidant capability. Scoparia dulcis was also found to potentiate nerve growth factor-like effects upon cell lines. Catharanthus roseus appears to inhibit acetylcholinesterase with relatively high potency, while Sesamum indicum demonstrated the strongest antioxidant ability. Comparisons with currently used plant derived therapeutics illustrate how these plants may be likely to have some therapeutic benefits in AD. The evidence presented also highlights how appropriate dietary supplementation with some of these plants in various cultural settings might have effects analogous or complementary to the so-called protective Mediterranean diet. However, prior to embarking on making any formal recommendations to this end, further rigorous evaluation is needed to better elucidate the breadth and potential toxicological aspects of medicinal properties harboured by these plants. This would be vital to ensuring a more informed and safe delivery of preparations of these plants if they were to be considered as a form of dietary supplementation and where appropriate, how these might interact with more formally established therapies in relation to AD.

Approaches to achieve high-level heterologous protein production in plants.

PubMed

Streatfield, Stephen J

2007-01-01

Plants offer an alternative to microbial fermentation and animal cell cultures for the production of recombinant proteins. For protein pharmaceuticals, plant systems are inherently safer than native and even recombinant animal sources. In addition, post-translational modifications, such as glycosylation, which cannot be achieved with bacterial fermentation, can be accomplished using plants. The main advantage foreseen for plant systems is reduced production costs. Plants should have a particular advantage for proteins produced in bulk, such as industrial enzymes, for which product pricing is low. In addition, edible plant tissues are well suited to the expression of vaccine antigens and pharmaceuticals for oral delivery. Three approaches have been followed to express recombinant proteins in plants: expression from the plant nuclear genome; expression from the plastid genome; and expression from plant tissues carrying recombinant plant viral sequences. The most important factor in moving plant-produced heterologous proteins from developmental research to commercial products is to ensure competitive production costs, and the best way to achieve this is to boost expression. Thus, considerable research effort has been made to increase the amount of recombinant protein produced in plants. This research includes molecular technologies to increase replication, to boost transcription, to direct transcription in tissues suited for protein accumulation, to stabilize transcripts, to optimize translation, to target proteins to subcellular locations optimal for their accumulation, and to engineer proteins to stabilize them. Other methods include plant breeding to increase transgene copy number and to utilize germplasm suited to protein accumulation. Large-scale commercialization of plant-produced recombinant proteins will require a combination of these technologies.

Distributed-Memory Breadth-First Search on Massive Graphs

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

Buluc, Aydin; Beamer, Scott; Madduri, Kamesh

This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.

Molecular breeding of transgenic rice plants expressing a bacterial chlorocatechol dioxygenase gene.

PubMed

Shimizu, Masami; Kimura, Tetsuya; Koyama, Takayoshi; Suzuki, Katsuhisa; Ogawa, Naoto; Miyashita, Kiyotaka; Sakka, Kazuo; Ohmiya, Kunio

2002-08-01

The cbnA gene encoding the chlorocatechol dioxygenase gene from Ralstonia eutropha NH9 was introduced into rice plants. The cbnA gene was expressed in transgenic rice plants under the control of a modified cauliflower mosaic virus 35S promoter. Western blot analysis using anti-CbnA protein indicated that the cbnA gene was expressed in leaf tissue, roots, culms, and seeds. Transgenic rice calluses expressing the cbnA gene converted 3-chlorocatechol to 2-chloromucote efficiently. Growth and morphology of the transgenic rice plants expressing the cbnA gene were not distinguished from those of control rice plants harboring only a Ti binary vector. It is thus possible to breed transgenic plants that degrade chloroaromatic compounds in soil and surface water.

On risk and plant-based biopharmaceuticals.

PubMed

Peterson, Robert K D; Arntzen, Charles J

2004-02-01

Research into plant-based expression of pharmaceutical proteins is proceeding at a blistering pace. Indeed, plants expressing pharmaceutical proteins are currently being grown in field environments throughout the USA. But how are these plants and proteins being assessed for environmental risk and how are they being regulated? Here, we examine the applicability of the risk assessment paradigm for assessing human and ecological risks from field-grown transgenic plants that express pharmaceutical proteins.

First complete sauropod dinosaur skull from the Cretaceous of the Americas and the evolution of sauropod dentition.

PubMed

Chure, Daniel; Britt, Brooks B; Whitlock, John A; Wilson, Jeffrey A

2010-04-01

Sauropod dinosaur bones are common in Mesozoic terrestrial sediments, but sauropod skulls are exceedingly rare--cranial materials are known for less than one third of sauropod genera and even fewer are known from complete skulls. Here we describe the first complete sauropod skull from the Cretaceous of the Americas, Abydosaurus mcintoshi, n. gen., n. sp., known from 104.46 +/- 0.95 Ma (megannum) sediments from Dinosaur National Monument, USA. Abydosaurus shares close ancestry with Brachiosaurus, which appeared in the fossil record ca. 45 million years earlier and had substantially broader teeth. A survey of tooth shape in sauropodomorphs demonstrates that sauropods evolved broad crowns during the Early Jurassic but did not evolve narrow crowns until the Late Jurassic, when they occupied their greatest range of crown breadths. During the Cretaceous, brachiosaurids and other lineages independently underwent a marked diminution in tooth breadth, and before the latest Cretaceous broad-crowned sauropods were extinct on all continental landmasses. Differential survival and diversification of narrow-crowned sauropods in the Late Cretaceous appears to be a directed trend that was not correlated with changes in plant diversity or abundance, but may signal a shift towards elevated tooth replacement rates and high-wear dentition. Sauropods lacked many of the complex herbivorous adaptations present within contemporaneous ornithischian herbivores, such as beaks, cheeks, kinesis, and heterodonty. The spartan design of sauropod skulls may be related to their remarkably small size--sauropod skulls account for only 1/200th of total body volume compared to 1/30th body volume in ornithopod dinosaurs.

Transplastomic expression of bacterial L-aspartate-alpha-decarboxylase enhances photosynthesis and biomass production in response to high temperature stress.

PubMed

Fouad, W M; Altpeter, F

2009-10-01

Metabolic engineering for beta-alanine over-production in plants is expected to enhance environmental stress tolerance. The Escherichia coli L-aspartate-alpha-decarboxylase (AspDC) encoded by the panD gene, catalyzes the decarboxylation of L-aspartate to generate beta-alanine and carbon dioxide. The constitutive E. coli panD expression cassette was co-introduced with the constitutive, selectable aadA expression cassette into the chloroplast genome of tobacco via biolistic gene transfer and homologous recombination. Site specific integration of the E. coli panD expression cassette into the chloroplast genome and generation of homotransplastomic plants were confirmed by PCR and Southern blot analysis, respectively, following plant regeneration and germination of seedlings on selective media. PanD expression was verified by assays based on transcript detection and in vitro enzyme activity. The AspDC activities in transplastomic plants expressing panD were drastically increased by high-temperature stress. beta-Alanine accumulated in transplastomic plants at levels four times higher than in wildtype plants. Analysis of chlorophyll fluorescence on plants subjected to severe heat stress at 45 degrees C under light verified that photosystem II (PSII) in transgenic plants had higher thermotolerance than in wildtype plants. The CO(2) assimilation of transplastomic plants expressing panD was more tolerant to high temperature stress than that of wildtype plants, resulting in the production of 30-40% more above ground biomass than wildtype control. The results presented indicate that chloroplast engineering of the beta-alanine pathway by over-expression of the E. coli panD enhances thermotolerance of photosynthesis and biomass production following high temperature stress.

Unravelling the mechanisms for plant survival on gypsum soils: an analysis of the chemical composition of gypsum plants from Turkey.

PubMed

Bolukbasi, A; Kurt, L; Palacio, S

2016-03-01

Depending on their specificity to gypsum, plants can be classified as gypsophiles (gypsum exclusive) and gypsovags (non-exclusive). The former may further be segregated into wide and narrow gypsophiles, depending on the breadth of their distribution area. Narrow gypsum endemics have a putative similar chemical composition to plants non-exclusive to gypsum (i.e. gypsovags), which may indicate their similar ecological strategy as stress-tolerant plant refugees on gypsum. However, this hypothesis awaits testing in different regions of the world. We compared the chemical composition of four narrow gypsum endemics, one widely distributed gypsophile and six gypsovags from Turkey. Further, we explored the plasticity in chemical composition of Turkish gypsovags growing on high- and low-gypsum content soils. Differences were explored with multivariate analyses (RDA) and mixed models (REML). Narrow gypsum endemics segregated from gypsovags in their chemical composition according to RDAs (mainly due to higher K and ash content in the former). Nevertheless, differences were small and disappeared when different nutrients were analysed individually. All the gypsovags studied accumulated more S and ash when growing on high-gypsum than on low-gypsum soils. Similar to narrow gypsum endemics from other regions of the world, most local gypsum endemics from Turkey show a similar chemical composition to gypsovags. This may indicate a shared ecological strategy as stress-tolerant plants not specifically adapted to gypsum. Nevertheless, the narrow gypsum endemic Gypsophila parva showed a chemical composition typical of gypsum specialists, indicating that various strategies are feasible within narrowly distributed gypsophiles. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

State regulation of nuclear power and national energy policy

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

Moeller, J.W.

1992-12-31

In April 1983 and January 1984, the United States Supreme Court rendered two decisions that redefined the metes and bounds of federal preemption of commercial nuclear power plant regulation. In Pacific Gas & Electric Co. v. State Energy Resources Conservation and Development Commission (PG&E), the court decided that the Atomic Energy Act of 1954, as amended (the Act), did not preempt a California state law that established a moratorium on commercial nuclear power plant construction. In Silkwood v. Kerr-McGee Corporation, the Court also decided that the Act did not preempt a claim for damages under state tort law for radiologicalmore » injuries suffered in a nuclear fuel facility regulated by the United States Nuclear Regulatory Commission (NRC). The two decisions redefined the extent of federal preemption, under the Act and other federal law, of nuclear plant regulation as well as the extend of state regulation of nuclear plants. In the eight years since PG&E and Silkwood, numerous other developments have eroded further the breadth of federal preemption of commercial nuclear power plant regulation. This Article explores the developments, since PG&E and Silkwood, that have expanded further the scope of state and local regulation of commercial nuclear power plants. Specifically, the Article first identifies the extent of state and local participation in nuclear power regulation provided by the Act and other federal loan relevant to commercial nuclear power. Second, it discusses in detail the PG&E and Silkwood decisions. The Article also considers the impact of seven specific developments on the legislative implementation of a national energy policy that contemplates a role for nuclear power.« less

Ecological release and venom evolution of a predatory marine snail at Easter Island.

PubMed

Duda, Thomas F; Lee, Taehwan

2009-05-20

Ecological release is coupled with adaptive radiation and ecological diversification yet little is known about the molecular basis of phenotypic changes associated with this phenomenon. The venomous, predatory marine gastropod Conus miliaris has undergone ecological release and exhibits increased dietary breadth at Easter Island. We examined the extent of genetic differentiation of two genes expressed in the venom of C. miliaris among samples from Easter Island, American Samoa and Guam. The population from Easter Island exhibits unique frequencies of alleles that encode distinct peptides at both loci. Levels of divergence at these loci exceed observed levels of divergence observed at a mitochondrial gene region at Easter Island. Patterns of genetic variation at two genes expressed in the venom of this C. miliaris suggest that selection has operated at these genes and contributed to the divergence of venom composition at Easter Island. These results show that ecological release is associated with strong selection pressures that promote the evolution of new phenotypes.

Phylogenetic relatedness and host plant growth form influence gene expression of the polyphagous comma butterfly (Polygonia c-album)

PubMed Central

Heidel-Fischer, Hanna M; Freitak, Dalial; Janz, Niklas; Söderlind, Lina; Vogel, Heiko; Nylin, Sören

2009-01-01

Background The mechanisms that shape the host plant range of herbivorous insect are to date not well understood but knowledge of these mechanisms and the selective forces that influence them can expand our understanding of the larger ecological interaction. Nevertheless, it is well established that chemical defenses of plants influence the host range of herbivorous insects. While host plant chemistry is influenced by phylogeny, also the growth forms of plants appear to influence the plant defense strategies as first postulated by Feeny (the "plant apparency" hypothesis). In the present study we aim to investigate the molecular basis of the diverse host plant range of the comma butterfly (Polygonia c-album) by testing differential gene expression in the caterpillars on three host plants that are either closely related or share the same growth form. Results In total 120 genes were identified to be differentially expressed in P. c-album after feeding on different host plants, 55 of them in the midgut and 65 in the restbody of the caterpillars. Expression patterns could be confirmed with an independent method for 14 of 27 tested genes. Pairwise similarities in upregulation in the midgut of the caterpillars were higher between plants that shared either growth form or were phylogenetically related. No known detoxifying enzymes were found to be differently regulated in the midgut after feeding on different host plants. Conclusion Our data suggest a complex picture of gene expression in response to host plant feeding. While each plant requires a unique gene regulation in the caterpillar, both phylogenetic relatedness and host plant growth form appear to influence the expression profile of the polyphagous comma butterfly, in agreement with phylogenetic studies of host plant utilization in butterflies. PMID:19878603

Phylogenetic relatedness and host plant growth form influence gene expression of the polyphagous comma butterfly (Polygonia c-album).

PubMed

Heidel-Fischer, Hanna M; Freitak, Dalial; Janz, Niklas; Söderlind, Lina; Vogel, Heiko; Nylin, Sören

2009-10-31

The mechanisms that shape the host plant range of herbivorous insect are to date not well understood but knowledge of these mechanisms and the selective forces that influence them can expand our understanding of the larger ecological interaction. Nevertheless, it is well established that chemical defenses of plants influence the host range of herbivorous insects. While host plant chemistry is influenced by phylogeny, also the growth forms of plants appear to influence the plant defense strategies as first postulated by Feeny (the "plant apparency" hypothesis). In the present study we aim to investigate the molecular basis of the diverse host plant range of the comma butterfly (Polygonia c-album) by testing differential gene expression in the caterpillars on three host plants that are either closely related or share the same growth form. In total 120 genes were identified to be differentially expressed in P. c-album after feeding on different host plants, 55 of them in the midgut and 65 in the restbody of the caterpillars. Expression patterns could be confirmed with an independent method for 14 of 27 tested genes. Pairwise similarities in upregulation in the midgut of the caterpillars were higher between plants that shared either growth form or were phylogenetically related. No known detoxifying enzymes were found to be differently regulated in the midgut after feeding on different host plants. Our data suggest a complex picture of gene expression in response to host plant feeding. While each plant requires a unique gene regulation in the caterpillar, both phylogenetic relatedness and host plant growth form appear to influence the expression profile of the polyphagous comma butterfly, in agreement with phylogenetic studies of host plant utilization in butterflies.

OH 83: A new early modern human fossil cranium from the Ndutu beds of Olduvai Gorge, Tanzania.

PubMed

Reiner, Whitney B; Masao, Fidelis; Sholts, Sabrina B; Songita, Agustino Venance; Stanistreet, Ian; Stollhofen, Harald; Taylor, R E; Hlusko, Leslea J

2017-11-01

Herein we introduce a newly recovered partial calvaria, OH 83, from the upper Ndutu Beds of Olduvai Gorge, Tanzania. We present the geological context of its discovery and a comparative analysis of its morphology, placing OH 83 within the context of our current understanding of the origins and evolution of Homo sapiens. We comparatively assessed the morphology of OH 83 using quantitative and qualitative data from penecontemporaneous fossils and the W.W. Howells modern human craniometric dataset. OH 83 is geologically dated to ca. 60-32 ka. Its morphology is indicative of an early modern human, falling at the low end of the range of variation for post-orbital cranial breadth, the high end of the range for bifrontal breadth, and near average in frontal length. There have been numerous attempts to use cranial anatomy to define the species Homo sapiens and identify it in the fossil record. These efforts have not met wide agreement by the scientific community due, in part, to the mosaic patterns of cranial variation represented by the fossils. The variable, mosaic pattern of trait expression in the crania of Middle and Late Pleistocene fossils implies that morphological modernity did not occur at once. However, OH 83 demonstrates that by ca. 60-32 ka modern humans in Africa included individuals that are at the fairly small and gracile range of modern human cranial variation. © 2017 Wiley Periodicals, Inc.

HIV-specific Fc effector function early in infection predicts the development of broadly neutralizing antibodies.

PubMed

Richardson, Simone I; Chung, Amy W; Natarajan, Harini; Mabvakure, Batsirai; Mkhize, Nonhlanhla N; Garrett, Nigel; Abdool Karim, Salim; Moore, Penny L; Ackerman, Margaret E; Alter, Galit; Morris, Lynn

2018-04-01

While the induction of broadly neutralizing antibodies (bNAbs) is a major goal of HIV vaccination strategies, there is mounting evidence to suggest that antibodies with Fc effector function also contribute to protection against HIV infection. Here we investigated Fc effector functionality of HIV-specific IgG plasma antibodies over 3 years of infection in 23 individuals, 13 of whom developed bNAbs. Antibody-dependent cellular phagocytosis (ADCP), complement deposition (ADCD), cellular cytotoxicity (ADCC) and cellular trogocytosis (ADCT) were detected in almost all individuals with levels of activity increasing over time. At 6 months post-infection, individuals with bNAbs had significantly higher levels of ADCD and ADCT that correlated with antibody binding to C1q and FcγRIIa respectively. In addition, antibodies from individuals with bNAbs showed more IgG subclass diversity to multiple HIV antigens which also correlated with Fc polyfunctionality. Germinal center activity represented by CXCL13 levels and expression of activation-induced cytidine deaminase (AID) was found to be associated with neutralization breadth, Fc polyfunctionality and IgG subclass diversity. Overall, multivariate analysis by random forest classification was able to group bNAb individuals with 85% sensitivity and 80% specificity based on the properties of their antibody Fc early in HIV infection. Thus, the Fc effector function profile predicted the development of neutralization breadth in this cohort, suggesting that intrinsic immune factors within the germinal center provide a mechanistic link between the Fc and Fab of HIV-specific antibodies.

HIV-specific Fc effector function early in infection predicts the development of broadly neutralizing antibodies

PubMed Central

Richardson, Simone I.; Mabvakure, Batsirai; Mkhize, Nonhlanhla N.; Moore, Penny L.; Alter, Galit

2018-01-01

While the induction of broadly neutralizing antibodies (bNAbs) is a major goal of HIV vaccination strategies, there is mounting evidence to suggest that antibodies with Fc effector function also contribute to protection against HIV infection. Here we investigated Fc effector functionality of HIV-specific IgG plasma antibodies over 3 years of infection in 23 individuals, 13 of whom developed bNAbs. Antibody-dependent cellular phagocytosis (ADCP), complement deposition (ADCD), cellular cytotoxicity (ADCC) and cellular trogocytosis (ADCT) were detected in almost all individuals with levels of activity increasing over time. At 6 months post-infection, individuals with bNAbs had significantly higher levels of ADCD and ADCT that correlated with antibody binding to C1q and FcγRIIa respectively. In addition, antibodies from individuals with bNAbs showed more IgG subclass diversity to multiple HIV antigens which also correlated with Fc polyfunctionality. Germinal center activity represented by CXCL13 levels and expression of activation-induced cytidine deaminase (AID) was found to be associated with neutralization breadth, Fc polyfunctionality and IgG subclass diversity. Overall, multivariate analysis by random forest classification was able to group bNAb individuals with 85% sensitivity and 80% specificity based on the properties of their antibody Fc early in HIV infection. Thus, the Fc effector function profile predicted the development of neutralization breadth in this cohort, suggesting that intrinsic immune factors within the germinal center provide a mechanistic link between the Fc and Fab of HIV-specific antibodies. PMID:29630668

Improvement of pest resistance in transgenic tobacco plants expressing dsRNA of an insect-associated gene EcR.

PubMed

Zhu, Jin-Qi; Liu, Shumin; Ma, Yao; Zhang, Jia-Qi; Qi, Hai-Sheng; Wei, Zhao-Jun; Yao, Qiong; Zhang, Wen-Qing; Li, Sheng

2012-01-01

The adoption of pest-resistant transgenic plants to reduce yield loss and pesticide utilization has been successful in the past three decades. Recently, transgenic plant expressing double-stranded RNA (dsRNA) targeting pest genes emerges as a promising strategy for improving pest resistance in crops. The steroid hormone, 20-hydroxyecdysone (20E), predominately controls insect molting via its nuclear receptor complex, EcR-USP. Here we report that pest resistance is improved in transgenic tobacco plants expressing dsRNA of EcR from the cotton bollworm, Helicoverpa armigera, a serious lepidopteran pest for a variety of crops. When H. armigera larvae were fed with the whole transgenic tobacco plants expressing EcR dsRNA, resistance to H. armigera was significantly improved in transgenic plants. Meanwhile, when H. armigera larvae were fed with leaves of transgenic tobacco plants expressing EcR dsRNA, its EcR mRNA level was dramatically decreased causing molting defects and larval lethality. In addition, the transgenic tobacco plants expressing H. armigera EcR dsRNA were also resistant to another lepidopteran pest, the beet armyworm, Spodoptera exigua, due to the high similarity in the nucleotide sequences of their EcR genes. This study provides additional evidence that transgenic plant expressing dsRNA targeting insect-associated genes is able to improve pest resistance.

Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress

PubMed Central

Bharti, Nidhi; Pandey, Shiv Shanker; Barnawal, Deepti; Patel, Vikas Kumar; Kalra, Alok

2016-01-01

Plant growth promoting rhizobacteria (PGPR) hold promising future for sustainable agriculture. Here, we demonstrate a carotenoid producing halotolerant PGPR Dietzia natronolimnaea STR1 protecting wheat plants from salt stress by modulating the transcriptional machinery responsible for salinity tolerance in plants. The expression studies confirmed the involvement of ABA-signalling cascade, as TaABARE and TaOPR1 were upregulated in PGPR inoculated plants leading to induction of TaMYB and TaWRKY expression followed by stimulation of expression of a plethora of stress related genes. Enhanced expression of TaST, a salt stress-induced gene, associated with promoting salinity tolerance was observed in PGPR inoculated plants in comparison to uninoculated control plants. Expression of SOS pathway related genes (SOS1 and SOS4) was modulated in PGPR-applied wheat shoots and root systems. Tissue-specific responses of ion transporters TaNHX1, TaHAK, and TaHKT1, were observed in PGPR-inoculated plants. The enhanced gene expression of various antioxidant enzymes such as APX, MnSOD, CAT, POD, GPX and GR and higher proline content in PGPR-inoculated wheat plants contributed to increased tolerance to salinity stress. Overall, these results indicate that halotolerant PGPR-mediated salinity tolerance is a complex phenomenon that involves modulation of ABA-signalling, SOS pathway, ion transporters and antioxidant machinery. PMID:27708387

Plants having modified response to ethylene

DOEpatents

Meyerowitz, Elliott M.; Chang, Caren; Bleecker, Anthony B.

1997-01-01

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

Plants having modified response to ethylene

DOEpatents

Meyerowitz, E.M.; Chang, C.; Bleecker, A.B.

1998-10-20

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype. 67 figs.

Plants having modified response to ethylene

DOEpatents

Meyerowitz, Elliot M.; Chang, Caren; Bleecker, Anthony B.

1998-01-01

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

Plants having modified response to ethylene

DOEpatents

Meyerowitz, E.M.; Chang, C.; Bleecker, A.B.

1997-11-18

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype. 31 figs.

Effectiveness of the High Dose/Refuge Strategy for Managing Pest Resistance to Bacillus thuringiensis (Bt) Plants Expressing One or Two Toxins

PubMed Central

Gryspeirt, Aiko; Grégoire, Jean-Claude

2012-01-01

To delay resistance development to Bacillus thuringiensis (Bt) plants expressing their own insecticide, the application of the Insect Resistance Management strategy called “High Dose/Refuge Strategy” (HD/R) is recommended by the US Environmental Protection Agency (US EPA). This strategy was developed for Bt plants expressing one toxin. Presently, however, new Bt plants that simultaneously express two toxins are on the market. We used a mathematical model to evaluate the efficiency of the HD/R strategy for both these Bt toxins. As the current two-toxin Bt plants do not express two new Cry toxins but reuse one toxin already in use with a one-toxin plant, we estimated the spread of resistance when the resistance alleles are not rare. This study assesses: (i) whether the two toxins have to be present in high concentration, and (ii) the impact of the relative size of the refuge zone on the evolution of resistance and population density. We concluded that for Bt plants expressing one toxin, a high concentration is an essential condition for resistance management. For the pyramided Bt plants, one toxin could be expressed at a low titer if the two toxins are used for the first time, and a small refuge zone is acceptable. PMID:23162699

Effectiveness of the high dose/refuge strategy for managing pest resistance to Bacillus thuringiensis (Bt) plants expressing one or two toxins.

PubMed

Gryspeirt, Aiko; Grégoire, Jean-Claude

2012-10-01

To delay resistance development to Bacillus thuringiensis (Bt) plants expressing their own insecticide, the application of the Insect Resistance Management strategy called "High Dose/Refuge Strategy" (HD/R) is recommended by the US Environmental Protection Agency (US EPA). This strategy was developed for Bt plants expressing one toxin. Presently, however, new Bt plants that simultaneously express two toxins are on the market. We used a mathematical model to evaluate the efficiency of the HD/R strategy for both these Bt toxins. As the current two-toxin Bt plants do not express two new Cry toxins but reuse one toxin already in use with a one-toxin plant, we estimated the spread of resistance when the resistance alleles are not rare. This study assesses: (i) whether the two toxins have to be present in high concentration, and (ii) the impact of the relative size of the refuge zone on the evolution of resistance and population density. We concluded that for Bt plants expressing one toxin, a high concentration is an essential condition for resistance management. For the pyramided Bt plants, one toxin could be expressed at a low titer if the two toxins are used for the first time, and a small refuge zone is acceptable.

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

Okita, T.W.

Part 1 of this research focuses on patterns of gene expression of ADPG-pyrophosphorylase in native and transgenic potato plants. To elucidate the mechanism controlling AGP expression during plant development, the expression of the potato tuber AGP small subunit (sAGP) gene was analyzed in transgenic potato plants using a promoter-{beta}-glucuronidase expression system. Part II evaluated the structure-function relationships of AGP.

The pollination ecology of an assemblage of grassland asclepiads in South Africa.

PubMed

Ollerton, Jeff; Johnson, Steven D; Cranmer, Louise; Kellie, Sam

2003-12-01

The KwaZulu-Natal region of South Africa hosts a large diversity of asclepiads (Apocynaceae: Asclepiadoideae), many of which are endemic to the area. The asclepiads are of particular interest because of their characteristically highly evolved floral morphology. During 3 months of fieldwork (November 2000 to January 2001) the flower visitors and pollinators to an assemblage of nine asclepiads at an upland grassland site were studied. These observations were augmented by laboratory studies of flower morphology (including scanning electron microscopy) and flower colour (using a spectrometer). Two of the specialized pollination systems that were documented are new to the asclepiads: fruit chafer pollination and pompilid wasp pollination. The latter is almost unique in the angiosperms. Taxa possessing these specific pollination systems cluster together in multidimensional phenotype space, suggesting that there has been convergent evolution in response to similar selection to attract identical pollinators. Pollination niche breadth varied from the very specialized species, with only one pollinator, to the more generalized, with up to ten pollinators. Pollinator sharing by the specialized taxa does not appear to have resulted in niche differentiation in terms of the temporal or spatial dimensions, or with regards to placement of pollinaria. Nestedness analysis of the data set showed that there was predictability and structure to the pattern of plant-pollinator interactions, with generalist insects visiting specialized plants and vice versa. The research has shown that there is still much to be learned about plant-pollinator interactions in areas of high plant diversity such as South Africa.

Wilhelm Hofmeister and the foundations of plant science.

PubMed

Martin, Cyrus

2017-09-11

On January 12 th 1877, the Grim Reaper visited Wilhelm Hofmeister (Figure 1) for the last time. Having recently witnessed the death of a wife, two daughters, and two sons (only two of his nine children survived him), the German botanist, perhaps succumbing to the weight of his own grief, suffered a series of strokes and then promptly died at the age of 52 in Lindenau, Germany. He has since faded into the dusty annals of 19 th century botany, his contributions to our knowledge about plants, how they come into being, develop and interact with their environment, mostly forgotten. In an ode to Hofmeister marking 100 years since his birth, Douglas Haughton Campbell of Stanford University, referring to Hofmeister's studies in comparative morphology, wrote, "…there is no question that Hofmeister's work will remain as probably the most brilliant contribution ever made to this fundamental department of botany" [1]. And in an essay published in Plant Physiology, Donald Kaplan and Todd Cooke went further still, writing, "Frederich Wilhelm Benedikt Hofmeister stands as one of the most remarkable figures in the history of botany and one who made fundamental contributions to all areas of plant biology" [2]. If that wasn't enough, Kaplan and Cooke added "In terms of native genius, he is certainly the peer of both Darwin and Mendel and may have even exceeded them in the breadth and depth of his talents." Copyright © 2017 Elsevier Ltd. All rights reserved.

Using heterologous expression systems to characterize potassium and sodium transport activities.

PubMed

Rodríguez, Alonso; Benito, Begoña; Cagnac, Olivier

2012-01-01

The expression of plant transporters in simple well-characterized cell systems is an irreplaceable technique for gaining insights into the kinetic and energetic features of plant transporters. Among all the available expression systems, yeast cells offer the highest simplicity and have the capacity to mimic the in vivo properties of plant transporters. Here, we describe the use of yeast mutants to express K(+) and Na(+) plant transporters and discuss some experimental problems that can produce misleading results.

Distributed Memory Breadth-First Search Revisited: Enabling Bottom-Up Search

DTIC Science & Technology

2013-01-03

Jun. 1972. [2] W. McLendon III, B. Hendrickson, S . J. Plimpton , and L. Rauchwerger, “Finding strongly connected components in distributed graphs,” J...Breadth-First Search Revisited: Enabling Bottom-Up Search 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT...NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) University of California at Berkeley,Electrical

Depth of Cervical Intraepithelial Neoplasia Grade 3 in Peruvian Women: Implications for Therapeutic Depth of Necrosis.

PubMed

Taxa, Luis; Jeronimo, Jose; Alonzo, Todd A; Gage, Julia; Castle, Philip E; Cremer, Miriam L; Felix, Juan C

2018-01-01

To determine the involvement of cervical intraepithelial neoplasia grade 3 (CIN3) in a population of women in a lower-resource setting. One hundred twelve consecutive cone excision specimens with histological diagnosis of CIN3 were retrieved from the National Institute of Neoplastic Diseases in Lima Peru. Two pathologists independently evaluated each specimen microscopically and confirmed 107 cases that could be measured by optical micrometry. Depth and breadth of the lesions were measured microscopically. The mean maximal depth of cervical involvement by CIN3 was 2 ± 0.13 mm; depth was less than 3.5 mm in 89.7% of cases and less than 5 mm in 93.5%. Mean breadth of CIN3 was 7.3 ± 4.4 mm; breadth was less than 15.9 mm in 95% of cases and less than 20.5 mm in 99.7%. The correlation coefficient between breadth and depth of CIN3 was 0.61. No significant correlation was found between age and depth. Depth of CIN3 involvement in a developing country is significantly deeper than that reported in the United States. Treatment selection for women with CIN3 and risk of treatment failure may vary between developing and developed countries because of the difference in the depth of lesions. Countries with underscreened populations need to consider the increased disease severity in devising treatment strategies.

The Breadth and Titer of Maternal HIV-1-Specific Heterologous Neutralizing Antibodies Are Not Associated with a Lower Rate of Mother-to-Child Transmission of HIV-1

PubMed Central

Chaillon, Antoine; Wack, Thierry; Braibant, Martine; Mandelbrot, Laurent; Blanche, Stéphane; Warszawski, Josiane

2012-01-01

It has been hypothesized that neutralizing antibodies (NAbs) should have broad specificity to be effective in protection against diverse HIV-1 variants. The mother-to-child transmission model of HIV-1 provides the opportunity to examine whether the breadth of maternal NAbs is associated with protection of infants from infection. Samples were obtained at delivery from 57 transmitting mothers (T) matched with 57 nontransmitting mothers (NT) enrolled in the multicenter French perinatal cohort (ANRS EPF CO1) between 1990 and 1996. Sixty-eight (59.6%) and 46 (40.4%) women were infected by B and non-B viruses, respectively. Neutralization assays were carried out with TZM-bl cells, using a panel of 10 primary isolates of 6 clades (A, B, C, F, CRF01_AE, and CRF02_AG), selected for their moderate or low sensitivity to neutralization. Neutralization breadths were not statistically different between T and NT mothers. However, a few statistically significant differences were observed, with higher frequencies or titers of NAbs toward several individual strains for NT mothers when the clade B-infected or non-clade B-infected mothers were analyzed separately. Our study confirms that the breadth of maternal NAbs is not associated with protection of infants from infection. PMID:22811522

Estimation of sex from the lower limb measurements of Sudanese adults.

PubMed

Ahmed, Altayeb Abdalla

2013-06-10

The sex estimation from mutilated and amputated limbs or body parts is one of the most vital steps in person identification in medical-legal autopsies. Sex estimation from lower limb anthropometric measurements has demonstrated a high degree of expected accuracy in a limited range of the global population. The aims of this study were to assess the degree of the sexual dimorphism in lower limb measurements and the accuracy of utilization of these measurements for estimation of sex in a contemporary adult Sudanese population. The tibial length, bimalleolar breadth, foot length, and foot breadth of 240 right-handed Sudanese Arab subjects (120 males and 120 females) aged between 25 and 30 years were measured following international anthropometric standards. Demarking points, sexual dimorphism indices and discriminant functions were developed from 200 subjects (100 males and 100 females) who comprised the study group. All variables were sexually dimorphic. The bimalleolar breadth and foot breadth significantly contributed to sex estimation. Leg dimensions showed a higher accuracy for sex estimation than foot dimensions. Cross-validated sex classification accuracy ranged between 78% and 89.5%. The reliability of these standards was assessed in a test sample of 20 males and 20 females, and the results showed accuracy between 75% and 90%. This study provides new forensic standards for sex estimation from lower limb measurements of Sudanese adults. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Are quality improvement methods a fashion for hospitals in Taiwan?

PubMed

Chung, Kuo-Piao; Yu, Tsung-Hsien

2012-08-01

This study reviews the rise and fall of the quality improvement (QI) methods implemented by hospitals in Taiwan, and examines the factors related to these methods. Cross-sectional, questionnaire-based survey. One hundred and thirty-nine district teaching hospitals, regional hospitals and medical centers. Directors or the persons in charge of implementing QI methods. s) None. s) Breadth and depth of the 18 QI methods. Seventy-two hospitals responded to the survey, giving a response rate of 52%. In terms of breadth based on the hospitals' self-reporting, the average number of QI methods adopted per hospital was 11.78 (range: 7-17). More than 80% of the surveyed hospitals had implemented eight QI methods, and >50% had implemented five QI methods. The QI methods adopted by over 80% of the surveyed hospitals had been implemented for a period of ∼7 years. On the basis of the authors' classification, seven of the eight QI methods (except for QI team in total quality management) had an implementation depth of almost 70% or higher in the surveyed hospitals. This study provides a snapshot of the QI methods implemented by hospitals in Taiwan. The results show that the average breadth of the QI methods adopted was 11.78; however, only 8.83 were implemented deeply. The hospitals' accreditation level was associated with the breadth and depth of QI method implementation.

Sex estimation by femur in modern Thai population.

PubMed

Monum, T; Prasitwattanseree, S; Das, S; Siriphimolwat, P; Mahakkanukrauh, P

2017-01-01

Sex estimation is an important step of postmortem investigation and the femur is a useful bone for sex estimation by using metric analysis method. Even though there have been a reported sex estimation method by using femur in Thais, the temporal change related to time and anthropological data need to be renewed. Thus the aim of this study is to re-evaluate sex estimation by femur in Thais. 97 adult male and 103 female femora were random chosen from Forensic osteology research center and 6 measurements were applied tend to. To compare with previous Thai data, mid shaft diameter to increase but femoral head and epicondylar breadth to stabilize and when tested previous discriminant function by vertical head diameter and epicondalar breadth, the accuracy of prediction was lower than previous report. From the new data, epicondalar breadth is the best variable for distinguishing male and female at 88.7 percent of accuracy, following by transverse and vertical head diameter at 86.7 percent and femoral neck diameter at 81.7 percent of accuracy. Multivariate discriminant analysis indicated transverse head diameter and epicondylar breadth performed highest rate of accuracy at 89.7 percent. The percent of accuracy of femur was close to previous reported sex estimation by talus and calcaneus in Thai population. Thus, for especially in case of lower limb remain, which absence of pelvis.

Integrating linear optimization with structural modeling to increase HIV neutralization breadth.

PubMed

Sevy, Alexander M; Panda, Swetasudha; Crowe, James E; Meiler, Jens; Vorobeychik, Yevgeniy

2018-02-01

Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods. We demonstrate the effectiveness of this method, which we call BROAD, by benchmarking the performance on increasing predicted breadth of anti-HIV antibodies. We use this novel method to increase predicted breadth of naturally-occurring antibody VRC23 against a panel of 180 divergent HIV viral strains and achieve 100% predicted binding against the panel. In addition, we compare the performance of this method to state-of-the-art multistate design in Rosetta and show that we can outperform the existing method significantly. We further demonstrate that sequences recovered by this method recover known binding motifs of broadly neutralizing anti-HIV antibodies. Finally, our approach is general and can be extended easily to other protein systems. Although our modeled antibodies were not tested in vitro, we predict that these variants would have greatly increased breadth compared to the wild-type antibody.

Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.

