Accurate evaluation of exchange fields in finite element micromagnetic solvers

NASA Astrophysics Data System (ADS)

Chang, R.; Escobar, M. A.; Li, S.; Lubarda, M. V.; Lomakin, V.

2012-04-01

Quadratic basis functions (QBFs) are implemented for solving the Landau-Lifshitz-Gilbert equation via the finite element method. This involves the introduction of a set of special testing functions compatible with the QBFs for evaluating the Laplacian operator. The results by using QBFs are significantly more accurate than those via linear basis functions. QBF approach leads to significantly more accurate results than conventionally used approaches based on linear basis functions. Importantly QBFs allow reducing the error of computing the exchange field by increasing the mesh density for structured and unstructured meshes. Numerical examples demonstrate the feasibility of the method.

Variation in Macro and Trace Elements in Progression of Type 2 Diabetes

PubMed Central

2014-01-01

Macro elements are the minerals of which the body needs more amounts and are more important than any other elements. Trace elements constitute a minute part of the living tissues and have various metabolic characteristics and functions. Trace elements participate in tissue and cellular and subcellular functions; these include immune regulation by humoral and cellular mechanisms, nerve conduction, muscle contractions, membrane potential regulations, and mitochondrial activity and enzyme reactions. The status of micronutrients such as iron and vanadium is higher in type 2 diabetes. The calcium, magnesium, sodium, chromium, cobalt, iodine, iron, selenium, manganese, and zinc seem to be low in type 2 diabetes while elements such as potassium and copper have no effect. In this review, we emphasized the status of macro and trace elements in type 2 diabetes and its advantages or disadvantages; this helps to understand the mechanism, progression, and prevention of type 2 diabetes due to the lack and deficiency of different macro and trace elements. PMID:25162051

Isolation and functional characterization of CE1 binding proteins.

PubMed

Lee, Sun-ji; Park, Ji Hye; Lee, Mi Hun; Yu, Ji-hyun; Kim, Soo Young

2010-12-16

Abscisic acid (ABA) is a plant hormone that controls seed germination, protective responses to various abiotic stresses and seed maturation. The ABA-dependent processes entail changes in gene expression. Numerous genes are regulated by ABA, and promoter analyses of the genes revealed that cis-elements sharing the ACGTGGC consensus sequence are ubiquitous among ABA-regulated gene promoters. The importance of the core sequence, which is generally known as ABA response element (ABRE), has been demonstrated by various experiments, and its cognate transcription factors known as ABFs/AREBs have been identified. Although necessary, ABRE alone is not sufficient, and another cis-element known as "coupling element (CE)" is required for full range ABA-regulation of gene expression. Several CEs are known. However, despite their importance, the cognate transcription factors mediating ABA response via CEs have not been reported to date. Here, we report the isolation of transcription factors that bind one of the coupling elements, CE1. To isolate CE1 binding proteins, we carried out yeast one-hybrid screens. Reporter genes containing a trimer of the CE1 element were prepared and introduced into a yeast strain. The yeast was transformed with library DNA that represents RNA isolated from ABA-treated Arabidopsis seedlings. From the screen of 3.6 million yeast transformants, we isolated 78 positive clones. Analysis of the clones revealed that a group of AP2/ERF domain proteins binds the CE1 element. We investigated their expression patterns and analyzed their overexpression lines to investigate the in vivo functions of the CE element binding factors (CEBFs). Here, we show that one of the CEBFs, AtERF13, confers ABA hypersensitivity in Arabidopsis, whereas two other CEBFs enhance sugar sensitivity. Our results indicate that a group of AP2/ERF superfamily proteins interacts with CE1. Several CEBFs are known to mediate defense or abiotic stress response, but the physiological functions of other CEBFs remain to be determined. Our in vivo functional analysis of several CEBFs suggests that they are likely to be involved in ABA and/or sugar response. Together with previous results reported by others, our current data raise an interesting possibility that the coupling element CE1 may function not only as an ABRE but also as an element mediating biotic and abiotic stress responses.

Trace element distribution in the rat cerebellum

NASA Astrophysics Data System (ADS)

Kwiatek, W. M.; Long, G. J.; Pounds, J. G.; Reuhl, K. R.; Hanson, A. L.; Jones, K. W.

1990-04-01

Spatial distributions and concentrations of trace elements (TE) in the brain are important because TE perform catalytic and structural functions in enzymes which regulate brain function and development. We have investigated the distributions of TE in rat cerebellum. Structures were sectioned and analyzed by the Synchrotron Radiation Induced X-ray Emission (SRIXE) method using the NSLS X-26 white-light microprobe facility. Advantages important for TE analysis of biological specimens with X-ray microscopy include short time of measurement, high brightness and flux, good spatial resolution, multielemental detection, good sensitivity, and nondestructive irradiation. Trace elements were measured in thin rat brain sections of 20 μm thickness. The analyses were performed on sample volumes as small as 0.2 nl with Minimum Detectable Limits (MDL) of 50 ppb wet weight for Fe, 100 ppb wet weight for Cu, and Zn, and 1 ppm wet weight for Pb. The distribution of TE in the molecular cell layer, granule cell layer and fiber tract of rat cerebella was investigated. Both point analyses and two-dimensional semiquantitative mapping of the TE distribution in a section were used. All analyzed elements were observed in each structure of the cerebellum except mercury which was not observed in granule cell layer or fiber tract. This approach permits an exacting correlation of the TE distribution in complex structure with the diet, toxic elements, and functional status of the animal.

Transposable elements in Drosophila.

PubMed

McCullers, Tabitha J; Steiniger, Mindy

2017-01-01

Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster .

Transposable elements in Drosophila

PubMed Central

McCullers, Tabitha J.; Steiniger, Mindy

2017-01-01

ABSTRACT Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster. PMID:28580197

What Aspects of Personal Care Are Most Important to Patients Undergoing Radiation Therapy for Prostate Cancer?

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

Foley, Kimberley A.; Department of Public Health Sciences, Queen's University, Kingston, Ontario; Feldman-Stewart, Deb

Purpose/Objective: The overall quality of patient care is a function of the quality of both its technical and its nontechnical components. The purpose of this study was to identify the elements of nontechnical (personal) care that are most important to patients undergoing radiation therapy for prostate cancer. Methods and Materials: We reviewed the literature and interviewed patients and health professionals to identify elements of personal care pertinent to patients undergoing radiation therapy for prostate cancer. We identified 143 individual elements relating to 10 aspects of personal care. Patients undergoing radical radiation therapy for prostate cancer completed a self-administered questionnaire inmore » which they rated the importance of each element. The overall importance of each element was measured by the percentage of respondents who rated it as “very important.” The importance of each aspect of personal care was measured by the mean importance of its elements. Results: One hundred eight patients completed the questionnaire. The percentage of patients who rated each element “very important” ranged from 7% to 95% (mean 61%). The mean importance rating of the elements of each aspect of care varied significantly: “perceived competence of caregivers,” 80%; “empathy and respectfulness of caregivers,” 67%; “adequacy of information sharing,” 67%; “patient centeredness,” 59%; “accessibility of caregivers,” 57%; “continuity of care,” 51%; “privacy,” 51%; “convenience,” 45%; “comprehensiveness of services,” 44%; and “treatment environment,” 30% (P<.0001). Neither age nor education was associated with importance ratings, but the patient's health status was associated with the rating of some elements of care. Conclusions: Many different elements of personal care are important to patients undergoing radiation therapy for prostate cancer, but the 3 aspects of care that most believe are most important are these: the perceived competence of their caregivers, the empathy and respectfulness of their caregivers, and the adequacy of information sharing.« less

Ionomics: The functional genomics of elements.

PubMed

Baxter, Ivan

2010-03-01

Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. This approach has been applied extensively in plants for forward and reverse genetics, screening diversity panels, and modeling of physiological states. In this review, I will discuss some of the advantages and limitations of the ionomics approach as well as the important parameters to consider when designing ionomics experiments, and how to evaluate ionomics data.

Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

PubMed Central

Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

2012-01-01

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

Metal transport across biomembranes: emerging models for a distinct chemistry.

PubMed

Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

2012-04-20

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

Multiple heteroatom substitution to graphene nanoribbon

PubMed Central

Meyer, Ernst

2018-01-01

Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)—a tool to directly resolve chemical structures—is one of the most promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution. This elemental-sensitive measurement takes an important step in the analysis of functionalized two-dimensional carbon materials. PMID:29662955

A Decade of Experience in Creating and Maintaining Data Elements for Structured Clinical Documentation in EHRs

PubMed Central

Zhou, Li; Collins, Sarah; Morgan, Stephen J.; Zafar, Neelam; Gesner, Emily J.; Fehrenbach, Martin; Rocha, Roberto A.

2016-01-01

Structured clinical documentation is an important component of electronic health records (EHRs) and plays an important role in clinical care, administrative functions, and research activities. Clinical data elements serve as basic building blocks for composing the templates used for generating clinical documents (such as notes and forms). We present our experience in creating and maintaining data elements for three different EHRs (one home-grown and two commercial systems) across different clinical settings, using flowsheet data elements as examples in our case studies. We identified basic but important challenges (including naming convention, links to standard terminologies, and versioning and change management) and possible solutions to address them. We also discussed more complicated challenges regarding governance, documentation vs. structured data capture, pre-coordination vs. post-coordination, reference information models, as well as monitoring, communication and training. PMID:28269927

Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.

PubMed

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De; Qin, Cheng-Feng

2013-06-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

PubMed Central

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De

2013-01-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5′ cyclization sequence (5′CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5′CS, and the presence of DCS-PK facilitates the formation of 5′-3′ RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution. PMID:23576500

Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice.

PubMed

Wang, Rui; Zhu, Menglin; Ye, Rongjian; Liu, Zuoxiong; Zhou, Fei; Chen, Hao; Lin, Yongjun

2015-12-11

As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.

Are there different requirements for trace elements in eumelanin- and pheomelanin-based color production? A case study of two passerine species.

PubMed

Zduniak, Piotr; Surmacki, Adrian; Erciyas-Yavuz, Kiraz; Chudzińska, Maria; Barałkiewicz, Danuta

2014-09-01

Melanin is the most common pigment in animal integuments including bird plumage. It has been shown that several trace elements may play roles in the production and signaling function of melanin-colored plumage. We investigated coloration and content of various metal elements in the rectrices of two insectivorous passerines, Common Redstarts (Phoenicurus phoenicurus) and Blackcaps (Sylvia atricapilla), which have eumelanin- and pheomelanin-based coloration, respectively. We hypothesized that 1) the two species would differ in concentrations of metals important in melanin synthesis (Ca, Fe, Cu, Zn), 2) differences in metal concentration levels would be related to feather coloration. Our study confirmed the first prediction and provides the first evidence that selected elements may play a greater role in pheomelanin than in eumelanin synthesis. Concentrations of three elements considered as important in melanin synthesis (Ca, Fe, Zn) were 52% to 93% higher in rusty colored Common Redstart feathers compared to the dark gray Blackcap feathers. However, element concentrations were not correlated with feather coloration or sex in either species. Our study suggests that, of the two melanin forms, pheomelanin synthesis may bear higher costs associated with the acquisition of specific elements or limited elements may create trade-offs between ornamentation and other physiological functions. Our findings warrant further investigations designed to better understand the roles of macro- and microelements in the synthesis of both forms of melanin. Copyright © 2014 Elsevier Inc. All rights reserved.

PhOBF1, a petunia OCS element binding factor, plays an important role in antiviral RNA silencing

USDA-ARS?s Scientific Manuscript database

Virus-induced gene silencing (VIGS) is a common strategy of reverse genetics for characterizing function of genes in plant. The detailed mechanism governing RNA silencing efficiency triggered by virus is largely unclear. Here, we revealed that a petunia (Petunia hybrida) ocs element binding factor, ...

Altruistic functions for selfish DNA.

PubMed

Faulkner, Geoffrey J; Carninci, Piero

2009-09-15

Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this "selfish DNA" or "junk DNA" dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.

The importance of trace element speciation in biomedical science.

PubMed

Templeton, Douglas M

2003-04-01

According to IUPAC terminology, trace element speciation reflects differences in chemical composition at multiple levels from nuclear and electronic structure to macromolecular complexation. In the medical sciences, all levels of composition are important in various circumstances, and each can affect the bioavailability, distribution, physiological function, toxicity, diagnostic utility, and therapeutic potential of an element. Here we discuss, with specific examples, three biological principles in the intimate relation between speciation and biological behavior: i) the kinetics of interconversion of species determines distribution within the organism, ii) speciation governs transport across various biological barriers, and iii) speciation can limit potentially undesirable interactions between physiologically essential elements. We will also describe differences in the speciation of iron in states of iron overload, to illustrate how speciation analysis can provide insight into cellular processes in human disease.

Simulation analysis and experimental verification of spiral-tube-type valveless piezoelectric pump with gyroscopic effect

NASA Astrophysics Data System (ADS)

Leng, Xuefei; Zhang, Jianhui; Jiang, Yan; Wang, Shouyin; Zhao, Chunsheng

2014-07-01

The current research of the valveless piezoelectric pump focuses on increasing the flow rate and pressure differential. Compared with the valve piezoelectric pump, the valveless one has excellent performances in simple structure, low cost, and easy miniaturization. So, their important development trend is the mitigation of their weakness, and the multi-function integration. The flow in a spiral tube element is sensitive to the element attitude caused by the Coriolis force, and that a valveless piezoelectric pump is designed by applying this phenomenon. The pump has gyroscopic effect, and has both the actuator function of fluid transfer and the sensor function, which can obtain the angular velocity when its attitude changes. First, the present paper analyzes the flow characteristics in the tube, obtains the calculation formula for the pump flow, and identifies the relationship between pump attitude and flow, which clarifies the impact of flow and driving voltage, frequency, spiral line type and element attitude, and verifies the gyroscopic effect of the pump. Then, the finite element simulation is used to verify the theory. Finally, a pump is fabricated for experimental testing of the relationship between pump attitude and pressure differential. Experimental results show that when Archimedes spiral θ=4π is selected for the tube design, and the rotation speed of the plate is 70 r/min, the pressure differential is 88.2 Pa, which is 1.5 times that of 0 r/min rotation speed. The spiral-tube-type valveless piezoelectric pump proposed can turn the element attitude into a form of pressure output, which is important for the multi-function integration of the valveless piezoelectric pump and for the development of civil gyroscope in the future.