PubMed

Jagtap, Soham; Shivaprasad, Padubidri V

2014-12-02

Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved. We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors. Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers

PubMed Central

2011-01-01

Background RNA silencing is used in plants as a major defence mechanism against invasive nucleic acids, such as viruses. Accordingly, plant viruses have evolved to produce counter defensive RNA-silencing suppressors (RSSs). These factors interfere in various ways with the RNA silencing machinery in cells, and thereby disturb the microRNA (miRNA) mediated endogene regulation and induce developmental and morphological changes in plants. In this study we have explored these effects using previously characterized transgenic tobacco plants which constitutively express (under CaMV 35S promoter) the helper component-proteinase (HC-Pro) derived from a potyviral genome. The transcript levels of leaves and flowers of these plants were analysed using microarray techniques (Tobacco 4 × 44 k, Agilent). Results Over expression of HC-Pro RSS induced clear phenotypic changes both in growth rate and in leaf and flower morphology of the tobacco plants. The expression of 748 and 332 genes was significantly changed in the leaves and flowers, respectively, in the HC-Pro expressing transgenic plants. Interestingly, these transcriptome alterations in the HC-Pro expressing tobacco plants were similar as those previously detected in plants infected with ssRNA-viruses. Particularly, many defense-related and hormone-responsive genes (e.g. ethylene responsive transcription factor 1, ERF1) were differentially regulated in these plants. Also the expression of several stress-related genes, and genes related to cell wall modifications, protein processing, transcriptional regulation and photosynthesis were strongly altered. Moreover, genes regulating circadian cycle and flowering time were significantly altered, which may have induced a late flowering phenotype in HC-Pro expressing plants. The results also suggest that photosynthetic oxygen evolution, sugar metabolism and energy levels were significantly changed in these transgenic plants. Transcript levels of S-adenosyl-L-methionine (SAM) were also decreased in these plants, apparently leading to decreased transmethylation capacity. The proteome analysis using 2D-PAGE indicated significantly altered proteome profile, which may have been both due to altered transcript levels, decreased translation, and increased proteosomal/protease activity. Conclusion Expression of the HC-Pro RSS mimics transcriptional changes previously shown to occur in plants infected with intact viruses (e.g. Tobacco etch virus, TEV). The results indicate that the HC-Pro RSS contributes a significant part of virus-plant interactions by changing the levels of multiple cellular RNAs and proteins. PMID:21507209

Cladosporium fulvum CfHNNI1 induces hypersensitive necrosis, defence gene expression and disease resistance in both host and nonhost plants.

PubMed

Cai, Xin-Zhong; Zhou, Xin; Xu, You-Ping; Joosten, Matthieu H A J; de Wit, Pierre J G M

2007-05-01

Nonhost resistance as a durable and broad-spectrum defence strategy is of great potential for agricultural applications. We have previously isolated a cDNA showing homology with genes encoding bZIP transcription factors from tomato leaf mould pathogen Cladosporium fulvum. Upon expression, the cDNA results in necrosis in C. fulvum host tomato and nonhost tobacco plants and is thus named CfHNNI1 (for C . f ulvum host and nonhost plant necrosis inducer 1). In the present study we report the induction of necrosis in a variety of nonhost plant species belonging to three families by the transient in planta expression of CfHNNI1 using virus-based vectors. Additionally, transient expression of CfHNNI1 also induced expression of the HR marker gene LeHSR203 and greatly reduced the accumulation of recombinant Potato virus X. Stable CfHNNI1 transgenic tobacco plants were generated in which the expression of CfHNNI1 is under the control of the pathogen-inducible hsr203J promoter. When infected with the oomycetes pathogen Phytophthora parasitica var. nicotianae, these transgenic plants manifested enhanced expression of CfHNNI1 and subsequent accumulation of CfHNNI1 protein, resulting in high expression of the HSR203J and PR genes, and strong resistance to the pathogen. The CfHNNI1 transgenic plants also exhibited induced resistance to Pseudomonas syringae pv. tabaci and Tobacco mosaic virus. Furthermore, CfHNNI1 was highly expressed and the protein was translocated into plant cells during the incompatible interactions between C. fulvum and host and nonhost plants. Our results demonstrate that CfHNNI1 is a potential general elicitor of hypersensitive response and nonhost resistance.

Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.

PubMed

Jiang, Zhenhong; He, Fei; Zhang, Ziding

2017-07-01

Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study will deepen our understanding of plant metabolism in plant immunity and provide new insights into disease-resistant crop improvement.

Inhibition of Snl6 expression for biofuel production

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

Bart, Rebecca; Chern, Mawsheng; Ronald, Pamela

The invention provides compositions and methods for inhibiting the expression of the gene Snl6 in plants. Plants with inhibited expression of Snl6 have use in biofuel production, e.g., by increasing the amount of soluble sugar that can be extracted from the plant.

Plants having modified response to ethylene by transformation with an ETR nucleic acid

DOEpatents

Meyerowitz, Elliott M.; Chang, Caren; Bleecker, Anthony B.

2001-01-01

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

Multi-sensor radiation detection, imaging, and fusion

NASA Astrophysics Data System (ADS)

Vetter, Kai

2016-01-01

Glenn Knoll was one of the leaders in the field of radiation detection and measurements and shaped this field through his outstanding scientific and technical contributions, as a teacher, his personality, and his textbook. His Radiation Detection and Measurement book guided me in my studies and is now the textbook in my classes in the Department of Nuclear Engineering at UC Berkeley. In the spirit of Glenn, I will provide an overview of our activities at the Berkeley Applied Nuclear Physics program reflecting some of the breadth of radiation detection technologies and their applications ranging from fundamental studies in physics to biomedical imaging and to nuclear security. I will conclude with a discussion of our Berkeley Radwatch and Resilient Communities activities as a result of the events at the Dai-ichi nuclear power plant in Fukushima, Japan more than 4 years ago.

Pathogen Phytosensing: Plants to Report Plant Pathogens.

PubMed

Mazarei, Mitra; Teplova, Irina; Hajimorad, M Reza; Stewart, C Neal

2008-04-14

Real-time systems that provide evidence of pathogen contamination in crops can be an important new line of early defense in agricultural centers. Plants possess defense mechanisms to protect against pathogen attack. Inducible plant defense is controlled by signal transduction pathways, inducible promoters and cis-regulatory elements corresponding to key genes involved in defense, and pathogen-specific responses. Identified inducible promoters and cis-acting elements could be utilized in plant sentinels, or 'phytosensors', by fusing these to reporter genes to produce plants with altered phenotypes in response to the presence of pathogens. Here, we have employed cis-acting elements from promoter regions of pathogen inducible genes as well as those responsive to the plant defense signal molecules salicylic acid, jasmonic acid, and ethylene. Synthetic promoters were constructed by combining various regulatory elements supplemented with the enhancer elements from the Cauliflower mosaic virus (CaMV) 35S promoter to increase basal level of the GUS expression. The inducibility of each synthetic promoter was first assessed in transient expression assays using Arabidopsis thaliana protoplasts and then examined for efficacy in stably transgenic Arabidopsis and tobacco plants. Histochemical and fluorometric GUS expression analyses showed that both transgenic Arabidopsis and tobacco plants responded to elicitor and phytohormone treatments with increased GUS expression when compared to untreated plants. Pathogen-inducible phytosensor studies were initiated by analyzing the sensitivity of the synthetic promoters against virus infection. Transgenic tobacco plants infected with Alfalfa mosaic virus showed an increase in GUS expression when compared to mock-inoculated control plants, whereas Tobacco mosaic virus infection caused no changes in GUS expression. Further research, using these transgenic plants against a range of different pathogens with the regulation of detectable reporter gene could provide biological evidence to define the functional differences between pathogens, and provide new technology and applications for transgenic plants as phytosensors.

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity

PubMed Central

Lumpkin, Will; Hurtado, Paul J.; Dyer, Lee A.

2018-01-01

Most of earth’s biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change. PMID:29579077

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

PubMed

Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

2018-01-01

Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change.

Expression of fungal pectin methylesterase in transgenic tobacco leads to alteration in cell wall metabolism and a dwarf phenotype.

PubMed

Hasunuma, Tomohisa; Fukusaki, Ei-ichiro; Kobayashi, Akio

2004-08-05

A transgenic tobacco plant (Nicotiana tabacum L.) expressing a fungal pectin methylesterase (PME; EC 3.1.1.11) gene derived from a black filamentous fungus, Aspergillus niger was created. Fungal PME should have a wider range of adaptability to substrate pectin compared with plant PME. As expected, the proportion of methyl esters in pectin was reduced in the transgenic tobacco. Consequently, the transgenic plant showed short internodes, small leaves and a dwarf phenotype. At a cellular level, the longitudinal lengths of stem epidermal cells were shorter than those of control plants. This is the first report that fungal PME promotes dwarfism in plants. It is worth noting that in the PME-expressing dwarf plant, the expression levels of cell wall metabolism related genes that included endo-1,4-beta-glucanase, cellulose synthase, endo-xyloglucan transferase and expansin gene were decreased. These results suggest that the expression of fungal PME in plants affects the cell wall metabolism.

Sexual dimorphism of the mandible in a contemporary Chinese Han population.

PubMed

Dong, Hongmei; Deng, Mohong; Wang, WenPeng; Zhang, Ji; Mu, Jiao; Zhu, Guanghui

2015-10-01

A present limitation of forensic anthropology practice in China is the lack of population-specific criteria on contemporary human skeletons. In this study, a sample of 203 maxillofacial Cone beam computed tomography (CBCT) images, including 96 male and 107 female cases (20-65 years old), was analyzed to explore mandible sexual dimorphism in a population of contemporary adult Han Chinese to investigate the potential use of the mandible as sex indicator. A three-dimensional image from mandible CBCT scans was reconstructed using the SimPlant Pro 11.40 software. Nine linear and two angular parameters were measured. Discriminant function analysis (DFA) and logistic regression analysis (LRA) were used to develop the mathematics models for sex determination. All of the linear measurements studied and one angular measurement were found to be sexually dimorphic, with the maximum mandibular length and bi-condylar breadth being the most dimorphic by univariate DFA and LRA respectively. The cross-validated sex allocation accuracies on multivariate were ranged from 84.2% (direct DFA), 83.5% (direct LRA), 83.3% (stepwise DFA) to 80.5% (stepwise LRA). In general, multivariate DFA yielded a higher accuracy and LRA obtained a lower sex bias, and therefore both DFA and LRA had their own advantages for sex determination by the mandible in this sample. These results suggest that the mandible expresses sexual dimorphism in the contemporary adult Han Chinese population, indicating an excellent sexual discriminatory ability. Cone beam computed tomography scanning can be used as alternative source for contemporary osteometric techniques. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Expression of Human Immunodeficiency Virus Type 1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus.

PubMed

Marcobal, Angela; Liu, Xiaowen; Zhang, Wenlei; Dimitrov, Antony S; Jia, Letong; Lee, Peter P; Fouts, Timothy R; Parks, Thomas P; Lagenaur, Laurel A

Eradication of human immunodeficiency virus type 1 (HIV-1) by vaccination with epitopes that produce broadly neutralizing antibodies is the ultimate goal for HIV prevention. However, generating appropriate immune responses has proven difficult. Expression of broadly neutralizing antibodies by vaginal colonizing lactobacilli provides an approach to passively target these antibodies to the mucosa. We tested the feasibility of expressing single-chain and single-domain antibodies (dAbs) in Lactobacillus to be used as a topical microbicide/live biotherapeutic. Lactobacilli provide an excellent platform to express anti-HIV proteins. Broadly neutralizing antibodies have been identified against epitopes on the HIV-1 envelope and have been made into active antibody fragments. We tested single-chain variable fragment m9 and dAb-m36 and its derivative m36.4 as prototype antibodies. We cloned and expressed the antibody fragments m9, m36, and m36.4 in Lactobacillus jensenii-1153 and tested the expression levels and functionality. We made a recombinant L. jensenii 1153-1128 that expresses dAb-m36.4. All antibody fragments m9, m36, and m36.4 were expressed by lactobacilli. However, we noted the smaller m36/m36.4 were expressed to higher levels, ≥3 μg/ml. All L. jensenii-expressed antibody fragments bound to gp120/CD4 complex; Lactobacillus-produced m36.4 inhibited HIV-1 BaL in a neutralization assay. Using a TZM-bl assay, we characterized the breadth of neutralization of the m36.4. Delivery of dAbs by Lactobacillus could provide passive transfer of these antibodies to the mucosa and longevity at the site of HIV-1 transmission.

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

PubMed

Proost, Sebastian; Mutwil, Marek

2018-05-01

The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

Gene encoding plant asparagine synthetase

DOEpatents

Coruzzi, Gloria M.; Tsai, Fong-Ying

1993-10-26

The identification and cloning of the gene(s) for plant asparagine synthetase (AS), an important enzyme involved in the formation of asparagine, a major nitrogen transport compound of higher plants is described. Expression vectors constructed with the AS coding sequence may be utilized to produce plant AS; to engineer herbicide resistant plants, salt/drought tolerant plants or pathogen resistant plants; as a dominant selectable marker; or to select for novel herbicides or compounds useful as agents that synchronize plant cells in culture. The promoter for plant AS, which directs high levels of gene expression and is induced in an organ specific manner and by darkness, is also described. The AS promoter may be used to direct the expression of heterologous coding sequences in appropriate hosts.

Conditional sterility in plants

DOEpatents

Meagher, Richard B.; McKinney, Elizabeth; Kim, Tehryung

2010-02-23

The present disclosure provides methods, recombinant DNA molecules, recombinant host cells containing the DNA molecules, and transgenic plant cells, plant tissue and plants which contain and express at least one antisense or interference RNA specific for a thiamine biosynthetic coding sequence or a thiamine binding protein or a thiamine-degrading protein, wherein the RNA or thiamine binding protein is expressed under the regulatory control of a transcription regulatory sequence which directs expression in male and/or female reproductive tissue. These transgenic plants are conditionally sterile; i.e., they are fertile only in the presence of exogenous thiamine. Such plants are especially appropriate for use in the seed industry or in the environment, for example, for use in revegetation of contaminated soils or phytoremediation, especially when those transgenic plants also contain and express one or more chimeric genes which confer resistance to contaminants.

Advancing Clouds Lifecycle Representation in Numerical Models Using Innovative Analysis Methods that Bridge ARM Observations and Models Over a Breadth of Scales

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

Kollias, Pavlos

2016-09-06

This the final report for the DE-SC0007096 - Advancing Clouds Lifecycle Representation in Numerical Models Using Innovative Analysis Methods that Bridge ARM Observations and Models Over a Breadth of Scales - PI: Pavlos Kollias. The final report outline the main findings of the research conducted using the aforementioned award in the area of cloud research from the cloud scale (10-100 m) to the mesoscale (20-50 km).

The Effects of the First Part of the CoRT Program for Teaching Thinking (BREADTH) on the Development of Communication Skills among a Sample of Students from Al al-Bayt University in Jordan

ERIC Educational Resources Information Center

Alshurman, Wael Mohammad

2017-01-01

This study aimed to investigate the effects of the first part of the CoRT program for teaching thinking (BREADTH) on the development of communication skills among a sample of students from Al al-Bayt University in Jordan. The study sample consisted of all the students enrolled in the training session for the first part of the CoRT program held by…

Daytime soybean transcriptome fluctuations during water deficit stress.

PubMed

Rodrigues, Fabiana Aparecida; Fuganti-Pagliarini, Renata; Marcolino-Gomes, Juliana; Nakayama, Thiago Jonas; Molinari, Hugo Bruno Correa; Lobo, Francisco Pereira; Harmon, Frank G; Nepomuceno, Alexandre Lima

2015-07-07

Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression. We identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55% were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were up-regulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period. Gene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

Ectopic Expression of Xylella fastidiosa rpfF Conferring Production of Diffusible Signal Factor in Transgenic Tobacco and Citrus Alters Pathogen Behavior and Reduces Disease Severity.

PubMed

Caserta, R; Souza-Neto, R R; Takita, M A; Lindow, S E; De Souza, A A

2017-11-01

The pathogenicity of Xylella fastidiosa is associated with its ability to colonize the xylem of host plants. Expression of genes contributing to xylem colonization are suppressed, while those necessary for insect vector acquisition are increased with increasing concentrations of diffusible signal factor (DSF), whose production is dependent on RpfF. We previously demonstrated that transgenic citrus plants ectopically expressing rpfF from a citrus strain of X. fastidiosa subsp. pauca exhibited less susceptibility to Xanthomonas citri subsp. citri, another pathogen whose virulence is modulated by DSF accumulation. Here, we demonstrate that ectopic expression of rpfF in both transgenic tobacco and sweet orange also confers a reduction in disease severity incited by X. fastidiosa and reduces its colonization of those plants. Decreased disease severity in the transgenic plants was generally associated with increased expression of genes conferring adhesiveness to the pathogen and decreased expression of genes necessary for active motility, accounting for the reduced population sizes achieved in the plants, apparently by limiting pathogen dispersal through the plant. Plant-derived DSF signal molecules in a host plant can, therefore, be exploited to interfere with more than one pathogen whose virulence is controlled by DSF signaling.

Metal resistant plants and phytoremediation of environmental contamination

DOEpatents

Meagher, Richard B.; Li, Yujing; Dhankher, Om P.

2010-04-20

The present disclosure provides a method of producing transgenic plants which are resistant to at least one metal ion by transforming the plant with a recombinant DNA comprising a nucleic acid encoding a bacterial arsenic reductase under the control of a plant expressible promoter, and a nucleic acid encoding a nucleotide sequence encoding a phytochelatin biosynthetic enzyme under the control of a plant expressible promoter. The invention also relates a method of phytoremediation of a contaminated site by growing in the site a transgenic plant expressing a nucleic acid encoding a bacterial arsenate reductase and a nucleic acid encoding a phytochelatin biosynthetic enzyme.

Expression of an Arabidopsis Ca2+/H+ antiporter CAX1 variant in petunia enhances cadmium tolerance and accumulation.

PubMed

Wu, Qingyu; Shigaki, Toshiro; Williams, Kimberly A; Han, Jeung-Sul; Kim, Chang Kil; Hirschi, Kendal D; Park, Sunghun

2011-01-15

Phytoremediation is a cost-effective and minimally invasive technology to cleanse soils contaminated with heavy metals. However, few plant species are suitable for phytoremediation of metals such as cadmium (Cd). Genetic engineering offers a powerful tool to generate plants that can hyperaccumulate Cd. An Arabidopsis CAX1 mutant (CAXcd), which confers enhanced Cd transport in yeast, was ectopically expressed in petunia to evaluate whether the CAXcd expression would enhance Cd tolerance and accumulation in planta. The CAXcd-expressing petunia plants showed significantly greater Cd tolerance and accumulation than the controls. After being treated with either 50 or 100μM CdCl(2) for 6 weeks, the CAXcd-expressing plants showed more vigorous growth compared with controls, and the transgenic plants accumulated significantly more Cd (up to 2.5-fold) than controls. Moreover, the accumulation of Cd did not affect the development and morphology of the CAXcd-expressing petunia plants until the flowering and ultimately the maturing of seeds. Therefore, petunia has the potential to serve as a model species for developing herbaceous, ornamental plants for phytoremediation. Copyright © 2010 Elsevier GmbH. All rights reserved.

High-level HIV-1 Nef transient expression in Nicotiana benthamiana using the P19 gene silencing suppressor protein of Artichoke Mottled Crinckle Virus

PubMed Central

2009-01-01

Background In recent years, different HIV antigens have been successfully expressed in plants by either stable transformation or transient expression systems. Among HIV proteins, Nef is considered a promising target for the formulation of a multi-component vaccine due to its implication in the first steps of viral infection. Attempts to express Nef as a single protein product (not fused to a stabilizing protein) in transgenic plants resulted in disappointingly low yields (about 0.5% of total soluble protein). In this work we describe a transient expression system based on co-agroinfiltration of plant virus gene silencing suppressor proteins in Nicotiana benthamiana, followed by a two-step affinity purification protocol of plant-derived Nef. Results The effect of three gene silencing viral suppressor proteins (P25 of Potato Virus X, P19 of either Artichoke Mottled Crinckle virus and Tomato Bushy Stunt virus) on Nef transient expression yield was evaluated. The P19 protein of Artichoke Mottled Crinckle virus (AMCV-P19) gave the highest expression yield in vacuum co-agroinfiltration experiments reaching 1.3% of total soluble protein, a level almost three times higher than that previously reported in stable transgenic plants. The high yield observed in the co-agroinfiltrated plants was correlated to a remarkable decrease of Nef-specific small interfering RNAs (siRNAs) indicating an effective modulation of RNA silencing mechanisms by AMCV-P19. Interestingly, we also showed that expression levels in top leaves of vacuum co-agroinfiltrated plants were noticeably reduced compared to bottom leaves. Moreover, purification of Nef from agroinfiltrated tissue was achieved by a two-step immobilized metal ion affinity chromatography protocol with yields of 250 ng/g of fresh tissue. Conclusion We demonstrated that expression level of HIV-1 Nef in plant can be improved using a transient expression system enhanced by the AMCV-P19 gene silencing suppressor protein. Moreover, plant-derived Nef was purified, with enhanced yield, exploiting a two-step purification protocol. These results represent a first step towards the development of a plant-derived HIV vaccine. PMID:19930574

High-level HIV-1 Nef transient expression in Nicotiana benthamiana using the P19 gene silencing suppressor protein of Artichoke Mottled Crinckle Virus.

PubMed

Lombardi, Raffaele; Circelli, Patrizia; Villani, Maria Elena; Buriani, Giampaolo; Nardi, Luca; Coppola, Valentina; Bianco, Linda; Benvenuto, Eugenio; Donini, Marcello; Marusic, Carla

2009-11-20

In recent years, different HIV antigens have been successfully expressed in plants by either stable transformation or transient expression systems. Among HIV proteins, Nef is considered a promising target for the formulation of a multi-component vaccine due to its implication in the first steps of viral infection. Attempts to express Nef as a single protein product (not fused to a stabilizing protein) in transgenic plants resulted in disappointingly low yields (about 0.5% of total soluble protein). In this work we describe a transient expression system based on co-agroinfiltration of plant virus gene silencing suppressor proteins in Nicotiana benthamiana, followed by a two-step affinity purification protocol of plant-derived Nef. The effect of three gene silencing viral suppressor proteins (P25 of Potato Virus X, P19 of either Artichoke Mottled Crinckle virus and Tomato Bushy Stunt virus) on Nef transient expression yield was evaluated. The P19 protein of Artichoke Mottled Crinckle virus (AMCV-P19) gave the highest expression yield in vacuum co-agroinfiltration experiments reaching 1.3% of total soluble protein, a level almost three times higher than that previously reported in stable transgenic plants. The high yield observed in the co-agroinfiltrated plants was correlated to a remarkable decrease of Nef-specific small interfering RNAs (siRNAs) indicating an effective modulation of RNA silencing mechanisms by AMCV-P19. Interestingly, we also showed that expression levels in top leaves of vacuum co-agroinfiltrated plants were noticeably reduced compared to bottom leaves. Moreover, purification of Nef from agroinfiltrated tissue was achieved by a two-step immobilized metal ion affinity chromatography protocol with yields of 250 ng/g of fresh tissue. We demonstrated that expression level of HIV-1 Nef in plant can be improved using a transient expression system enhanced by the AMCV-P19 gene silencing suppressor protein. Moreover, plant-derived Nef was purified, with enhanced yield, exploiting a two-step purification protocol. These results represent a first step towards the development of a plant-derived HIV vaccine.

Microbial terroir for wine grapes

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

Gilbert, J. A.; van der Lelie, D.; Zarraonaindia, I.

2013-12-05

The viticulture industry has been selectively growing vine cultivars with different traits (grape size, shape, color, flavor, yield of fruit, and so forth) for millennia, and small variations in soil composition, water management, climate, and the aspect of vineyards have long been associated with shifts in these traits. As such, many different clonal varieties of vines exist, even within given grape varieties, such as merlot, pinot noir, and chardonnay. The commensal microbial flora that coexists with the plant may be one of the key factors that influence these traits. To date, the role of microbes has been largely ignored, outsidemore » of microbial pathogens, mainly because the technologies did not exist to allow us to look in any real depth or breadth at the community structure of the multitudes of bacterial and fungal species associated with each plant. In PNAS, Bokulich et al. (1) used next-generation sequencing of 16S rRNA and internal transcribed spacer ribosomal sequence to determine the relative abundances of bacteria and fungi, respectively, from grape must (freshly pressed grape juice, containing the skins and seeds) from plants in eight vineyards representing four of the major wine growing regions in California. The authors show that the microbiomes (bacterial and fungal taxonomic structure) associated with this early fermentation stage show defined biogeography, illustrating that different wine-growing regions maintain different microbial communities, with some influences from the grape variety and the year of production.« less

Soil nutrients influence spatial distributions of tropical tree species.

PubMed

John, Robert; Dalling, James W; Harms, Kyle E; Yavitt, Joseph B; Stallard, Robert F; Mirabello, Matthew; Hubbell, Stephen P; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B

2007-01-16

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search

PubMed Central

Tang, Xiwei; Wang, Jianxin; Li, Min; He, Yiming; Pan, Yi

2014-01-01

Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes from the weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the weighted density, ClusterBFS detects protein complexes of the weighted network by the breadth first search algorithm, which originates from a given seed protein used as starting-point. The experimental results show that ClusterBFS performs significantly better than the other computational approaches in terms of the identification of protein complexes. PMID:24818139

The influence of psychological resilience on the relation between automatic stimulus evaluation and attentional breadth for surprised faces.

PubMed

Grol, Maud; De Raedt, Rudi

2015-01-01

The broaden-and-build theory relates positive emotions to resilience and cognitive broadening. The theory proposes that the broadening effects underly the relation between positive emotions and resilience, suggesting that resilient people can benefit more from positive emotions at the level of cognitive functioning. Research has investigated the influence of positive emotions on attentional broadening, but the stimulus in the target of attention may also influence attentional breadth, depending on affective stimulus evaluation. Surprised faces are particularly interesting as they are valence ambiguous, therefore, we investigated the relation between affective evaluation--using an affective priming task--and attentional breadth for surprised faces, and how this relation is influenced by resilience. Results show that more positive evaluations are related to more attentional broadening at high levels of resilience, while this relation is reversed at low levels. This indicates that resilient individuals can benefit more from attending to positively evaluated stimuli at the level of attentional broadening.

Anthropometric characteristics of elite male junior rowers

PubMed Central

Bourgois, J.; Claessens, A.; Vrijens, J.; Philippaerts, R.; Van Renterghem, B.; Thomis, M.; Janssens, M.; Loos, R.; Lefevre, J.

2000-01-01

During the 1997 Fédération Internationale des Sociétés d'Aviron World Junior Rowing Championships, anthropometric data on 383 male junior rowers were assessed. With 430 participating athletes, the sample represented 89% of the population. In addition to age, 27 dimensions were measured: body mass, six heights or lengths, four breadths, 10 girths, and six skinfolds. The elite male junior rowers were tall (187.4 (5.8) cm; mean (SD)) and heavy (82.2 (7.4) kg), with larger length, breadth, and girth dimensions than a nationally representative sample of Belgian boys of the same chronological age. A rowing specific anthropometric profile chart with norms was constructed. The stature of the junior rowers is similar to that of adult heavyweight elite rowers, except that the junior rowers are lighter. Compared with non-finalists, finalists are heavier (but still lighter than the adult heavyweight elite rower) and taller, with greater length, breadth (except for the bicristal diameter), and girth dimensions. Key Words: anthropometry; body size; males; junior; rowers PMID:10854024

Optimization of conditions for transient Agrobacterium-mediated gene expression assays in Arabidopsis.

PubMed

Kim, Mi Jung; Baek, Kon; Park, Chung-Mo

2009-08-01

Transient genetic transformation of plant organs is an indispensable way of studying gene function in plants. This study was aimed to develop an optimized system for transient Agrobacterium-mediated transformation of the Arabidopsis leaves. The beta-glucuronidase (GUS) reporter gene was employed to evaluate growth and biochemical parameters that influence the levels of transient expression. The effects of plant culture conditions, Agrobacterial genetic backgrounds, densities of Agrobacterial cell suspensions, and of several detergents were analyzed. We found that optimization of plant culture conditions is the most critical factor among the parameters analyzed. Higher levels of transient expression were observed in plants grown under short day conditions (SDs) than in plants grown under long day conditions (LDs). Furthermore, incubation of the plants under SDs at high relative humidity (85-90%) for 24 h after infiltration greatly improved the levels of transient expression. Under the optimized culture conditions, expression of the reporter gene reached the peak 3 days after infiltration and was rapidly decreased after the peak. Among the five Agrobacterial strains examined, LAB4404 produced the highest levels of expression. We also examined the effects of detergents, including Triton X-100, Tween-20, and Silwet L-77. Supplementation of the infiltration media either with 0.01% Triton X-100 or 0.01% Tween-20 improved the levels of expression by approximately 1.6-fold. Our observations indicate that transient transformation of the Arabidopsis leaves in the infiltration media supplemented with 0.01% Triton X-100 and incubation of the infiltrated plants under SDs at high relative humidity are necessary for maximal levels of expression.

Overview of expression of hepatitis B surface antigen in transgenic plants.

PubMed

Guan, Zheng-jun; Guo, Bin; Huo, Yan-lin; Guan, Zheng-ping; Wei, Ya-hui

2010-10-28

Hepatitis B virus (HBV), a pathogen for chronic liver infection, afflicts more than 350 million people world-wide. The effective way to control the virus is to take HBV vaccine. Hepatitis B surface antigen (HBsAg) is an effective protective antigen suitable for vaccine development. At present, "edible" vaccine based on transgenic plants is one of the most promising directions in novel types of vaccines. HBsAg production from transgenic plants has been carried out, and the transgenic plant expression systems have developed from model plants (such as tobacco, potato and tomato) to other various plant platforms. Crude or purified extracts of transformed plants have been found to conduct immunological responses and clinical trials for hepatitis B, which gave the researches of plant-based HBsAg production a big boost. The aim of this review was to summarize the recent data about plant-based HBsAg development including molecular biology of HBsAg gene, selection of expression vector, the expression of HBsAg gene in plants, as well as corresponding immunological responses in animal models or human. Copyright © 2010 Elsevier Ltd. All rights reserved.

A Perspective on the Development of Plant-Made Vaccines in the Fight against Ebola Virus

PubMed Central

Rosales-Mendoza, Sergio; Nieto-Gómez, Ricardo; Angulo, Carlos

2017-01-01

The Ebola virus (EBOV) epidemic indicated a great need for prophylactic and therapeutic strategies. The use of plants for the production of biopharmaceuticals is a concept being adopted by the pharmaceutical industry, with an enzyme for human use currently commercialized since 2012 and some plant-based vaccines close to being commercialized. Although plant-based antibodies against EBOV are under clinical evaluation, the development of plant-based vaccines against EBOV essentially remains an unexplored area. The current technologies for the production of plant-based vaccines include stable nuclear expression, transient expression mediated by viral vectors, and chloroplast expression. Specific perspectives on how these technologies can be applied for developing anti-EBOV vaccines are provided, including possibilities for the design of immunogens as well as the potential of the distinct expression modalities to produce the most relevant EBOV antigens in plants considering yields, posttranslational modifications, production time, and downstream processing. PMID:28344580

Rule-Based Design of Plant Expression Vectors Using GenoCAD.

PubMed

Coll, Anna; Wilson, Mandy L; Gruden, Kristina; Peccoud, Jean

2015-01-01

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

Phytodegradation of organophosphorus compounds by transgenic plants expressing a bacterial organophosphorus hydrolase.

PubMed

Wang, Xiaoxue; Wu, Ningfeng; Guo, Jun; Chu, Xiaoyu; Tian, Jian; Yao, Bin; Fan, Yunliu

2008-01-18

Organophosphorus (OP) compounds are widely used as pesticides in agriculture but cause broad-area environmental pollution. In this work, we have expressed a bacterial organophosphorus hydrolase (OPH) gene in tobacco plants. An assay of enzyme activity showed that transgenic plants could secrete OPH into the growth medium. The transgenic plants were resistant to methyl parathion (Mep), an OP pesticide, as evidenced by a toxicity test showing that the transgenic plants produced greater shoot and root biomass than did the wild-type plants. Furthermore, at 0.02% (v/v) Mep, the transgenic plants degraded more than 99% of Mep after 14 days of growth. Our work indicates that transgenic plants expressing an OPH gene may provide a new strategy for decontaminating OP pollutants.

Immunodiagnostic Properties of Wucheraria bancrofti SXP-1, a Potential Filarial Diagnostic Candidate Expressed in Tobacco Plant, Nicotiana tabacum.

PubMed

Ganapathy, Mathangi; Chakravarthi, M; Charles, S Jason; Harunipriya, P; Jaiganesh, S; Subramonian, N; Kaliraj, P

2015-08-01

Transgenic tobacco plants were developed expressing WbSXP-1, a diagnostic antigen isolated from the cDNA library of L3 stage larvae of Wucheraria bancrofti. This antigen produced by recombinant Escherichia coli has been demonstrated by to be successful as potential diagnostic candidate against lymphatic filariasis. A rapid format simple and qualitative flow through immune-filtration diagnostic kit has been developed for the identification of IgG antibodies to the recombinant WbSXP-1 and is being marketed by M/S Span Diagnostics Ltd in India and Africa. Here, we present the results of experiments on the transformation and expression of the same filarial antigen, WbSXP-1, in tobacco plant, Nicotiana tabacum, to produce plant-based diagnostic antigen. It was possible to successfully transform the tobacco plant with WbSXP-1, the integration of the parasite-specific gene in plants was confirmed by PCR amplification and the expression of the filarial protein by Western blotting. The immunoreactivity of the plant-produced WbSXP-1 was assessed based on its reaction with the monoclonal antibodies developed against the E. coli-produced protein. Immunological screening using clinical sera from patients indicates that the plant-produced protein is comparable to E. coli-produced diagnostic antigen. The result demonstrated that plants can be used as suitable expression systems for the production of diagnostic proteins against lymphatic filariasis, a neglected tropical infectious disease which has a negative impact on socioeconomic development. This is the first report of the integration, expression and efficacy of a diagnostic candidate of lymphatic filariasis in plants.Key MessageTransgenic tobacco plants with WbSXP-1, a filarial diagnostic candidate, were developed. The plant-produced protein showed immunoreactivity on par with the E. coli product.

Contribution of transposable elements in the plant's genome.

PubMed

Sahebi, Mahbod; Hanafi, Mohamed M; van Wijnen, Andre J; Rice, David; Rafii, M Y; Azizi, Parisa; Osman, Mohamad; Taheri, Sima; Bakar, Mohd Faizal Abu; Isa, Mohd Noor Mat; Noor, Yusuf Muhammad

2018-07-30

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms. Copyright © 2018 Elsevier B.V. All rights reserved.

Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae

PubMed Central

Hodgins-Davis, Andrea; Adomas, Aleksandra B.; Warringer, Jonas; Townsend, Jeffrey P.

2012-01-01

Genetic variation for plastic phenotypes potentially contributes phenotypic variation to populations that can be selected during adaptation to novel ecological contexts. However, the basis and extent of plastic variation that manifests in diverse environments remains elusive. Here, we characterize copper reaction norms for mRNA abundance among five Saccharomyces cerevisiae strains to 1) describe population variation across the full range of ecologically relevant copper concentrations, from starvation to toxicity, and 2) to test the hypothesis that plastic networks exhibit increased population variation for gene expression. We find that although the vast majority of the variation is small in magnitude (considerably <2-fold), not just some, but most genes demonstrate variable expression across environments, across genetic backgrounds, or both. Plastically expressed genes included both genes regulated directly by copper-binding transcription factors Mac1 and Ace1 and genes indirectly responding to the downstream metabolic consequences of the copper gradient, particularly genes involved in copper, iron, and sulfur homeostasis. Copper-regulated gene networks exhibited more similar behavior within the population in environments where those networks have a large impact on fitness. Nevertheless, expression variation in genes like Cup1, important to surviving copper stress, was linked with variation in mitotic fitness and in the breadth of differential expression across the genome. By revealing a broader and deeper range of population variation, our results provide further evidence for the interconnectedness of genome-wide mRNA levels, their dependence on environmental context and genetic background, and the abundance of variation in gene expression that can contribute to future evolution. PMID:23019066

Anthropometric Variables and Somatotype of Young and Professional Male Basketball Players

PubMed Central

Kopiczko, Anna; Mikołajec, Kazimierz; Musalek, Martin

2018-01-01

Background: Determining somatic models and profiles in young athletes has recently become a fundamental element in selecting basketball playing positions. The aim of this study was to assess the relationship between the body build of young and adult elite male basketball players at different playing positions. Methods: Participants consisted of 35 young (age: 14.09 ± 0.30 years, n = 35) and 35 adult professional basketball players (age: 24.45 ± 5.40 years, n = 35) competing in elite leagues. The anthropometric characteristics assessed included body mass, body height, skinfolds, somatotypes, girths, and breadths. Results: The centers in both age groups were significantly taller and heavier (p < 0.001) compared to forwards and guards. The greatest difference between categories were in the guards’ personal height (from 169.36 to 186.68 = 17.32 cm). The guards from the professional team were closest in height to the forwards (difference = 7.17 cm) compared to young players where the difference between guards and forwards was 13.23 cm. Young competitors were more ectomorphic (2.12-3.75-4.17), while professional players were more mesomorphic (2.26-4.57-3.04). Significant criteria for center selection at professional level seems to be personal height and arm span ratio. Conclusions: The results indicate that the selection for basketball playing positions should include the analysis of body height and mass, shoulder breadth, humerus breadth, femur breadth and specifically for centers the difference between personal the height and arm span.