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

PubMed Central

Chandrashekar, Darshan Shimoga; Dey, Poulami; Acharya, Kshitish K.

2015-01-01

Background Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. Result We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species. Conclusion GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various contexts/regions. GREAM is freely available at http://resource.ibab.ac.in/GREAM/. PMID:26208093

Mapping functional connectivity

Treesearch

Peter Vogt; Joseph R. Ferrari; Todd R. Lookingbill; Robert H. Gardner; Kurt H. Riitters; Katarzyna Ostapowicz

2009-01-01

An objective and reliable assessment of wildlife movement is important in theoretical and applied ecology. The identification and mapping of landscape elements that may enhance functional connectivity is usually a subjective process based on visual interpretations of species movement patterns. New methods based on mathematical morphology provide a generic, flexible,...

Functional and mechanistic diversity of distal transcription enhancers

PubMed Central

Bulger, Michael; Groudine, Mark

2013-01-01

Biological differences among metazoans, and between cell types in a given organism, arise in large part due to differences in gene expression patterns. The sequencing of multiple metazoan genomes, coupled with recent advances in genome-wide analysis of histone modifications and transcription factor binding, has revealed that among regulatory DNA sequences, gene-distal enhancers appear to exhibit the greatest diversity and cell-type specificity. Moreover, such elements are emerging as important targets for mutations that can give rise to disease and to genetic variability that underlies evolutionary change. Studies of long-range interactions between distal genomic sequences in the nucleus indicate that enhancers are often important determinants of nuclear organization, contributing to a general model for enhancer function that involves direct enhancer-promoter contact. In a number of systems, however, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse. PMID:21295696

The impact of transposable elements on mammalian development

PubMed Central

Garcia-Perez, Jose L.; Widmann, Thomas J.; Adams, Ian R.

2018-01-01

Summary Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that significantly impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and how the somatic activity of TEs can influence gene regulatory networks. PMID:27875251

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

The genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin.

PubMed

Yazaki, Junshi; Kikuchi, Shoshi

2005-01-01

We now have the various genomics tools for monocot (Oryza sativa) and a dicot (Arabidopsis thaliana) plant. Plant is not only a very important agricultural resource but also a model organism for biological research. It is important that the interaction between ABA and GA is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. These studies have investigated the relationship between dormancy and germination using genomics tools. Genomics tools identified genes that had never before been annotated as ABA- or GA-responsive genes in plant, detected new interactions between genes responsive to the two hormones, comprehensively characterized cis-elements of hormone-responsive genes, and characterized cis-elements of rice and Arabidopsis. In these research, ABA- and GA-regulated genes have been classified as functional proteins (proteins that probably function in stress or PR tolerance) and regulatory proteins (protein factors involved in further regulation of signal transduction). Comparison between ABA and/or GA-responsive genes in rice and those in Arabidopsis has shown that the cis-element has specificity in each species. cis-Elements for the dehydration-stress response have been specified in Arabidopsis but not in rice. cis-Elements for protein storage are remarkably richer in the upstream regions of the rice gene than in those of Arabidopsis.

Functional Grammar and Teaching of Reading--A Pedagogy Based on Graded Teaching of College English in China

ERIC Educational Resources Information Center

Xu, Tuo; Zhang, Beili

2015-01-01

This article discusses the importance of functional grammar and demonstrates its application to the teaching of reading among graded college students. Functional grammar holds that a discourse is composed of two levels: the interior level and the exterior level. Therefore, reading activities involve both linguistic elements and contexts.…

Regulatory elements in vivo in the promoter of the abscisic acid responsive gene rab17 from maize.

PubMed

Busk, P K; Jensen, A B; Pagès, M

1997-06-01

The rab17 gene from maize is transcribed in late embryonic development and is responsive to abscisic acid and water stress in embryo and vegetative tissues. In vivo footprinting and transient transformation of rab17 were performed in embryos and vegetative tissues to characterize the cis-elements involved in regulation of the gene. By in vivo footprinting, protein binding was observed to nine elements in the promoter, which correspond to five putative ABREs (abscisic acid responsive elements) and four other sequences. The footprints indicated that distinct proteins interact with these elements in the two developmental stages. In transient transformation, six of the elements were important for high level expression of the rab17 promoter in embryos, whereas only three elements were important in leaves. The cis-acting sequences can be divided in embryo-specific, ABA-specific and leaf-specific elements on the basis of protein binding and the ability to confer expression of rab17. We found one positive, new element, called GRA, with the sequence CACTGGCCGCCC. This element was important for transcription in leaves but not in embryos. Two other non-ABRE elements that stimulated transcription from the rab17 promoter resemble previously described abscisic acid and drought-inducible elements. There were differences in protein binding and function of the five ABREs in the rab17 promoter. The possible reasons for these differences are discussed. The in vivo data obtained suggest that an embryo-specific pathway regulates transcription of the rab genes during development, whereas another pathway is responsible for induction in response to ABA and drought in vegetative tissues.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

PubMed

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A; Kluger, Yuval

2016-10-14

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3'Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

PubMed Central

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P.; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A.; Kluger, Yuval

2016-01-01

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3′Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. PMID:27439714

Wetland biogeochemistry and ecological risk assessment

NASA Astrophysics Data System (ADS)

Bai, Junhong; Huang, Laibin; Gao, Haifeng; Zhang, Guangliang

2017-02-01

Wetlands are an important ecotone between terrestrial and aquatic ecosystems and can provide great ecological service functions. Soils/sediments are one of the important components of wetland ecosystems, which support wetland plants and microorganisms and influence wetland productivity. Moreover, wetland soils/sediments serve as sources, sinks and transfers of carbon, nitrogen, phosphorus and chemical contaminants such as heavy metals. In natural wetland ecosystems, wetland soils/sediments play a great role in improving water quality as these chemical elements can be retained in wetland soils/sediments for a long time. Moreover, the biogeochemical processes of the abovementioned elements in wetland soils/sediments can drive wetland evolution and development, and their changes will considerably affect wetland ecosystem health. Therefore, a better understanding of wetland soil biogeochemistry will contribute to improving wetland ecological service functions.

Genetic dissection of the α-globin super-enhancer in vivo

PubMed Central

Hay, Deborah; Hughes, Jim R.; Rode, Christina; Li, Pik-Shan; Pennacchio, Len A.; Sloane-Stanley, Jacqueline A.; Ayyub, Helena; Butler, Sue; Sauka-Spengler, Tatjana; Gibbons, Richard J.; Smith, Andrew J.H.; Wood, William G.; Higgs, Douglas R.

2016-01-01

Many genes determining cell identity are regulated by clusters of mediator-bound enhancer elements collectively referred to as super-enhancers. These have been proposed to manifest higher-order properties important in development and disease. Here, we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer singly and in informative combinations, we demonstrate that each constituent enhancer appears to act independently and in an additive fashion with respect to hematologic phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation. PMID:27376235

The impact of transposable elements on mammalian development.

PubMed

Garcia-Perez, Jose L; Widmann, Thomas J; Adams, Ian R

2016-11-15

Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks. © 2016. Published by The Company of Biologists Ltd.

The contribution of nature to people: Applying concepts of values and properties to rate the management importance of natural elements.

PubMed

Smith, Michael J; Wagner, Christian; Wallace, Ken J; Pourabdollah, Amir; Lewis, Loretta

2016-06-15

An important, and yet unresolved question in natural resource management is how best to manage natural elements and their associated values to ensure human wellbeing. Specifically, there is a lack of measurement tools to assess the contribution of nature to people. We present one approach to overcome this global issue and show that the preferred state of any system element, in terms of realising human values, is a function of element properties. Consequently, natural resource managers need to understand the nature of the relationships between element properties and values if they are to successfully manage for human wellbeing. In two case studies of applied planning, we demonstrate how to identify key element properties, quantify their relationships to priority human values, and combine this information to model the contribution of elements to human wellbeing. In one of the two case studies we also compared the modelling outputs with directly elicited stakeholder opinions regarding the importance of the elements for realising the given priority values. The two, largely congruent outputs provide additional support for the approach. The study shows that rating sets of elements on their relative overall value for human wellbeing, or utility, provides critical information for subsequent management decisions and a basis for productive new research. We consider that the described approach is broadly applicable within the domain of natural resource management. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

A conserved RNA structural element within the hepatitis B virus post-transcriptional regulatory element enhance nuclear export of intronless transcripts and repress the splicing mechanism.

PubMed

Visootsat, Akasit; Payungporn, Sunchai; T-Thienprasert, Nattanan P

2015-12-01

Hepatitis B virus (HBV) infection is a primary cause of hepatocellular carcinoma and liver cirrhosis worldwide. To develop novel antiviral drugs, a better understanding of HBV gene expression regulation is vital. One important aspect is to understand how HBV hijacks the cellular machinery to export unspliced RNA from the nucleus. The HBV post-transcriptional regulatory element (HBV PRE) has been proposed to be the HBV RNA nuclear export element. However, the function remains controversial, and the core element is unclear. This study, therefore, aimed to identify functional regulatory elements within the HBV PRE and investigate their functions. Using bioinformatics programs based on sequence conservation and conserved RNA secondary structures, three regulatory elements were predicted, namely PRE 1151-1410, PRE 1520-1620 and PRE 1650-1684. PRE 1151-1410 significantly increased intronless and unspliced luciferase activity in both HepG2 and COS-7 cells. Likewise, PRE 1151-1410 significantly elevated intronless and unspliced HBV surface transcripts in liver cancer cells. Moreover, motif analysis predicted that PRE 1151-1410 contains several regulatory motifs. This study reported the roles of PRE 1151-1410 in intronless transcript nuclear export and the splicing mechanism. Additionally, these results provide knowledge in the field of HBV RNA regulation. Moreover, PRE 1151-1410 may be used to enhance the expression of other mRNAs in intronless reporter plasmids.

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion.

PubMed

Vaschetto, Luis María

2018-04-01

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.

Genetic evidence for conserved non-coding element function across species–the ears have it

PubMed Central

Turner, Eric E.; Cox, Timothy C.

2014-01-01

Comparison of genomic sequences from diverse vertebrate species has revealed numerous highly conserved regions that do not appear to encode proteins or functional RNAs. Often these “conserved non-coding elements,” or CNEs, can direct gene expression to specific tissues in transgenic models, demonstrating they have regulatory function. CNEs are frequently found near “developmental” genes, particularly transcription factors, implying that these elements have essential regulatory roles in development. However, actual examples demonstrating CNE regulatory functions across species have been few, and recent loss-of-function studies of several CNEs in mice have shown relatively minor effects. In this Perspectives article, we discuss new findings in “fancy” rats and Highland cattle demonstrating that function of a CNE near the Hmx1 gene is crucial for normal external ear development and when disrupted can mimic loss-of function Hmx1 coding mutations in mice and humans. These findings provide important support for conserved developmental roles of CNEs in divergent species, and reinforce the concept that CNEs should be examined systematically in the ongoing search for genetic causes of human developmental disorders in the era of genome-scale sequencing. PMID:24478720

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters.

PubMed

Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

2005-02-01

cis-Acting regulatory elements are important molecular switches involved in the transcriptional regulation of a dynamic network of gene activities controlling various biological processes, including abiotic stress responses, hormone responses and developmental processes. In particular, understanding regulatory gene networks in stress response cascades depends on successful functional analyses of cis-acting elements. The ever-improving accuracy of transcriptome expression profiling has led to the identification of various combinations of cis-acting elements in the promoter regions of stress-inducible genes involved in stress and hormone responses. Here we discuss major cis-acting elements, such as the ABA-responsive element (ABRE) and the dehydration-responsive element/C-repeat (DRE/CRT), that are a vital part of ABA-dependent and ABA-independent gene expression in osmotic and cold stress responses.

Technology-Critical Elements: Economic and Policy Perspectives

NASA Astrophysics Data System (ADS)

Eggert, R. G.

2017-12-01

Critical elements are those that provide essential functionality to modern engineered materials, have few ready substitutes and are subject to supply-chain risks or concerns about long-run availability. This paper provides economic and public-policy perspectives on critical elements. It suggests: that which elements are critical is situational and changes over time; that we are not running out of mineral-derived raw materials in a geologic sense but rather, for some elements, face scarcities that are technological, environmental, political or economic in nature; and that public policy's most important role over the longer term is fostering scientific and technological innovation, especially early stage research, that has the potential to overcome these scarcities.

Characterization of promoter of EgPAL1, a novel PAL gene from the oil palm Elaeis guineensis Jacq.

PubMed

Yusuf, Chong Yu Lok; Abdullah, Janna Ong; Shaharuddin, Noor Azmi; Abu Seman, Idris; Abdullah, Mohd Puad

2018-02-01

The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop. In this study, the 5' regulatory sequence of a highly divergent oil palm PAL gene (EgPAL1) was isolated and fused with GUS in Arabidopsis to create two transgenic plants carrying the minimal promoter with (2302 bp) and without its regulatory elements (139 bp). The regulatory sequence contained cis-acting elements known to be important for plant development and stress response including the AC-II element for lignin biosynthesis and several stress responsive elements. The promoter and its regulatory region were fully functional in Arabidopsis. Its activities were characterised by two common fundamental features of PAL which are responsive to plant internal developmental programme and external factors. The promoter was developmentally regulated in certain organs; highly active in young organs but less active or inactive in mature organs. The presence of the AC elements and global activity of the EgPAL1 promoter in all organs resembled the property of lignin-related genes. The existence of the MBS element and enhancement of the promoter activity by PEG reflected the behaviour of drought-responsive genes. Our findings provide a platform for evaluating oil palm gene promoters in the heterologous system of Arabidopsis and give insights into the activities of EgPAL1 promoter in oil palm.