Anthropometric Variables and Somatotype of Young and Professional Male Basketball Players.

PubMed

Gryko, Karol; Kopiczko, Anna; Mikołajec, Kazimierz; Stasny, Petr; Musalek, Martin

2018-01-29

Determining somatic models and profiles in young athletes has recently become a fundamental element in selecting basketball playing positions. The aim of this study was to assess the relationship between the body build of young and adult elite male basketball players at different playing positions. Participants consisted of 35 young (age: 14.09 ± 0.30 years, n = 35) and 35 adult professional basketball players (age: 24.45 ± 5.40 years, n = 35) competing in elite leagues. The anthropometric characteristics assessed included body mass, body height, skinfolds, somatotypes, girths, and breadths. The centers in both age groups were significantly taller and heavier ( p < 0.001) compared to forwards and guards. The greatest difference between categories were in the guards' personal height (from 169.36 to 186.68 = 17.32 cm). The guards from the professional team were closest in height to the forwards (difference = 7.17 cm) compared to young players where the difference between guards and forwards was 13.23 cm. Young competitors were more ectomorphic (2.12-3.75-4.17), while professional players were more mesomorphic (2.26-4.57-3.04). Significant criteria for center selection at professional level seems to be personal height and arm span ratio. The results indicate that the selection for basketball playing positions should include the analysis of body height and mass, shoulder breadth, humerus breadth, femur breadth and specifically for centers the difference between personal the height and arm span.

Estimation of stature from hand and foot dimensions in a Korean population.

PubMed

Kim, Wonjoon; Kim, Yong Min; Yun, Myung Hwan

2018-04-01

The estimation of stature using foot and hand dimensions is essential in the process of personal identification. The shapes of feet and hands vary depending on races and gender, and it is of great importance to design an adequate equation in consideration of variances to estimate stature. This study is based on a total of 5,195 South Korean males and females, aged from 20 to 59 years. Body dimensions of stature, hand length, hand breadth, foot length, and foot breadth were measured according to standard anthropometric procedures. The independent t-test was performed in order to verify significant gender-induced differences and the results showed that there was significant difference between males and females for all the foot-hand dimensions (p<0.01). All dimensions showed a positive and statistically significant relation with stature in both genders (p<0.01). For both genders, the foot length showed highest correlation, whereas the hand breadth showed least correlation. The stepwise regression analysis was conducted, and the results showed that males had the highest prediction accuracy in the regression equation consisting of foot length and hand length (R 2 =0.532), whereas females had the highest accuracy in the regression model consisting of foot length and hand breadth (R 2 =0.437) The findings of this study indicated that hand and foot dimensions can be used to predict the stature of South Korean in the forensic science field. Copyright © 2018 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Expression and Chloroplast Targeting of Cholesterol Oxidase in Transgenic Tobacco Plants

PubMed Central

Corbin, David R.; Grebenok, Robert J.; Ohnmeiss, Thomas E.; Greenplate, John T.; Purcell, John P.

2001-01-01

Cholesterol oxidase represents a novel type of insecticidal protein with potent activity against the cotton boll weevil (Anthonomus grandis grandis Boheman). We transformed tobacco (Nicotiana tabacum) plants with the cholesterol oxidase choM gene and expressed cytosolic and chloroplast-targeted versions of the ChoM protein. Transgenic leaf tissues expressing cholesterol oxidase exerted insecticidal activity against boll weevil larvae. Our results indicate that cholesterol oxidase can metabolize phytosterols in vivo when produced cytosolically or when targeted to chloroplasts. The transgenic plants exhibiting cytosolic expression accumulated low levels of saturated sterols known as stanols, and displayed severe developmental aberrations. In contrast, the transgenic plants expressing chloroplast-targeted cholesterol oxidase maintained a greater accumulation of stanols, and appeared phenotypically and developmentally normal. These results are discussed within the context of plant sterol distribution and metabolism. PMID:11457962

Regulation of galactan synthase expression to modify galactan content in plants

DOEpatents

None

2017-08-22

The disclosure provides methods of engineering plants to modulate galactan content. Specifically, the disclosure provides methods for engineering a plant to increase the galactan content in a plant tissue by inducing expression of beta-1,4-galactan synthase (GALS), modulated by a heterologous promoter. Further disclosed are the methods of modulating expression level of GALS under the regulation of a transcription factor, as well as overexpression of UDP-galactose epimerse in the same plant tissue. Tissue specific promoters and transcription factors can be used in the methods are also provided.

The HSP terminator of Arabidopsis thaliana increases gene expression in plant cells.

PubMed

Nagaya, Shingo; Kawamura, Kazue; Shinmyo, Atsuhiko; Kato, Ko

2010-02-01

To express a foreign gene in plants effectively, a good expression system is required. Here we describe the identification of a transcriptional terminator that supports increased levels of expression. The terminators of several Arabidopsis genes were examined in transfected Arabidopsis T87 protoplasts. The heat shock protein 18.2 (HSP) terminator was the most effective in supporting increased levels of expression. The HSP terminator increases mRNA levels of both transiently and stably expressed transgenes approximately 2-fold more than the NOS (nopaline synthase) terminator. When combined with the HSP terminator, a translational enhancer increased gene expression levels approximately 60- to 100-fold in transgenic plants.

Regulatory functions of SnRK1 in stress-responsive gene expression and in plant growth and development.

PubMed

Cho, Young-Hee; Hong, Jung-Woo; Kim, Eun-Chul; Yoo, Sang-Dong

2012-04-01

Sucrose-nonfermentation1-related protein kinase1 (SnRK1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. Efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. To overcome these limitations and study SnRK1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable expression in transgenic plants. We found that both rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) SnRK1 activities critically influence stress-inducible gene expression and the induction of stress tolerance. Genetic, molecular, and chromatin immunoprecipitation analyses further revealed that the nuclear SnRK1 modulated target gene transcription in a submergence-dependent manner. From early seedling development through late senescence, SnRK1 activities appeared to modulate developmental processes in the plants. Our findings offer insight into the regulatory functions of plant SnRK1 in stress-responsive gene regulation and in plant growth and development throughout the life cycle.

Material and methods to increase plant growth and yield

DOEpatents

Kirst, Matias

2015-09-15

The present invention relates to materials and methods for modulating growth rates, yield, and/or resistance to drought conditions in plants. In one embodiment, a method of the invention comprises increasing expression of an hc1 gene (or a homolog thereof that provides for substantially the same activity), or increasing expression or activity of the protein encoded by an hc1 gene thereof, in a plant, wherein expression of the hc1 gene or expression or activity of the protein encoded by an hc1 gene results in increased growth rate, yield, and/or drought resistance in the plant.

Materials and methods to increase plant growth and yield

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

Kirst, Matias

The present invention relates to materials and methods for modulating growth rates, yield, and/or resistance to drought conditions in plants. In one embodiment, a method of the invention comprises increasing expression of an hc1 gene (or a homolog thereof that provides for substantially the same activity), or increasing expression or activity of the protein encoded by an hc1 gene thereof, in a plant, wherein expression of the hc1 gene or expression or activity of the protein encoded by an hc1 gene results in increased growth rate, yield, and/or drought resistance in the plant.

Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

PubMed Central

Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A.; Parra-Tabla, Víctor

2015-01-01

Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and –within each of these two plot types– mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity. PMID:26241962

Plant and algal cell walls: diversity and functionality

PubMed Central

Popper, Zoë A.; Ralet, Marie-Christine; Domozych, David S.

2014-01-01

Background Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore, wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes (plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. Scope The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research. PMID:25453142

Plant and algal cell walls: diversity and functionality.

PubMed

Popper, Zoë A; Ralet, Marie-Christine; Domozych, David S

2014-10-01

Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore,wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes ( plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research.

HIV-1 Antibody Neutralization Breadth Is Associated with Enhanced HIV-Specific CD4+ T Cell Responses

PubMed Central

Soghoian, Damien Z.; Lindqvist, Madelene; Ghebremichael, Musie; Donaghey, Faith; Carrington, Mary; Seaman, Michael S.; Kaufmann, Daniel E.; Walker, Bruce D.

2015-01-01

ABSTRACT Antigen-specific CD4+ T helper cell responses have long been recognized to be a critical component of effective vaccine immunity. CD4+ T cells are necessary to generate and maintain humoral immune responses by providing help to antigen-specific B cells for the production of antibodies. In HIV infection, CD4+ T cells are thought to be necessary for the induction of Env-specific broadly neutralizing antibodies. However, few studies have investigated the role of HIV-specific CD4+ T cells in association with HIV neutralizing antibody activity in vaccination or natural infection settings. Here, we conducted a comprehensive analysis of HIV-specific CD4+ T cell responses in a cohort of 34 untreated HIV-infected controllers matched for viral load, with and without neutralizing antibody breadth to a panel of viral strains. Our results show that the breadth and magnitude of Gag-specific CD4+ T cell responses were significantly higher in individuals with neutralizing antibodies than in those without neutralizing antibodies. The breadth of Gag-specific CD4+ T cell responses was positively correlated with the breadth of neutralizing antibody activity. Furthermore, the breadth and magnitude of gp41-specific, but not gp120-specific, CD4+ T cell responses were significantly elevated in individuals with neutralizing antibodies. Together, these data suggest that robust Gag-specific CD4+ T cells and, to a lesser extent, gp41-specific CD4+ T cells may provide important intermolecular help to Env-specific B cells that promote the generation or maintenance of Env-specific neutralizing antibodies. IMPORTANCE One of the earliest discoveries related to CD4+ T cell function was their provision of help to B cells in the development of antibody responses. Yet little is known about the role of CD4+ T helper responses in the setting of HIV infection, and no studies to date have evaluated the impact of HIV-specific CD4+ T cells on the generation of antibodies that can neutralize multiple different strains of HIV. Here, we addressed this question by analyzing HIV-specific CD4+ T cell responses in untreated HIV-infected persons with and without neutralizing antibodies. Our results indicate that HIV-infected persons with neutralizing antibodies have significantly more robust CD4+ T cell responses targeting Gag and gp41 proteins than individuals who lack neutralizing antibodies. These associations suggest that Gag- and gp41-specific CD4+ T cell responses may provide robust help to B cells for the generation or maintenance of neutralizing antibodies in natural HIV-infection. PMID:26656715

Remote sensing of gene expression in Planta: transgenic plants as monitors of exogenous stress perception in extraterrestrial environments

NASA Technical Reports Server (NTRS)

Manak, Michael S.; Paul, Anna-Lisa; Sehnke, Paul C.; Ferl, Robert J.

2002-01-01

Transgenic arabidopsis plants containing the alcohol dehydrogenase (Adh) gene promoter fused to the green fluorescent protein (GFP) reporter gene were developed as biological sensors for monitoring physiological responses to unique environments. Plants were monitored in vivo during exposure to hypoxia, high salt, cold, and abcissic acid in experiments designed to characterize the utility and responses of the Adh/GFP biosensors. Plants in the presence of environmental stimuli that induced the Adh promoter responded by expressing GFP, which in turn generated a detectable fluorescent signal. The GFP signal degraded when the inducing stimulus was removed. Digital imaging of the Adh/GFP plants exposed to each of the exogenous stresses demonstrated that the stress-induced gene expression could be followed in real time. The experimental results established the feasibility of using a digital monitoring system for collecting gene expression data in real time from Transgenic Arabidopsis Gene Expression System (TAGES) biosensor plants during space exploration experiments.

Metal resistance sequences and transgenic plants

DOEpatents

Meagher, Richard Brian; Summers, Anne O.; Rugh, Clayton L.

1999-10-12

The present invention provides nucleic acid sequences encoding a metal ion resistance protein, which are expressible in plant cells. The metal resistance protein provides for the enzymatic reduction of metal ions including but not limited to divalent Cu, divalent mercury, trivalent gold, divalent cadmium, lead ions and monovalent silver ions. Transgenic plants which express these coding sequences exhibit increased resistance to metal ions in the environment as compared with plants which have not been so genetically modified. Transgenic plants with improved resistance to organometals including alkylmercury compounds, among others, are provided by the further inclusion of plant-expressible organometal lyase coding sequences, as specifically exemplified by the plant-expressible merB coding sequence. Furthermore, these transgenic plants which have been genetically modified to express the metal resistance coding sequences of the present invention can participate in the bioremediation of metal contamination via the enzymatic reduction of metal ions. Transgenic plants resistant to organometals can further mediate remediation of organic metal compounds, for example, alkylmetal compounds including but not limited to methyl mercury, methyl lead compounds, methyl cadmium and methyl arsenic compounds, in the environment by causing the freeing of mercuric or other metal ions and the reduction of the ionic mercury or other metal ions to the less toxic elemental mercury or other metals.

A universal expression/silencing vector in plants.

PubMed

Peretz, Yuval; Mozes-Koch, Rita; Akad, Fuad; Tanne, Edna; Czosnek, Henryk; Sela, Ilan

2007-12-01

A universal vector (IL-60 and auxiliary constructs), expressing or silencing genes in every plant tested to date, is described. Plants that have been successfully manipulated by the IL-60 system include hard-to-manipulate species such as wheat (Triticum duram), pepper (Capsicum annuum), grapevine (Vitis vinifera), citrus, and olive (Olea europaea). Expression or silencing develops within a few days in tomato (Solanum lycopersicum), wheat, and most herbaceous plants and in up to 3 weeks in woody trees. Expression, as tested in tomato, is durable and persists throughout the life span of the plant. The vector is, in fact, a disarmed form of Tomato yellow leaf curl virus, which is applied as a double-stranded DNA and replicates as such. However, the disarmed virus does not support rolling-circle replication, and therefore viral progeny single-stranded DNA is not produced. IL-60 does not integrate into the plant's genome, and the construct, including the expressed gene, is not heritable. IL-60 is not transmitted by the Tomato yellow leaf curl virus's natural insect vector. In addition, artificial satellites were constructed that require a helper virus for replication, movement, and expression. With IL-60 as the disarmed helper "virus," transactivation occurs, resulting in an inducible expressing/silencing system. The system's potential is demonstrated by IL-60-derived suppression of a viral-silencing suppressor of Grapevine virus A, resulting in Grapevine virus A-resistant/tolerant plants.

RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants

USDA-ARS?s Scientific Manuscript database

The whitefly Bemisia tabaci (Genn.) is a pest and vector of plant viruses affecting plants worldwide. Using RNA interference (RNAi) to downregulate whitefly genes by expressing their homologous double stranded RNAs in plants has great potential for management of whiteflies to reduce plant virus dise...

Chaco Chachalaca (Ortalis canicollis, Wagler, 1830) feeding ecology in a gallery forest in the South Pantanal (Brazil).

PubMed

Ragusa-Netto, J

2015-01-01

Cracids are generalist frugivores, which often exploit plant food resources such as flowers and leaves, mainly when fruit production declines. The Chaco chachalaca (Ortalis canicollis) is the most abundant cracid in the Pantanal (Brazil), and particularly common in the gallery forests. However, the factors related to their occurrence in this habitat type are unclear. In this study I describe the feeding habits and feeding niche breadth fluctuations of the Chaco chachalaca in relation to food resources abundance and diversity at the Miranda river gallery forest (Southern Pantanal). I also analyzed the relationships between Chaco chachalacas feeding activity and food resources abundance. This parameter (flowers and fruits) exhibited significant seasonal differences of abundance in which flowers were plentiful at the end of the dry, while fruits were abundant during the early wet season. However, food resources diversity to Chaco chachalacas exhibited no seasonal difference. Their feeding activity paralleled the availability of food resources, so that when some items were massively available an enhanced number of Chaco chachalacas foraged in the gallery forest, particularly during the prolonged dry season when they extensively used flowers and Genipa americana fruits. In fact, the Chaco chachalaca feeding niche breadth value presented low values in this period, while high values were common in the rest of the year. The flexible diet of this cracid, potentially favors their year round presence in the gallery forest, mainly during the prolonged dry season when the propensity for famine might be high. Since the Chaco chachalaca is among the largest and most abundant canopy frugivores in the gallery forest, it may contribute to forest regeneration, an underscored role due to the impact of annual floods and meandering dynamics on tree loss.

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants.

PubMed

Lukan, Tjaša; Machens, Fabian; Coll, Anna; Baebler, Špela; Messerschmidt, Katrin; Gruden, Kristina

2018-01-01

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science.

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

PubMed Central

Machens, Fabian; Coll, Anna; Baebler, Špela; Messerschmidt, Katrin; Gruden, Kristina

2018-01-01

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science. PMID:29300787

Pathogen Phytosensing: Plants to Report Plant Pathogens

PubMed Central

Mazarei, Mitra; Teplova, Irina; Hajimorad, M. Reza; Stewart, C. Neal

2008-01-01

Real-time systems that provide evidence of pathogen contamination in crops can be an important new line of early defense in agricultural centers. Plants possess defense mechanisms to protect against pathogen attack. Inducible plant defense is controlled by signal transduction pathways, inducible promoters and cis-regulatory elements corresponding to key genes involved in defense, and pathogen-specific responses. Identified inducible promoters and cis-acting elements could be utilized in plant sentinels, or ‘phytosensors’, by fusing these to reporter genes to produce plants with altered phenotypes in response to the presence of pathogens. Here, we have employed cis-acting elements from promoter regions of pathogen inducible genes as well as those responsive to the plant defense signal molecules salicylic acid, jasmonic acid, and ethylene. Synthetic promoters were constructed by combining various regulatory elements supplemented with the enhancer elements from the Cauliflower mosaic virus (CaMV) 35S promoter to increase basal level of the GUS expression. The inducibility of each synthetic promoter was first assessed in transient expression assays using Arabidopsis thaliana protoplasts and then examined for efficacy in stably transgenic Arabidopsis and tobacco plants. Histochemical and fluorometric GUS expression analyses showed that both transgenic Arabidopsis and tobacco plants responded to elicitor and phytohormone treatments with increased GUS expression when compared to untreated plants. Pathogen-inducible phytosensor studies were initiated by analyzing the sensitivity of the synthetic promoters against virus infection. Transgenic tobacco plants infected with Alfalfa mosaic virus showed an increase in GUS expression when compared to mock-inoculated control plants, whereas Tobacco mosaic virus infection caused no changes in GUS expression. Further research, using these transgenic plants against a range of different pathogens with the regulation of detectable reporter gene could provide biological evidence to define the functional differences between pathogens, and provide new technology and applications for transgenic plants as phytosensors. PMID:27879840

Historical mathematics in the French eighteenth century.

PubMed

Richards, Joan L

2006-12-01

At least since the seventeenth century, the strange combination of epistemological certainty and ontological power that characterizes mathematics has made it a major focus of philosophical, social, and cultural negotiation. In the eighteenth century, all of these factors were at play as mathematical thinkers struggled to assimilate and extend the analysis they had inherited from the seventeenth century. A combination of educational convictions and historical assumptions supported a humanistic mathematics essentially defined by its flexibility and breadth. This mathematics was an expression of l'esprit humain, which was unfolding in a progressive historical narrative. The French Revolution dramatically altered the historical and educational landscapes that had supported this eighteenth-century approach, and within thirty years Augustin Louis Cauchy had radically reconceptualized and restructured mathematics to be rigorous rather than narrative.

Morphological, Genome and Gene Expression Changes in Newly Induced Autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino.

PubMed

Gao, Ri; Wang, Haibin; Dong, Bin; Yang, Xiaodong; Chen, Sumei; Jiang, Jiafu; Zhang, Zhaohe; Liu, Chen; Zhao, Nan; Chen, Fadi

2016-10-09

Autopolyploidy is widespread in higher plants and plays an important role in the process of evolution. The present study successfully induced autotetraploidys from Chrysanthemum lavandulifolium by colchicine. The plant morphology, genomic, transcriptomic, and epigenetic changes between tetraploid and diploid plants were investigated. Ligulate flower, tubular flower and leaves of tetraploid plants were greater than those of the diploid plants. Compared with diploid plants, the genome changed as a consequence of polyploidization in tetraploid plants, namely, 1.1% lost fragments and 1.6% novel fragments occurred. In addition, DNA methylation increased after genome doubling in tetraploid plants. Among 485 common transcript-derived fragments (TDFs), which existed in tetraploid and diploid progenitors, 62 fragments were detected as differentially expressed TDFs, 6.8% of TDFs exhibited up-regulated gene expression in the tetraploid plants and 6.0% exhibited down-regulation. The present study provides a reference for further studying the autopolyploidization role in the evolution of C. lavandulifolium. In conclusion, the autopolyploid C. lavandulifolium showed a global change in morphology, genome and gene expression compared with corresponding diploid.

Transgenic rice plants expressing a Bacillus subtilis protoporphyrinogen oxidase gene are resistant to diphenyl ether herbicide oxyfluorfen.

PubMed

Lee, H J; Lee, S B; Chung, J S; Han, S U; Han, O; Guh, J O; Jeon, J S; An, G; Back, K

2000-06-01

Protoporphyrinogen oxidase (Protox), the penultimate step enzyme of the branch point for the biosynthetic pathway of Chl and hemes, is the target site of action of diphenyl ether (DPE) herbicides. However, Bacillus subtilis Protox is known to be resistant to the herbicides. In order to develop the herbicide-resistant plants, the transgenic rice plants were generated via expression of B. subtilis Protox gene under ubiquitin promoter targeted to the cytoplasm or to the plastid using Agrobacterium-mediated gene transformation. The integration and expression of the transgene were investigated at T0 generation by DNA and RNA blots. Most transgenic rice plants revealed one copy transgene insertion into the rice genome, but some with 3 copies. The expression levels of B. subtilis Protox mRNA appeared to correlate with the copy number. Furthermore, the plastidal transgenic lines exhibited much higher expression of the Protox mRNA than the cytoplasmic transgenic lines. The transgenic plants expressing the B. subtilis Protox gene at T0 generation were found to be resistant to oxyfluorfen when judged by cellular damage with respect to cellular leakage, Chl loss, and lipid peroxidation. The transgenic rice plants targeted to the plastid exhibited higher resistance to the herbicide than the transgenic plants targeted to the cytoplasm. In addition, possible resistance mechanisms in the transgenic plants to DPE herbicides are discussed.

[Protective immune response of guinea pigs against challenge with foot and mouth disease virus by immunization with foliar extracts from transgenic tomato plants expressing the FMDV structural protein VP1].

PubMed

Pan, Li; Zhang, Yong-Guang; Wang, Yong-Lu; Wang, Bao-Qin; Xie, Qing-Ge

2006-10-01

The plant constitutive expression vector pBin438/VP1 for VP1 gene of foot-and-mouth disease virus strain O/ China/99 was constructed. Mediated with Agrobacterium tumefaciens GV3101 harboring pBin438/VP1, VP1 gene was transferred into cotyledons of tomato. After selected by Kanamysin, sixty resistant lines were obtained. The integration and transcription of the VP1 gene in transformed plants was detected by PCR and RT-PCR. After being detected by sandwich-ELISA assays, about 40% transformed plants confirmed to express the recombinant protein. The leave extracts of two positive lines were respectively emulsified in Freund's adjuvant and guinea pigs were intramuscular inoculation at days 0, 15 and 30d. According to the sera antibody levels and the protection of the vaccinated guinea pigs against challenge with 100ID50 FMDV, probed into the immunogenicity of the target protein expressed in transgenic plants. Experimental results showed that the plant expression vector was successfully constructed. PCR and RT-PCR analyses confirmed VP1 gene was transformed into tomato plants and got expression at the transcription levels. The expressed VP1 protein of FMDV, which was identified by ELISA and Western blot, can be specifically recognized by polyclonal antibodies against FMDV. Indirect-ELISA antibody titers reached 1:64 twenty-one days after the third inoculation. In the challenge test, the protection against FMDV challenge in two groups was 80% and 40% respectively. The immunization test in guinea pigs indicated that the expression product of transgenic tomato plants had immunogenicity and could effectively induce the specific antibodies against FMDV.

Can absolute and proportional anthropometric characteristics distinguish stronger and weaker powerlifters?

PubMed

Keogh, Justin W L; Hume, Patria A; Pearson, Simon N; Mellow, Peter J

2009-11-01

This study sought to compare the anthropometric profiles of 17 weaker and 17 stronger Australasian and Pacific powerlifters who had competed in a regional-, national-, or international-level powerlifting competition in New Zealand. Stronger lifters were defined as those having a Wilks score greater than 410, whereas those in the weaker group had a Wilks score less than 370. Each powerlifter was assessed for 37 anthropometric dimensions by International Society for the Advancement of Kinanthropometry (ISAK) level II and III accredited anthropometrists. Because all powerlifters were highly mesomorphic and possessed large girths and bone breadths, both in absolute terms and when expressed as Phantom-Z scores compared through the Phantom, relatively few significant anthropometric differences were observed. However, stronger lifters had significantly greater muscle mass and larger muscular girths in absolute terms as well as greater Brugsch Index (chest girth/height) and "Phantom"-normalized muscle mass, upper arm, chest, and forearm girths. In terms of the segment lengths and bone breadths, the only significant difference was that stronger lifters had a significantly shorter lower leg than weaker lifters. Because the majority of the significant differences were for muscle mass and muscular girths, it would appear likely that these differences contributed to the stronger lifters' superior performance. Powerlifters may therefore need to devote some of their training to the development of greater levels of muscular hypertrophy if they wish to continue to improve their performance. To better understand the anthropometric determinants of muscular strength, future research should recruit larger samples (particularly of elite lifters) and follow these subjects prospectively.

Breadth of neutralizing antibodies elicited by stable, homogeneous clade A and clade C HIV-1 gp140 envelope trimers in guinea pigs.

PubMed

Nkolola, Joseph P; Peng, Hanqin; Settembre, Ethan C; Freeman, Michael; Grandpre, Lauren E; Devoy, Colleen; Lynch, Diana M; La Porte, Annalena; Simmons, Nathaniel L; Bradley, Ritu; Montefiori, David C; Seaman, Michael S; Chen, Bing; Barouch, Dan H

2010-04-01

The native envelope (Env) spike on the surface of human immunodeficiency virus type 1 (HIV-1) is trimeric, and thus trimeric Env vaccine immunogens are currently being explored in preclinical immunogenicity studies. Key challenges have included the production and purification of biochemically homogeneous and stable trimers and the evaluation of these immunogens utilizing standardized virus panels for neutralization assays. Here we report the binding and neutralizing antibody (NAb) responses elicited by clade A (92UG037.8) and clade C (CZA97.012) Env gp140 trimer immunogens in guinea pigs. These trimers have been selected and engineered for optimal biochemical stability and have defined antigenic properties. Purified gp140 trimers with Ribi adjuvant elicited potent, cross-clade NAb responses against tier 1 viruses as well as detectable but low-titer NAb responses against select tier 2 viruses from clades A, B, and C. In particular, the clade C trimer elicited NAbs that neutralized 27%, 20%, and 47% of tier 2 viruses from clades A, B, and C, respectively. Heterologous DNA prime, protein boost as well as DNA prime, recombinant adenovirus boost regimens expressing these antigens, however, did not result in an increased magnitude or breadth of NAb responses in this system. These data demonstrate the immunogenicity of stable, homogeneous clade A and clade C gp140 trimers and exemplify the utility of standardized tier 1 and tier 2 virus panels for assessing the NAb responses of candidate HIV-1 Env immunogens.

An Oomycete CRN Effector Reprograms Expression of Plant HSP Genes by Targeting their Promoters

PubMed Central

Song, Tianqiao; Ma, Zhenchuan; Shen, Danyu; Li, Qi; Li, Wanlin; Su, Liming; Ye, Tingyue; Zhang, Meixiang; Wang, Yuanchao; Dou, Daolong

2015-01-01

Oomycete pathogens produce a large number of CRN effectors to manipulate plant immune responses and promote infection. However, their functional mechanisms are largely unknown. Here, we identified a Phytophthora sojae CRN effector PsCRN108 which contains a putative DNA-binding helix-hairpin-helix (HhH) motif and acts in the plant cell nucleus. Silencing of the PsCRN108 gene reduced P. sojae virulence to soybean, while expression of the gene in Nicotiana benthamiana and Arabidopsis thaliana enhanced plant susceptibility to P. capsici. Moreover, PsCRN108 could inhibit expression of HSP genes in A. thaliana, N. benthamiana and soybean. Both the HhH motif and nuclear localization signal of this effector were required for its contribution to virulence and its suppression of HSP gene expression. Furthermore, we found that PsCRN108 targeted HSP promoters in an HSE- and HhH motif-dependent manner. PsCRN108 could inhibit the association of the HSE with the plant heat shock transcription factor AtHsfA1a, which initializes HSP gene expression in response to stress. Therefore, our data support a role for PsCRN108 as a nucleomodulin in down-regulating the expression of plant defense-related genes by directly targeting specific plant promoters. PMID:26714171

An Oomycete CRN Effector Reprograms Expression of Plant HSP Genes by Targeting their Promoters.

PubMed

Song, Tianqiao; Ma, Zhenchuan; Shen, Danyu; Li, Qi; Li, Wanlin; Su, Liming; Ye, Tingyue; Zhang, Meixiang; Wang, Yuanchao; Dou, Daolong

2015-12-01

Oomycete pathogens produce a large number of CRN effectors to manipulate plant immune responses and promote infection. However, their functional mechanisms are largely unknown. Here, we identified a Phytophthora sojae CRN effector PsCRN108 which contains a putative DNA-binding helix-hairpin-helix (HhH) motif and acts in the plant cell nucleus. Silencing of the PsCRN108 gene reduced P. sojae virulence to soybean, while expression of the gene in Nicotiana benthamiana and Arabidopsis thaliana enhanced plant susceptibility to P. capsici. Moreover, PsCRN108 could inhibit expression of HSP genes in A. thaliana, N. benthamiana and soybean. Both the HhH motif and nuclear localization signal of this effector were required for its contribution to virulence and its suppression of HSP gene expression. Furthermore, we found that PsCRN108 targeted HSP promoters in an HSE- and HhH motif-dependent manner. PsCRN108 could inhibit the association of the HSE with the plant heat shock transcription factor AtHsfA1a, which initializes HSP gene expression in response to stress. Therefore, our data support a role for PsCRN108 as a nucleomodulin in down-regulating the expression of plant defense-related genes by directly targeting specific plant promoters.

Influence of lunar cycles on growth of Ashwagandha (Withania somnifera [L.] Dunal).

PubMed

Tavhare, Swagata D; Nishteswar, K; Shukla, Vinay J

2015-01-01

Ayurvedic classics have advocated to collect the medicinal plants according to part used and seasons in order to get desired pharmacological action and therapeutic benefits. The logic behind this principle is being validated by recent researches. To analyze the influence of lunar cycles on growth of Ashwagandha in Shishira and Greeshma Ritu (winter and summer season). Fourteen small crops of Ashwagandha of average size 10 cm were collected on October 7, 2013, from institute campus and then replantation was done at Charaka Herbal Garden, Gujarat Ayurved University, Jamnagar in an area of 60 cm × 60 cm (l × b). No fertilizers or pesticides were used. The plants were watered daily and plants were uprooted as per lunar cycles for analysis. Eight samples were collected and observed during Shishira and Greeshma season on Pournima (full moon) and Amavasya (new moon) days. The measurements were taken thrice and average values were taken into consideration for study purpose. The variations in morphological characteristics such as length, breadth, weight, and number of roots and twigs were studied through statistical procedure of principle component analysis, which makes interpretation of all possible related variables. Root weight (RW), pith diameter (PD) and internodal distance (ID) were found to be increased on full moon days as compared to new moon days. The maximum RW was observed during Greeshma Aashadha Pournima. The study has shown a definite influence of lunar cycles on the growth of the plant parts assessed by RW, PD, and ID that have found to be increased on full moon days as compared to new moon days.

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response

PubMed Central

Tsai, Alex Yi-Lin; Chan, Kin; Ho, Chi-Yip; Canam, Thomas; Capron, Resmi; Master, Emma R.; Bräutigam, Katharina

2017-01-01

The plant cell wall is an abundant and renewable resource for lignocellulosic applications such as the production of biofuel. Due to structural and compositional complexities, the plant cell wall is, however, recalcitrant to hydrolysis and extraction of platform sugars. A cell wall engineering strategy to reduce this recalcitrance makes use of microbial cell wall modifying enzymes that are expressed directly in plants themselves. Previously, we constructed transgenic Arabidopsis thaliana constitutively expressing the fungal hemicellulases: Phanerochaete carnosa glucurnoyl esterase (PcGCE) and Aspergillus nidulans α-arabinofuranosidase (AnAF54). While the PcGCE lines demonstrated improved xylan extractability, they also displayed chlorotic leaves leading to the hypothesis that expression of such enzymes in planta resulted in plant stress. The objective of this study is to investigate the impact of transgenic expression of the aforementioned microbial hemicellulases in planta on the host arabidopsis. More specifically, we investigated transcriptome profiles by short read high throughput sequencing (RNAseq) from developmentally distinct parts of the plant stem. When compared to non-transformed wild-type plants, a subset of genes was identified that showed differential transcript abundance in all transgenic lines and tissues investigated. Intriguingly, this core set of genes was significantly enriched for those involved in plant defense and biotic stress responses. While stress and defense-related genes showed increased transcript abundance in the transgenic plants regardless of tissue or genotype, genes involved in photosynthesis (light harvesting) were decreased in their transcript abundance potentially reflecting wide-spread effects of heterologous microbial transgene expression and the maintenance of plant homeostasis. Additionally, an increase in transcript abundance for genes involved in salicylic acid signaling further substantiates our finding that transgenic expression of microbial cell wall modifying enzymes induces transcriptome responses similar to those observed in defense responses. PMID:28253318

Fall armyworm (Lepidoptera: Noctuidae) development survivorship and damage on cotton plants expressing insecticidal plant-incorporated protectants

USDA-ARS?s Scientific Manuscript database

Cotton, Gossypium hirsutum (L.), plants expressing insecticidal crystal (Cry) proteins of Bacillus thuringiensis (Bt) Berliner are planted on significant acreage across the Southern region of the United States. Fall armyworm, Spodoptera frugiperda (J. E. Smith), can be a significant cotton pest in ...

Minimizing the unpredictability of transgene expression in plants: the role of genetic insulators

USDA-ARS?s Scientific Manuscript database

The genetic transformation of plants has become a necessary tool for fundamental plant biology research, as well as the generation of engineered plants exhibiting improved agronomic and industrial traits. However, this technology is significantly hindered by the fact that transgene expression is hi...

Report of the Defense Science Board Task Force on Military Applications of New-Generation Computing Technologies.

DTIC Science & Technology

1984-12-01

1980’s we are seeing enhancement of breadth, power, and accessibility of computers in many dimensions: o Pov~erfu1, costly fragile mainframes for...During the 1980’s we are seeing enhancement of breadth, power and accessibility of computers in many dimensions. (1) Powerful, costly, fragile mainframes... X A~ ’ EMORANDlUM FOR THE t-RAIRMAN, DEFENSE<. ’ ’...’"" S!B.FECT: Defense Science Board T is F- Supercomputei Applicai io, Yoi are requested to

Anthropometric Survey of US Army Personnel (1988): Correlation Coefficients and Regression Equations. Part 4. Bivariate Regression Tables

DTIC Science & Technology

1990-05-01

THUMBBR THUMB BREADTH NO. VARIABLE CONSTANT REGRESS. COEF. ST.ERROR ADJUQTED (.ERR OF ESTIMATE E4 58 HANDBRTH 7.623 0.183 ( 0.006) 1.124 .319 59 HANDCIRC...945, 956, 965 TRAGION TO TOP OF HEAD (TRAGT, 255) 39,51, 718, 851, 899, 945, 956, 965 Trapezius Post 23 Trochanter 23 TROCHArNTERION HEIGHT (TROQINT...THGHCLR, 105) 33, 40, 673, M08 881,927, 955, 964 Thigh Poia 23 THUMB BREADTH (THUMBBR, 106) 34, 49, 674,88 882,94955, 964 ThumlAip 23 THUMBTIP REACH

A rice chloroplast transit peptide sequence does not alter the cytoplasmic localization of sheep serotonin N-acetyltransferase expressed in transgenic rice plants.