Supervised Classification Processes for the Characterization of Heritage Elements, Case Study: Cuenca-Ecuador

NASA Astrophysics Data System (ADS)

Briones, J. C.; Heras, V.; Abril, C.; Sinchi, E.

2017-08-01

The proper control of built heritage entails many challenges related to the complexity of heritage elements and the extent of the area to be managed, for which the available resources must be efficiently used. In this scenario, the preventive conservation approach, based on the concept that prevent is better than cure, emerges as a strategy to avoid the progressive and imminent loss of monuments and heritage sites. Regular monitoring appears as a key tool to identify timely changes in heritage assets. This research demonstrates that the supervised learning model (Support Vector Machines - SVM) is an ideal tool that supports the monitoring process detecting visible elements in aerial images such as roofs structures, vegetation and pavements. The linear, gaussian and polynomial kernel functions were tested; the lineal function provided better results over the other functions. It is important to mention that due to the high level of segmentation generated by the classification procedure, it was necessary to apply a generalization process through opening a mathematical morphological operation, which simplified the over classification for the monitored elements.

Finite Element Simulation and Experimental Verification of Internal Stress of Quenched AISI 4140 Cylinders

NASA Astrophysics Data System (ADS)

Liu, Yu; Qin, Shengwei; Hao, Qingguo; Chen, Nailu; Zuo, Xunwei; Rong, Yonghua

2017-03-01

The study of internal stress in quenched AISI 4140 medium carbon steel is of importance in engineering. In this work, the finite element simulation (FES) was employed to predict the distribution of internal stress in quenched AISI 4140 cylinders with two sizes of diameter based on exponent-modified (Ex-Modified) normalized function. The results indicate that the FES based on Ex-Modified normalized function proposed is better consistent with X-ray diffraction measurements of the stress distribution than FES based on normalized function proposed by Abrassart, Desalos and Leblond, respectively, which is attributed that Ex-Modified normalized function better describes transformation plasticity. Effect of temperature distribution on the phase formation, the origin of residual stress distribution and effect of transformation plasticity function on the residual stress distribution were further discussed.

Atom-scale depth localization of biologically important chemical elements in molecular layers.

PubMed

Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

2016-08-23

In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces.

Atom-scale depth localization of biologically important chemical elements in molecular layers

PubMed Central

Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

2016-01-01

In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers’ global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

Insights into Structural and Mechanistic Features of Viral IRES Elements

PubMed Central

Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.

2018-01-01

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113

Cre/lox-recombinase-mediated cassette exchange for reversible site-specific genomic targeting of the disease vector, Aedes aegypti

USDA-ARS?s Scientific Manuscript database

Site-specific genome modification is an important tool for mosquito functional genomics studies that help to uncover gene functions, identify gene regulatory elements, and perform comparative gene expression studies, all of which contribute to a better understanding of mosquito biology and are thus ...

Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover.

PubMed

Young, Robert S

2016-07-01

Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage-specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover - where the activity of a locus is specific to one lineage, but the underlying DNA remains conserved - can also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage-specific regions may play an important but previously underappreciated role in human biology and disease. © 2016 The Authors BioEssays Published by WILEY Periodicals, Inc.

Features analysis of five-element theory and its basal effects on construction of visceral manifestation theory.

PubMed

Ma, Zimi; Jia, Chunhua; Guo, Jin; Gu, Haorong; Miao, Yanhuan

2014-02-01

To study the Chinese ancient five-element theory, one of the philosophical foundations of Traditional Chinese Medicine (TCM) theory construction, from the perspective of comtemporary cognitive science, and to reveal the important functions of five-element theory in the construction of TCM theory. The basic effects of five-element theory in the construction of TCM theory are intensively expounded and proved from the following aspects: embodiment of five-element theory in cognizing the world, quasi axiom of five-element theory in essence, classification thery of family resemblance and deductive inference pattern of five-element theory, and the openness and expansibility of five-element theory. If five-element theory is considered a cognitive pattern or cognitive system related to culture, then there should be features of cognitive embodiment in the cognitive system. If five-element theory is regarded as a symbolic system, however, then there should be a quasi-axiom for the system, and inferential deduction. If, however, five-element theory is taken as a theoretical constructive metaphor, then there should be features of opening and expansibility for the metaphor. Based on five-element theory, this study provides a cognitive frame for the construction of TCM (a medicine that originated in China, and is characterized by holism and treatment based on pattern identification differentiation) theory with the function of constructing a concept base, thereby implying further research strategies. Useful information may be produced from the creative inferences obtained from the incorporation of five-element theory.

A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion

PubMed Central

Sommer, Morten OA; Church, George M; Dantas, Gautam

2010-01-01

Sustainable biofuel alternatives to fossil fuel energy are hampered by recalcitrance and toxicity of biomass substrates to microbial biocatalysts. To address this issue, we present a culture-independent functional metagenomic platform for mining Nature's vast enzymatic reservoir and show its relevance to biomass conversion. We performed functional selections on 4.7 Gb of metagenomic fosmid libraries and show that genetic elements conferring tolerance toward seven important biomass inhibitors can be identified. We select two metagenomic fosmids that improve the growth of Escherichia coli by 5.7- and 6.9-fold in the presence of inhibitory concentrations of syringaldehyde and 2-furoic acid, respectively, and identify the individual genes responsible for these tolerance phenotypes. Finally, we combine the individual genes to create a three-gene construct that confers tolerance to mixtures of these important biomass inhibitors. This platform presents a route for expanding the repertoire of genetic elements available to synthetic biology and provides a starting point for efforts to engineer robust strains for biofuel generation. PMID:20393580

Genetic dissection of the α-globin super-enhancer in vivo

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

Hay, Deborah; Hughes, Jim R.; Babbs, Christian

Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. Furthermore, these super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation,more » without clear evidence of synergistic or higher-order effects. This study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.« less

Genetic dissection of the α-globin super-enhancer in vivo

DOE PAGES

Hay, Deborah; Hughes, Jim R.; Babbs, Christian; ...

2016-07-04

Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. Furthermore, these super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation,more » without clear evidence of synergistic or higher-order effects. This study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.« less

Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

NASA Astrophysics Data System (ADS)

Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

2015-11-01

Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex: simple models of technological equipment, conveyors models, models of the obstacles and like that. Using these elements it could be formed various production spaces (robotized workcells), in which it is possible to virtually track the operation of an industrial robot arm modelled in the system.