PubMed

Byeon, Yeong; Lee, Hyoung Yool; Lee, Kyungjin; Back, Kyoungwhan

2014-09-01

Ectopic overexpression of melatonin biosynthetic genes of animal origin has been used to generate melatonin-rich transgenic plants to examine the functional roles of melatonin in plants. However, the subcellular localization of these proteins expressed in the transgenic plants remains unknown. We studied the localization of sheep (Ovis aries) serotonin N-acetyltransferase (OaSNAT) and a translational fusion of a rice SNAT transit peptide to OaSNAT (TS:OaSNAT) in plants. Laser confocal microscopy analysis revealed that both OaSNAT and TS:OaSNAT proteins were localized to the cytoplasm even with the addition of the transit sequence to OaSNAT. Transgenic rice plants overexpressing the TS:OaSNAT fusion transgene exhibited high SNAT enzyme activity relative to untransformed wild-type plants, but lower activity than transgenic rice plants expressing the wild-type OaSNAT gene. Melatonin levels in both types of transgenic rice plant corresponded well with SNAT enzyme activity levels. The TS:OaSNAT transgenic lines exhibited increased seminal root growth relative to wild-type plants, but less than in the OaSNAT transgenic lines, confirming that melatonin promotes root growth. Seed-specific OaSNAT expression under the control of a rice prolamin promoter did not confer high levels of melatonin production in transgenic rice seeds compared with seeds from transgenic plants expressing OaSNAT under the control of the constitutive maize ubiquitin promoter. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Overexpression of an Arabidopsis heterogeneous nuclear ribonucleoprotein gene, AtRNP1, affects plant growth and reduces plant tolerance to drought and salt stresses

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

Wang, Zhenyu, E-mail: wzy72609@163.com; Zhao, Xiuyang, E-mail: xiuzh@psb.vib-ugent.be; Wang, Bing, E-mail: wangbing@ibcas.ac.cn

Heterogeneous nuclear ribonucleoproteins (hnRNPs) participate in diverse regulations of plant growth and environmental stress responses. In this work, an Arabidopsis hnRNP of unknown function, AtRNP1, was investigated. We found that AtRNP1 gene is highly expressed in rosette and cauline leaves, and slightly induced under drought, salt, osmotic and ABA stresses. AtRNP1 protein is localized to both the nucleus and cytoplasm. We performed homologous overexpression of AtRNP1 and found that the transgenic plants showed shortened root length and plant height, and accelerated flowering. In addition, the transgenic plants also showed reduced tolerance to drought, salt, osmotic and ABA stresses. Further studiesmore » revealed that under both normal and stress conditions, the proline contents in the transgenic plants are markedly decreased, associated with reduced expression levels of a proline synthase gene and several stress-responsive genes. These results suggested that the overexpression of AtRNP1 negatively affects plant growth and abiotic stress tolerance. - Highlights: • AtRNP1 is a widely expressed gene and its expression is slightly induced under abiotic stresses. • AtRNP1 protein is localized to both the nucleus and cytoplasm. • Overexpression of AtRNP1 affects plant growth. • Overexpression of AtRNP1 reduces plant tolerance to drought and salt stresses. • AtRNP1 overexpression plants show decreased proline accumulation and stress-responsive gene expressions.« less

Molecular pharming - VLPs made in plants.

PubMed

Marsian, Johanna; Lomonossoff, George P

2016-02-01

Plant-based expression offers a safe, inexpensive and potentially limitless way to produce therapeutics in a quick and flexible manner. Plants require only simple inorganic nutrients, water, carbon dioxide and sunlight for efficient growth. Virus-like particles (VLPs) are convincing look-alikes of viruses but without carrying infectious genomic material. However, they can still elicit a very potent immune response which makes them ideal vaccine candidates. In this review the different methods of plant expression are described together with the most recent developments in the field of transiently-expressed plant-made VLPs. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Improvement of the Trivalent Inactivated Flu Vaccine Using PapMV Nanoparticles

PubMed Central

Savard, Christian; Guérin, Annie; Drouin, Karine; Bolduc, Marilène; Laliberté-Gagné, Marie-Eve; Dumas, Marie-Christine; Majeau, Nathalie; Leclerc, Denis

2011-01-01

Commercial seasonal flu vaccines induce production of antibodies directed mostly towards hemaglutinin (HA). Because HA changes rapidly in the circulating virus, the protection remains partial. Several conserved viral proteins, e.g., nucleocapsid (NP) and matrix proteins (M1), are present in the vaccine, but are not immunogenic. To improve the protection provided by these vaccines, we used nanoparticles made of the coat protein of a plant virus (papaya mosaic virus; PapMV) as an adjuvant. Immunization of mice and ferrets with the adjuvanted formulation increased the magnitude and breadth of the humoral response to NP and to highly conserved regions of HA. They also triggered a cellular mediated immune response to NP and M1, and long-lasting protection in animals challenged with a heterosubtypic influenza strain (WSN/33). Thus, seasonal flu vaccine adjuvanted with PapMV nanoparticles can induce universal protection to influenza, which is a major advancement when facing a pandemic. PMID:21747909

“Real time” genetic manipulation: a new tool for ecological field studies

PubMed Central

Schäfer, Martin; Brütting, Christoph; Gase, Klaus; Reichelt, Michael; Baldwin, Ian; Meldau, Stefan

2014-01-01

Summary Field experiments with transgenic plants often reveal the functional significance of genetic traits important for plant performance in their natural environments. Until now, only constitutive overexpression, ectopic expression and gene silencing methods have been used to analyze gene-related phenotypes in natural habitats. These methods do not allow sufficient control over gene expression to study ecological interactions in real-time, genetic traits playing essential roles in development, or dose-dependent effects. We applied the sensitive dexamethasone (DEX)-inducible pOp6/LhGR expression system to the ecological model plant Nicotiana attenuata and established a lanolin-based DEX application method to facilitate ectopic gene expression and RNAi mediated gene silencing in the field and under challenging conditions (e.g. high temperature, wind and UV radiation). Fully established field-grown plants were used to silence phytoene desaturase and thereby cause photobleaching only in specific plant sectors, and to activate expression of the cytokinin (CK) biosynthesis gene isopentenyl transferase (ipt). We used ipt expression to analyze the role of CK’s in both the glasshouse and field to understand resistance to the native herbivore Tupiocoris notatus, which attack plants at small spatial scales. By spatially restricting ipt expression and elevating CK levels in single leaves, T. notatus damage increased, demonstrating CK’s role in this plant-herbivore interaction at a small scale. As the arena of most ecological interactions is highly constrained in time and space, these tools will advance the genetic analysis of dynamic traits that matter for plant performance in nature. PMID:23906159

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

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

Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

DOE PAGES

Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.; ...

2016-11-01

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN

PubMed Central

Soifer, Ilya; Barad, Omer; Shem-Tov, Doron; Baruch, Kobi; Lu, Fei; Hernandez, Alvaro G.; Wright, Chris L.; Koehler, Klaus; Buell, C. Robin; de Leon, Natalia

2016-01-01

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools. PMID:27803309

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

PubMed Central

da Silva, Carlos R. M.; Andrade, Alan C.; Marraccini, Pierre; Teixeira, João B.; Carazzolle, Marcelo F.; Pereira, Gonçalo A. G.; Pereira, Luiz Filipe P.; Vanzela, André L. L.; Wang, Lu; Jordan, I. King; Carareto, Claudia M. A.

2013-01-01

Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. PMID:24244387

Expression of geminiviral AC2 RNA silencing suppressor changes sugar and jasmonate responsive gene expression in transgenic tobacco plants

PubMed Central

2012-01-01

Background RNA-silencing is a conserved gene regulation and surveillance machinery, which in plants, is also used as major defence mechanism against viruses. Various virus-specific dsRNA structures are recognized by the silencing machinery leading to degradation of the viral RNAs or, as in case of begomoviruses, to methylation of their DNA genomes. Viruses produce specific RNA silencing suppressor (RSS) proteins to prevent these host defence mechanisms, and as these interfere with the silencing machinery they also disturb the endogenous silencing reactions. In this paper, we describe how expression of AC2 RSS, derived from African cassava mosaic geminivirus changes transcription profile in tobacco (Nicotiana tabacum) leaves and in flowers. Results Expression of AC2 RSS in transgenic tobacco plants induced clear phenotypic changes both in leaves and in flowers. Transcriptomes of these plants were strongly altered, with total of 1118 and 251 differentially expressed genes in leaves and flowers, respectively. The three most up-regulated transcript groups were related to stress, cell wall modifications and signalling, whereas the three most down-regulated groups were related to translation, photosynthesis and transcription. It appears that many of the gene expression alterations appeared to be related to enhanced biosynthesis of jasmonate and ethylene, and consequent enhancement of the genes and pathways that are regulated by these hormones, or to the retrograde signalling caused by the reduced photosynthetic activity and sugar metabolism. Comparison of these results to a previous transcriptional profiling of HC-Pro RSS-expressing plants revealed that some of same genes were induced by both RSSs, but their expression levels were typically higher in AC2 than in HC-Pro RSS expressing plants. All in all, a large number of transcript alterations were found to be specific to each of the RSS expressing transgenic plants. Conclusions AC2 RSS in transgenic tobacco plants interferes with the silencing machinery. It causes stress and defence reactions for instance via induction of the jasmonate and ethylene biosynthesis, and by consequent gene expression alteration regulated by these hormones. The changed sugar metabolism may cause significant down-regulation of genes encoding ribosomal proteins, thus reducing the general translation level. PMID:23130567

Plants with elevated levels of glucan

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

Pauly, Markus; Kraemer, Florian J.; Hake, Sarah

The present disclosure relates to mutations in licheninase genes encoding polypeptides with decreased licheninase activity, which when expressed in plants results in elevated levels of glucan in the plants. In particular, the disclosure relates to licheninase nucleic acids and polypeptides related to glucan accumulation in plants, plants with reduced expression of a licheninase nucleic acid, and methods related to the generation of plants with increased glucan content in the cell walls of leaf tissue.

Foliar extracts from transgenic tomato plants expressing the structural polyprotein, P1-2A, and protease, 3C, from foot-and-mouth disease virus elicit a protective response in guinea pigs.

PubMed

Pan, Li; Zhang, Yongguang; Wang, Yonglu; Wang, Baoqin; Wang, Wenxiu; Fang, Yuzhen; Jiang, Shoutian; Lv, Jianliang; Wang, Wei; Sun, Yuan; Xie, Qingge

2008-01-15

The expression of recombinant antigens in transgenic plants is increasingly used as an alternative method of producing experimental immunogens. In this report, we describe the production of transgenic tomato plants that express the structural polyprotein, P1-2A, and protease, 3C, from foot-and-mouth disease (FMDV). P1-2A3C was inserted into the plant binary vector, pBin438, and transformed into tomato plants using Agrobacterium tumefaciens strain, GV3101. The presence of P1-2A3C was confirmed by PCR, transcription was verified by RT-PCR, and recombinant protein expression was confirmed by sandwich-ELISA and Western blot analyses. Guinea pigs immunized intramuscularly with foliar extracts from P1-2A3C-transgenic tomato plants were found to develop a virus-specific antibody response against FMDV. Vaccinated guinea pigs were fully protected against a challenge infection, while guinea pigs injected with untransformed plant extracts failed to elicit an antibody response and were not protected against challenge. These results demonstrate that transgenic tomato plants expressing the FMDV structural polyprotein, P1-2A, and the protease, 3C, can be used as a source of recombinant antigen for vaccine production.

Glutathione Transferase from Trichoderma virens Enhances Cadmium Tolerance without Enhancing Its Accumulation in Transgenic Nicotiana tabacum

PubMed Central

Dixit, Prachy; Mukherjee, Prasun K.; Ramachandran, V.; Eapen, Susan

2011-01-01

Background Cadmium (Cd) is a major heavy metal pollutant which is highly toxic to plants and animals. Vast agricultural areas worldwide are contaminated with Cd. Plants take up Cd and through the food chain it reaches humans and causes toxicity. It is ideal to develop plants tolerant to Cd, without enhanced accumulation in the edible parts for human consumption. Glutathione transferases (GST) are a family of multifunctional enzymes known to have important roles in combating oxidative stresses induced by various heavy metals including Cd. Some GSTs are also known to function as glutathione peroxidases. Overexpression/heterologous expression of GSTs is expected to result in plants tolerant to heavy metals such as Cd. Results Here, we report cloning of a glutathione transferase gene from Trichoderma virens, a biocontrol fungus and introducing it into Nicotiana tabacum plants by Agrobacterium-mediated gene transfer. Transgenic nature of the plants was confirmed by Southern blot hybridization and expression by reverse transcription PCR. Transgene (TvGST) showed single gene Mendelian inheritance. When transgenic plants expressing TvGST gene were exposed to different concentrations of Cd, they were found to be more tolerant compared to wild type plants, with transgenic plants showing lower levels of lipid peroxidation. Levels of different antioxidant enzymes such as glutathione transferase, superoxide dismutase, ascorbate peroxidase, guiacol peroxidase and catalase showed enhanced levels in transgenic plants expressing TvGST compared to control plants, when exposed to Cd. Cadmium accumulation in the plant biomass in transgenic plants were similar or lower than wild-type plants. Conclusion The results of the present study suggest that transgenic tobacco plants expressing a Trichoderma virens GST are more tolerant to Cd, without enhancing its accumulation in the plant biomass. It should be possible to extend the present results to crop plants for developing Cd tolerance and in limiting Cd availability in the food chain. PMID:21283689

Expression of Antisense Long Noncoding RNAs as Potential Regulators in Rainbow Trout with Different Tolerance to Plant-Based Diets.

PubMed

Abernathy, Jason; Overturf, Ken

2018-01-04

Reformulation of aquafeeds in salmonid diets to include more plant proteins is critical for sustainable aquaculture. However, increasing plant proteins can lead to stunted growth and enteritis. Toward an understanding of the regulatory mechanisms behind plant protein utilization, directional RNA sequencing of liver tissues from a rainbow trout strain selected for growth on an all plant-protein diet and a control strain, both fed a plant diet for 12 weeks, were utilized to construct long noncoding RNAs. Antisense long noncoding RNAs were selected for differential expression and functional analyses since they have been shown to have regulatory actions within a genome. A total of 142 unique antisense long noncoding RNAs were differentially expressed between strains, 60 of which could be mapped to a gene. Genes underlying these noncoding RNAs are indicated in lipid metabolism and immunity. Six noncoding transcripts were also found to overlap with differentially expressed protein-coding genes, all of which were co-expressed. Associating variation in regulatory elements between rainbow trout strains with differing tolerance to plant-protein diets will assist in future studies toward increased gains throughout carnivorous aquaculture.

Light availability affects sex lability in a gynodioecious plant.

PubMed

Varga, Sandra; Kytöviita, Minna-Maarit

2016-11-01

Sex lability (i.e., gender diphasy) in plants is classically linked to the larger resource needs associated with the female sexual function (i.e., seed production) compared to the male function (i.e., pollen production). Sex lability in response to the environment is extensively documented in dioecious species, but has been largely overlooked in gynodioecious plants. Here, we tested whether environmental conditions induce sex lability in the gynodioecious Geranium sylvaticum. We conducted a transplantation experiment in the field where plants with different sex expression were reciprocally transplanted between high light and low light habitats. We measured plants' reproductive output and sex expression over four years. Our results show that sex expression was labile over the study period. The light level at the destination habitat had a significant effect on sexual expression and reproductive output, because plants decreased their reproductive output when transplanted to the low light habitat. Transplantation origin did not affect any parameter measured. This study shows that sex expression in Geranium sylvaticum is labile and related to light availability. Sexually labile plants did not produce more seeds or pollen, and thus, there was no apparent fitness gain in sexually labile individuals. Sex lability in gynodioecious plants may be more common than previously believed because detection of sex lability necessitates data on the same individuals over time, which is rare in sexually dimorphic herbaceous plants. © 2016 Botanical Society of America.

GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis.

PubMed

Coll, Anna; Wilson, Mandy L; Gruden, Kristina; Peccoud, Jean

2016-01-01

With the rapid advances in prediction tools for discovery of new promoters and their cis-elements, there is a need to improve plant expression methodologies in order to facilitate a high-throughput functional validation of these promoters in planta. The promoter-reporter analysis is an indispensible approach for characterization of plant promoters. It requires the design of complex plant expression vectors, which can be challenging. Here, we describe the use of a plant grammar implemented in GenoCAD that will allow the users to quickly design constructs for promoter analysis experiments but also for other in planta functional studies. The GenoCAD plant grammar includes a library of plant biological parts organized in structural categories to facilitate their use and management and a set of rules that guides the process of assembling these biological parts into large constructs.

More than 400 million years of evolution and some plants still can't make it on their own: Plant stress tolerance via fungal symbiosis

USGS Publications Warehouse

Rodriguez, R.; Redman, R.

2008-01-01

All plants in natural ecosystems are thought to be symbiotic with mycorrhizal and/or endophytic fungi. Collectively, these fungi express different symbiotic lifestyles ranging from parasitism to mutualism. Analysis of Colletotrichum species indicates that individual isolates can express either parasitic or mutualistic lifestyles depending on the host genotype colonized. The endophyte colonization pattern and lifestyle expression indicate that plants can be discerned as either disease, non-disease, or non-hosts. Fitness benefits conferred by fungi expressing mutualistic lifestyles include biotic and abiotic stress tolerance, growth enhancement, and increased reproductive success. Analysis of plant-endophyte associations in high stress habitats revealed that at least some fungal endophytes confer habitat-specific stress tolerance to host plants. Without the habitat-adapted fungal endophytes, the plants are unable to survive in their native habitats. Moreover, the endophytes have a broad host range encompassing both monocots and eudicots, and confer habitat-specific stress tolerance to both plant groups. ?? The Author [2008]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.

Photo anthropometric variations in Japanese facial features: Establishment of large-sample standard reference data for personal identification using a three-dimensional capture system.

PubMed

Ogawa, Y; Wada, B; Taniguchi, K; Miyasaka, S; Imaizumi, K

2015-12-01

This study clarifies the anthropometric variations of the Japanese face by presenting large-sample population data of photo anthropometric measurements. The measurements can be used as standard reference data for the personal identification of facial images in forensic practices. To this end, three-dimensional (3D) facial images of 1126 Japanese individuals (865 male and 261 female Japanese individuals, aged 19-60 years) were acquired as samples using an already validated 3D capture system, and normative anthropometric analysis was carried out. In this anthropometric analysis, first, anthropological landmarks (22 items, i.e., entocanthion (en), alare (al), cheilion (ch), zygion (zy), gonion (go), sellion (se), gnathion (gn), labrale superius (ls), stomion (sto), labrale inferius (li)) were positioned on each 3D facial image (the direction of which had been adjusted to the Frankfort horizontal plane as the standard position for appropriate anthropometry), and anthropometric absolute measurements (19 items, i.e., bientocanthion breadth (en-en), nose breadth (al-al), mouth breadth (ch-ch), bizygomatic breadth (zy-zy), bigonial breadth (go-go), morphologic face height (se-gn), upper-lip height (ls-sto), lower-lip height (sto-li)) were exported using computer software for the measurement of a 3D digital object. Second, anthropometric indices (21 items, i.e., (se-gn)/(zy-zy), (en-en)/(al-al), (ls-li)/(ch-ch), (ls-sto)/(sto-li)) were calculated from these exported measurements. As a result, basic statistics, such as the mean values, standard deviations, and quartiles, and details of the distributions of these anthropometric results were shown. All of the results except "upper/lower lip ratio (ls-sto)/(sto-li)" were normally distributed. They were acquired as carefully as possible employing a 3D capture system and 3D digital imaging technologies. The sample of images was much larger than any Japanese sample used before for the purpose of personal identification. The measurements will be useful as standard reference data for forensic practices and as material data for future studies in this field. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Breadth of Coverage, Ease of Use, and Quality of Mobile Point-of-Care Tool Information Summaries: An Evaluation

PubMed Central

Ren, Jinma

2016-01-01

Background With advances in mobile technology, accessibility of clinical resources at the point of care has increased. Objective The objective of this research was to identify if six selected mobile point-of-care tools meet the needs of clinicians in internal medicine. Point-of-care tools were evaluated for breadth of coverage, ease of use, and quality. Methods Six point-of-care tools were evaluated utilizing four different devices (two smartphones and two tablets). Breadth of coverage was measured using select International Classification of Diseases, Ninth Revision, codes if information on summary, etiology, pathophysiology, clinical manifestations, diagnosis, treatment, and prognosis was provided. Quality measures included treatment and diagnostic inline references and individual and application time stamping. Ease of use covered search within topic, table of contents, scrolling, affordance, connectivity, and personal accounts. Analysis of variance based on the rank of score was used. Results Breadth of coverage was similar among Medscape (mean 6.88), Uptodate (mean 6.51), DynaMedPlus (mean 6.46), and EvidencePlus (mean 6.41) (P>.05) with DynaMed (mean 5.53) and Epocrates (mean 6.12) scoring significantly lower (P<.05). Ease of use had DynaMedPlus with the highest score, and EvidencePlus was lowest (6.0 vs 4.0, respectively, P<.05). For quality, reviewers rated the same score (4.00) for all tools except for Medscape, which was rated lower (P<.05). Conclusions For breadth of coverage, most point-of-care tools were similar with the exception of DynaMed. For ease of use, only UpToDate and DynaMedPlus allow for search within a topic. All point-of-care tools have remote access with the exception of UpToDate and Essential Evidence Plus. All tools except Medscape covered criteria for quality evaluation. Overall, there was no significant difference between the point-of-care tools with regard to coverage on common topics used by internal medicine clinicians. Selection of point-of-care tools is highly dependent on individual preference based on ease of use and cost of the application. PMID:27733328

HIV-1 Envelope Glycoproteins from Diverse Clades Differentiate Antibody Responses and Durability among Vaccinees

PubMed Central

2018-01-01

ABSTRACT Induction of broadly cross-reactive antiviral humoral responses with the capacity to target globally diverse circulating strains is a key goal for HIV-1 immunogen design. A major gap in the field is the identification of diverse HIV-1 envelope antigens to evaluate vaccine regimens for binding antibody breadth. In this study, we define unique antigen panels to map HIV-1 vaccine-elicited antibody breadth and durability. Diverse HIV-1 envelope glycoproteins were selected based on genetic and geographic diversity to cover the global epidemic, with a focus on sexually acquired transmitted/founder viruses with a tier 2 neutralization phenotype. Unique antigenicity was determined by nonredundancy (Spearman correlation), and antigens were clustered using partitioning around medoids (PAM) to identify antigen diversity. Cross-validation demonstrated that the PAM method was better than selection by reactivity and random selection. Analysis of vaccine-elicited V1V2 binding antibody in longitudinal samples from the RV144 clinical trial revealed the striking heterogeneity among individual vaccinees in maintaining durable responses. These data support the idea that a major goal for vaccine development is to improve antibody levels, breadth, and durability at the population level. Elucidating the level and durability of vaccine-elicited binding antibody breadth needed for protection is critical for the development of a globally efficacious HIV vaccine. IMPORTANCE The path toward an efficacious HIV-1 vaccine will require characterization of vaccine-induced immunity that can recognize and target the highly genetically diverse virus envelope glycoproteins. Antibodies that target the envelope glycoproteins, including diverse sequences within the first and second hypervariable regions (V1V2) of gp120, were identified as correlates of risk for the one partially efficacious HIV-1 vaccine. To build upon this discovery, we experimentally and computationally evaluated humoral responses to define envelope glycoproteins representative of the antigenic diversity of HIV globally. These diverse envelope antigens distinguished binding antibody breadth and durability among vaccine candidates, thus providing insights for advancing the most promising HIV-1 vaccine candidates. PMID:29386288

A plant EPF-type zinc-finger protein, CaPIF1, involved in defence against pathogens.

PubMed

Oh, Sang-Keun; Park, Jeong Mee; Joung, Young Hee; Lee, Sanghyeob; Chung, Eunsook; Kim, Soo-Yong; Yu, Seung Hun; Choi, Doil

2005-05-01

SUMMARY To understand better the defence responses of plants to pathogen attack, we challenged hot pepper plants with bacterial pathogens and identified transcription factor-encoding genes whose expression patterns were altered during the subsequent hypersensitive response. One of these genes, CaPIF1 (Capsicum annuum Pathogen-Induced Factor 1), was characterized further. This gene encodes a plant-specific EPF-type protein that contains two Cys(2)/His(2) zinc fingers. CaPIF1 expression was rapidly and specifically induced when pepper plants were challenged with bacterial pathogens to which they are resistant. In contrast, challenge with a pathogen to which the plants are susceptible only generated weak CaPIF1 expression. CaPIF1 expression was also strongly induced in pepper leaves by the exogenous application of ethephon, an ethylene-releasing compound, and salicylic acid, whereas methyl jasmonate had only moderate effects. CaPIF1 localized to the nuclei of onion epidermis when expressed as a CaPIF1-smGFP fusion protein. Transgenic tobacco plants over-expressing CaPIF1 driven by the CaMV 35S promoter showed increased resistance to challenge with a tobacco-specific pathogen or non-host bacterial pathogens. These plants also showed constitutive up-regulation of multiple defence-related genes. Moreover, virus-induced silencing of the CaPIF1 orthologue in Nicotiana benthamiana enhanced susceptibility to the same host or non-host bacterial pathogens. These observations provide evidence that an EPF-type Cys(2)/His(2) zinc-finger protein plays a crucial role in the activation of the pathogen defence response in plants.

Plant Expression of a Bacterial Cytochrome P450 That Catalyzes Activation of a Sulfonylurea Pro-Herbicide.

PubMed Central

O'Keefe, D. P.; Tepperman, J. M.; Dean, C.; Leto, K. J.; Erbes, D. L.; Odell, J. T.

1994-01-01

The Streptomyces griseolus gene encoding herbicide-metabolizing cytochrome P450SU1 (CYP105A1) was expressed in transgenic tobacco (Nicotiana tabacum). Because this P450 can be reduced by plant chloroplast ferredoxin in vitro, chloroplast-targeted and nontargeted expression were compared. Whereas P450SU1 antigen was found in the transgenic plants regardless of the targeting, only those with chloroplast-directed enzyme performed P450SU1-mediated N-dealkylation of the sulfonylurea 2-methylethyl-2,3-dihydro-N-[(4,6-dimethoxypyrimidin-2-yl)aminocarbonyl]-1, 2-benzoisothiazole- 7-sulfonamide-1,1-dioxide (R7402). Chloroplast targeting appears to be essential for the bacterial P450 to function in the plant. Because the R7402 metabolite has greater phytotoxicity than R7402 itself, plants bearing active P450SU1 are susceptible to injury from R7402 treatment that is harmless to plants without P450SU1. Thus, P450SU1 expression and R7402 treatment can be used as a negative selection system in plants. Furthermore, expression of P450SU1 from a tissue-specific promoter can sequester production of the phytotoxic R7402 metabolite to a single plant tissue. In tobacco expressing P450SU1 from a tapetum-specific promoter, treatment of immature flower buds with R7402 caused dramatically lowered pollen viability. Such treatment could be the basis for a chemical hybridizing agent. PMID:12232216

Physiological and molecular responses of Lactuca sativa to colonization by Salmonella enterica serovar Dublin.

PubMed

Klerks, M M; van Gent-Pelzer, M; Franz, E; Zijlstra, C; van Bruggen, A H C

2007-08-01

This paper describes the physiological and molecular interactions between the human-pathogenic organism Salmonella enterica serovar Dublin and the commercially available mini Roman lettuce cv. Tamburo. The association of S. enterica serovar Dublin with lettuce plants was first determined, which indicated the presence of significant populations outside and inside the plants. The latter was evidenced from significant residual concentrations after highly efficient surface disinfection (99.81%) and fluorescence microscopy of S. enterica serovar Dublin in cross sections of lettuce at the root-shoot transition region. The plant biomass was reduced significantly compared to that of noncolonized plants upon colonization with S. enterica serovar Dublin. In addition to the physiological response, transcriptome analysis by cDNA amplified fragment length polymorphism analysis also provided clear differential gene expression profiles between noncolonized and colonized lettuce plants. From these, generally and differentially expressed genes were selected and identified by sequence analysis, followed by reverse transcription-PCR displaying the specific gene expression profiles in time. Functional grouping of the expressed genes indicated a correlation between colonization of the plants and an increase in expressed pathogenicity-related genes. This study indicates that lettuce plants respond to the presence of S. enterica serovar Dublin at physiological and molecular levels, as shown by the reduction in growth and the concurrent expression of pathogenicity-related genes. In addition, it was confirmed that Salmonella spp. can colonize the interior of lettuce plants, thus potentially imposing a human health risk when processed and consumed.

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray.

PubMed

Samolski, Ilanit; de Luis, Alberto; Vizcaíno, Juan Antonio; Monte, Enrique; Suárez, M Belén

2009-10-13

It has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density oligonucleotide (HDO) microarray encompassing 14,081 Expressed Sequence Tag (EST)-based transcripts from eight Trichoderma spp. and 9,121 genome-derived transcripts of T. reesei, and we have used this microarray to examine the gene expression of T. harzianum either alone or in the presence of tomato plants, chitin, or glucose. Global microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues. The effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of plant colonization, as well as for expression studies in other Trichoderma spp. represented on it. Using this microarray, we have been able to define a number of genes probably involved in the transcriptional response of T. harzianum within the first hours of contact with tomato plant roots, which may provide new insights into the mechanisms and roles of this fungus in the Trichoderma-plant interaction.

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray

PubMed Central

2009-01-01

Background It has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density oligonucleotide (HDO) microarray encompassing 14,081 Expressed Sequence Tag (EST)-based transcripts from eight Trichoderma spp. and 9,121 genome-derived transcripts of T. reesei, and we have used this microarray to examine the gene expression of T. harzianum either alone or in the presence of tomato plants, chitin, or glucose. Results Global microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues. Conclusion The effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of plant colonization, as well as for expression studies in other Trichoderma spp. represented on it. Using this microarray, we have been able to define a number of genes probably involved in the transcriptional response of T. harzianum within the first hours of contact with tomato plant roots, which may provide new insights into the mechanisms and roles of this fungus in the Trichoderma-plant interaction. PMID:19825185

Construct validity of adolescents' self-reported big five personality traits: importance of conceptual breadth and initial validation of a short measure.

PubMed

Morizot, Julien

2014-10-01

While there are a number of short personality trait measures that have been validated for use with adults, few are specifically validated for use with adolescents. To trust such measures, it must be demonstrated that they have adequate construct validity. According to the view of construct validity as a unifying form of validity requiring the integration of different complementary sources of information, this article reports the evaluation of content, factor, convergent, and criterion validities as well as reliability of adolescents' self-reported personality traits. Moreover, this study sought to address an inherent potential limitation of short personality trait measures, namely their limited conceptual breadth. In this study, starting with items from a known measure, after the language-level was adjusted for use with adolescents, items tapping fundamental primary traits were added to determine the impact of added conceptual breadth on the psychometric properties of the scales. The resulting new measure was named the Big Five Personality Trait Short Questionnaire (BFPTSQ). A group of expert judges considered the items to have adequate content validity. Using data from a community sample of early adolescents, the results confirmed the factor validity of the Big Five structure in adolescence as well as its measurement invariance across genders. More important, the added items did improve the convergent and criterion validities of the scales, but did not negatively affect their reliability. This study supports the construct validity of adolescents' self-reported personality traits and points to the importance of conceptual breadth in short personality measures. © The Author(s) 2014.

Age-related factors in the relationship between foot measurements and living stature and body weight.

PubMed

Atamturk, Derya; Duyar, Izzet

2008-11-01

The measurements of feet and footprints are especially important in forensic identification, as they have been used to predict the body height and weight of victims or suspects. It can be observed that the subjects of forensic-oriented studies are generally young adults. That is to say, researchers rarely take into consideration the body's proportional changes with age. Hence, the aim of this study is to generate equations which take age and sex into consideration, when stature and body weight are estimated from foot and footprints dimensions. With this aim in mind, we measured the stature, body weight, foot length and breadth, heel breadth, footprint length and breadth, and footprint heel breadth of 516 volunteers (253 males and 263 females) aged between 17.6 and 82.9 years using standard measurement techniques. The sample population was divided randomly into two groups. Group 1, the study group, consisted of 80% of the sample (n = 406); the remaining 20% were assigned to the cross-validation group or Group 2 (n = 110). In the first stage of the study, we produced equations for estimating stature and weight using a stepwise regression technique. Then, their reliability was tested on Group 2 members. Statistical analyses showed that the ratios of foot dimensions to stature and body weight change considerably with age and sex. Consequently, the regression equations which include these variables yielded more reliable results. Our results indicated that age and sex should be taken into consideration when predicting human body height and weight for forensic purposes.

Automated Discovery of Functional Generality of Human Gene Expression Programs

PubMed Central

Gerber, Georg K; Dowell, Robin D; Jaakkola, Tommi S; Gifford, David K

2007-01-01

An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-κB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal “cross-talk,” and genes from high generality programs may maintain common physiological responses that go awry in disease states. Further, our method is multipurpose, and can be applied readily to novel compendia of biological data. PMID:17696603

AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana.

PubMed

Han, Zhaofen; Yu, Huimin; Zhao, Zhong; Hunter, David; Luo, Xinjuan; Duan, Jun; Tian, Lining

2016-01-01

The histone deacetylases play important roles in the regulation of gene expression and the subsequent control of a number of important biological processes, including those involved in the response to environmental stress. A specific group of histone deacetylase genes, HD2, is present in plants. In Arabidopsis, HD2s include HD2A, HD2B, HD2C, and HD2D. Previous research showed that HD2A, HD2B, and HD2C are more related in terms of expression and function, but not HD2D. In this report, we studied different aspects of AtHD2D in Arabidopsis with respect to plant response to drought and other abiotic stresses. Bioinformatics analysis indicates that HD2D is distantly related to other HD2 genes. Transient expression in Nicotiana benthamiana and stable expression in Arabidopsis of AtHD2D fused with gfp showed that AtHD2D was expressed in the nucleus. Overexpression of AtHD2D resulted in developmental changes including fewer main roots, more lateral roots, and a higher root:shoot ratio. Seed germination and plant flowering time were delayed in transgenic plants expressing AtHD2D, but these plants exhibited higher degrees of tolerance to abiotic stresses, including drought, salt, and cold stresses. Physiological studies indicated that the malondialdehyde (MDA) content was high in wild-type plants but in plants overexpressing HD2D the MDA level increased slowly in response to stress conditions of drought, cold, and salt stress. Furthermore, electrolyte leakage in leaf cells of wild type plants increased but remained stable in transgenic plants. Our results indicate that AtHD2D is unique among HD2 genes and it plays a role in plant growth and development regulation and these changes can modulate plant stress responses.

Relationship between Hexokinase and the Aquaporin PIP1 in the Regulation of Photosynthesis and Plant Growth

PubMed Central

Kelly, Gilor; Sade, Nir; Attia, Ziv; Secchi, Francesca; Zwieniecki, Maciej; Holbrook, N. Michele; Levi, Asher; Alchanatis, Victor; Moshelion, Menachem; Granot, David

2014-01-01

Increased expression of the aquaporin NtAQP1, which is known to function as a plasmalemma channel for CO2 and water, increases the rate of both photosynthesis and transpiration. In contrast, increased expression of Arabidopsis hexokinase1 (AtHXK1), a dual-function enzyme that mediates sugar sensing, decreases the expression of photosynthetic genes and the rate of transpiration and inhibits growth. Here, we show that AtHXK1 also decreases root and stem hydraulic conductivity and leaf mesophyll CO2 conductance (g m). Due to their opposite effects on plant development and physiology, we examined the relationship between NtAQP1 and AtHXK1 at the whole-plant level using transgenic tomato plants expressing both genes simultaneously. NtAQP1 significantly improved growth and increased the transpiration rates of AtHXK1-expressing plants. Reciprocal grafting experiments indicated that this complementation occurs when both genes are expressed simultaneously in the shoot. Yet, NtAQP1 had only a marginal effect on the hydraulic conductivity of the double-transgenic plants, suggesting that the complementary effect of NtAQP1 is unrelated to shoot water transport. Rather, NtAQP1 significantly increased leaf mesophyll CO2 conductance and enhanced the rate of photosynthesis, suggesting that NtAQP1 facilitated the growth of the double-transgenic plants by enhancing mesophyll conductance of CO2. PMID:24498392

In planta expression of HIV-1 p24 protein using an RNA plant virus-based expression vector.

PubMed

Zhang, G; Leung, C; Murdin, L; Rovinski, B; White, K A

2000-02-01

Plant viruses show significant potential as expression vectors for the production of foreign proteins (e.g., antigens) in plants. The HIV-1 p24 nucleocapsid protein is an important early marker of HIV infection and has been used as an antigen in the development of HIV vaccines. Toward developing a plant-based expression system for the production of p24, we have investigated the use of a (positive)-strand RNA plant virus, tomato bushy stunt virus (TBSV), as an expression vector. The HIV p24 open reading frame (ORF) was introduced into a cloned cDNA copy of the TBSV genome as an in-frame fusion with a 5'-terminal portion of the TBSV coat protein ORF. In vitro-generated RNA transcripts corresponding to the engineered virus vector were infectious when inoculated into plant protoplasts; Northern and Western blot analyses verified the accumulation of a predicted p24-encoding viral subgenomic mRNA and the production of p24 fusion product. Whole-plant infections with the viral vector led to the accumulation of p24 fusion protein in inoculated leaves, which cross-reacted with p24-specific antibodies, thus confirming the maintenance of key antigenic determinants. This study is the first to demonstrate that TBSV can be engineered to express a complete foreign protein of clinical importance. Strategies for optimizing protein yield from this viral vector are discussed.

The size and shape of the attentional "spotlight" varies with differences in sports expertise.

PubMed

Hüttermann, Stefanie; Memmert, Daniel; Simons, Daniel J

2014-06-01

Focused attention enhances processing of some aspects of the world at the expense of unattended items. Although focused attention has been studied for decades, few studies have measured individual and group differences in how people distribute attention. In three studies, we explored differences in the breadth and distribution of attention as a function of athletic expertise. Study 1 found 25% greater attention breadth in expert athletes than in novices. Study 2 found that the distribution of focused attention for experts varied as a function of the type of athletic expertise: Experts in sports that demand greater horizontal distribution of attention (e.g., soccer) showed greater horizontal breadth of attention than did those whose sports demand more vertical attention (e.g., volleyball), and vice versa. Study 3 used a slightly modified design to replicate the results of Studies 1 and 2. Overall, the findings reveal a systematic association between the measured "shape" of focused attention in a laboratory task and expertise in a real-world skill. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Distinctiveness as a function of spatial expansion in verbal working memory: comment on Kreitz, Furley, Memmert, and Simons (2015).

PubMed

Guida, Alessandro; van Dijck, Jean-Philippe; Abrahamse, Elger

2017-05-01

In a recent study, Kreitz et al. (Psychological Research 79:1034-1041, 2015) reported on a relationship between verbal working memory capacity and visuo-spatial attentional breadth. The authors hinted at attentional control to be the major link underlying this relationship. We put forward an alternative explanation by framing it within the context of a recent theory on serial order in memory: verbal item sequences entering in working memory are coded by adding a spatial context that can be derived from reading/writing habits. The observation by Kreitz et al. (Psychological Research 79:1034-1041, 2015) enriches this framework by suggesting that a larger visuo-spatial attentional breadth allows for internal coding of the verbal items in a more (spatially) distinct manner-thereby increasing working memory performance. As such, Kreitz et al. (Psychological Research 79:1034-1041, 2015) is the first study revealing a functional link between visuo-spatial attentional breadth and verbal working memory size, which strengthens spatial accounts of serial order coding in working memory.

HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.

PubMed

Landais, Elise; Murrell, Ben; Briney, Bryan; Murrell, Sasha; Rantalainen, Kimmo; Berndsen, Zachary T; Ramos, Alejandra; Wickramasinghe, Lalinda; Smith, Melissa Laird; Eren, Kemal; de Val, Natalia; Wu, Mengyu; Cappelletti, Audrey; Umotoy, Jeffrey; Lie, Yolanda; Wrin, Terri; Algate, Paul; Chan-Hui, Po-Ying; Karita, Etienne; Ward, Andrew B; Wilson, Ian A; Burton, Dennis R; Smith, Davey; Pond, Sergei L Kosakovsky; Poignard, Pascal

2017-11-21

Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The Brassicaceae Family Displays Divergent, Shoot-Skewed NLR Resistance Gene Expression.

PubMed

Munch, David; Gupta, Vikas; Bachmann, Asger; Busch, Wolfgang; Kelly, Simon; Mun, Terry; Andersen, Stig Uggerhøj

2018-02-01

Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from nine plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape ( Brassica napus ) and the model plant Arabidopsis ( Arabidopsis thaliana ), were unique in showing NLR expression skewed toward the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae are also outliers in the sense that they have lost the common symbiosis signaling pathway, which enables intracellular infection by root symbionts. While it is unclear if these two events are related, the NLR expression shift identified here suggests that the Brassicaceae may have evolved unique pattern-recognition receptors and antimicrobial root metabolites to substitute for NLR protection. Such innovations in root protection could potentially be exploited in crop rotation schemes or for enhancing root defense systems of non-Brassicaceae crops. © 2018 American Society of Plant Biologists. All Rights Reserved.

Cytokinin oxidase/dehydrogenase overexpression modifies antioxidant defense against heat, drought and their combination in Nicotiana tabacum plants.

PubMed

Lubovská, Zuzana; Dobrá, Jana; Storchová, Helena; Wilhelmová, Naďa; Vanková, Radomíra

2014-11-01

Cytokinins (CKs) as well as the antioxidant enzyme system (AES) play important roles in plant stress responses. The expression and activity of antioxidant enzymes (AE) were determined in drought, heat and combination of both stresses, comparing the response of tobacco plants overexpressing the main cytokinin degrading enzyme, cytokinin oxidase/dehydrogenase, under the control of root-specific WRKY6 promoter (W6:CKX1 plants) or constitutive promoter (35S:CKX1 plants) and the corresponding wild-type (WT). Expression levels as well as activities of cytosolic ascorbate peroxidase, catalase 3, and cytosolic superoxide dismutase were low under optimal conditions and increased after heat and combined stress in all genotypes. Unlike catalase 3, two other peroxisomal enzymes, catalase 1 and catalase 2, were transcribed extensively under control conditions. Heat stress, in contrast to drought or combined stress, increased catalase 1 and reduced catalase 2 expression in WT and W6:CKX1 plants. In 35S:CKX1, catalase 1 expression was enhanced by heat or drought, but not under combined stress conditions. Mitochondrial superoxide dismutase expression was generally higher in 35S:CKX1 plants than in WT. Genes encoding for chloroplastic AEs, stromatal ascorbate peroxidase, thylakoidal ascorbate peroxidase and chloroplastic superoxide dismutase, were strongly transcribed under control conditions. All stresses down-regulated their expression in WT and W6:CKX1, whereas more stress-tolerant 35S:CKX1 plants maintained high expression during drought and heat. The achieved data show that the effect of down-regulation of CK levels on AES may be mediated by altered habit, resulting in improved stress tolerance, which is associated with diminished stress impact on photosynthesis, and changes in source/sink relations. Copyright © 2014 Elsevier GmbH. All rights reserved.

Roles of Soybean Plasma Membrane Intrinsic Protein GmPIP2;9 in Drought Tolerance and Seed Development.

PubMed

Lu, Linghong; Dong, Changhe; Liu, Ruifang; Zhou, Bin; Wang, Chuang; Shou, Huixia

2018-01-01

Aquaporins play an essential role in water uptake and transport in vascular plants. The soybean genome contains a total of 22 plasma membrane intrinsic protein (PIP) genes. To identify candidate PIPs important for soybean yield and stress tolerance, we studied the transcript levels of all 22 soybean PIPs. We found that a GmPIP2 subfamily member, GmPIP2;9, was predominately expressed in roots and developing seeds. Here, we show that GmPIP2;9 localized to the plasma membrane and had high water channel activity when expressed in Xenopus oocytes. Using transgenic soybean plants expressing a native GmPIP2;9 promoter driving a GUS-reporter gene, it was found high GUS expression in the roots, in particular, in the endoderm, pericycle, and vascular tissues of the roots of transgenic plants. In addition, GmPIP2;9 was also highly expressed in developing pods. GmPIP2;9 expression significantly increased in short term of polyethylene glycol (PEG)-mediated drought stress treatment. GmPIP2;9 overexpression increased tolerance to drought stress in both solution cultures and soil plots. Drought stress in combination with GmPIP2;9 overexpression increased net CO 2 assimilation of photosynthesis, stomata conductance, and transpiration rate, suggesting that GmPIP2;9- overexpressing transgenic plants were less stressed than wild-type (WT) plants. Furthermore, field experiments showed that GmPIP2;9 -overexpressing plants had significantly more pod numbers and larger seed sizes than WT plants. In summary, the study demonstrated that GmPIP2;9 has water transport activity. Its relative high expression levels in roots and developing pods are in agreement with the phenotypes of GmPIP2;9 -overexpressing plants in drought stress tolerance and seed development.

Roles of Soybean Plasma Membrane Intrinsic Protein GmPIP2;9 in Drought Tolerance and Seed Development

PubMed Central

Lu, Linghong; Dong, Changhe; Liu, Ruifang; Zhou, Bin; Wang, Chuang; Shou, Huixia

2018-01-01

Aquaporins play an essential role in water uptake and transport in vascular plants. The soybean genome contains a total of 22 plasma membrane intrinsic protein (PIP) genes. To identify candidate PIPs important for soybean yield and stress tolerance, we studied the transcript levels of all 22 soybean PIPs. We found that a GmPIP2 subfamily member, GmPIP2;9, was predominately expressed in roots and developing seeds. Here, we show that GmPIP2;9 localized to the plasma membrane and had high water channel activity when expressed in Xenopus oocytes. Using transgenic soybean plants expressing a native GmPIP2;9 promoter driving a GUS-reporter gene, it was found high GUS expression in the roots, in particular, in the endoderm, pericycle, and vascular tissues of the roots of transgenic plants. In addition, GmPIP2;9 was also highly expressed in developing pods. GmPIP2;9 expression significantly increased in short term of polyethylene glycol (PEG)-mediated drought stress treatment. GmPIP2;9 overexpression increased tolerance to drought stress in both solution cultures and soil plots. Drought stress in combination with GmPIP2;9 overexpression increased net CO2 assimilation of photosynthesis, stomata conductance, and transpiration rate, suggesting that GmPIP2;9-overexpressing transgenic plants were less stressed than wild-type (WT) plants. Furthermore, field experiments showed that GmPIP2;9-overexpressing plants had significantly more pod numbers and larger seed sizes than WT plants. In summary, the study demonstrated that GmPIP2;9 has water transport activity. Its relative high expression levels in roots and developing pods are in agreement with the phenotypes of GmPIP2;9-overexpressing plants in drought stress tolerance and seed development. PMID:29755491

Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants.

PubMed

Davin, Nicolas; Edger, Patrick P; Hefer, Charles A; Mizrachi, Eshchar; Schuetz, Mathias; Smets, Erik; Myburg, Alexander A; Douglas, Carl J; Schranz, Michael E; Lens, Frederic

2016-06-01

Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used the soc1ful loss of function mutant - the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis - to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woody soc1ful plants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/signaling during wood formation in soc1ful plants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Arabidopsis gene expression patterns during spaceflight

NASA Astrophysics Data System (ADS)

Paul, A.-L.; Ferl, R. J.

The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments resulted in the differential expression of hundreds of genes. A 5 day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β -Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on two fronts. First, expression patterns visualized with the Adh/GUS transgene were used to address specifically the possibility that spaceflight induces a hypoxic stress response, and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. (Paul et al., Plant Physiol. 2001, 126:613). Second, genome-wide patterns of native gene expression were evaluated utilizing the Affymetrix ATH1 GeneChip? array of 8,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes identified with the arrays was further characterized with quantitative Real-Time RT PCR (ABI - TaqmanTM). Comparison of the patterns of expression for arrays of hybridized with RNA isolated from plants exposed to spaceflight compared to the control arrays revealed hundreds of genes that were differentially expressed in response to spaceflight, yet most genes that are hallmarks of hypoxic stress were unaffected. These results will be discussed in light of current models for plant responses to the spaceflight environment, and with regard to potential future flight opportunities.

Ectopic expression of class 1 KNOX genes induce adventitious shoot regeneration and alter growth and development of tobacco (Nicotiana tabacum L) and European plum (Prunus domestica L).

PubMed

Srinivasan, C; Liu, Zongrang; Scorza, Ralph

2011-04-01

Transgenic plants of tobacco (Nicotiana tabacum L) and European plum (Prunus domestica L) were produced by transforming with the apple class 1 KNOX genes (MdKN1 and MdKN2) or corn KNOX1 gene. Transgenic tobacco plants were regenerated in vitro from transformed leaf discs cultured in a medium lacking cytokinin. Ectopic expression of KNOX genes retarded shoot growth by suppressing elongation of internodes in transgenic tobacco plants. Expression of each of the three KNOX1 genes induced malformation and extensive lobbing in tobacco leaves. In situ regeneration of adventitious shoots was observed from leaves and roots of transgenic tobacco plants expressing each of the three KNOX genes. In vitro culture of leaf explants and internode sections excised from in vitro grown MdKN1 expressing tobacco shoots regenerated adventitious shoots on MS (Murashige and Skoog 1962) basal medium in the absence of exogenous cytokinin. Transgenic plum plants that expressed the MdKN2 or corn KNOX1 gene grew normally but MdKN1 caused a significant reduction in plant height, leaf shape and size and produced malformed curly leaves. A high frequency of adventitious shoot regeneration (96%) was observed in cultures of leaf explants excised from corn KNOX1-expressing transgenic plum shoots. In contrast to KNOX1-expressing tobacco, leaf and internode explants of corn KNOX1-expressing plum required synthetic cytokinin (thidiazuron) in the culture medium to induce adventitious shoot regeneration. The induction of high-frequency regeneration of adventitious shoots in vitro from leaves and stem internodal sections of plum through the ectopic expression of a KNOX1 gene is the first such report for a woody perennial fruit trees.

An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves.

PubMed

Rosenthal, Sun Hee; Diamos, Andrew G; Mason, Hugh S

2018-03-01

We have found interesting features of a plant gene (extensin) 3' flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3'-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.

Constitutive expression of nitrate reductase allows normal growth and development of Nicotiana plumbaginifolia plants.

PubMed Central

Vincentz, M; Caboche, M

1991-01-01

A nitrate reductase (NR) deficient mutant of Nicotiana plumbaginifolia totally impaired in the production of NR transcript and protein was restored for NR activity by transformation with a chimaeric NR gene. This gene was composed of a full-length tobacco NR cDNA fused to the CaMV 35S promoter and to termination signals from the tobacco NR gene. The transgenic plants we obtained were viable and fertile and expressed from one-fifth to three times the wild-type NR activity in their leaves. The analysis of chimeric NR gene expression in these plants showed, by comparison with wild-type plants, that the regulation of NR gene expression by light, nitrate and circadian rhythm takes place at the transcriptional level. However, unlike nitrate, light was required for the accumulation of NR protein in transgenic plants, suggesting that NR expression is also controlled at the translational and/or post-translational level. Images PMID:2022181

Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes.

PubMed

Shen, Jiangshan J; Wang, Ting-You; Yang, Wanling

2017-11-02

Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs). To investigate the regulation of sex-biased differentially expressed genes (sDEG), we conducted pathway and transcription factor enrichment analyses on the sDEGs, as well as analyses on the genomic distribution of sDEGs. Evolutionary analyses were also conducted on both sDEGs and escape genes. Genome-wide, we characterized differential gene expression between sexes in 462 RNA-seq samples and identified 587 sex-biased genes, or 3.2% of the genes surveyed. On the X chromosome, sDEGs were distributed in evolutionary strata in a similar pattern as escape genes. We found a trend of negative correlation between the gene expression breadth and nonsynonymous over synonymous mutation (dN/dS) ratios, showing a possible pleiotropic constraint on evolution of genes. Genome-wide, nine transcription factors were found enriched in binding to the regions surrounding the transcription start sites of female-biased genes. Many pathways and protein domains were enriched in sex-biased genes, some of which hint at sex-biased physiological processes. These findings lend insight into the regulatory and evolutionary forces shaping sex-biased gene expression and their involvement in the physiological and pathological processes in human health and diseases.

Application of succulent plant leaves for Agrobacterium infiltration-mediated protein production

USDA-ARS?s Scientific Manuscript database

Infiltration of tobacco leaves with a suspension of Agrobacterium tumefaciens harboring a binary plant expression plasmid provides a convenient method for laboratory scale protein production. When expressing plant cell wall degrading enzymes in the widely used tobacco (Nicotiana benthamiana), diffic...

Enhanced salt stress tolerance of rice plants expressing a vacuolar H+-ATPase subunit c1 (SaVHAc1) gene from the halophyte grass Spartina alterniflora Löisel

USDA-ARS?s Scientific Manuscript database

The physiological role of a vacuolar ATPase subunit c1 (SaVHAc1) from a halophyte grass Spartina alterniflora was studied through its expression in rice. The SaVHAc1– expressing plants showed enhanced tolerance to salt stress than the wild-type plants, mainly through adjustments in early stage and p...

Co-Expression of Monodehydroascorbate Reductase and Dehydroascorbate Reductase from Brassica rapa Effectively Confers Tolerance to Freezing-Induced Oxidative Stress

PubMed Central

Shin, Sun-Young; Kim, Myung-Hee; Kim, Yul-Ho; Park, Hyang-Mi; Yoon, Ho-Sung

2013-01-01

Plants are exposed to various environmental stresses and have therefore developed antioxidant enzymes and molecules to protect their cellular components against toxicity derived from reactive oxygen species (ROS). Ascorbate is a very important antioxidant molecule in plants, and monodehydroascorbate reductase (MDHAR; EC 1.6.5.4) and dehydroascorbate reductase (DHAR; EC 1.8.5.1) are essential to regeneration of ascorbate for maintenance of ROS scavenging ability. The MDHAR and DHAR genes from Brassica rapa were cloned, transgenic plants overexpressing either BrMDHAR and BrDHAR were established, and then, each transgenic plant was hybridized to examine the effects of co-expression of both genes conferring tolerance to freezing. Transgenic plants co-overexpressing BrMDHAR and BrDHAR showed activated expression of relative antioxidant enzymes, and enhanced levels of glutathione and phenolics under freezing condition. Then, these alteration caused by co-expression led to alleviated redox status and lipid peroxidation and consequently conferred improved tolerance against severe freezing stress compared to transgenic plants overexpressing single gene. The results of this study suggested that although each expression of BrMDHAR or BrDHAR was available to according tolerance to freezing, the simultaneous expression of two genes generated synergistic effects conferring improved tolerance more effectively even severe freezing. PMID:24170089

Constitutive expression of transgenes encoding derivatives of the synthetic antimicrobial peptide BP100: impact on rice host plant fitness

PubMed Central

2012-01-01

Background The Biopeptide BP100 is a synthetic and strongly cationic α-helical undecapeptide with high, specific antibacterial activity against economically important plant-pathogenic bacteria, and very low toxicity. It was selected from a library of synthetic peptides, along with other peptides with activities against relevant bacterial and fungal species. Expression of the BP100 series of peptides in plants is of major interest to establish disease-resistant plants and facilitate molecular farming. Specific challenges were the small length, peptide degradation by plant proteases and toxicity to the host plant. Here we approached the expression of the BP100 peptide series in plants using BP100 as a proof-of-concept. Results Our design considered up to three tandemly arranged BP100 units and peptide accumulation in the endoplasmic reticulum (ER), analyzing five BP100 derivatives. The ER retention sequence did not reduce the antimicrobial activity of chemically synthesized BP100 derivatives, making this strategy possible. Transformation with sequences encoding BP100 derivatives (bp100der) was over ten-fold less efficient than that of the hygromycin phosphotransferase (hptII) transgene. The BP100 direct tandems did not show higher antimicrobial activity than BP100, and genetically modified (GM) plants constitutively expressing them were not viable. In contrast, inverted repeats of BP100, whether or not elongated with a portion of a natural antimicrobial peptide (AMP), had higher antimicrobial activity, and fertile GM rice lines constitutively expressing bp100der were produced. These GM lines had increased resistance to the pathogens Dickeya chrysanthemi and Fusarium verticillioides, and tolerance to oxidative stress, with agronomic performance comparable to untransformed lines. Conclusions Constitutive expression of transgenes encoding short cationic α-helical synthetic peptides can have a strong negative impact on rice fitness. However, GM plants expressing, for example, BP100 based on inverted repeats, have adequate agronomic performance and resistant phenotypes as a result of a complex equilibrium between bp100der toxicity to plant cells, antimicrobial activity and transgene-derived plant stress response. It is likely that these results can be extended to other peptides with similar characteristics. PMID:22947243

Constitutive expression of transgenes encoding derivatives of the synthetic antimicrobial peptide BP100: impact on rice host plant fitness.

PubMed

Nadal, Anna; Montero, Maria; Company, Nuri; Badosa, Esther; Messeguer, Joaquima; Montesinos, Laura; Montesinos, Emilio; Pla, Maria

2012-09-04

The Biopeptide BP100 is a synthetic and strongly cationic α-helical undecapeptide with high, specific antibacterial activity against economically important plant-pathogenic bacteria, and very low toxicity. It was selected from a library of synthetic peptides, along with other peptides with activities against relevant bacterial and fungal species. Expression of the BP100 series of peptides in plants is of major interest to establish disease-resistant plants and facilitate molecular farming. Specific challenges were the small length, peptide degradation by plant proteases and toxicity to the host plant. Here we approached the expression of the BP100 peptide series in plants using BP100 as a proof-of-concept. Our design considered up to three tandemly arranged BP100 units and peptide accumulation in the endoplasmic reticulum (ER), analyzing five BP100 derivatives. The ER retention sequence did not reduce the antimicrobial activity of chemically synthesized BP100 derivatives, making this strategy possible. Transformation with sequences encoding BP100 derivatives (bp100der) was over ten-fold less efficient than that of the hygromycin phosphotransferase (hptII) transgene. The BP100 direct tandems did not show higher antimicrobial activity than BP100, and genetically modified (GM) plants constitutively expressing them were not viable. In contrast, inverted repeats of BP100, whether or not elongated with a portion of a natural antimicrobial peptide (AMP), had higher antimicrobial activity, and fertile GM rice lines constitutively expressing bp100der were produced. These GM lines had increased resistance to the pathogens Dickeya chrysanthemi and Fusarium verticillioides, and tolerance to oxidative stress, with agronomic performance comparable to untransformed lines. Constitutive expression of transgenes encoding short cationic α-helical synthetic peptides can have a strong negative impact on rice fitness. However, GM plants expressing, for example, BP100 based on inverted repeats, have adequate agronomic performance and resistant phenotypes as a result of a complex equilibrium between bp100der toxicity to plant cells, antimicrobial activity and transgene-derived plant stress response. It is likely that these results can be extended to other peptides with similar characteristics.

Coexpression of CD14 and CD326 discriminate hepatic precursors in the human fetal liver.

PubMed

Fomin, Marina E; Tai, Lung-Kuo; Bárcena, Alicia; Muench, Marcus O

2011-07-01

The molecular and cellular profile of liver cells during early human development is incomplete, complicating the isolation and study of hepatocytes, cholangiocytes, and hepatic stem cells from the complex amalgam of hepatic and hematopoietic cells, that is, the fetal liver. Epithelial cell adhesion molecule, CD326, has emerged as a marker of hepatic stem cells, and lipopolysaccharide receptor CD14 is known to be expressed on adult hepatocytes. Using flow cytometry, we studied the breadth of CD326 and CD14 expression in midgestation liver. Both CD45(+) hematopoietic and CD45(-) nonhematopoietic cells expressed CD326. Moreover, diverse cell types expressing CD326 were revealed among CD45(-) cells by costaining for CD14. Fluorescence-activated cell sorting was used to isolate nonhematopoietic cells distinguished by expression of high levels of CD326 and low CD14 (CD326(++)CD14(lo)), which were characterized for gene expression associated with liver development. CD326(++)CD14(lo) cells expressed the genes albumin, α-fetoprotein, hepatic nuclear factor 3α, prospero-related homeobox 1, cytochrome P450 3A7, α(1)-antitrypsin, and transferrin. Proteins expressed included cell-surface CD24, CD26, CD29, CD34, CD49f, CD243, and CD324 and, in the cytoplasm, cytokeratins-7/8 (CAM 5.2 antigen) and some cytokeratin-19. Cultured CD326(++)CD14(lo) cells yielded albumin(+) hepatocytes, cytokeratin-19(+) cholangiocytes, and hepatoblasts expressing both markers. Using epifluorescence microscopy we observed CD326 and CD14 expression on fetal hepatocytes comprising the liver parenchyma, as well as on cells associated with ductal plates and surrounding large vessels. These findings indicate that expression of CD14 and CD326 can be used to identify functionally distinct subsets of fetal liver cells, including CD326(++)CD14(lo) cells, representing a mixture of parenchymal cells, cholangiocytes, and hepatoblasts.

International Towing Tank Conference ITTC Symbols and Terminology List. Final Version 1996

DTIC Science & Technology

1997-05-13

law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB...of water-plane aft of mWA midship 2 A AWF Area of water-plane forward mWF of midship 2 A AX Area of maximum transverse mX section 2 B B Beam or...design water line B BWL Maximum moulded breadth mWL at design water line B BX Breadth, moulded of mX maximum section area at design water line d,T T

Two decades of change in European general practice service profiles: conditions associated with the developments in 28 countries between 1993 and 2012.

PubMed

Schäfer, Willemijn L A; Boerma, Wienke G W; Spreeuwenberg, Peter; Schellevis, François G; Groenewegen, Peter P

2016-01-01

Evidence regarding the benefits of strong primary care has influenced health policy and practice. This study focuses on changes in the breadth of services provided by general practitioners (GPs) in Europe between 1993 and 2012 and offers possible explanations for these changes. Data on the breadth of service profiles were used from two cross-sectional surveys in 28 countries: the 1993 European GP Task Profile study (6321 GPs) and the 2012 QUALICOPC study (6044 GPs). GPs' involvement in four areas of clinical activity (first contact care, treatment of diseases, medical procedures, and prevention) was established using ecometric analyses. The changes were measured by the relative increase in the breadth of service profiles. Associations between changes and national-level conditions were examined though regression analyses. Data on the national conditions were used from various other public databases including the World Databank and the PHAMEU (Primary Health care Activity Monitor) database. A total of 28 European countries. GPs. Changes in the breadth of GP service profiles. A general trend of increased involvement of European GPs in treatment of diseases and decreased involvement in preventive activities was observed. Conditions at the national level were associated with changes in the involvement of GPs in first contact care, treatment of diseases and, to a limited extent, prevention. Especially in countries with stronger growth of health care expenditures between 1993 and 2012 the service profiles have expanded. In countries where family values are more dominant the breadth in service profiles decreased. A stronger professional status of GPs was positively associated with the change in first contact care. GPs in former communist countries and Turkey have increased their involvement in the provision of services. Developments in Western Europe were less evident. The developments in the service profiles could only to a very limited extent be explained by national conditions. A main driver of reform seems to be the changes in health care expenditure, which may indicate a notion of urgency because there may be a pressure to curb the rising expenditures. Broad GP service profiles are an indicator of strong primary care in a country. It is expected that developments in the breadth of GP service profiles are influenced by various national conditions related to the urgency to reform, politics, and means. Between 1993 and 2012 the involvement of GPs in European countries in treatment of diseases increased and their involvement preventive activities decreased. The national conditions were found to be associated with changes in GPs' involvement as first contact of care, treatment of diseases, and, to a limited extent, prevention. More specifically, in countries with a stronger growth in health care expenditures, service profiles of European GPs have expanded more in the past decades.

Mycorrhizal fungi influence on silver uptake and membrane protein gene expression following silver nanoparticle exposure

NASA Astrophysics Data System (ADS)

Noori, Azam; White, Jason C.; Newman, Lee A.

2017-02-01

The rapid growth of nanotechnology and the high demand for nanomaterial use have greatly increased the risk of particle release into the environment. Understanding nanomaterial interactions with crop species and their associated microorganisms is critical to food safety and security. In the current study, tomato was inoculated with mycorrhizal fungi and subsequently exposed to 12, 24, or 36 mg/kg of 2- or 15-nm silver nanoparticles (Ag-NPs). Mycorrhizal (M) and non-mycorrhizal (NM) tomatoes exposed to 36 mg/kg of 2-nm Ag-NPs accumulated 1300 and 1600 μg/g silver in their tissues, respectively. Mycorrhizal plants accumulated 14% less silver compared to non-mycorrhizal plants. To begin to understand the mechanisms by which plants accumulate NPs, the expression of two aquaporin channel genes, the plasma membrane intrinsic protein (PIP) and the tonoplast membrane intrinsic protein (TIP), and one potassium channel (KC) gene were studied. In non-mycorrhizal plants, the expression of KC, PIP, and TIP was eight, five, and nine times higher than the control, respectively. These expressions for mycorrhizal plants were 5.8, 3.5, and 2 times higher than controls, respectively. The expression of KC and PIP, which are located on the plasma membrane, was 3.5 and 2.5, respectively, times higher than TIP, which is located on the tonoplast. PIP expression was significantly higher in NM tomatoes exposed to 12 mg/kg of 2-nm Ag-NPs compared to M plants. These results show that mycorrhizal colonization decreases Ag accumulation in NP-exposed plants and also moderates changes in expression level of membrane transport proteins.

Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria.

PubMed

Troxell, Bryan; Hassan, Hosni M

2013-01-01

In the ancient anaerobic environment, ferrous iron (Fe(2+)) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe(3+)) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe(3+), bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe(3+). However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe(2+) as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.

Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria

PubMed Central

Troxell, Bryan; Hassan, Hosni M.

2013-01-01

In the ancient anaerobic environment, ferrous iron (Fe2+) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe3+) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe3+, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe3+. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe2+ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria. PMID:24106689

Biologically Active Secondary Metabolites from the Fungi.

PubMed

Bills, Gerald F; Gloer, James B

2016-11-01

Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.

Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa).

PubMed

Nguyen Dinh, Sy; Sai, Than Zaw Tun; Nawaz, Ghazala; Lee, Kwanuk; Kang, Hunseung

2016-08-20

Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

UV-C-Induced alleviation of transcriptional gene silencing through plant-plant communication: Key roles of jasmonic acid and salicylic acid pathways.

PubMed

Xu, Wei; Wang, Ting; Xu, Shaoxin; Li, Fanghua; Deng, Chenguang; Wu, Lijun; Wu, Yuejin; Bian, Po

2016-08-01

Plant stress responses at the epigenetic level are expected to allow more permanent changes of gene expression and potentially long-term adaptation. While it has been reported that plants subjected to adverse environments initiate various stress responses in their neighboring plants, little is known regarding epigenetic responses to external stresses mediated by plant-plant communication. In this study, we show that DNA repetitive elements of Arabidopsis thaliana, whose expression is inhibited epigenetically by transcriptional gene silencing (TGS) mechanism, are activated by UV-C irradiation through airborne plant-plant and plant-plant-plant communications, accompanied by DNA demethylation at CHH sites. Moreover, the TGS is alleviated by direct treatments with exogenous methyl jasmonate (MeJA) and methyl salicylate (MeSA). Further, the plant-plant and plant-plant-plant communications are blocked by mutations in the biosynthesis or signaling of jasmonic acid (JA) or salicylic acid (SA), indicating that JA and SA pathways are involved in the interplant communication for epigenetic responses. For the plant-plant-plant communication, stress cues are relayed to the last set of receiver plants by promoting the production of JA and SA signals in relaying plants, which exhibit upregulated expression of genes for JA and SA biosynthesis and enhanced emanation of MeJA and MeSA. Copyright © 2016 Elsevier B.V. All rights reserved.

Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status

PubMed Central

Bao, Aili; Liang, Zhijun; Zhao, Zhuqing; Cai, Hongmei

2015-01-01

AMT1-3 encodes the high affinity NH4+ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants. PMID:25915023

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores.

PubMed

Kartzinel, Tyler R; Chen, Patricia A; Coverdale, Tyler C; Erickson, David L; Kress, W John; Kuzmina, Maria L; Rubenstein, Daniel I; Wang, Wei; Pringle, Robert M

2015-06-30

Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species-even pairs of grazers matched in size, digestive physiology, and location-and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized.

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

PubMed Central

Kartzinel, Tyler R.; Chen, Patricia A.; Coverdale, Tyler C.; Erickson, David L.; Kress, W. John; Kuzmina, Maria L.; Rubenstein, Daniel I.; Wang, Wei; Pringle, Robert M.

2015-01-01

Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species—even pairs of grazers matched in size, digestive physiology, and location—and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized. PMID:26034267

Stress-Inducible Expression of an F-box Gene TaFBA1 from Wheat Enhanced the Drought Tolerance in Transgenic Tobacco Plants without Impacting Growth and Development.

PubMed

Kong, Xiangzhu; Zhou, Shumei; Yin, Suhong; Zhao, Zhongxian; Han, Yangyang; Wang, Wei

2016-01-01

E3 ligase plays an important role in the response to many environment stresses in plants. In our previous study, constitutive overexpression of an F-box protein gene TaFBA1 driven by 35S promoter improved the drought tolerance in transgenic tobacco plants, but the growth and development in transgenic plants was altered in normal conditions. In this study, we used stress-inducible promoter RD29A instead of 35S promoter, as a results, the stress-inducible transgenic tobacco plants exhibit a similar phenotype with wild type (WT) plants. However, the drought tolerance of the transgenic plants with stress-inducible expressed TaFBA1 was enhanced. The improved drought tolerance of transgenic plants was indicated by their higher seed germination rate and survival rate, greater biomass and photosynthesis than those of WT under water stress, which may be related to their greater water retention capability and osmotic adjustment. Moreover, the transgenic plants accumulated less reactive oxygen species, kept lower MDA content and membrane leakage under water stress, which may be related to their higher levels of antioxidant enzyme activity and upregulated gene expression of some antioxidant enzymes. These results suggest that stress induced expression of TaFBA1 confers drought tolerance via the improved water retention and antioxidative compete ability. Meanwhile, this stress-inducible expression strategy by RD29A promoter can minimize the unexpectable effects by 35S constitutive promoter on phenotypes of the transgenic plants.

Stable heterologous expression of biologically active terpenoids in green plant cells

PubMed Central

Ikram, N. Kusaira B. K.; Zhan, Xin; Pan, Xi-Wu; King, Brian C.; Simonsen, Henrik T.

2015-01-01

Plants biosynthesize a great diversity of biologically active small molecules of interest for fragrances, flavors, and pharmaceuticals. Among specialized metabolites, terpenoids represent the greatest molecular diversity. Many terpenoids are very complex, and total chemical synthesis often requires many steps and difficult chemical reactions, resulting in a low final yield or incorrect stereochemistry. Several drug candidates with terpene skeletons are difficult to obtain by chemical synthesis due to their large number of chiral centers. Thus, biological production remains the preferred method for industrial production for many of these compounds. However, because these chemicals are often found in low abundance in the native plant, or are produced in plants which are difficult to cultivate, there is great interest in engineering increased production or expression of the biosynthetic pathways in heterologous hosts. Although there are many examples of successful engineering of microbes such as yeast or bacteria to produce these compounds, this often requires extensive changes to the host organism's metabolism. Optimization of plant gene expression, post-translational protein modifications, subcellular localization, and other factors often present challenges. To address the future demand for natural products used as drugs, new platforms are being established that are better suited for heterologous production of plant metabolites. Specifically, direct metabolic engineering of plants can provide effective heterologous expression for production of valuable plant-derived natural products. In this review, our primary focus is on small terpenoids and we discuss the benefits of plant expression platforms and provide several successful examples of stable production of small terpenoids in plants. PMID:25852702

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response

DOE PAGES

Tsai, Alex Yi-Lin; Chan, Kin; Ho, Chi-Yip; ...

2017-03-02

The plant cell wall is an abundant and renewable resource for lignocellulosic applications such as the production of biofuel. Due to structural and compositional complexities, the plant cell wall is, however, recalcitrant to hydrolysis and extraction of platform sugars. A cell wall engineering strategy to reduce this recalcitrance makes use of microbial cell wall modifying enzymes that are expressed directly in plants themselves. Previously, we constructed transgenic Arabidopsis thaliana constitutively expressing the fungal hemicellulases: Phanerochaete carnosa glucurnoyl esterase (PcGCE) and Aspergillus nidulans α-arabinofuranosidase (AnAF54). While the PcGCE lines demonstrated improved xylan extractability, they also displayed chlorotic leaves leading to themore » hypothesis that expression of such enzymes in planta resulted in plant stress. The objective of this study is to investigate the impact of transgenic expression of the aforementioned microbial hemicellulases in planta on the host arabidopsis. More specifically, we investigated transcriptome profiles by short read high throughput sequencing (RNAseq) from developmentally distinct parts of the plant stem. When compared to non-transformed wild-type plants, a subset of genes was identified that showed differential transcript abundance in all transgenic lines and tissues investigated. Intriguingly, this core set of genes was significantly enriched for those involved in plant defense and biotic stress responses. While stress and defense-related genes showed increased transcript abundance in the transgenic plants regardless of tissue or genotype, genes involved in photosynthesis (light harvesting) were decreased in their transcript abundance potentially reflecting wide-spread effects of heterologous microbial transgene expression and the maintenance of plant homeostasis. Additionally, an increase in transcript abundance for genes involved in salicylic acid signaling further substantiates our finding that transgenic expression of microbial cell wall modifying enzymes induces transcriptome responses similar to those observed in defense responses.« less

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response

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

Tsai, Alex Yi-Lin; Chan, Kin; Ho, Chi-Yip

The plant cell wall is an abundant and renewable resource for lignocellulosic applications such as the production of biofuel. Due to structural and compositional complexities, the plant cell wall is, however, recalcitrant to hydrolysis and extraction of platform sugars. A cell wall engineering strategy to reduce this recalcitrance makes use of microbial cell wall modifying enzymes that are expressed directly in plants themselves. Previously, we constructed transgenic Arabidopsis thaliana constitutively expressing the fungal hemicellulases: Phanerochaete carnosa glucurnoyl esterase (PcGCE) and Aspergillus nidulans α-arabinofuranosidase (AnAF54). While the PcGCE lines demonstrated improved xylan extractability, they also displayed chlorotic leaves leading to themore » hypothesis that expression of such enzymes in planta resulted in plant stress. The objective of this study is to investigate the impact of transgenic expression of the aforementioned microbial hemicellulases in planta on the host arabidopsis. More specifically, we investigated transcriptome profiles by short read high throughput sequencing (RNAseq) from developmentally distinct parts of the plant stem. When compared to non-transformed wild-type plants, a subset of genes was identified that showed differential transcript abundance in all transgenic lines and tissues investigated. Intriguingly, this core set of genes was significantly enriched for those involved in plant defense and biotic stress responses. While stress and defense-related genes showed increased transcript abundance in the transgenic plants regardless of tissue or genotype, genes involved in photosynthesis (light harvesting) were decreased in their transcript abundance potentially reflecting wide-spread effects of heterologous microbial transgene expression and the maintenance of plant homeostasis. Additionally, an increase in transcript abundance for genes involved in salicylic acid signaling further substantiates our finding that transgenic expression of microbial cell wall modifying enzymes induces transcriptome responses similar to those observed in defense responses.« less

Production of phytotoxic cationic α-helical antimicrobial peptides in plant cells using inducible promoters.

PubMed

Company, Nuri; Nadal, Anna; Ruiz, Cristina; Pla, Maria

2014-01-01

Synthetic linear antimicrobial peptides with cationic α-helical structures, such as BP100, have potent and specific activities against economically important plant pathogenic bacteria. They are also recognized as valuable therapeutics and preservatives. However, highly active BP100 derivatives are often phytotoxic when expressed at high levels as recombinant peptides in plants. Here we demonstrate that production of recombinant phytotoxic peptides in transgenic plants is possible by strictly limiting transgene expression to certain tissues and conditions, and specifically that minimization of this expression during transformation and regeneration of transgenic plants is essential to obtain viable plant biofactories. On the basis of whole-genome transcriptomic data available online, we identified the Os.hsp82 promoter that fulfilled this requirement and was highly induced in response to heat shock. Using this strategy, we generated transgenic rice lines producing moderate yields of severely phytotoxic BP100 derivatives on exposure to high temperature. In addition, a threshold for gene expression in selected tissues and stages was experimentally established, below which the corresponding promoters should be suitable for driving the expression of recombinant phytotoxic proteins in genetically modified plants. In view of the growing transcriptomics data available, this approach is of interest to assist promoter selection for specific purposes.