Parenteral trace element provision: recent clinical research and practical conclusions

PubMed Central

Stehle, P; Stoffel-Wagner, B; Kuhn, K S

2016-01-01

The aim of this systematic review (PubMed, www.ncbi.nlm.nih.gov/pubmed and Cochrane, www.cochrane.org; last entry 31 December 2014) was to present data from recent clinical studies investigating parenteral trace element provision in adult patients and to draw conclusions for clinical practice. Important physiological functions in human metabolism are known for nine trace elements: selenium, zinc, copper, manganese, chromium, iron, molybdenum, iodine and fluoride. Lack of, or an insufficient supply of, these trace elements in nutrition therapy over a prolonged period is associated with trace element deprivation, which may lead to a deterioration of existing clinical symptoms and/or the development of characteristic malnutrition syndromes. Therefore, all parenteral nutrition prescriptions should include a daily dose of trace elements. To avoid trace element deprivation or imbalances, physiological doses are recommended. PMID:27049031

Coordinated transcriptional regulation of two key genes in the lignin branch pathway - CAD and CCR - is mediated through MYB- binding sites

PubMed Central

2010-01-01

Background Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the final steps in the biosynthesis of monolignols, the monomeric units of the phenolic lignin polymers which confer rigidity, imperviousness and resistance to biodegradation to cell walls. We have previously shown that the Eucalyptus gunnii CCR and CAD2 promoters direct similar expression patterns in vascular tissues suggesting that monolignol production is controlled, at least in part, by the coordinated transcriptional regulation of these two genes. Although consensus motifs for MYB transcription factors occur in most gene promoters of the whole phenylpropanoid pathway, functional evidence for their contribution to promoter activity has only been demonstrated for a few of them. Here, in the lignin-specific branch, we studied the functional role of MYB elements as well as other cis-elements identified in the regulatory regions of EgCAD2 and EgCCR promoters, in the transcriptional activity of these gene promoters. Results By using promoter deletion analysis and in vivo footprinting, we identified an 80 bp regulatory region in the Eucalyptus gunnii EgCAD2 promoter that contains two MYB elements, each arranged in a distinct module with newly identified cis-elements. A directed mutagenesis approach was used to introduce block mutations in all putative cis-elements of the EgCAD2 promoter and in those of the 50 bp regulatory region previously delineated in the EgCCR promoter. We showed that the conserved MYB elements in EgCAD2 and EgCCR promoters are crucial both for the formation of DNA-protein complexes in EMSA experiments and for the transcriptional activation of EgCAD2 and EgCCR promoters in vascular tissues in planta. In addition, a new regulatory cis-element that modulates the balance between two DNA-protein complexes in vitro was found to be important for EgCAD2 expression in the cambial zone. Conclusions Our assignment of functional roles to the identified cis-elements clearly demonstrates the importance of MYB cis-elements in the transcriptional regulation of two genes of the lignin-specific pathway and support the hypothesis that MYB elements serve as a common means for the coordinated regulation of genes in the entire lignin biosynthetic pathway. PMID:20584286

Discovery of functional non-coding conserved regions in the α-synuclein gene locus

PubMed Central

Sterling, Lori; Walter, Michael; Ting, Dennis; Schüle, Birgitt

2014-01-01

Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein ( SNCA) gene have consistently been shown to be associated with Parkinson’s disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in the SNCA genomic region regulate expression of SNCA, and that SNPs in these regions could be functionally modulating the expression of SNCA, thus contributing to neuronal demise and predisposing to Parkinson’s disease. In a pair-wise comparison of a 206kb genomic region encompassing the SNCA gene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of the SNCA gene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of the SNCA gene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream of SNCA had a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity. Our results demonstrate that the SNCA gene contains cis-regulatory regions that might regulate the transcription and expression of SNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson’s disease-associated SNPs and its function in the disease process. PMID:25566351

COMPARISONS OF THE FINITE-ELEMENT-WITH-DISCONTIGUOUS-SUPPORT METHOD TO CONTINUOUS-ENERGY MONTE CARLO FOR PIN-CELL PROBLEMS

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

A. T. Till; M. Hanuš; J. Lou

The standard multigroup (MG) method for energy discretization of the transport equation can be sensitive to approximations in the weighting spectrum chosen for cross-section averaging. As a result, MG often inaccurately treats important phenomena such as self-shielding variations across a material. From a finite-element viewpoint, MG uses a single fixed basis function (the pre-selected spectrum) within each group, with no mechanism to adapt to local solution behavior. In this work, we introduce the Finite-Element-with-Discontiguous-Support (FEDS) method, whose only approximation with respect to energy is that the angular flux is a linear combination of unknowns multiplied by basis functions. A basismore » function is non-zero only in the discontiguous set of energy intervals associated with its energy element. Discontiguous energy elements are generalizations of bands and are determined by minimizing a norm of the difference between snapshot spectra and their averages over the energy elements. We begin by presenting the theory of the FEDS method. We then compare to continuous-energy Monte Carlo for one-dimensional slab and two-dimensional pin-cell problem. We find FEDS to be accurate and efficient at producing quantities of interest such as reaction rates and eigenvalues. Results show that FEDS converges at a rate that is approximately first-order in the number of energy elements and that FEDS is less sensitive to weighting spectrum than standard MG.« less

Trace elements in parenteral nutrition: a practical guide for dosage and monitoring for adult patients.

PubMed

Fessler, Theresa A

2013-12-01

Parenteral nutrition (PN) is a life-sustaining therapy for hundreds of thousands of people who have severe impairment of gastrointestinal function. Trace elements are a small but very important part of PN that can be overlooked during busy practice. Serious complications can result from trace element deficiencies and toxicities, and this is especially problematic during times of product shortages. Practical information on parenteral trace element use can be gleaned from case reports, some retrospective studies, and very few randomized controlled trials. A general knowledge of trace element metabolism and excretion, deficiency and toxicity symptoms, products, optimal dosages, and strategies for supplementation, restriction, and monitoring will equip practitioners to provide optimal care for their patients who depend on PN.

Safety Benefits of Access Spacing

DOT National Transportation Integrated Search

1997-01-01

The spacing of driveways and streets is an important element in roadway planning, design, and operation. Access points are the main source of accidents and congestion. Their location and spacing affects the safety and functional integrity of streets ...