Production of Phytotoxic Cationic α-Helical Antimicrobial Peptides in Plant Cells Using Inducible Promoters

PubMed Central

Company, Nuri; Nadal, Anna; Ruiz, Cristina; Pla, Maria

2014-01-01

Synthetic linear antimicrobial peptides with cationic α-helical structures, such as BP100, have potent and specific activities against economically important plant pathogenic bacteria. They are also recognized as valuable therapeutics and preservatives. However, highly active BP100 derivatives are often phytotoxic when expressed at high levels as recombinant peptides in plants. Here we demonstrate that production of recombinant phytotoxic peptides in transgenic plants is possible by strictly limiting transgene expression to certain tissues and conditions, and specifically that minimization of this expression during transformation and regeneration of transgenic plants is essential to obtain viable plant biofactories. On the basis of whole-genome transcriptomic data available online, we identified the Os.hsp82 promoter that fulfilled this requirement and was highly induced in response to heat shock. Using this strategy, we generated transgenic rice lines producing moderate yields of severely phytotoxic BP100 derivatives on exposure to high temperature. In addition, a threshold for gene expression in selected tissues and stages was experimentally established, below which the corresponding promoters should be suitable for driving the expression of recombinant phytotoxic proteins in genetically modified plants. In view of the growing transcriptomics data available, this approach is of interest to assist promoter selection for specific purposes. PMID:25387106

Effects of growth form and functional traits on response of woody plants to clearing and fragmentation of subtropical rainforest.

PubMed

Kooyman, R M; Zanne, A E; Gallagher, R V; Cornwell, W; Rossetto, M; O'Connor, P; Parkes, E A; Catterall, C F; Laffan, S W; Lusk, C H

2013-12-01

The conservation implications of large-scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free-standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free-standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind-dispersed seeds. Connections between the patchy spatial distribution of free-standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free-standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow-growing mature-phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest-area reduction and fragmentation. Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical. © 2013 Society for Conservation Biology.

Preferential expression and immunogenicity of HIV-1 Tat fusion protein expressed in tomato plant.

PubMed

Cueno, Marni E; Hibi, Yurina; Karamatsu, Katsuo; Yasutomi, Yasuhiro; Imai, Kenichi; Laurena, Antonio C; Okamoto, Takashi

2010-10-01

HIV-1 Tat plays a major role in viral replication and is essential for AIDS development making it an ideal vaccine target providing that both humoral and cellular immune responses are induced. Plant-based antigen production, due to its cheaper cost, appears ideal for vaccine production. In this study, we created a plant-optimized tat and mutant (Cys30Ala/Lys41Ala) tat (mtat) gene and ligated each into a pBI121 expression vector with a stop codon and a gusA gene positioned immediately downstream. The vector construct was bombarded into tomato leaf calli and allowed to develop. We thus generated recombinant tomato plants preferentially expressing a Tat-GUS fusion protein over a Tat-only protein. In addition, plants bombarded with either tat or mtat genes showed no phenotypic difference and produced 2-4 microg Tat-GUS fusion protein per milligram soluble plant protein. Furthermore, tomato extracts intradermally inoculated into mice were found to induce a humoral and, most importantly, cellular immunity.

Quantitative characterization of genetic parts and circuits for plant synthetic biology.

PubMed

Schaumberg, Katherine A; Antunes, Mauricio S; Kassaw, Tessema K; Xu, Wenlong; Zalewski, Christopher S; Medford, June I; Prasad, Ashok

2016-01-01

Plant synthetic biology promises immense technological benefits, including the potential development of a sustainable bio-based economy through the predictive design of synthetic gene circuits. Such circuits are built from quantitatively characterized genetic parts; however, this characterization is a significant obstacle in work with plants because of the time required for stable transformation. We describe a method for rapid quantitative characterization of genetic plant parts using transient expression in protoplasts and dual luciferase outputs. We observed experimental variability in transient-expression assays and developed a mathematical model to describe, as well as statistical normalization methods to account for, this variability, which allowed us to extract quantitative parameters. We characterized >120 synthetic parts in Arabidopsis and validated our method by comparing transient expression with expression in stably transformed plants. We also tested >100 synthetic parts in sorghum (Sorghum bicolor) protoplasts, and the results showed that our method works in diverse plant groups. Our approach enables the construction of tunable gene circuits in complex eukaryotic organisms.

The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)

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

Karen S. Browning; Marie Petrocek; Bonnie Bartel

2006-06-01

The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional genemore » expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.« less

Overexpression of the Wheat Expansin Gene TaEXPA2 Improved Seed Production and Drought Tolerance in Transgenic Tobacco Plants.

PubMed

Chen, Yanhui; Han, Yangyang; Zhang, Meng; Zhou, Shan; Kong, Xiangzhu; Wang, Wei

2016-01-01

Expansins are cell wall proteins that are grouped into two main families, α-expansins and β-expansins, and they are implicated in the control of cell extension via the disruption of hydrogen bonds between cellulose and matrix glucans. TaEXPA2 is an α-expansin gene identified in wheat. Based on putative cis-regulatory elements in the TaEXPA2 promoter sequence and the expression pattern induced when polyethylene glycol (PEG) is used to mimic water stress, we hypothesized that TaEXPA2 is involved in plant drought tolerance and plant development. Through transient expression of 35S::TaEXPA2-GFP in onion epidermal cells, TaEXPA2 was localized to the cell wall. Constitutive expression of TaEXPA2 in tobacco improved seed production by increasing capsule number, not seed size, without having any effect on plant growth patterns. The transgenic tobacco exhibited a significantly greater tolerance to water-deficiency stress than did wild-type (WT) plants. We found that under drought stress, the transgenic plants maintained a better water status. The accumulated content of osmotic adjustment substances, such as proline, in TaEXPA2 transgenic plants was greater than that in WT plants. Transgenic plants also displayed greater antioxidative competence as indicated by their lower malondialdehyde (MDA) content, relative electrical conductivity, and reactive oxygen species (ROS) accumulation than did WT plants. This result suggests that the transgenic plants suffer less damage from ROS under drought conditions. The activities of some antioxidant enzymes as well as expression levels of several genes encoding key antioxidant enzymes were higher in the transgenic plants than in the WT plants under drought stress. Collectively, our results suggest that ectopic expression of the wheat expansin gene TaEXPA2 improves seed production and drought tolerance in transgenic tobacco plants.

Overexpression of the Wheat Expansin Gene TaEXPA2 Improved Seed Production and Drought Tolerance in Transgenic Tobacco Plants

PubMed Central

Chen, Yanhui; Han, Yangyang; Zhang, Meng; Zhou, Shan; Kong, Xiangzhu; Wang, Wei

2016-01-01

Expansins are cell wall proteins that are grouped into two main families, α-expansins and β-expansins, and they are implicated in the control of cell extension via the disruption of hydrogen bonds between cellulose and matrix glucans. TaEXPA2 is an α-expansin gene identified in wheat. Based on putative cis-regulatory elements in the TaEXPA2 promoter sequence and the expression pattern induced when polyethylene glycol (PEG) is used to mimic water stress, we hypothesized that TaEXPA2 is involved in plant drought tolerance and plant development. Through transient expression of 35S::TaEXPA2-GFP in onion epidermal cells, TaEXPA2 was localized to the cell wall. Constitutive expression of TaEXPA2 in tobacco improved seed production by increasing capsule number, not seed size, without having any effect on plant growth patterns. The transgenic tobacco exhibited a significantly greater tolerance to water-deficiency stress than did wild-type (WT) plants. We found that under drought stress, the transgenic plants maintained a better water status. The accumulated content of osmotic adjustment substances, such as proline, in TaEXPA2 transgenic plants was greater than that in WT plants. Transgenic plants also displayed greater antioxidative competence as indicated by their lower malondialdehyde (MDA) content, relative electrical conductivity, and reactive oxygen species (ROS) accumulation than did WT plants. This result suggests that the transgenic plants suffer less damage from ROS under drought conditions. The activities of some antioxidant enzymes as well as expression levels of several genes encoding key antioxidant enzymes were higher in the transgenic plants than in the WT plants under drought stress. Collectively, our results suggest that ectopic expression of the wheat expansin gene TaEXPA2 improves seed production and drought tolerance in transgenic tobacco plants. PMID:27073898

Diversification of Root Hair Development Genes in Vascular Plants.

PubMed

Huang, Ling; Shi, Xinhui; Wang, Wenjia; Ryu, Kook Hui; Schiefelbein, John

2017-07-01

The molecular genetic program for root hair development has been studied intensively in Arabidopsis ( Arabidopsis thaliana ). To understand the extent to which this program might operate in other plants, we conducted a large-scale comparative analysis of root hair development genes from diverse vascular plants, including eudicots, monocots, and a lycophyte. Combining phylogenetics and transcriptomics, we discovered conservation of a core set of root hair genes across all vascular plants, which may derive from an ancient program for unidirectional cell growth coopted for root hair development during vascular plant evolution. Interestingly, we also discovered preferential diversification in the structure and expression of root hair development genes, relative to other root hair- and root-expressed genes, among these species. These differences enabled the definition of sets of genes and gene functions that were acquired or lost in specific lineages during vascular plant evolution. In particular, we found substantial divergence in the structure and expression of genes used for root hair patterning, suggesting that the Arabidopsis transcriptional regulatory mechanism is not shared by other species. To our knowledge, this study provides the first comprehensive view of gene expression in a single plant cell type across multiple species. © 2017 American Society of Plant Biologists. All Rights Reserved.

Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns.

PubMed

Benedetti, Manuel; Pontiggia, Daniela; Raggi, Sara; Cheng, Zhenyu; Scaloni, Flavio; Ferrari, Simone; Ausubel, Frederick M; Cervone, Felice; De Lorenzo, Giulia

2015-04-28

Oligogalacturonides (OGs) are fragments of pectin that activate plant innate immunity by functioning as damage-associated molecular patterns (DAMPs). We set out to test the hypothesis that OGs are generated in planta by partial inhibition of pathogen-encoded polygalacturonases (PGs). A gene encoding a fungal PG was fused with a gene encoding a plant polygalacturonase-inhibiting protein (PGIP) and expressed in transgenic Arabidopsis plants. We show that expression of the PGIP-PG chimera results in the in vivo production of OGs that can be detected by mass spectrometric analysis. Transgenic plants expressing the chimera under control of a pathogen-inducible promoter are more resistant to the phytopathogens Botrytis cinerea, Pectobacterium carotovorum, and Pseudomonas syringae. These data provide strong evidence for the hypothesis that OGs released in vivo act as a DAMP signal to trigger plant immunity and suggest that controlled release of these molecules upon infection may be a valuable tool to protect plants against infectious diseases. On the other hand, elevated levels of expression of the chimera cause the accumulation of salicylic acid, reduced growth, and eventually lead to plant death, consistent with the current notion that trade-off occurs between growth and defense.

Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns

PubMed Central

Benedetti, Manuel; Pontiggia, Daniela; Raggi, Sara; Cheng, Zhenyu; Scaloni, Flavio; Ferrari, Simone; Ausubel, Frederick M.; Cervone, Felice; De Lorenzo, Giulia

2015-01-01

Oligogalacturonides (OGs) are fragments of pectin that activate plant innate immunity by functioning as damage-associated molecular patterns (DAMPs). We set out to test the hypothesis that OGs are generated in planta by partial inhibition of pathogen-encoded polygalacturonases (PGs). A gene encoding a fungal PG was fused with a gene encoding a plant polygalacturonase-inhibiting protein (PGIP) and expressed in transgenic Arabidopsis plants. We show that expression of the PGIP–PG chimera results in the in vivo production of OGs that can be detected by mass spectrometric analysis. Transgenic plants expressing the chimera under control of a pathogen-inducible promoter are more resistant to the phytopathogens Botrytis cinerea, Pectobacterium carotovorum, and Pseudomonas syringae. These data provide strong evidence for the hypothesis that OGs released in vivo act as a DAMP signal to trigger plant immunity and suggest that controlled release of these molecules upon infection may be a valuable tool to protect plants against infectious diseases. On the other hand, elevated levels of expression of the chimera cause the accumulation of salicylic acid, reduced growth, and eventually lead to plant death, consistent with the current notion that trade-off occurs between growth and defense. PMID:25870275

Hoarseness.

PubMed

Sulica, Lucian

2011-06-01

Hoarseness is the colloquial expression for dysphonia ; these terms are often used interchangeably in medicine to refer to altered voice quality. Hoarseness may be both a symptom and a sign of dysfunction of the phonatory apparatus. It is never a diagnosis, despite having a corresponding International Classification of Diseases code and sometimes serving as such for purposes of administrative convenience. The same anatomical and physiological features that make the vocal folds uniquely suited for the high-speed vibration necessary for sound production render them exquisitely sensitive to a wide range of abnormalities. The breadth of pathologic conditions that can cause hoarseness makes a unified overview a challenge; hoarseness is simply not a homogeneous category after the initial laryngoscopy. Moreover, the available literature predominantly focuses on specific diagnoses rather than on hoarseness as a whole, so scant published data exist to support an evidence-based approach. Nevertheless, certain unifying principles exist.

A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium

PubMed Central

Hoshi, Ayaka; Oshima, Kenro; Kakizawa, Shigeyuki; Ishii, Yoshiko; Ozeki, Johji; Hashimoto, Masayoshi; Komatsu, Ken; Kagiwada, Satoshi; Yamaji, Yasuyuki; Namba, Shigetou

2009-01-01

One of the most important themes in agricultural science is the identification of virulence factors involved in plant disease. Here, we show that a single virulence factor, tengu-su inducer (TENGU), induces witches' broom and dwarfism and is a small secreted protein of the plant-pathogenic bacterium, phytoplasma. When tengu was expressed in Nicotiana benthamiana plants, these plants showed symptoms of witches' broom and dwarfism, which are typical of phytoplasma infection. Transgenic Arabidopsis thaliana lines expressing tengu exhibited similar symptoms, confirming the effects of tengu expression on plants. Although the localization of phytoplasma was restricted to the phloem, TENGU protein was detected in apical buds by immunohistochemical analysis, suggesting that TENGU was transported from the phloem to other cells. Microarray analyses showed that auxin-responsive genes were significantly down-regulated in the tengu-transgenic plants compared with GUS-transgenic control plants. These results suggest that TENGU inhibits auxin-related pathways, thereby affecting plant development. PMID:19329488

A novel RNA binding protein affects rbcL gene expression and is specific to bundle sheath chloroplasts in C4 plants

PubMed Central

2013-01-01

Background Plants that utilize the highly efficient C4 pathway of photosynthesis typically possess kranz-type leaf anatomy that consists of two morphologically and functionally distinct photosynthetic cell types, the bundle sheath (BS) and mesophyll (M) cells. These two cell types differentially express many genes that are required for C4 capability and function. In mature C4 leaves, the plastidic rbcL gene, encoding the large subunit of the primary CO2 fixation enzyme Rubisco, is expressed specifically within BS cells. Numerous studies have demonstrated that BS-specific rbcL gene expression is regulated predominantly at post-transcriptional levels, through the control of translation and mRNA stability. The identification of regulatory factors associated with C4 patterns of rbcL gene expression has been an elusive goal for many years. Results RLSB, encoded by the nuclear RLSB gene, is an S1-domain RNA binding protein purified from C4 chloroplasts based on its specific binding to plastid-encoded rbcL mRNA in vitro. Co-localized with LSU to chloroplasts, RLSB is highly conserved across many plant species. Most significantly, RLSB localizes specifically to leaf bundle sheath (BS) cells in C4 plants. Comparative analysis using maize (C4) and Arabidopsis (C3) reveals its tight association with rbcL gene expression in both plants. Reduced RLSB expression (through insertion mutation or RNA silencing, respectively) led to reductions in rbcL mRNA accumulation and LSU production. Additional developmental effects, such as virescent/yellow leaves, were likely associated with decreased photosynthetic function and disruption of associated signaling networks. Conclusions Reductions in RLSB expression, due to insertion mutation or gene silencing, are strictly correlated with reductions in rbcL gene expression in both maize and Arabidopsis. In both plants, accumulation of rbcL mRNA as well as synthesis of LSU protein were affected. These findings suggest that specific accumulation and binding of the RLSB binding protein to rbcL mRNA within BS chloroplasts may be one determinant leading to the characteristic cell type-specific localization of Rubisco in C4 plants. Evolutionary modification of RLSB expression, from a C3 “default” state to BS cell-specificity, could represent one mechanism by which rbcL expression has become restricted to only one cell type in C4 plants. PMID:24053212

Arabidopsis gene expression patterns are altered during spaceflight

NASA Astrophysics Data System (ADS)

Paul, Anna-Lisa; Popp, Michael P.; Gurley, William B.; Guy, Charles; Norwood, Kelly L.; Ferl, Robert J.

The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments results in differential gene expression. A 5-day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β-Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on gene expression patterns initially by using the Adh/GUS transgene to address specifically the possibility that spaceflight induces a hypoxic stress response (Paul, A.L., Daugherty, C.J., Bihn, E.A., Chapman, D.K., Norwood, K.L., Ferl, R.J., 2001. Transgene expression patterns indicate that spaceflight affects stress signal perception and transduction in arabidopsis, Plant Physiol. 126, 613-621). As a follow-on to the reporter gene analysis, we report here the evaluation of genome-wide patterns of native gene expression within Arabidopsis shoots utilizing the Agilent DNA array of 21,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes was further characterized with quantitative Real-Time RT PCR (ABI - Taqman®). Comparison of the patterns of expression for arrays probed with RNA isolated from plants exposed to spaceflight compared to RNA isolated from ground control plants revealed 182 genes that were differentially expressed in response to the spaceflight mission by more than 4-fold, and of those only 50 genes were expressed at levels chosen to support a conservative change call. None of the genes that are hallmarks of hypoxic stress were induced to this level. However, genes related to heat shock were dramatically induced - but in a pattern and under growth conditions that are not easily explained by elevated temperatures. These gene expression data are discussed in light of current models for plant responses to the spaceflight environment and with regard to potential future spaceflight experiment opportunities.

Compositions and methods for improved plant feedstock

DOEpatents

Shen, Hui; Chen, Fang; Dixon, Richard A

2014-12-02

The invention provides methods for modifying lignin content and composition in plants and achieving associated benefits therefrom involving altered expression of newly discovered MYB4 transcription factors. Nucleic acid constructs for modifying MYB4 transcription factor expression are described. By over-expressing the identified MYB4 transcription factors, for example, an accompanying decrease in lignin content may be achieved. Plants are provided by the invention comprising such modifications, as are methods for their preparation and use.

Main Strategies of Plant Expression System Glycoengineering for Producing Humanized Recombinant Pharmaceutical Proteins.

PubMed

Rozov, S M; Permyakova, N V; Deineko, E V

2018-03-01

Most the pharmaceutical proteins are derived not from their natural sources, rather their recombinant analogs are synthesized in various expression systems. Plant expression systems, unlike mammalian cell cultures, combine simplicity and low cost of procaryotic systems and the ability for posttranslational modifications inherent in eucaryotes. More than 50% of all human proteins and more than 40% of the currently used pharmaceutical proteins are glycosylated, that is, they are glycoproteins, and their biological activity, pharmacodynamics, and immunogenicity depend on the correct glycosylation pattern. This review examines in detail the similarities and differences between N- and O-glycosylation in plant and mammalian cells, as well as the effect of plant glycans on the activity, pharmacokinetics, immunity, and intensity of biosynthesis of pharmaceutical proteins. The main current strategies of glycoengineering of plant expression systems aimed at obtaining fully humanized proteins for pharmaceutical application are summarized.

Transgenic soybean plants expressing Spb18S dsRNA exhibit enhanced resistance to the soybean pod borer Leguminivora glycinivorella (Lepidoptera: Olethreutidae).

PubMed

Wang, Zhanchun; Li, Tianyu; Ni, Hejia; Wang, Guoyue; Liu, Xinxin; Cao, Yingxue; Li, Wenbin; Meng, Fanli

2018-06-01

The soybean pod borer [SPB; Leguminivora glycinivorella (Mats.) Obraztsov] is a major soybean pest in northeastern Asia. A useful method for addressing this problem is the generation of transgenic plants producing double-stranded RNA (dsRNA) that target essential insect genes. In this study, we confirmed that 18S ribosomal RNA is critical for SPB development. Downregulated Spb18S expression induced by dsRNA injection increased larval mortality rates and resulted in early pupation. We also assessed whether Spb18S is silenced in SPB larvae fed on transgenic soybean expressing Spb18S dsRNA. Transgenic plants downregulated Spb18S expression levels and second-instar larval survival rates. Moreover, such plants were less damaged by SPB larvae than control plants under field conditions. © 2018 Wiley Periodicals, Inc.

Transgenic tobacco expressing Pinellia ternata agglutinin confers enhanced resistance to aphids.

PubMed

Yao, Jianhong; Pang, Yongzhen; Qi, Huaxiong; Wan, Bingliang; Zhao, Xiuyun; Kong, Weiwen; Sun, Xiaofen; Tang, Kexuan

2003-12-01

Tobacco leaf discs were transformed with a plasmid, pBIPTA, containing the selectable marker neomycin phosphotransferase gene (nptII) and Pinellia ternata agglutinin gene (pta) via Agrobacterium tumefaciens-mediated transformation. Thirty-two independent transgenic tobacco plants were regenerated. PCR and Southern blot analyses confirmed that the pta gene had integrated into the plant genome and northern blot analysis revealed transgene expression at various levels in transgenic plants. Genetic analysis confirmed Mendelian segregation of the transgene in T1 progeny. Insect bioassays showed that transgenic plants expressing PTA inhibited significantly the growth of peach potato aphid (Myzus persicae Sulzer). This is the first report that transgenic plants expressing pta confer enhanced resistance to aphids. Our study indicates that the pta gene can be used as a supplement to the snowdrop (Galanthus nivalis) lectin gene (gna) in the control of aphids, a sap-sucking insect pest causing significant yield losses of crops.

Expression and characterization of a recombinant single-domain monoclonal antibody against MUC1 mucin in tobacco plants.

PubMed

Rajabi-Memari, H; Jalali-Javaran, M; Rasaee, M J; Rahbarizadeh, F; Forouzandeh-Moghadam, M; Esmaili, A

2006-08-01

A promising alternative to conventional antibodies is the single-domain antibody fragment of the Camelidae (V(HH)), which (because of features such as small length, high expression, solubility, and stability) is preferred to other antibody derivatives. In this report, a recombinant single-domain antibody (V(HH)) against MUC1 mucin in the tobacco plant, which may be considered as a suitable and economical alternative expression system, was produced. This antibody was expressed under the control of a strong constitutive promoter, CaMV35S, and NOS terminator. A plant high-expression sequence (Kozak sequence) was linked at the 5' end for overexpression of the V(HH) gene. The constructed cassette (pBIV(HH)) was transferred to agrobacterium, and the VHH gene was inserted into the plant genome by agrobacterium-mediated transformation. Transgenic lines were selected on kanamycin (100 mg/L) and maintained in soil, and subsequent generations were obtained. The presence and expression of the transgene was confirmed in the transformants by polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), and Western blot. Tobacco transgenic lines leave expressed V(HH) at levels varying from 1.12% to 1.63% of the total soluble protein. This report examines the transformation and expression of recombinant single-domain antibody (V(HH)) against antigen-associated tumor in tobacco plants.

Induced over-expression of AtDREB2A CA improves drought tolerance in sugarcane.

PubMed

Reis, Rafaela Ribeiro; da Cunha, Bárbara Andrade Dias Brito; Martins, Polyana Kelly; Martins, Maria Thereza Bazzo; Alekcevetch, Jean Carlos; Chalfun, Antônio; Andrade, Alan Carvalho; Ribeiro, Ana Paula; Qin, Feng; Mizoi, Junya; Yamaguchi-Shinozaki, Kazuko; Nakashima, Kazuo; Carvalho, Josirley de Fátima Corrêa; de Sousa, Carlos Antônio Ferreira; Nepomuceno, Alexandre Lima; Kobayashi, Adilson Kenji; Molinari, Hugo Bruno Correa

2014-05-01

Drought is one of the most challenging agricultural issues limiting sustainable sugarcane production and, in some cases, yield losses caused by drought are nearly 50%. DREB proteins play vital regulatory roles in abiotic stress responses in plants. The transcription factor DREB2A interacts with a cis-acting DRE sequence to activate the expression of downstream genes that are involved in drought-, salt- and heat-stress response in Arabidopsis thaliana. In the present study, we evaluated the effects of stress-inducible over-expression of AtDREB2A CA on gene expression, leaf water potential (ΨL), relative water content (RWC), sucrose content and gas exchanges of sugarcane plants submitted to a four-days water deficit treatment in a rhizotron-grown root system. The plants were also phenotyped by scanning the roots and measuring morphological parameters of the shoot. The stress-inducible expression of AtDREB2A CA in transgenic sugarcane led to the up-regulation of genes involved in plant response to drought stress. The transgenic plants maintained higher RWC and ΨL over 4 days after withholding water and had higher photosynthetic rates until the 3rd day of water-deficit. Induced expression of AtDREB2A CA in sugarcane increased sucrose levels and improved bud sprouting of the transgenic plants. Our results indicate that induced expression of AtDREB2A CA in sugarcane enhanced its drought tolerance without biomass penalty. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Seed specific expression and analysis of recombinant human adenosine deaminase (hADA) in three host plant species.

PubMed

Doshi, Ketan M; Loukanina, Natalia N; Polowick, Patricia L; Holbrook, Larry A

2016-10-01

The plant seed is a leading platform amongst plant-based storage systems for the production of recombinant proteins. In this study, we compared the activity of human adenosine deaminase (hADA) expressed in transgenic seeds of three different plant species: pea (Pisum sativum L.), Nicotiana benthamiana L. and tarwi (Lupinus mutabilis Sweet). All three species were transformed with the same expression vector containing the hADA gene driven by the seed-specific promoter LegA2 with an apoplast targeting pinII signal peptide. During the study, several independent transgenic lines were generated and screened from each plant species and only lines with a single copy of the gene of interest were used for hADA expression analysis. A stable transgenic canola line expressing the ADA protein, under the control of 35S constitutive promoter was used as both as a positive control and for comparative study with the seed specific promoter. Significant differences were detected in the expression of hADA. The highest activity of the hADA enzyme (Units/g seed) was reported in tarwi (4.26 U/g) followed by pea (3.23 U/g) and Nicotiana benthamiana (1.69 U/g). The expression of mouse ADA in canola was very low in both seed and leaf tissue compared to other host plants, confirming higher activity of seed specific promoter. Altogether, these results suggest that tarwi could be an excellent candidate for the production of valuable recombinant proteins.

Transformation of an edible crop with the pagA gene of Bacillus anthracis.

PubMed

Aziz, Mohammad Azhar; Sikriwal, Deepa; Singh, Samer; Jarugula, Sridhar; Kumar, P Anand; Bhatnagar, Rakesh

2005-09-01

Vaccination against anthrax is the most important strategy to combat the disease. This study describes a generation of edible transgenic crop expressing, functional protective antigen (PA). In vitro studies showed that the plant-expressed antigen is qualitatively similar to recombinant PA. Immunization studies in mouse animal models indicated the generation of PA-specific neutralizing antibodies and stressed the need for improving expression levels to generate higher antibody titers. Genetic engineering of a plant organelle offers immense scope for increasing levels of antigen expression. An AT-rich PA gene (pagA) coding for the 83-kDa PA molecule was thus cloned and expressed in tobacco chloroplasts. Biolistics was used for the transformation of a chloroplast genome under a set of optimized conditions. The expression of the pagA gene with 69% AT content was highly favored by an AT-rich chloroplast genome. A multifold expression level of functional PA was obtained as compared with the nuclear transgenic tobacco plants. This report describes for the first time a comprehensive study on generating transgenic plants expressing PA, which may serve as a source of an edible vaccine against anthrax. Two important achievements of expressing PA in an edible crop and use of chloroplast technology to enhance the expression levels are discussed here.

Ntann12 annexin expression is induced by auxin in tobacco roots

PubMed Central

Baucher, Marie; Oukouomi Lowe, Yves; Vandeputte, Olivier M.; Mukoko Bopopi, Johnny; Moussawi, Jihad; Vermeersch, Marjorie; Mol, Adeline; El Jaziri, Mondher; Homblé, Fabrice; Pérez-Morga, David

2011-01-01

Ntann12, encoding a polypeptide homologous to annexins, was found previously to be induced upon infection of tobacco with the bacterium Rhodococcus fascians. In this study, Ntann12 is shown to bind negatively charged phospholipids in a Ca2+-dependent manner. In plants growing in light conditions, Ntann12 is principally expressed in roots and the corresponding protein was mainly immunolocalized in the nucleus. Ntann12 expression was inhibited following plant transfer to darkness and in plants lacking the aerial part. However, an auxin (indole-3-acetic acid) treatment restored the expression of Ntann12 in the root system in dark conditions. Conversely, polar auxin transport inhibitors such as 1-naphthylphthalamic acid (NPA) or 2,3,5-triiodobenzoic acid (TIBA) inhibited Ntann12 expression in light condition. These results indicate that the expression of Ntann12 in the root is linked to the perception of a signal in the aerial part of the plant that is transmitted to the root via polar auxin transport. PMID:21543519

Contribution of systematic reviews to management decisions.

PubMed

Cook, Carly N; Possingham, Hugh P; Fuller, Richard A

2013-10-01

Systematic reviews comprehensively summarize evidence about the effectiveness of conservation interventions. We investigated the contribution to management decisions made by this growing body of literature. We identified 43 systematic reviews of conservation evidence, 23 of which drew some concrete conclusions relevant to management. Most reviews addressed conservation interventions relevant to policy decisions; only 35% considered practical on-the-ground management interventions. The majority of reviews covered only a small fraction of the geographic and taxonomic breadth they aimed to address (median = 13% of relevant countries and 16% of relevant taxa). The likelihood that reviews contained at least some implications for management tended to increase as geographic coverage increased and to decline as taxonomic breadth increased. These results suggest the breadth of a systematic review requires careful consideration. Reviews identified a mean of 312 relevant primary studies but excluded 88% of these because of deficiencies in design or a failure to meet other inclusion criteria. Reviews summarized on average 284 data sets and 112 years of research activity, yet the likelihood that their results had at least some implications for management did not increase as the amount of primary research summarized increased. In some cases, conclusions were elusive despite the inclusion of hundreds of data sets and years of cumulative research activity. Systematic reviews are an important part of the conservation decision making tool kit, although we believe the benefits of systematic reviews could be significantly enhanced by increasing the number of reviews focused on questions of direct relevance to on-the-ground managers; defining a more focused geographic and taxonomic breadth that better reflects available data; including a broader range of evidence types; and appraising the cost-effectiveness of interventions. © 2013 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site.

PubMed

Cheng, Hao D; Grimm, Sebastian K; Gilman, Morgan Sa; Gwom, Luc Christian; Sok, Devin; Sundling, Christopher; Donofrio, Gina; Hedestam, Gunilla B Karlsson; Bonsignori, Mattia; Haynes, Barton F; Lahey, Timothy P; Maro, Isaac; von Reyn, C Fordham; Gorny, Miroslaw K; Zolla-Pazner, Susan; Walker, Bruce D; Alter, Galit; Burton, Dennis R; Robb, Merlin L; Krebs, Shelly J; Seaman, Michael S; Bailey-Kellogg, Chris; Ackerman, Margaret E

2018-03-08

Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth. To begin to address this discrepancy between recombinant protein recognition and virus neutralization, we studied the fine epitope specificity of a panel of CD4-binding site (CD4bs) antibodies to define the molecular recognition features of functionally potent humoral responses targeting the HIV-1 envelope site bound by CD4. Whereas previous studies have used neutralization data and machine-learning methods to provide epitope maps, here, this approach was reversed, demonstrating that simple binding assays of fine epitope specificity can prospectively identify broadly neutralizing CD4bs-specific mAbs. Building on this result, we show that epitope mapping and prediction of neutralization breadth can also be accomplished in the assessment of polyclonal serum responses. Thus, this study identifies a set of CD4bs bnAb signature amino acid residues and demonstrates that sensitivity to mutations at signature positions is sufficient to predict neutralization breadth of polyclonal sera with a high degree of accuracy across cohorts and across clades.

Determination of sex from various hand dimensions of Koreans.

PubMed

Jee, Soo-Chan; Bahn, Sangwoo; Yun, Myung Hwan

2015-12-01

In the case of disasters or crime scenes, forensic anthropometric methods have been utilized as a reliable way to quickly confirm the identification of victims using only a few parts of the body. A total of 321 measurement data (from 167 males and 154 females) were analyzed to investigate the suitability of detailed hand dimensions as discriminators of sex. A total of 29 variables including length, breadth, thickness, and circumference of fingers, palm, and wrist were measured. The obtained data were analyzed using descriptive statistics and t-test. The accuracy of sex indication from the hand dimensions data was found using discriminant analysis. The age effect and interaction effect according to age and sex on hand dimensions were analyzed by ANOVA. The prediction accuracy on a wide age range was also compared. According to the results, the maximum hand circumference showed the highest accuracy of 88.6% for predicting sex for males and 89.6% for females. Although the breadth, circumference, and thickness of hand parts generally showed higher accuracy than the lengths of hand parts in predicting the sex of the participant, the breadth and circumference of some finger joints showed a significant difference according to age and gender. Thus, the dimensions of hand parts which are not affected by age or gender, such as hand length, palm length, hand breadth, and maximum hand thickness, are recommended to be used first in sex determination for a wide age range group. The results suggest that the detailed hand dimensions can also be used to identify sex for better accuracy; however, the aging effects need to be considered in estimating aged suspects. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Comparing 3D foot scanning with conventional measurement methods.

PubMed

Lee, Yu-Chi; Lin, Gloria; Wang, Mao-Jiun J

2014-01-01

Foot dimension information on different user groups is important for footwear design and clinical applications. Foot dimension data collected using different measurement methods presents accuracy problems. This study compared the precision and accuracy of the 3D foot scanning method with conventional foot dimension measurement methods including the digital caliper, ink footprint and digital footprint. Six commonly used foot dimensions, i.e. foot length, ball of foot length, outside ball of foot length, foot breadth diagonal, foot breadth horizontal and heel breadth were measured from 130 males and females using four foot measurement methods. Two-way ANOVA was performed to evaluate the sex and method effect on the measured foot dimensions. In addition, the mean absolute difference values and intra-class correlation coefficients (ICCs) were used for precision and accuracy evaluation. The results were also compared with the ISO 20685 criteria. The participant's sex and the measurement method were found (p < 0.05) to exert significant effects on the measured six foot dimensions. The precision of the 3D scanning measurement method with mean absolute difference values between 0.73 to 1.50 mm showed the best performance among the four measurement methods. The 3D scanning measurements showed better measurement accuracy performance than the other methods (mean absolute difference was 0.6 to 4.3 mm), except for measuring outside ball of foot length and foot breadth horizontal. The ICCs for all six foot dimension measurements among the four measurement methods were within the 0.61 to 0.98 range. Overall, the 3D foot scanner is recommended for collecting foot anthropometric data because it has relatively higher precision, accuracy and robustness. This finding suggests that when comparing foot anthropometric data among different references, it is important to consider the differences caused by the different measurement methods.

Morphometric distances among five ethnic groups and evaluation of the secular trend in historical Libya.

PubMed

Danubio, Maria Enrica; Martorella, Domenico; Rufo, Fabrizio; Vecchi, Elvira; Sanna, Emanuele

2011-01-01

This study analysed the variations, both in space and time, of 10 body dimensions and 2 anthropometric indexes of 745 adult males belonging to 5 ethnic groups of historical Lybia (el-Haràbi, el-Baraghìts, Marabtìn, Oases inhabitants and Tuareg). The data were collected in the years 1928 and 1932 by Puccioni and Cipriani, two Italian anthropologists. The aim was to reconstruct the biological history of Libya at the time, and thus contribute to the ongoing debate on the evolution of the biological standard of living in developing Countries. The subjects were analysed by ethnicity and by 10-year age groups, after adjusting for age. The results of ANCOVA and Tukey's post-hoc test show that among and between groups there are statistical significant differences overall for armspan, height, head breadth, bizygomatic breadth, biiliac breadth/height and head breadth/head length indexes. By means of the cluster analysis, the el-Haràbi, el-Baraghìts and Marabtìn groups cluster together, whereas the Tuareg and Oases inhabitants cluster separately one from the other and both from the other three ethnic groups. Within-group variations are not very marked in all ethnicities. In general, there is the tendency, not statistically significant, to the reduction and/or stasis of body dimensions from the older to the younger, and the differences are greater among the older than the younger age classes. In conclusion, it can be argued that these groups, all different culturally and geographically, were following the same tendency of stasis of the secular trend of the body dimensions considered in this study, and such stasis persisted since, at least, the last twenty years of the 19th century, when the older were born.

Species' Traits as Predictors of Range Shifts Under Contemporary Climate Change: A Meta-analysis

NASA Astrophysics Data System (ADS)

MacLean, S. A.; Beissinger, S. R.