Rockfall exposures in Montserrat mountain

NASA Astrophysics Data System (ADS)

Fontquerni Gorchs, Sara; Vilaplana Fernández, Joan Manuel; Guinau Sellés, Marta; Jesús Royán Cordero, Manuel

2015-04-01

This study shows the developed methodology to analyze the exposure level on a 1:25000 scale, and the results obtained by applying it to an important part of the Monataña de Montserrat Natural Park for vehicles with and without considering their occupants. The development of this proposal is part of an ongoing study which focuses more in-depth in the analysis of the rockfall risk exposure in different scales and in different natural and social contexts. This research project applies a methodology to evaluate the rockfall exposure level based on the product of the frequency of occurrence of the event by an exposure function of the vulnerable level on a 1:25,000 scale although the scale used for the study was 1:10,000. The proposed methodology to calculate the exposure level is based on six phases: 1- Identification, classification and inventory of every element potentially under risk. 2- Zoning of the frequency of occurrence of the event in the studied area. 3- Design of the exposure function for each studied element. 4- Obtaining the Exposure index, it can be defined as the product of the frequency of occurrence by the exposure function of the vulnerable element through SIG analysis obtained with ArcGis software (ESRI) 5- Obtaining exposure level by grouping into categories the numerical values of the exposure index. 6- Production of the exposition zoning map. The different types of vulnerable elements considered in the totality of the study are: Vehicles in motion, people in vehicles in motion, people on paths, permanent elements and people in buildings. Each defined typology contains all elements with same characteristics and an exposure function has been designed for each of them. For the exposure calculation, two groups of elements have been considered; firstly the group of elements with no people involved and afterwards same group of elements but with people involved. This is a first comprehensive and synthetic work about rockfall exposure on the Montserrat Mountain. It is important to mention that the exposure level calculation has been obtained from natural hazard data do not protected by defense works. Results of this work enable us to consider best strategies to reduce rockfalls risk in the PNMM. It is clear that, apart from the required structural defense works, some of them already made, implementation of strategies not involving structural defense is, in the medium and long term, the best policy to mitigate the risk. In the PNMM case, rethinking of mobility and traffic management on the mountain access would be definitely helpful to achieve a minimized geological risk.

Differential Item Functioning Analysis of High-Stakes Test in Terms of Gender: A Rasch Model Approach

ERIC Educational Resources Information Center

Alavi, Seyed Mohammad; Bordbar, Soodeh

2017-01-01

Differential Item Functioning (DIF) analysis is a key element in evaluating educational test fairness and validity. One of the frequently cited sources of construct-irrelevant variance is gender which has an important role in the university entrance exam; therefore, it causes bias and consequently undermines test validity. The present study aims…

Synaptic Efficacy as a Function of Ionotropic Receptor Distribution: A Computational Study

PubMed Central

Allam, Sushmita L.; Bouteiller, Jean-Marie C.; Hu, Eric Y.; Ambert, Nicolas; Greget, Renaud; Bischoff, Serge; Baudry, Michel; Berger, Theodore W.

2015-01-01

Glutamatergic synapses are the most prevalent functional elements of information processing in the brain. Changes in pre-synaptic activity and in the function of various post-synaptic elements contribute to generate a large variety of synaptic responses. Previous studies have explored postsynaptic factors responsible for regulating synaptic strength variations, but have given far less importance to synaptic geometry, and more specifically to the subcellular distribution of ionotropic receptors. We analyzed the functional effects resulting from changing the subsynaptic localization of ionotropic receptors by using a hippocampal synaptic computational framework. The present study was performed using the EONS (Elementary Objects of the Nervous System) synaptic modeling platform, which was specifically developed to explore the roles of subsynaptic elements as well as their interactions, and that of synaptic geometry. More specifically, we determined the effects of changing the localization of ionotropic receptors relative to the presynaptic glutamate release site, on synaptic efficacy and its variations following single pulse and paired-pulse stimulation protocols. The results indicate that changes in synaptic geometry do have consequences on synaptic efficacy and its dynamics. PMID:26480028

Synaptic Efficacy as a Function of Ionotropic Receptor Distribution: A Computational Study.

PubMed

Allam, Sushmita L; Bouteiller, Jean-Marie C; Hu, Eric Y; Ambert, Nicolas; Greget, Renaud; Bischoff, Serge; Baudry, Michel; Berger, Theodore W

2015-01-01

Glutamatergic synapses are the most prevalent functional elements of information processing in the brain. Changes in pre-synaptic activity and in the function of various post-synaptic elements contribute to generate a large variety of synaptic responses. Previous studies have explored postsynaptic factors responsible for regulating synaptic strength variations, but have given far less importance to synaptic geometry, and more specifically to the subcellular distribution of ionotropic receptors. We analyzed the functional effects resulting from changing the subsynaptic localization of ionotropic receptors by using a hippocampal synaptic computational framework. The present study was performed using the EONS (Elementary Objects of the Nervous System) synaptic modeling platform, which was specifically developed to explore the roles of subsynaptic elements as well as their interactions, and that of synaptic geometry. More specifically, we determined the effects of changing the localization of ionotropic receptors relative to the presynaptic glutamate release site, on synaptic efficacy and its variations following single pulse and paired-pulse stimulation protocols. The results indicate that changes in synaptic geometry do have consequences on synaptic efficacy and its dynamics.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?

PubMed

Kaur, Simranjeet; Pociot, Flemming

2015-07-13

Despite numerous studies implicating Alu repeat elements in various diseases, there is sparse information available with respect to the potential functional and biological roles of the repeat elements in Type 1 diabetes (T1D). Therefore, we performed a genome-wide sequence analysis of T1D candidate genes to identify embedded Alu elements within these genes. We observed significant enrichment of Alu elements within the T1D genes (p-value < 10e-16), which highlights their importance in T1D. Functional annotation of T1D genes harboring Alus revealed significant enrichment for immune-mediated processes (p-value < 10e-6). We also identified eight T1D genes harboring inverted Alus (IRAlus) within their 3' untranslated regions (UTRs) that are known to regulate the expression of host mRNAs by generating double stranded RNA duplexes. Our in silico analysis predicted the formation of duplex structures by IRAlus within the 3'UTRs of T1D genes. We propose that IRAlus might be involved in regulating the expression levels of the host T1D genes.

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory.

PubMed

Welti, Nina; Striebel, Maren; Ulseth, Amber J; Cross, Wyatt F; DeVilbiss, Stephen; Glibert, Patricia M; Guo, Laodong; Hirst, Andrew G; Hood, Jim; Kominoski, John S; MacNeill, Keeley L; Mehring, Andrew S; Welter, Jill R; Hillebrand, Helmut

2017-01-01

Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES) often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1) changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2) changing trophic dynamics influences the transformation and fluxes of matter across environmental boundaries; (3) changing ecosystem metabolism will alter the chemical diversity of the non-living environment. Finally, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment.

The ENCODE project: implications for psychiatric genetics.

PubMed

Kavanagh, D H; Dwyer, S; O'Donovan, M C; Owen, M J

2013-05-01

The ENCyclopedia Of DNA Elements (ENCODE) project is a public research consortium that aims to identify all functional elements of the human genome sequence. The project comprised 1640 data sets, from 147 different cell type and the findings were released in a coordinated set of 34 publications across several journals. The ENCODE publications report that 80.4% of the human genome displays some functionality. These data have important implications for interpreting results from large-scale genetics studies. We reviewed some of the key findings from the ENCODE publications and discuss how they can influence or inform further investigations into the genetic factors contributing to neuropsychiatric disorders.