2016-12-01

A growing body of literature seeks to explain variation in range shifts using species' ecological and life history traits, with expectations that shifts should be greater in species with greater dispersal ability, reproductive potential, and ecological generalization. If trait-based arguments, hold, then traits would provide valuable evidence-based tools for conservation and management that could increase the accuracy of future range projections, vulnerability assessments, and predictions of novel community assemblages. However, empirical support is limited in extent and consensus, and trait-based relationships remain largely unvalidated. We conducted a comprehensive literature review of species' traits as predictors of range shifts, collecting results from over 11,000 species' responses across multiple taxa from studies that directly compared 20th century and contemporary distributions for multispecies assemblages. We then performed a meta-analysis to calculate the mean study-level effects of body size, fecundity, diet breadth, habitat breadth, and historic range limit, while directly controlling for ecological and methodological heterogeneity across studies that could bias reported effect sizes. We show that ecological and life history traits have had limited success in accounting for variation among species in range shifts over the past century. Of the five traits analyzed, only habitat breadth and historic range limit consistently supported range shift predictions across multiple studies. Fecundity, body size, and diet breadth showed no clear relationship with range shifts, and some traits identified in our literature review (e.g. migratory ecology) have consistently contradicted range shift predictions. Current understanding of species' traits as predictors of range shifts is limited, and standardized study is needed before traits can be reliably incorporated into projections of climate change impacts.

Prevention of bubonic and pneumonic plague using plant-derived vaccines.

PubMed

Alvarez, M Lucrecia; Cardineau, Guy A

2010-01-01

Yersinia pestis, the causative agent of bubonic and pneumonic plague, is an extremely virulent bacterium but there are currently no approved vaccines for protection against this organism. Plants represent an economical and safer alternative to fermentation-based expression systems for the production of therapeutic proteins. The recombinant plague vaccine candidates produced in plants are based on the two most immunogenic antigens of Y. pestis: the fraction-1 capsular antigen (F1) and the low calcium response virulent antigen (V) either in combination or as a fusion protein (F1-V). These antigens have been expressed in plants using all three known possible strategies: nuclear transformation, chloroplast transformation and plant-virus-based expression vectors. These plant-derived plague vaccine candidates were successfully tested in animal models using parenteral, oral, or prime/boost immunization regimens. This review focuses on the recent research accomplishments towards the development of safe and effective pneumonic and bubonic plague vaccines using plants as bioreactors.

Characterization of a tryptophan 2-monooxygenase gene from Puccinia graminis f. sp. tritici involved in auxin biosynthesis and rust pathogenicity.

PubMed

Yin, Chuntao; Park, Jeong-Jin; Gang, David R; Hulbert, Scot H

2014-03-01

The plant hormone indole-3-acetic acid (IAA) is best known as a regulator of plant growth and development but its production can also affect plant-microbe interactions. Microorganisms, including numerous plant-associated bacteria and several fungi, are also capable of producing IAA. The stem rust fungus Puccinia graminis f. sp. tritici induced wheat plants to accumulate auxin in infected leaf tissue. A gene (Pgt-IaaM) encoding a putative tryptophan 2-monooxygenase, which makes the auxin precursor indole-3-acetamide (IAM), was identified in the P. graminis f. sp. tritici genome and found to be expressed in haustoria cells in infected plant tissue. Transient silencing of the gene in infected wheat plants indicated that it was required for full pathogenicity. Expression of Pgt-IaaM in Arabidopsis caused a typical auxin expression phenotype and promoted susceptibility to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000.

Arabidopsis thaliana plants expressing Rift Valley fever virus antigens: Mice exhibit systemic immune responses as the result of oral administration of the transgenic plants.

PubMed

Kalbina, Irina; Lagerqvist, Nina; Moiane, Bélisario; Ahlm, Clas; Andersson, Sören; Strid, Åke; Falk, Kerstin I

2016-11-01

The zoonotic Rift Valley fever virus affects livestock and humans in Africa and on the Arabian Peninsula. The economic impact of this pathogen due to livestock losses, as well as its relevance to public health, underscores the importance of developing effective and easily distributed vaccines. Vaccines that can be delivered orally are of particular interest. Here, we report the expression in transformed plants (Arabidopsis thaliana) of Rift Valley fever virus antigens. The antigens used in this study were the N protein and a deletion mutant of the Gn glycoprotein. Transformed lines were analysed for specific mRNA and protein content by RT-PCR and Western blotting, respectively. Furthermore, the plant-expressed antigens were evaluated for their immunogenicity in mice fed the transgenic plants. After oral intake of fresh transgenic plant material, a proportion of the mice elicited specific IgG antibody responses, as compared to the control animals that were fed wild-type plants and of which none sero-converted. Thus, we show that transgenic plants can be readily used to express and produce Rift Valley Fever virus proteins, and that the plants are immunogenic when given orally to mice. These are promising findings and provide a basis for further studies on edible plant vaccines against the Rift Valley fever virus. Copyright © 2016 Elsevier Inc. All rights reserved.

Enhanced Whitefly Resistance in Transgenic Tobacco Plants Expressing Double Stranded RNA of v-ATPase A Gene

PubMed Central

Thakur, Nidhi; Upadhyay, Santosh Kumar; Verma, Praveen C.; Chandrashekar, Krishnappa; Tuli, Rakesh; Singh, Pradhyumna K.

2014-01-01

Background Expression of double strand RNA (dsRNA) designed against important insect genes in transgenic plants have been shown to give protection against pests through RNA interference (RNAi), thus opening the way for a new generation of insect-resistant crops. We have earlier compared the efficacy of dsRNAs/siRNAs, against a number of target genes, for interference in growth of whitefly (Bemisia tabaci) upon oral feeding. The v-ATPase subunit A (v-ATPaseA) coding gene was identified as a crucial target. We now report the effectiveness of transgenic tobacco plants expressing siRNA to silence v-ATPaseA gene expression for the control of whitefly infestation. Methodology/Principal Findings Transgenic tobacco lines were developed for the expression of long dsRNA precursor to make siRNA and knock down the v-ATPaseA mRNA in whitefly. Molecular analysis and insecticidal properties of the transgenic plants established the formation of siRNA targeting the whitefly v-ATPaseA, in the leaves. The transcript level of v-ATPaseA in whiteflies was reduced up to 62% after feeding on the transgenic plants. Heavy infestation of whiteflies on the control plants caused significant loss of sugar content which led to the drooping of leaves. The transgenic plants did not show drooping effect. Conclusions/Significance Host plant derived pest resistance was achieved against whiteflies by genetic transformation of tobacco which generated siRNA against the whitefly v-ATPaseA gene. Transgenic tobacco lines expressing dsRNA of v-ATPaseA, delivered sufficient siRNA to whiteflies feeding on them, mounting a significant silencing response, leading to their mortality. The transcript level of the target gene was reduced in whiteflies feeding on transgenic plants. The strategy can be taken up for genetic engineering of plants to control whiteflies in field crops. PMID:24595215

New contributions to the molecular systematics and the evolution of host-plant associations in the genus Chrysolina (Coleoptera, Chrysomelidae, Chrysomelinae)

PubMed Central

Jurado-Rivera, José A.; Petitpierre, Eduard

2015-01-01

Abstract The taxonomic circumscription of the large and diverse leaf beetle genus Chrysolina Motschulsky is not clear, and its discrimination from the closely related genus Oreina Chevrolat has classically been controversial. In addition, the subgeneric arrangement of the species is unstable, and proposals segregating Chrysolina species into new genera have been recently suggested. In this context, the availability of a phylogenetic framework would provide the basis for a stable taxonomic system, but the existing phylogenies are based on few taxa and have low resolution. In the present study we perform a phylogenetic analysis based on mitochondrial (cox1 and rrnL) and nuclear (H3) DNA sequences from a sample of fifty-two Chrysolina species representing almost half of the subgeneric diversity of the group (thirty out of sixty-five subgenera) and most of the morphological, ecological and karyological variation in the genus. In addition, five Oreina species from two subgenera have also been analysed. The resulting phylogeny is used to evaluate some of the most relevant taxonomic hypotheses for Chrysolina, and also to reconstruct its ancestral host plant associations in a Bayesian framework. Our findings support the paraphyly of Chrysolina as currently defined due to the inclusion of Oreina, the monophyly of the Chrysolina (plus Oreina) species including the divergent Chrysolina (Polysticta) vigintimaculata (Clark, 1864), and enable inferences of deep-level evolutionary relationships among the studied subgenera. The plant family Lamiaceae is inferred as the ancestral host of the study group, whose evolution is characterized by continuous host-shifting among pre-existing host plant families. Some Chrysolina clades include mixtures of species with different levels of diet breadth, indicating that niche width has varied through time. PMID:26798320

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate.

PubMed

Valeeva, Lia R; Nyamsuren, Chuluuntsetseg; Sharipova, Margarita R; Shakirov, Eugene V

2018-01-01

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo -inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases) and 168phyA (BPP family) under the control of root-specific inducible promoter Pht1;2 . The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate that future crop biotechnologies involving such enzymes will require a very careful evaluation of phytase source and activity. Overall, our data suggest feasibility of using bacterial phytases to improve plant growth in conditions of phosphorus deficiency and demonstrate that inducible expression of recombinant enzymes should be investigated further as a viable approach to plant biotechnology.

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate

PubMed Central

Valeeva, Lia R.; Nyamsuren, Chuluuntsetseg; Sharipova, Margarita R.; Shakirov, Eugene V.

2018-01-01

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases) and 168phyA (BPP family) under the control of root-specific inducible promoter Pht1;2. The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate that future crop biotechnologies involving such enzymes will require a very careful evaluation of phytase source and activity. Overall, our data suggest feasibility of using bacterial phytases to improve plant growth in conditions of phosphorus deficiency and demonstrate that inducible expression of recombinant enzymes should be investigated further as a viable approach to plant biotechnology. PMID:29515604

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

PubMed Central

2012-01-01

Background Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related genes with the highest accuracy is a very important task because these genes might serve as tumor biomarkers, which is of great benefit to not only tumor molecular diagnosis but also drug development. Results This paper proposes a novel gene selection method with rich biomedical meaning based on Heuristic Breadth-first Search Algorithm (HBSA) to find as many optimal gene subsets as possible. Due to the curse of dimensionality, this type of method could suffer from over-fitting and selection bias problems. To address these potential problems, a HBSA-based ensemble classifier is constructed using majority voting strategy from individual classifiers constructed by the selected gene subsets, and a novel HBSA-based gene ranking method is designed to find important tumor-related genes by measuring the significance of genes using their occurrence frequencies in the selected gene subsets. The experimental results on nine tumor datasets including three pairs of cross-platform datasets indicate that the proposed method can not only obtain better generalization performance but also find many important tumor-related genes. Conclusions It is found that the frequencies of the selected genes follow a power-law distribution, indicating that only a few top-ranked genes can be used as potential diagnosis biomarkers. Moreover, the top-ranked genes leading to very high prediction accuracy are closely related to specific tumor subtype and even hub genes. Compared with other related methods, the proposed method can achieve higher prediction accuracy with fewer genes. Moreover, they are further justified by analyzing the top-ranked genes in the context of individual gene function, biological pathway, and protein-protein interaction network. PMID:22830977

Achieving Potent Autologous Neutralizing Antibody Responses against Tier 2 HIV-1 Viruses by Strategic Selection of Envelope Immunogens.

PubMed

Hessell, Ann J; Malherbe, Delphine C; Pissani, Franco; McBurney, Sean; Krebs, Shelly J; Gomes, Michelle; Pandey, Shilpi; Sutton, William F; Burwitz, Benjamin J; Gray, Matthew; Robins, Harlan; Park, Byung S; Sacha, Jonah B; LaBranche, Celia C; Fuller, Deborah H; Montefiori, David C; Stamatatos, Leonidas; Sather, D Noah; Haigwood, Nancy L

2016-04-01

Advancement in immunogen selection and vaccine design that will rapidly elicit a protective Ab response is considered critical for HIV vaccine protective efficacy. Vaccine-elicited Ab responses must therefore have the capacity to prevent infection by neutralization-resistant phenotypes of transmitted/founder (T/F) viruses that establish infection in humans. Most vaccine candidates to date have been ineffective at generating Abs that neutralize T/F or early variants. In this study, we report that coimmunizing rhesus macaques with HIV-1 gp160 DNA and gp140 trimeric protein selected from native envelope gene sequences (envs) induced neutralizing Abs against Tier 2 autologous viruses expressing cognate envelope (Env). The Env immunogens were selected from envs emerging during the earliest stages of neutralization breadth developing within the first 2 years of infection in two clade B-infected human subjects. Moreover, the IgG responses in macaques emulated the targeting to specific regions of Env known to be associated with autologous and heterologous neutralizing Abs developed within the human subjects. Furthermore, we measured increasing affinity of macaque polyclonal IgG responses over the course of the immunization regimen that correlated with Tier 1 neutralization. In addition, we report firm correlations between Tier 2 autologous neutralization and Tier 1 heterologous neutralization, as well as overall TZM-bl breadth scores. Additionally, the activation of Env-specific follicular helper CD4 T cells in lymphocytes isolated from inguinal lymph nodes of vaccinated macaques correlated with Tier 2 autologous neutralization. These results demonstrate the potential for native Env derived from subjects at the time of neutralization broadening as effective HIV vaccine elements. Copyright © 2016 by The American Association of Immunologists, Inc.

A Genetic Approach to the Identification of Plant Genes Involved in Viral Movement

DTIC Science & Technology

1999-09-30

Arabidopsis.. We plan to create two transgenic plant lines of Arabidopsis, one that expresses the firefly luciferase (Luc) gene, and one that... transgenic plant lines that express Luc or CD upon infection with RCNMV. Phenotypically these lines will either be luminescent (Luc) or sensitive to 5

Overexpression of Arabidopsis AnnAt8 Alleviates Abiotic Stress in Transgenic Arabidopsis and Tobacco

PubMed Central

Yadav, Deepanker; Ahmed, Israr; Shukla, Pawan; Boyidi, Prasanna; Kirti, Pulugurtha Bharadwaja

2016-01-01

Abiotic stress results in massive loss of crop productivity throughout the world. Because of our limited knowledge of the plant defense mechanisms, it is very difficult to exploit the plant genetic resources for manipulation of traits that could benefit multiple stress tolerance in plants. To achieve this, we need a deeper understanding of the plant gene regulatory mechanisms involved in stress responses. Understanding the roles of different members of plant gene families involved in different stress responses, would be a step in this direction. Arabidopsis, which served as a model system for the plant research, is also the most suitable system for the functional characterization of plant gene families. Annexin family in Arabidopsis also is one gene family which has not been fully explored. Eight annexin genes have been reported in the genome of Arabidopsis thaliana. Expression studies of different Arabidopsis annexins revealed their differential regulation under various abiotic stress conditions. AnnAt8 (At5g12380), a member of this family has been shown to exhibit ~433 and ~175 fold increase in transcript levels under NaCl and dehydration stress respectively. To characterize Annexin8 (AnnAt8) further, we have generated transgenic Arabidopsis and tobacco plants constitutively expressing AnnAt8, which were evaluated under different abiotic stress conditions. AnnAt8 overexpressing transgenic plants exhibited higher seed germination rates, better plant growth, and higher chlorophyll retention when compared to wild type plants under abiotic stress treatments. Under stress conditions transgenic plants showed comparatively higher levels of proline and lower levels of malondialdehyde compared to the wild-type plants. Real-Time PCR analyses revealed that the expression of several stress-regulated genes was altered in AnnAt8 over-expressing transgenic tobacco plants, and the enhanced tolerance exhibited by the transgenic plants can be correlated with altered expressions of these stress-regulated genes. Our findings suggest a role for AnnAt8 in enhancing abiotic stress tolerance at different stages of plant growth and development. PMID:27135239

Expression of multiple proteins in transgenic plants

DOEpatents

Vierstra, Richard D.; Walker, Joseph M.

2002-01-01

A method is disclosed for the production of multiple proteins in transgenic plants. A DNA construct for introduction into plants includes a provision to express a fusion protein of two proteins of interest joined by a linking domain including plant ubiquitin. When the fusion protein is produced in the cells of a transgenic plant transformed with the DNA construction, native enzymes present in plant cells cleave the fusion protein to release both proteins of interest into the cells of the transgenic plant. Since the proteins are produced from the same fusion protein, the initial quantities of the proteins in the cells of the plant are approximately equal.

Shoot to root communication is necessary to control the expression of iron-acquisition genes in Strategy I plants.

PubMed

García, María J; Romera, Francisco J; Stacey, Minviluz G; Stacey, Gary; Villar, Eduardo; Alcántara, Esteban; Pérez-Vicente, Rafael

2013-01-01

Previous research showed that auxin, ethylene, and nitric oxide (NO) can activate the expression of iron (Fe)-acquisition genes in the roots of Strategy I plants grown with low levels of Fe, but not in plants grown with high levels of Fe. However, it is still an open question as to how Fe acts as an inhibitor and which pool of Fe (e.g., root, phloem, etc.) in the plant acts as the key regulator for gene expression control. To further clarify this, we studied the effect of the foliar application of Fe on the expression of Fe-acquisition genes in several Strategy I plants, including wild-type cultivars of Arabidopsis [Arabidopsis thaliana (L.) Heynh], pea [Pisum sativum L.], tomato [Solanum lycopersicon Mill.], and cucumber [Cucumis sativus L.], as well as mutants showing constitutive expression of Fe-acquisition genes when grown under Fe-sufficient conditions [Arabidopsis opt3-2 and frd3-3, pea dgl and brz, and tomato chln (chloronerva)]. The results showed that the foliar application of Fe blocked the expression of Fe-acquisition genes in the wild-type cultivars and in the frd3-3, brz, and chln mutants, but not in the opt3-2 and dgl mutants, probably affected in the transport of a Fe-related repressive signal in the phloem. Moreover, the addition of either ACC (ethylene precursor) or GSNO (NO donor) to Fe-deficient plants up-regulated the expression of Fe-acquisition genes, but this effect did not occur in Fe-deficient plants sprayed with foliar Fe, again suggesting the existence of a Fe-related repressive signal moving from leaves to roots.

Functional diversity of arbuscular mycorrhizas extends to the expression of plant genes involved in P nutrition.

PubMed

Burleigh, Stephen H; Cavagnaro, Tim; Jakobsen, Iver

2002-07-01

This study of functional diversity considers symbiotic associations between two plant species, Medicago truncatula and Lycopersicon esculentum, and seven species of arbuscular mycorrhizal fungi (AMF). The objective was to integrate physiological analyses with molecular techniques to test whether functional diversity between AMF species is not only apparent at the level of mycorrhiza formation, plant nutrient uptake and plant growth, but also at the molecular level as observed by variation in the root expression of plant genes involved in the plant's P-starvation response. The seven species of AMF varied widely in their influence on the root expression of MtPT2 and Mt4 from M. truncatula and LePT1 and TPSI1 from L. esculentum. At one extreme was Glomus mosseae, whereby its colonization of M. truncatula resulted in the greatest reduction in MtPT2 and Mt4 gene expression and the highest level of P uptake and growth, while at the other extreme was Gigaspora rosea, whereby colonization resulted in the highest levels of MtPT2 and Mt4 gene expression and the lowest P uptake and growth. The expression of LePT1 and TPSI1 within the roots of L. esculentum was low and relatively uniform across the seven mycorrhizas, reflecting the ability of this cultivar to maintain low and constant shoot P levels despite root colonization by a broad selection of AMF. This study extends current understanding of functional diversity and shows that plants can respond differently to AMF, not only at the level of colonization, nutrient uptake and growth, but also at the level of gene expression.

Ectopic expression of a fruit phytoene synthase from Citrus paradisi Macf. promotes abiotic stress tolerance in transgenic tobacco.

PubMed

Cidade, Luciana C; de Oliveira, Tahise M; Mendes, Amanda F S; Macedo, Amanda F; Floh, Eny I S; Gesteira, Abelmon S; Soares-Filho, Walter S; Costa, Marcio G C

2012-12-01

Abscisic acid (ABA) is an important regulator of plant responses to environmental stresses and an absolute requirement for stress tolerance. Recently, a third phytoene synthase (PSY3) gene paralog was identified in monocots and demonstrated to play a specialized role in stress-induced ABA formation, thus suggesting that the first committed step in carotenogenesis is a key limiting step in ABA biosynthesis. To examine whether the ectopic expression of PSY, other than PSY3, would similarly affect ABA level and stress tolerance, we have produced transgenic tobacco containing a fruit-specific PSY (CpPSY) of grapefruit (Citrus paradisi Macf.). The transgenic plants contained a single- or double-locus insertion and expressed CpPSY at varying transcript levels. In comparison with the wild-type plants, the CpPSY expressing transgenic plants showed a significant increase on root length and shoot biomass under PEG-, NaCl- and mannitol-induced osmotic stress. The enhanced stress tolerance of transgenic plants was correlated with the increased endogenous ABA level and expression of stress-responsive genes, which in turn was correlated with the CpPSY copy number and expression level in different transgenic lines. Collectively, these results provide further evidence that PSY is a key enzyme regulating ABA biosynthesis and that the altered expression of other PSYs in transgenic plants may provide a similar function to that of the monocot's PSY3 in ABA biosynthesis and stress tolerance. The results also pave the way for further use of CpPSY, as well as other PSYs, as potential candidate genes for engineering tolerance to drought and salt stress in crop plants.

Intraspecific leaf trait variability along a boreal-to-tropical community diversity gradient

PubMed Central

Bastias, Cristina C.; Fortunel, Claire; Valladares, Fernando; Baraloto, Christopher; Benavides, Raquel; Cornwell, William; Markesteijn, Lars; de Oliveira, Alexandre A.; Sansevero, Jeronimo B. B.; Vaz, Marcel C.; Kraft, Nathan J. B.

2017-01-01

Disentangling the mechanisms that shape community assembly across diversity gradients is a central matter in ecology. While many studies have explored community assembly through species average trait values, there is a growing understanding that intraspecific trait variation (ITV) can also play a critical role in species coexistence. Classic biodiversity theory hypothesizes that higher diversity at species-rich sites can arise from narrower niches relative to species-poor sites, which would be reflected in reduced ITV as species richness increases. To explore how ITV in woody plant communities changes with species richness, we compiled leaf trait data (leaf size and specific leaf area) in a total of 521 woody plant species from 21 forest communities that differed dramatically in species richness, ranging from boreal to tropical rainforests. At each forest, we assessed ITV as an estimate of species niche breadth and we quantified the degree of trait overlap among co-occurring species as a measure of species functional similarity. We found ITV was relatively invariant across the species richness gradient. In addition, we found that species functional similarity increased with diversity. Contrary to the expectation from classic biodiversity theory, our results rather suggest that neutral processes or equalizing mechanisms can be acting as potential drivers shaping community assembly in hyperdiverse forests. PMID:28241033

UC Berkeley Nuclear Engineering Curriculum and Research Enhancement. Final report, February 14, 1993--February 14, 1995

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

Fowler, T.K.; Peterson, P.F.

1995-05-11

This is a report for the 2/14/93 to 2/14/95 period of the five-year program proposed and initiated in 1992, for curriculum and research enhancement for the Department of Nuclear Engineering at the University of California, Berkeley. The program is designed to strengthen the departmental academic infrastructure and improve the education breadth of nuclear engineering students. The DOE funds have supported scholarships and a novel educational program which includes summer coursework at the Diablo Canyon Nuclear Power Plant. The summer course provides an important introduction to reactor safety and operations to students who will in the future be responsible for runningmore » many of our existing nuclear power plants. The work was funded under DOE contract DE-FG0393ER75856, with a matching gift to the Department from the Pacific Gas and Electric Company (PG&E). The program described in the original grant proposal has been successful implemented with an enthusiastic response from our students and faculty. The program consisted of two parts, one for innovative additions to our curriculum funded by the DOE, and the other for distinguished lectureships and support for basic research funded by gifts from PG&E.« less

Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?

PubMed

Arnold, A Elizabeth; Lutzoni, F

2007-03-01

Fungal endophytes are found in asymptomatic photosynthetic tissues of all major lineages of land plants. The ubiquity of these cryptic symbionts is clear, but the scale of their diversity, host range, and geographic distributions are unknown. To explore the putative hyperdiversity of tropical leaf endophytes, we compared endophyte communities along a broad latitudinal gradient from the Canadian arctic to the lowland tropical forest of central Panama. Here, we use molecular sequence data from 1403 endophyte strains to show that endophytes increase in incidence, diversity, and host breadth from arctic to tropical sites. Endophyte communities from higher latitudes are characterized by relatively few species from many different classes of Ascomycota, whereas tropical endophyte assemblages are dominated by a small number of classes with a very large number of endophytic species. The most easily cultivated endophytes from tropical plants have wide host ranges, but communities are dominated by a large number of rare species whose host range is unclear. Even when only the most easily cultured species are considered, leaves of tropical trees represent hotspots of fungal species diversity, containing numerous species not yet recovered from other biomes. The challenge remains to recover and identify those elusive and rarely cultured taxa with narrower host ranges, and to elucidate the ecological roles of these little-known symbionts in tropical forests.

Utility operations review of North Carolina State University BSNE curriculum

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

Bishop, E.A.; Faggart, E.M.; Jackson, G.D.

1988-01-01

The industry advisors group of the North Carolina State University (NCSU) Department of Nuclear Engineering raised the question of how well the curriculum for a bachelor of science in nuclear engineering (BSNE) meets the needs of educating students to enter the nuclear operations field. The concern was that the nuclear industry has evolved from a design to an operations mode, but that the BSNE curriculum may not have responded to this evolution. To address this issue, a group of four persons qualified as senior reactor operators with operational experience from different utilities was selected. The authors are the members ofmore » this review group. All are degreed personnel, with three BSNE graduates from NCSU, and all have participated in nuclear plant startups and currently work at nuclear plant sites. The group prepared by reviewing the curriculum before arriving on campus, including the report developed for the Accreditation Board for Engineering and Technology. During our two-day campus visit, we reviewed course materials, interviewed professors, and toured laboratory and reactor facilities in order to get more insight into the breadth and thrust of the BSNE curriculum. The observations and recommendations contained in this paper were developed based on these reviews and discussions and represent the opinions of the authors and not necessarily their companies.« less

Expression of the human hepatitis B virus large surface antigen gene in transgenic tomato plants.

PubMed

Lou, Xiao-Ming; Yao, Quan-Hong; Zhang, Zhen; Peng, Ri-He; Xiong, Ai-Sheng; Wang, Hua-Kun

2007-04-01

The original hepatitis B virus (HBV) large surface antigen gene was synthesized. In order to optimize the expression of this gene in tomato plants, the tobacco pathogenesis-related protein S signal peptide was fused to the 5' end of the modified gene and the sequence encoding amino acids S, E, K, D, E, and L was placed at the 3' end. The gene encoding the modified HBV large surface antigen under the control of a fruit-specific promoter was constructed and expressed in transgenic tomato plants. The expression of the antigen from transgenic plants was confirmed by PCR and reverse transcriptase PCR. Enzyme-linked immunoassays using a monoclonal antibody directed against human serum-derived HBsAg revealed that the maximal level of HBsAg was about 0.02% of the soluble protein in transgenic tomato fruit. The amount of HBsAg in mature fruits was found to be 65- to 171-fold larger than in small or medium fruits and leaf tissues. Examination of transgenic plant samples by transmission electron microscopy proved that HBsAg had been expressed and had accumulated. The HBsAg protein was capable of assembling into capsomers and virus-like particles. To our knowledge, this is the first time the HBV large surface antigen has been expressed in plants. This work suggests the possibility of producing a new alternative vaccine for human HBV.

Boosted expression of the SARS-CoV nucleocapsid protein in tobacco and its immunogenicity in mice.

PubMed

Zheng, Nuoyan; Xia, Ran; Yang, Cuiping; Yin, Bojiao; Li, Yin; Duan, Chengguo; Liang, Liming; Guo, Huishan; Xie, Qi

2009-08-06

Vaccines produced in plant systems are safe and economical; however, the extensive application of plant-based vaccines is mainly hindered by low expression levels of heterologous proteins in plant systems. Here, we demonstrated that the post-transcriptional gene silencing suppressor p19 protein from tomato bushy stunt virus substantially enhanced the transient expression of recombinant SARS-CoV nucleocapsid (rN) protein in Nicotiana benthamiana. The rN protein in the agrobacteria-infiltrated plant leaf accumulated up to a concentration of 79 microg per g fresh leaf weight at 3 days post infiltration. BALB/c mice were intraperitoneally vaccinated with pre-treated plant extract emulsified in Freund's adjuvant. The rN protein-specific IgG in the mouse sera attained a titer about 1:1,800 following three doses of immunization, which suggested effective B-cell maturation and differentiation in mice. Antibodies of the subclasses IgG1 and IgG2a were abundantly present in the mouse sera. During vaccination of rN protein, the expression of IFN-gamma and IL-10 was evidently up-regulated in splenocytes at different time points, while the expression of IL-2 and IL-4 was not. Up to now, this is the first study that plant-expressed recombinant SARS-CoV N protein can induce strong humoral and cellular responses in mice.

Enhanced Tolerance of Transgenic Potato Plants Over-Expressing Non-specific Lipid Transfer Protein-1 (StnsLTP1) against Multiple Abiotic Stresses

PubMed Central

Gangadhar, Baniekal H.; Sajeesh, Kappachery; Venkatesh, Jelli; Baskar, Venkidasamy; Abhinandan, Kumar; Yu, Jae W.; Prasad, Ram; Mishra, Raghvendra K.

2016-01-01

Abiotic stresses such as heat, drought, and salinity are major environmental constraints that limit potato (Solanum tuberosum L.) production worldwide. Previously, we found a potential thermo-tolerance gene, named StnsLTP1 from potato using yeast functional screening. Here, we report the functional characterization of StnsLTP1 and its role in multiple abiotic stresses in potato plants. Computational analysis of StnsLTP1 with other plant LTPs showed eight conserved cysteine residues, and four α-helices stabilized by four disulfide bridges. Expression analysis of StnsLTP1 gene showed differential expression under heat, water-deficit and salt stresses. Transgenic potato lines over-expressing StnsLTP1 gene displayed enhanced cell membrane integrity under stress conditions, as indicated by reduced membrane lipid per-oxidation, and hydrogen peroxide content relative to untransformed (UT) control plants. In addition, transgenic lines over-expressing StLTP1 also exhibited increased antioxidant enzyme activity with enhanced accumulation of ascorbates, and up-regulation of stress-related genes including StAPX, StCAT, StSOD, StHsfA3, StHSP70, and StsHSP20 compared with the UT plants. These results suggests that StnsLTP1 transgenic plants acquired improved tolerance to multiple abiotic stresses through enhanced activation of antioxidative defense mechanisms via cyclic scavenging of reactive oxygen species and regulated expression of stress-related genes. PMID:27597854

The promoter of a plant defensin gene directs specific expression in nematode-induced syncytia in Arabidopsis roots.

PubMed

Siddique, Shahid; Wieczorek, Krzysztof; Szakasits, Dagmar; Kreil, David P; Bohlmann, Holger

2011-10-01

The beet cyst nematode Heterodera schachtii induces a feeding site, called syncytium, in roots of host plants. In Arabidopsis, one of the genes whose expression is strongly induced in these structures is Pdf2.1 which codes for an antimicrobial plant defensin. Arabidopsis has 13 plant defensin genes. Besides Pdf2.1, the Pdf2.2 and Pdf2.3 genes were strongly expressed in syncytia and therefore the expression of all three Pdf genes was studied in detail. The promoter of the Pdf2.1 gene turned out to be an interesting candidate to drive a syncytium-specific expression of foreign genes as RT-PCR showed that apart from the feeding site it was only expressed in siliques (seeds). The Pdf2.2 and Pdf2.3 genes were in addition expressed in seedlings, roots, leaves, stems, and flowers. These results were supported by the analysis of promoter::GUS lines. After infection with H. schachtii all GUS lines showed a strong staining in syncytia at 5 and 15 dpi. This expression pattern was confirmed by in situ RT-PCR. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Intraspecific competition facilitates the evolution of tolerance to insect damage in the perennial plant Solanum carolinense.

PubMed

McNutt, David W; Halpern, Stacey L; Barrows, Kahaili; Underwood, Nora

2012-12-01

Tolerance to herbivory (the degree to which plants maintain fitness after damage) is a key component of plant defense, so understanding how natural selection and evolutionary constraints act on tolerance traits is important to general theories of plant-herbivore interactions. These factors may be affected by plant competition, which often interacts with damage to influence trait expression and fitness. However, few studies have manipulated competitor density to examine the evolutionary effects of competition on tolerance. In this study, we tested whether intraspecific competition affects four aspects of the evolution of tolerance to herbivory in the perennial plant Solanum carolinense: phenotypic expression, expression of genetic variation, the adaptive value of tolerance, and costs of tolerance. We manipulated insect damage and intraspecific competition for clonal lines of S. carolinense in a greenhouse experiment, and measured tolerance in terms of sexual and asexual fitness components. Compared to plants growing at low density, plants growing at high density had greater expression of and genetic variation in tolerance, and experienced greater fitness benefits from tolerance when damaged. Tolerance was not costly for plants growing at either density, and only plants growing at low density benefited from tolerance when undamaged, perhaps due to greater intrinsic growth rates of more tolerant genotypes. These results suggest that competition is likely to facilitate the evolution of tolerance in S. carolinense, and perhaps in other plants that regularly experience competition, while spatio-temporal variation in density may maintain genetic variation in tolerance.

Differential effects of Pseudomonas mendocina and Glomus intraradices on lettuce plants physiological response and aquaporin PIP2 gene expression under elevated atmospheric CO2 and drought.

PubMed

Alguacil, Maria Del Mar; Kohler, Josef; Caravaca, Fuensanta; Roldán, Antonio

2009-11-01

Arbuscular mycorrhizal (AM) symbiosis and plant-growth-promoting rhizobacterium (PGPR) can alleviate the effects of water stress in plants, but it is unknown whether these benefits can be maintained at elevated CO2. Therefore, we carried out a study where seedlings of Lactuca sativa were inoculated with the AM fungus (AMF) Glomus intraradices N.C. Schenk & G.S. Sm. or the PGPR Pseudomonas mendocina Palleroni and subjected to two levels of watering and two levels of atmospheric CO2 to ascertain their effects on plant physiological parameters and gene expression of one PIP aquaporin in roots. The inoculation with PGPR produced the greatest growth in lettuce plants under all assayed treatments as well as the highest foliar potassium concentration and leaf relative water content under elevated [CO2] and drought. However, under such conditions, the PIP2 gene expression remained almost unchanged. G. intraradices increased significantly the AMF colonization, foliar phosphorus concentration and leaf relative water content in plants grown under drought and elevated [CO2]. Under drought and elevated [CO2], the plants inoculated with G. intraradices showed enhanced expression of the PIP2 gene as compared to P. mendocina or control plants. Our results suggest that both microbial inoculation treatments could help to alleviate drought at elevated [CO2]. However, the PIP2 gene expression was increased only by the AMF but not by the PGPR under these conditions.

Expression of anti-tumor necrosis factor alpha (TNFα) single-chain variable fragment (scFv) in Spirodela punctata plants transformed with Agrobacterium tumefaciens.

PubMed

Balaji, Parthasarathy; Satheeshkumar, P K; Venkataraman, Krishnan; Vijayalakshmi, M A

2016-05-01

Therapeutic antibodies against tumor necrosis factor alpha (TNFα) have been considered effective for some of the autoimmune diseases such as rheumatoid arthritis, Crohn's diseases, and so on. But associated limitations of the current therapeutics in terms of cost, availability, and immunogenicity have necessitated the need for alternative candidates. Single-chain variable fragment (scFv) can negate the limitations tagged with the anti-TNFα therapeutics to a greater extent. In the present study, Spirodela punctata plants were transformed with anti-TNFα through in planta transformation using Agrobacterium tumefaciens strain, EHA105. Instead of cefotaxime, garlic extract (1 mg/mL) was used to remove the agrobacterial cells after cocultivation. To the best of our knowledge, this report shows for the first time the application of plant extracts in transgenic plant development. 95% of the plants survived screening under hygromycin. ScFv cDNA integration in the plant genomic DNA was confirmed at the molecular level by PCR. The transgenic protein expression was followed up to 10 months. Expression of scFv was confirmed by immunodot blot. Protein expression levels of up to 6.3% of total soluble protein were observed. β-Glucuronidase and green fluorescent protein expressions were also detected in the antibiotic resistant plants. The paper shows the generation of transgenic Spirodela punctuata plants through in planta transformation. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

A novel platform for biologically active recombinant human interleukin-13 production.

PubMed

Wang, David J; Brandsma, Martin; Yin, Ziqin; Wang, Aiming; Jevnikar, Anthony M; Ma, Shengwu

2008-06-01

Interleukin-13 (IL-13) is a pleiotropic regulatory cytokine with the potential for treating several human diseases, including type-1 diabetes. Thus far, conventional expression systems for recombinant IL-13 production have proven difficult and are limited by efficiency. In this study, transgenic plants were used as a novel expression platform for the production of human IL-13 (hIL-13). DNA constructs containing hIL-13 cDNA were introduced into tobacco plants. Transcriptional expression of the hIL-13 gene in transgenic plants was confirmed by reverse transcriptase-polymerase chain reaction and Northern blotting. Western blot analysis showed that the hIL-13 protein was efficiently accumulated in transgenic plants and present in multiple molecular forms, with an expression level as high as 0.15% of total soluble protein in leaves. The multiple forms of plant-derived recombinant hIL-13 (rhIL-13) are a result of differential N-linked glycosylation, as revealed by enzymatic and chemical deglycosylation, but not of disulphide-linked oligomerization. In vitro trypsin digestion indicated that plant rhIL-13 was more resistant than unglycosylated control rhIL-13 to proteolysis. The stability of plant rhIL-13 to digestion was further supported with simulated gastric and intestinal fluid digestion. In vitro bioassays using a factor-dependent human erythroleukaemic cell line (TF-1 cells) showed that plant rhIL-13 retained the biological functions of the authentic hIL-13 protein. These results demonstrate that transgenic plants are superior to conventional cell-based expression systems for the production of rhIL-13. Moreover, transgenic plants synthesizing high levels of rhIL-13 may prove to be an attractive delivery system for direct oral administration of IL-13 in the treatment of clinical diseases such as type-1 diabetes.

The C-terminal propeptide of a plant defensin confers cytoprotective and subcellular targeting functions

PubMed Central

2014-01-01

Background Plant defensins are small (45–54 amino acids), basic, cysteine-rich proteins that have a major role in innate immunity in plants. Many defensins are potent antifungal molecules and are being evaluated for their potential to create crop plants with sustainable disease resistance. Defensins are produced as precursor molecules which are directed into the secretory pathway and are divided into two classes based on the absence (class I) or presence (class II) of an acidic C-terminal propeptide (CTPP) of about 33 amino acids. The function of this CTPP had not been defined. Results By transgenically expressing the class II plant defensin NaD1 with and without its cognate CTPP we have demonstrated that NaD1 is phytotoxic to cotton plants when expressed without its CTPP. Transgenic cotton plants expressing constructs encoding the NaD1 precursor with the CTPP had the same morphology as non-transgenic plants but expression of NaD1 without the CTPP led to plants that were stunted, had crinkled leaves and were less viable. Immunofluorescence microscopy and transient expression of a green fluorescent protein (GFP)-CTPP chimera were used to confirm that the CTPP is sufficient for vacuolar targeting. Finally circular dichroism and NMR spectroscopy were used to show that the CTPP adopts a helical confirmation. Conclusions In this report we have described the role of the CTPP on NaD1, a class II defensin from Nicotiana alata flowers. The CTPP of NaD1 is sufficient for vacuolar targeting and plays an important role in detoxification of the defensin as it moves through the plant secretory pathway. This work may have important implications for the use of defensins for disease protection in transgenic crops. PMID:24495600

Nictaba Homologs from Arabidopsis thaliana Are Involved in Plant Stress Responses

PubMed Central

Eggermont, Lore; Stefanowicz, Karolina; Van Damme, Els J. M.

2018-01-01

Plants are constantly exposed to a wide range of environmental stresses, but evolved complicated adaptive and defense mechanisms which allow them to survive in unfavorable conditions. These mechanisms protect and defend plants by using different immune receptors located either at the cell surface or in the cytoplasmic compartment. Lectins or carbohydrate-binding proteins are widespread in the plant kingdom and constitute an important part of these immune receptors. In the past years, lectin research has focused on the stress-inducible lectins. The Nicotiana tabacum agglutinin, abbreviated as Nictaba, served as a model for one family of stress-related lectins. Here we focus on three non-chimeric Nictaba homologs from Arabidopsis thaliana, referred to as AN3, AN4, and AN5. Confocal microscopy of ArathNictaba enhanced green fluorescent protein (EGFP) fusion constructs transiently expressed in N. benthamiana or stably expressed in A. thaliana yielded fluorescence for AN4 and AN5 in the nucleus and the cytoplasm of the plant cell, while fluorescence for AN3 was only detected in the cytoplasm. RT-qPCR analysis revealed low expression for all three ArathNictabas in different tissues throughout plant development. Stress application altered the expression levels, but all three ArathNictabas showed a different expression pattern. Pseudomonas syringae infection experiments with AN4 and AN5 overexpression lines demonstrated a significantly higher tolerance of several transgenic lines to P. syringae compared to wild type plants. Finally, AN4 was shown to interact with two enzymes involved in plant defense, namely TGG1 and BGLU23. Taken together, our data suggest that the ArathNictabas represent stress-regulated proteins with a possible role in plant stress responses. On the long term this research can contribute to the development of more stress-resistant plants. PMID:29375596

The Xanthomonas campestris pv. vesicatoria Type-3 Effector XopB Inhibits Plant Defence Responses by Interfering with ROS Production

PubMed Central

Priller, Johannes Peter Roman; Reid, Stephen; Konein, Patrick; Dietrich, Petra

2016-01-01

The bacterial pathogen Xanthomonas campestris pv. vesicatoria 85–10 (Xcv) translocates about 30 type-3 effector proteins (T3Es) into pepper plants (Capsicum annuum) to suppress plant immune responses. Among them is XopB which interferes with PTI, ETI and sugar-mediated defence responses, but the underlying molecular mechanisms and direct targets are unknown so far. Here, we examined the XopB-mediated suppression of plant defence responses in more detail. Infection of susceptible pepper plants with Xcv lacking xopB resulted in delayed symptom development compared to Xcv wild type infection concomitant with an increased formation of salicylic acid (SA) and expression of pathogenesis-related (PR) genes. Expression of xopB in Arabidopsis thaliana promoted the growth of the virulent Pseudomonas syringae pv. tomato (Pst) DC3000 strain. This was paralleled by a decreased SA-pool and a lower induction of SA-dependent PR gene expression. The expression pattern of early flg22-responsive marker genes indicated that MAPK signalling was not altered in the presence of XopB. However, XopB inhibited the flg22-triggered burst of reactive oxygen species (ROS). Consequently, the transcript accumulation of AtOXI1, a ROS-dependent marker gene, was reduced in xopB-expressing Arabidopsis plants as well as callose deposition. The lower ROS production correlated with a low level of basal and flg22-triggered expression of apoplastic peroxidases and the NADPH oxidase RBOHD. Conversely, deletion of xopB in Xcv caused a higher production of ROS in leaves of susceptible pepper plants. Together our results demonstrate that XopB modulates ROS responses and might thereby compromise plant defence. PMID:27398933

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

Jeon, En Hee; Pak, Jung Hun; Kim, Mi Jin

Highlights: Black-Right-Pointing-Pointer We isolated a novel E2 ubiquitin-conjugating enzyme from leaves of wild rice plants. Black-Right-Pointing-Pointer The OgUBC1 was highly expressed in leaves treated with SA and UV-B radiation. Black-Right-Pointing-Pointer The recombinant OgUBC1 has an enzymatic activity of E2 in vitro. Black-Right-Pointing-Pointer The OgUBC1 could protect disruption of plant cells by UV-B radiation. Black-Right-Pointing-Pointer OgUBC1 confers disease resistance and UV-B tolerance in transgenic Arabidopsis plants. -- Abstract: A previously unidentified gene encoding ubiquitin-conjugating enzyme was isolated from leaves of wild rice plant treated with wounding and microbe-associated molecular patterns. The OgUBC1 gene was composed of 148 amino acids and containedmore » a typical active site and 21 ubiquitin thioester intermediate interaction residues and 4 E3 interaction residues. Both exogenous application of salicylic acid and UV-B irradiation triggered expression of OgUBC1 in leaves of wild rice. Recombinant OgUBC1 proteins bound to ubiquitins in vitro, proposing that the protein might act as E2 enzyme in planta. Heterologous expression of the OgUBC1 in Arabidopsis thaliana protected plants from cellular damage caused by an excess of UV-B radiation. A stable expression of chalcone synthase gene was detected in leaves of OgUBC1-expressing Arabidopsis, resulting in producing higher amounts of anthocyanin than those in wild-type Col-0 plants. Additionally, both pathogenesis-related gene1 and 5 were transcribed in the transgenic Arabidopsis in the absence of pathogen infection. The OgUBC1-expressing plants were resistant to the infection of Botrytis cinerea. Taken together, we suggested that the OgUBC1 is involved in ubiquitination process important for cellular response against biotic and abiotic stresses in plants.« less

Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors

PubMed Central

Giritch, Anatoli; Marillonnet, Sylvestre; Engler, Carola; van Eldik, Gerben; Botterman, Johan; Klimyuk, Victor; Gleba, Yuri

2006-01-01

Plant viral vectors allow expression of heterologous proteins at high yields, but so far, they have been unable to express heterooligomeric proteins efficiently. We describe here a rapid and indefinitely scalable process for high-level expression of functional full-size mAbs of the IgG class in plants. The process relies on synchronous coinfection and coreplication of two viral vectors, each expressing a separate antibody chain. The two vectors are derived from two different plant viruses that were found to be noncompeting. Unlike vectors derived from the same virus, noncompeting vectors effectively coexpress the heavy and light chains in the same cell throughout the plant body, resulting in yields of up to 0.5 g of assembled mAbs per kg of fresh-leaf biomass. This technology allows production of gram quantities of mAbs for research purposes in just several days, and the same protocol can be used on an industrial scale in situations requiring rapid response, such as pandemic or terrorism events. PMID:16973752

Transient Expression of Lumbrokinase (PI239) in Tobacco (Nicotiana tabacum) Using a Geminivirus-Based Single Replicon System Dissolves Fibrin and Blood Clots.

PubMed

Dickey, Alexia; Wang, Nan; Cooper, Edwin; Tull, Lauren; Breedlove, Drew; Mason, Hugh; Liu, Dehu; Wang, Kevin Yueju

2017-01-01

Lumbrokinases, a group of fibrinolytic enzymes extracted from earthworm, have been widely used to prevent and treat various cardiovascular diseases. They specifically target fibrin to effectively degrade thrombi without major side effects. Plant expression systems are becoming potential alternative expression platforms for producing pharmaceutical proteins. In this work, a lumbrokinase (PI239) was produced from a plant system. Both wild-type (WT) and plant codon-optimized (OP) PI239 gene sequences were synthesized and cloned into a geminivirus-based single-vector DNA replicon system. Both vectors were independently expressed in tobacco (Nicotiana tabacum) leaves transiently by agroinfiltration. Overexpressed PI239 resulted in sudden tissue necrosis 3 days after infiltration. Remaining proteins were purified through His-tag affinity chromatography and analyzed with SDS-PAGE and Western blot methods. Purified PI239 successfully degraded artificial fibrin with relative activity of 13,400 U/mg when compared with commercial lumbrokinase product. In vitro tests demonstrated that plant-derived PI239 dissolved human blood clots and that the plant expression system is capable of producing functional PI239.

Transgenic Cotton Plants Expressing the HaHR3 Gene Conferred Enhanced Resistance to Helicoverpa armigera and Improved Cotton Yield

PubMed Central

Han, Qiang; Wang, Zhenzhen; He, Yunxin; Xiong, Yehui; Lv, Shun; Li, Shupeng; Zhang, Zhigang; Qiu, Dewen; Zeng, Hongmei

2017-01-01

RNA interference (RNAi) has been developed as an efficient technology. RNAi insect-resistant transgenic plants expressing double-stranded RNA (dsRNA) that is ingested into insects to silence target genes can affect the viability of these pests or even lead to their death. HaHR3, a molt-regulating transcription factor gene, was previously selected as a target expressed in bacteria and tobacco plants to control Helicoverpa armigera by RNAi technology. In this work, we selected the dsRNA-HaHR3 fragment to silence HaHR3 in cotton bollworm for plant mediated-RNAi research. A total of 19 transgenic cotton lines expressing HaHR3 were successfully cultivated, and seven generated lines were used to perform feeding bioassays. Transgenic cotton plants expressing dsHaHR3 were shown to induce high larval mortality and deformities of pupation and adult eclosion when used to feed the newly hatched larvae, and 3rd and 5th instar larvae of H. armigera. Moreover, HaHR3 transgenic cotton also demonstrated an improved cotton yield when compared with controls. PMID:28867769

Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species.

PubMed

Stanton-Geddes, John; Nguyen, Andrew; Chick, Lacy; Vincent, James; Vangala, Mahesh; Dunn, Robert R; Ellison, Aaron M; Sanders, Nathan J; Gotelli, Nicholas J; Cahan, Sara Helms

2016-03-02

The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism's transcriptome measured across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth. We found that at least 2 % of all genes changed expression with temperature. The majority of upregulation was specific to exposure to low temperatures. The cool-adapted A. picea induced expression of more genes in response to extreme temperatures than did A. carolinensis, consistent with the enhanced response hypothesis. In contrast, under high temperatures the warm-adapted A. carolinensis downregulated many of the genes upregulated in A. picea, and required more extreme temperatures to induce down-regulation in gene expression, consistent with the tolerance hypothesis. We found no evidence for a trade-off between constitutive and inducible gene expression as predicted by the genetic assimilation hypothesis. These results suggest that increases in upper thermal limits may require an evolutionary shift in response mechanism away from damage repair toward tolerance and prevention.

miR394 and LCR are involved in Arabidopsis salt and drought stress responses in an abscisic acid-dependent manner

PubMed Central

2013-01-01

Background MicroRNAs (miRNAs) are a class of short, endogenous non-coding small RNAs that have ability to base pair with their target mRNAs to induce their degradation in plants. miR394a/b are conserved small RNAs and its target gene LCR (LEAF CURLING RESPONSIVENESS) encodes an F-box protein (SKP1-Cullin/CDC53-F-box) but whether miR394a/b and its target gene LCR are involved in regulation of plant response to abscisic acid (ABA) and abiotic stresses is unknown. Results Mature miR394 and precursor miR394a/b are shown to be slightly induced by ABA. By contrast, LCR expression is depressed by ABA. Analysis of LCR and its promoter (pLCR::GUS) revealed that LCR is expressed at all development stages. MIR394a/b over-expression (35S::MIR394a/b) and lcr (LCR loss of function) mutant plants are hypersensitive to salt stress, but LCR over-expressing (35S::m5LCR) plants display the salt-tolerant phenotype. Both 35S::MIR394a/b and lcr plants are highly tolerant to severe drought stress compared with wild-type, but 35S::m5LCR plants are susceptible to water deficiency. Over-expression of MIR394a/b led to ABA hypersensitivity and ABA-associated phenotypes, whereas 35S::m5LCR plants show ABA resistance phenotypes. Moreover, 35S::MIR394a/b plants accumulated higher levels of ABA-induced hydrogen peroxide and superoxide anion radicals than wild-type and 35S::m5LCR plants. Expressions of ABA- and stress-responsive genes, ABI3, ABI4, ABI5, ABF3, and ABF4 are up-regulated in MIR394a/b over-expressing plants but down-regulated in 35S::m5LCR plants. Over-expression of MIR394a in abi4-1 or abi5-1 background resulted in loss of ABA-sensitivity in 35S::MIR394a plants. Conclusions The silencing of LCR mRNA by miR394 is essential to maintain a certain phenotype favorable for the adaptive response to abiotic stresses. The contrasting phenotypes of salt and drought responses may be mediated by a functional balance between miR394 and LCR. If the balance is perturbed in case of the abiotic stress, an identical phenotype related to the stress response occurs, resulting in either ABA sensitive or insensitive response. Thus, miR394-regulated LCR abundance may allow plants to fine-tune their responses to ABA and abiotic stress. PMID:24330668

miR394 and LCR are involved in Arabidopsis salt and drought stress responses in an abscisic acid-dependent manner.

PubMed

Song, Jian Bo; Gao, Shuai; Sun, Di; Li, Hua; Shu, Xia Xia; Yang, Zhi Min

2013-12-11

MicroRNAs (miRNAs) are a class of short, endogenous non-coding small RNAs that have ability to base pair with their target mRNAs to induce their degradation in plants. miR394a/b are conserved small RNAs and its target gene LCR (LEAF CURLING RESPONSIVENESS) encodes an F-box protein (SKP1-Cullin/CDC53-F-box) but whether miR394a/b and its target gene LCR are involved in regulation of plant response to abscisic acid (ABA) and abiotic stresses is unknown. Mature miR394 and precursor miR394a/b are shown to be slightly induced by ABA. By contrast, LCR expression is depressed by ABA. Analysis of LCR and its promoter (pLCR::GUS) revealed that LCR is expressed at all development stages. MIR394a/b over-expression (35S::MIR394a/b) and lcr (LCR loss of function) mutant plants are hypersensitive to salt stress, but LCR over-expressing (35S::m5LCR) plants display the salt-tolerant phenotype. Both 35S::MIR394a/b and lcr plants are highly tolerant to severe drought stress compared with wild-type, but 35S::m5LCR plants are susceptible to water deficiency. Over-expression of MIR394a/b led to ABA hypersensitivity and ABA-associated phenotypes, whereas 35S::m5LCR plants show ABA resistance phenotypes. Moreover, 35S::MIR394a/b plants accumulated higher levels of ABA-induced hydrogen peroxide and superoxide anion radicals than wild-type and 35S::m5LCR plants. Expressions of ABA- and stress-responsive genes, ABI3, ABI4, ABI5, ABF3, and ABF4 are up-regulated in MIR394a/b over-expressing plants but down-regulated in 35S::m5LCR plants. Over-expression of MIR394a in abi4-1 or abi5-1 background resulted in loss of ABA-sensitivity in 35S::MIR394a plants. The silencing of LCR mRNA by miR394 is essential to maintain a certain phenotype favorable for the adaptive response to abiotic stresses. The contrasting phenotypes of salt and drought responses may be mediated by a functional balance between miR394 and LCR. If the balance is perturbed in case of the abiotic stress, an identical phenotype related to the stress response occurs, resulting in either ABA sensitive or insensitive response. Thus, miR394-regulated LCR abundance may allow plants to fine-tune their responses to ABA and abiotic stress.

MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development1

PubMed Central

Sharma, Deepika; Tiwari, Manish; Pandey, Ashutosh; Bhatia, Chitra; Sharma, Ashish; Trivedi, Prabodh Kumar

2016-01-01

MicroRNAs (miRNAs) are endogenous, noncoding small RNAs that function as critical regulators of gene expression. In plants, miRNAs have shown their potential as regulators of growth, development, signal transduction, and stress tolerance. Although the miRNA-mediated regulation of several processes is known, the involvement of miRNAs in regulating secondary plant product biosynthesis is poorly understood. In this study, we functionally characterized Arabidopsis (Arabidopsis thaliana) miR858a, which putatively targets R2R3-MYB transcription factors involved in flavonoid biosynthesis. Overexpression of miR858a in Arabidopsis led to the down-regulation of several MYB transcription factors regulating flavonoid biosynthesis. In contrast to the robust growth and early flowering of miR858OX plants, reduction of plant growth and delayed flowering were observed in Arabidopsis transgenic lines expressing an artificial miRNA target mimic (MIM858). Genome-wide expression analysis using transgenic lines suggested that miR858a targets a number of regulatory factors that modulate the expression of downstream genes involved in plant development and hormonal and stress responses. Furthermore, higher expression of MYBs in MIM858 lines leads to redirection of the metabolic flux towards the synthesis of flavonoids at the cost of lignin synthesis. Altogether, our study has established the potential role of light-regulated miR858a in flavonoid biosynthesis and plant growth and development. PMID:27208307

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants

PubMed Central

Wu, Xiaohui; Zhang, Yumin; Li, Qingshun Q.

2016-01-01

Alternative polyadenylation (APA) is an important layer of gene regulation that produces mRNAs that have different 3′ ends and/or encode diverse protein isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers of poly(A) sites collected in various plant species demand new methods and tools to access and mine these data. We have created an open-access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(A) sites in plants. PlantAPA provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions. Particularly, through PlantAPA, users can analyze poly(A) sites in extended 3′ UTR regions, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing. In addition, it also provides tools for analyzing poly(A) site selections, 3′ UTR lengthening or shortening, non-canonical APA site switching, and differential gene expression between conditions, making it more powerful for the study of APA-mediated gene expression regulation. More importantly, PlantAPA offers a bioinformatics pipeline that allows users to upload their own short reads or ESTs for poly(A) site extraction, enabling users to further explore poly(A) site selection using stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To date, PlantAPA hosts the largest database of APA sites in plants, including Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas reinhardtii. As a user-friendly web service, PlantAPA will be a valuable addition to the community of biologists studying APA mechanisms and gene expression regulation in plants. PMID:27446120

Multiple Different Defense Mechanisms Are Activated in the Young Transgenic Tobacco Plants Which Express the Full Length Genome of the Tobacco Mosaic Virus, and Are Resistant against this Virus

PubMed Central

Jada, Balaji; Soitamo, Arto J.; Siddiqui, Shahid Aslam; Murukesan, Gayatri; Aro, Eva-Mari; Salakoski, Tapio; Lehto, Kirsi

2014-01-01

Previously described transgenic tobacco lines express the full length infectious Tobacco mosaic virus (TMV) genome under the 35S promoter (Siddiqui et al., 2007. Mol Plant Microbe Interact, 20: 1489–1494). Through their young stages these plants exhibit strong resistance against both the endogenously expressed and exogenously inoculated TMV, but at the age of about 7–8 weeks they break into TMV infection, with typical severe virus symptoms. Infections with some other viruses (Potato viruses Y, A, and X) induce the breaking of the TMV resistance and lead to synergistic proliferation of both viruses. To deduce the gene functions related to this early resistance, we have performed microarray analysis of the transgenic plants during the early resistant stage, and after the resistance break, and also of TMV-infected wild type tobacco plants. Comparison of these transcriptomes to those of corresponding wild type healthy plants indicated that 1362, 1150 and 550 transcripts were up-regulated in the transgenic plants before and after the resistance break, and in the TMV-infected wild type tobacco plants, respectively, and 1422, 1200 and 480 transcripts were down-regulated in these plants, respectively. These transcriptome alterations were distinctly different between the three types of plants, and it appears that several different mechanisms, such as the enhanced expression of the defense, hormone signaling and protein degradation pathways contributed to the TMV-resistance in the young transgenic plants. In addition to these alterations, we also observed a distinct and unique gene expression alteration in these plants, which was the strong suppression of the translational machinery. This may also contribute to the resistance by slowing down the synthesis of viral proteins. Viral replication potential may also be suppressed, to some extent, by the reduction of the translation initiation and elongation factors eIF-3 and eEF1A and B, which are required for the TMV replication complex. PMID:25244327

Related Research and Arthroscopy: Increasing the Breadth of Arthroscopy and Arthroscopy Techniques.

PubMed

Wetzler, Merrick J; Brand, Jefferson C; Rossi, Michael J; Lubowitz, James H

2017-11-01

An editorial goal is to increase the breadth of Arthroscopy and Arthroscopy Techniques. Our readers are more than arthroscopic surgeons and scientists. Rather, the health care providers and scientists who read our journals are, first and foremost, physicians, allied health practitioners, and academic intellectuals whose interests include improving individual and public health and welfare across a wide spectrum of scholarly topics. By reaching a broader audience, we hope to expand our contribution to arthroscopic and related surgery and continue to develop the potential of our subspecialty. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Erratum: Erratum: Denoising Phase Unwrapping Algorithm for Precise Phase Shifting Interferometry

NASA Astrophysics Data System (ADS)

Phuc, Phan Huy; Rhee, Hyug-Gyo; Ghim, Young-Sik

2018-06-01

This is a revision of the reference list reported in the original article. In order to clear the contribution of the previous work on the incremental breadth-first search (IBFS) method applied to the PUMA algorithm, we add one more reference to the existing reference list, as in this erratum. Page 83 : In this paper, we propose an algorithm that modifies the Boykov-Kolmogorov (BK) algorithm using the incremental breadth-first search (IBFS) method [27, 28] to find paths from the source to the sink of a graph. [28] S. Ali, H. Khan, I. Shaik and F. Ali, Int. J. Eng. and Technol. 7, 254 (2015).

How Does Electronic Health Information Exchange Affect Hospital Performance Efficiency? The Effects of Breadth and Depth of Information Sharing.

PubMed

Cho, Na-Eun; Ke, Weiling; Atems, Bebonchu; Chang, Jongwha

2018-01-01

This research was motivated by the large investment in health information technology (IT) by hospitals and the inconsistent findings related to the effects of health IT adoption on hospital performance. Building on resource orchestration theory and the information systems literature, the authors developed a research model to investigate how the configuration strategies for sharing information under health IT systems affect hospital efficiency. The hypotheses were tested using data from the 2010 annual and IT surveys of the American Hospital Association, Centers for Medicare & Medicaid Services case mix index, and U.S. Census Bureau's small-area income and poverty estimates. The study revealed that in health IT systems, the breadth (extent) and depth (level of detail) of digital information sharing among stakeholders each has a curvilinear relationship with hospital efficiency. In addition, breadth and depth reinforce each other's positive effects and attenuate each other's negative effects, and their balance has a positive effect on hospital efficiency. The results of this research have the potential to enrich the literature on the value of adopting health IT systems as well as in providing practitioner guidelines for meaningful use.

Repetitive thinking about the mother during distress moderates the link between children's attentional breadth around the mother and depressive symptoms in middle childhood.

PubMed

Van de Walle, Magali; Bijttebier, Patricia; De Raedt, Rudi; Bosmans, Guy

2017-03-01

It has been suggested that an increased attentional focus on the mother should be maladaptive in middle childhood. However, the effect of a more narrow attentional field around the mother may depend on the mother-child relationship. The current study tested whether a more narrow attentional field around the mother is mainly maladaptive for children who tend to think repetitively about their mother (RTm) during distress. More specifically, it investigates whether RTm during distress provides the context in which an increased attentional focus on the mother is linked to depressive symptoms in middle childhood. RTm was measured using a self-report questionnaire. The breadth of children's attentional field around the mother was measured with the Attentional Breadth Task. This computer task assesses the extent to which children have a more narrow attentional field around the mother compared to unfamiliar women. Results of the current study (N = 157) support the hypothesis that 9-12 year old children who have a more narrow attentional field around the mother and who at the same time report more RTm during distress, have more depressive symptoms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Scorpion-Toxin Mimics of CD4 in Complex with Human Immunodeficiency Virus gp120: Crystal Structures, Molecular Mimicry, and Neutralization Breadth

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

Huang, Chih-chin; Stricher, Francois; Martin, Loic

The binding surface on CD4 for the HIV-1 gp120 envelope glycoprotein has been transplanted previously onto a scorpion-toxin scaffold. Here, we use X-ray crystallography to characterize atomic-level details of gp120 with this transplant, CD4M33. Despite known envelope flexibility, the conformation of gp120 induced by CD4M33 was so similar to that induced by CD4 that localized measures were required to distinguish ligand-induced differences from lattice variation. To investigate relationships between structure, function, and mimicry, an F23 analog of CD4M33 was devised. Structural and thermodynamic analyses showed F23 to be a better molecular mimic of CD4 than CD4M33. F23 also showed increasedmore » neutralization breadth, against diverse isolates of HIV-1, HIV-2, and SIVcpz. Our results lend insight into the stability of the CD4 bound conformation of gp120, define measures that quantify molecular mimicry as a function of evolutionary distance, and suggest how such evaluations might be useful in developing mimetic antagonists with increased neutralization breadth.« less

Diversification of Root Hair Development Genes in Vascular Plants1[OPEN

PubMed Central

Shi, Xinhui; Wang, Wenjia; Ryu, Kook Hui

2017-01-01

The molecular genetic program for root hair development has been studied intensively in Arabidopsis (Arabidopsis thaliana). To understand the extent to which this program might operate in other plants, we conducted a large-scale comparative analysis of root hair development genes from diverse vascular plants, including eudicots, monocots, and a lycophyte. Combining phylogenetics and transcriptomics, we discovered conservation of a core set of root hair genes across all vascular plants, which may derive from an ancient program for unidirectional cell growth coopted for root hair development during vascular plant evolution. Interestingly, we also discovered preferential diversification in the structure and expression of root hair development genes, relative to other root hair- and root-expressed genes, among these species. These differences enabled the definition of sets of genes and gene functions that were acquired or lost in specific lineages during vascular plant evolution. In particular, we found substantial divergence in the structure and expression of genes used for root hair patterning, suggesting that the Arabidopsis transcriptional regulatory mechanism is not shared by other species. To our knowledge, this study provides the first comprehensive view of gene expression in a single plant cell type across multiple species. PMID:28487476

A Novel 5-Enolpyruvylshikimate-3-Phosphate Synthase Shows High Glyphosate Tolerance in Escherichia coli and Tobacco Plants

PubMed Central

Zhang, Shengxue; Yang, Xuewen; Chen, Rongrong; Zhang, Yuwen; Lu, Wei; Liu, Yan; Wang, Jianhua; Lin, Min; Wang, Guoying

2012-01-01

A key enzyme in the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the primary target of the broad-spectrum herbicide glyphosate. Identification of new aroA genes coding for EPSPS with a high level of glyphosate tolerance is essential for the development of glyphosate-tolerant crops. In the present study, the glyphosate tolerance of five bacterial aroA genes was evaluated in the E. coli aroA-defective strain ER2799 and in transgenic tobacco plants. All five aroA genes could complement the aroA-defective strain ER2799, and AM79 aroA showed the highest glyphosate tolerance. Although glyphosate treatment inhibited the growth of both WT and transgenic tobacco plants, transgenic plants expressing AM79 aroA tolerated higher concentration of glyphosate and had a higher fresh weight and survival rate than plants expressing other aroA genes. When treated with high concentration of glyphosate, lower shikimate content was detected in the leaves of transgenic plants expressing AM79 aroA than transgenic plants expressing other aroA genes. These results suggest that AM79 aroA could be a good candidate for the development of transgenic glyphosate-tolerant crops. PMID:22715408

Plant nitrogen regulatory P-PII genes

DOEpatents

Coruzzi, Gloria M.; Lam, Hon-Ming; Hsieh, Ming-Hsiun

2001-01-01

The present invention generally relates to plant nitrogen regulatory PII gene (hereinafter P-PII gene), a gene involved in regulating plant nitrogen metabolism. The invention provides P-PII nucleotide sequences, expression constructs comprising said nucleotide sequences, and host cells and plants having said constructs and, optionally expressing the P-PII gene from said constructs. The invention also provides substantially pure P-PII proteins. The P-PII nucleotide sequences and constructs of the

Expression of ORF2 partial gene of hepatitis E virus in tomatoes and immunoactivity of expression products.

PubMed

Ma, Ying; Lin, Shun-Quan; Gao, Yi; Li, Mei; Luo, Wen-Xin; Zhang, Jun; Xia, Ning-Shao

2003-10-01

To transfer hepatitis E virus (HEV) ORF2 partial gene to tomato plants, to investigate its expression in transformants and the immunoactivity of expression products, and to explore the feasibility of developing a new type of plant-derived HEV oral vaccine. Plant binary expression vector p1301E2, carrying a fragment of HEV open reading frame-2 (named HEV-E2), was constructed by linking the fragment to a constitutive CaMV35s promoter and nos terminator, then directly introduced into Agrobacterium tumefaciens EHA105. With leaf-disc method, tomato plants medicated by EHA105 were transformed and hygromycin-resistant plantlets were obtained in selective medium containing hygromycin. The presence and integration of foreign DNA in transgenic tomato genome were confirmed by Gus gene expression, PCR amplification and Southern dot blotting. The immunoactivity of recombinant protein extracted from transformed plants was examined by enzyme-linked immunosorbant assay (ELISA) using a monoclonal antibody specifically against HEV. ELISA was also used to estimate the recombinant protein content in leaves and fruits of the transformants. Seven positive lines of HEV-E2-transgenic tomato plants confirmed by PCR and Southern blotting were obtained and the immunoactivity of recombinant protein could be detected in extracts of transformants. The expression levels of recombinant protein were 61.22 ng/g fresh weight in fruits and 6.37-47.9 ng/g fresh weight in leaves of the transformants. HEV-E2 gene was correctly expressed in transgenic tomatoes and the recombinant antigen derived from them has normal immunoactivity. Transgenic tomatoes may hold a good promise for producing a new type of low-cost oral vaccine for hepatitis E virus.

Sugar and hexokinase suppress expression of PIP aquaporins and reduce leaf hydraulics that preserves leaf water potential.

PubMed

Kelly, Gilor; Sade, Nir; Doron-Faigenboim, Adi; Lerner, Stephen; Shatil-Cohen, Arava; Yeselson, Yelena; Egbaria, Aiman; Kottapalli, Jayaram; Schaffer, Arthur A; Moshelion, Menachem; Granot, David

2017-07-01

Sugars affect central aspects of plant physiology, including photosynthesis, stomatal behavior and the loss of water through the stomata. Yet, the potential effects of sugars on plant aquaporins (AQPs) and water conductance have not been examined. We used database and transcriptional analyses, as well as cellular and whole-plant functional techniques to examine the link between sugar-related genes and AQPs. Database analyses revealed a high level of correlation between the expression of AQPs and that of sugar-related genes, including the Arabidopsis hexokinases 1 (AtHXK1). Increased expression of AtHXK1, as well as the addition of its primary substrate, glucose (Glc), repressed the expression of 10 AQPs from the plasma membrane-intrinsic proteins (PIP) subfamily (PIP-AQPs) and induced the expression of two stress-related PIP-AQPs. The osmotic water permeability of mesophyll protoplasts of AtHXK1-expressing plants and the leaf hydraulic conductance of those plants were significantly reduced, in line with the decreased expression of PIP-AQPs. Conversely, hxk1 mutants demonstrated a higher level of hydraulic conductance, with increased water potential in their leaves. In addition, the presence of Glc reduced leaf water potential, as compared with an osmotic control, indicating that Glc reduces the movement of water from the xylem into the mesophyll. The production of sugars entails a significant loss of water and these results suggest that sugars and AtHXK1 affect the expression of AQP genes and reduce leaf water conductance, to coordinate sugar levels with the loss of water through transpiration. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Gramene 2016: comparative plant genomics and pathway resources

PubMed Central

Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

2016-01-01

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

Dramatic transcriptional changes in an intracellular parasite enable host switching between plant and insect.

PubMed

Oshima, Kenro; Ishii, Yoshiko; Kakizawa, Shigeyuki; Sugawara, Kyoko; Neriya, Yutaro; Himeno, Misako; Minato, Nami; Miura, Chihiro; Shiraishi, Takuya; Yamaji, Yasuyuki; Namba, Shigetou

2011-01-01

Phytoplasmas are bacterial plant pathogens that have devastating effects on the yields of crops and plants worldwide. They are intracellular parasites of both plants and insects, and are spread among plants by insects. How phytoplasmas can adapt to two diverse environments is of considerable interest; however, the mechanisms enabling the "host switching" between plant and insect hosts are poorly understood. Here, we report that phytoplasmas dramatically alter their gene expression in response to "host switching" between plant and insect. We performed a detailed characterization of the dramatic change that occurs in the gene expression profile of Candidatus Phytoplasma asteris OY-M strain (approximately 33% of the genes change) upon host switching between plant and insect. The phytoplasma may use transporters, secreted proteins, and metabolic enzymes in a host-specific manner. As phytoplasmas reside within the host cell, the proteins secreted from phytoplasmas are thought to play crucial roles in the interplay between phytoplasmas and host cells. Our microarray analysis revealed that the expression of the gene encoding the secreted protein PAM486 was highly upregulated in the plant host, which is also observed by immunohistochemical analysis, suggesting that this protein functions mainly when the phytoplasma grows in the plant host. Additionally, phytoplasma growth in planta was partially suppressed by an inhibitor of the MscL osmotic channel that is highly expressed in the plant host, suggesting that the osmotic channel might play an important role in survival in the plant host. These results also suggest that the elucidation of "host switching" mechanism may contribute to the development of novel pest controls.

Antimicrobial peptide production and plant-based expression systems for medical and agricultural biotechnology.

PubMed

Holaskova, Edita; Galuszka, Petr; Frebort, Ivo; Oz, M Tufan

2015-11-01

Antimicrobial peptides (AMPs) are vital components of the innate immune system of nearly all living organisms. They generally act in the first line of defense against various pathogenic bacteria, parasites, enveloped viruses and fungi. These low molecular mass peptides are considered prospective therapeutic agents due to their broad-spectrum rapid activity, low cytotoxicity to mammalian cells and unique mode of action which hinders emergence of pathogen resistance. In addition to medical use, AMPs can also be employed for development of innovative approaches for plant protection in agriculture. Conferred disease resistance by AMPs might help us surmount losses in yield, quality and safety of agricultural products due to plant pathogens. Heterologous expression in plant-based systems, also called plant molecular farming, offers cost-effective large-scale production which is regarded as one of the most important factors for clinical or agricultural use of AMPs. This review presents various types of AMPs as well as plant-based platforms ranging from cell suspensions to whole plants employed for peptide production. Although AMP production in plants holds great promises for medicine and agriculture, specific technical limitations regarding product yield, function and stability still remain. Additionally, establishment of particular stable expression systems employing plants or plant tissues generally requires extended time scale for platform development compared to certain other heterologous systems. Therefore, fast and promising tools for evaluation of plant-based expression strategies and assessment of function and stability of the heterologously produced AMPs are critical for molecular farming and plant protection. Copyright © 2015 Elsevier Inc. All rights reserved.

Sweet smells prepare plants for future stress: airborne induction of plant disease immunity.

PubMed

Yi, Hwe-Su; Ryu, Choong-Min; Heil, Martin

2010-05-01

Plants require protection against a wide range of attackers such as insects and pathogens. The adequate plant defense responses are regulated via sophisticated signal cascades, which are activated following the perception of specific cues of the attackers. Plants might, however, gain a significant fitness advantage when pre-empting enemy attack before it actually occurs. Monitoring cues from attacked neighbors can permit plants to reach this goal. We have recently found airborne disease resistance against a bacterial pathogen in uninfected lima bean plants when these were located close to conspecific, resistance-expressing neighbors. The emitters could be chemically induced with benzothiadiazole or biologically with an avirulent pathogen. Unexpectedly, receiver plants, although expressing a functioning resistance, did not show reduced growth rates, which represent a common side-effect of directly induced pathogen resistance. Nonanal was identified as an active volatile and, rather than directly inducing full resistance, primed defense gene expression, which became fully activated only when the plants were subsequently challenged by a virulent pathogen. Priming by airborne signals allows for a more efficient and less costly preparation of plants for future attack and airborne signaling can affect resistance against both major groups of plant enemies: herbivores and pathogens.