Multiscale structural gradients enhance the biomechanical functionality of the spider fang

PubMed Central

Bar-On, Benny; Barth, Friedrich G.; Fratzl, Peter; Politi, Yael

2014-01-01

The spider fang is a natural injection needle, hierarchically built from a complex composite material comprising multiscale architectural gradients. Considering its biomechanical function, the spider fang has to sustain significant mechanical loads. Here we apply experiment-based structural modelling of the fang, followed by analytical mechanical description and Finite-Element simulations, the results of which indicate that the naturally evolved fang architecture results in highly adapted effective structural stiffness and damage resilience. The analysis methods and physical insights of this work are potentially important for investigating and understanding the architecture and structural motifs of sharp-edge biological elements such as stingers, teeth, claws and more. PMID:24866935

Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function

PubMed Central

Chillón, Isabel; Pyle, Anna M.

2016-01-01

LincRNA-p21 is a long intergenic non-coding RNA (lincRNA) involved in the p53-mediated stress response. We sequenced the human lincRNA-p21 (hLincRNA-p21) and found that it has a single exon that includes inverted repeat Alu elements (IRAlus). Sense and antisense Alu elements fold independently of one another into a secondary structure that is conserved in lincRNA-p21 among primates. Moreover, the structures formed by IRAlus are involved in the localization of hLincRNA-p21 in the nucleus, where hLincRNA-p21 colocalizes with paraspeckles. Our results underscore the importance of IRAlus structures for the function of hLincRNA-p21 during the stress response. PMID:27378782

Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro–costo–mandibular syndrome

PubMed Central

Lynch, Danielle C.; Revil, Timothée; Schwartzentruber, Jeremy; Bhoj, Elizabeth J.; Innes, A. Micheil; Lamont, Ryan E.; Lemire, Edmond G.; Chodirker, Bernard N.; Taylor, Juliet P.; Zackai, Elaine H.; McLeod, D. Ross; Kirk, Edwin P.; Hoover-Fong, Julie; Fleming, Leah; Savarirayan, Ravi; Boycott, Kym; MacKenzie, Alex; Brudno, Michael; Bulman, Dennis; Dyment, David; Majewski, Jacek; Jerome-Majewska, Loydie A.; Parboosingh, Jillian S.; Bernier, Francois P.

2014-01-01

Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro–costo–mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development. PMID:25047197

Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome.

PubMed

Lynch, Danielle C; Revil, Timothée; Schwartzentruber, Jeremy; Bhoj, Elizabeth J; Innes, A Micheil; Lamont, Ryan E; Lemire, Edmond G; Chodirker, Bernard N; Taylor, Juliet P; Zackai, Elaine H; McLeod, D Ross; Kirk, Edwin P; Hoover-Fong, Julie; Fleming, Leah; Savarirayan, Ravi; Majewski, Jacek; Jerome-Majewska, Loydie A; Parboosingh, Jillian S; Bernier, Francois P

2014-07-22

Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro-costo-mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development.

Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance.

PubMed

Ferris, Elliott; Abegglen, Lisa M; Schiffman, Joshua D; Gregg, Christopher

2018-03-06

The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ∼33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

A bacterium that can grow by using arsenic instead of phosphorus

USGS Publications Warehouse

Wolfe-Simon, Felisa; Blum, J.S.; Kulp, T.R.; Gordon, G.W.; Hoeft, S.E.; Pett-Ridge, J.; Stolz, J.F.; Webb, S.M.; Weber, P.K.; Davies, P.C.W.; Anbar, A.D.; Oremland, R.S.

2011-01-01

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

The influence of printing parameters on selected mechanical properties of FDM/FFF 3D-printed parts

NASA Astrophysics Data System (ADS)

Ćwikła, G.; Grabowik, C.; Kalinowski, K.; Paprocka, I.; Ociepka, P.

2017-08-01

Rapid Prototyping technologies, especially 3D printing are becoming increasingly popular due to their usability and the constant decrease in price of printing equipment and materials. The article focuses on the study of selected mechanical strength properties of 3D-printed elements, which are not very important if the element is only a model for further manufacturing techniques, but which are important when 3D-printed elements will be a part of a functioning device, e.g. a part of unique scientific equipment. The research was carried out on a set of standardised samples, printed with low-cost standard materials (ABS), using a cheap 3D printer. The influence of parameters (such as the type of infill pattern, infill density, shell thickness, printing temperature, the type of material) on selected mechanical properties of the samples, were tested. The obtained results allows making conscious decisions on the printing of elements to be durable enough, either on a non-professional printer, or when to ordered by a professional manufacturer.

Atomic adsorption on pristine graphene along the Periodic Table of Elements - From PBE to non-local functionals

NASA Astrophysics Data System (ADS)

Pašti, Igor A.; Jovanović, Aleksandar; Dobrota, Ana S.; Mentus, Slavko V.; Johansson, Börje; Skorodumova, Natalia V.

2018-04-01

The understanding of atomic adsorption on graphene is of high importance for many advanced technologies. Here we present a complete database of the atomic adsorption energies for the elements of the Periodic Table up to the atomic number 86 (excluding lanthanides) on pristine graphene. The energies have been calculated using the projector augmented wave (PAW) method with PBE, long-range dispersion interaction corrected PBE (PBE+D2, PBE+D3) as well as non-local vdW-DF2 approach. The inclusion of dispersion interactions leads to an exothermic adsorption for all the investigated elements. Dispersion interactions are found to be of particular importance for the adsorption of low atomic weight earth alkaline metals, coinage and s-metals (11th and 12th groups), high atomic weight p-elements and noble gases. We discuss the observed adsorption trends along the groups and rows of the Periodic Table as well some computational aspects of modelling atomic adsorption on graphene.

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation

PubMed Central

Engel, Krysta L.; Mackiewicz, Mark; Hardigan, Andrew A.; Myers, Richard M.; Savic, Daniel

2016-01-01

Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. PMID:27224938

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

PubMed

Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

2016-09-01

Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. Copyright © 2016 Elsevier Ltd. All rights reserved.

Abundance and Distribution of Geographically Isolated Wetlands across the Conterminous United States

EPA Science Inventory

Geographically isolated wetlands (GIWS) are important landscape elements involved in hydrologic, biogeochemical, and biological functioning. Their influence, under certain circumstances, can significantly affect other waters of the Unites States. However, there have been no data-...

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

PubMed

Smyth, Redmond P; Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe; von Kleist, Max; Marquet, Roland

2018-05-18

Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

PubMed Central

Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe

2018-01-01

Abstract Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5′ region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5′ PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production. PMID:29514260

Appropriate Objective Functions for Quantifying Iris Mechanical Properties Using Inverse Finite Element Modeling.

PubMed

Pant, Anup D; Dorairaj, Syril K; Amini, Rouzbeh

2018-07-01

Quantifying the mechanical properties of the iris is important, as it provides insight into the pathophysiology of glaucoma. Recent ex vivo studies have shown that the mechanical properties of the iris are different in glaucomatous eyes as compared to normal ones. Notwithstanding the importance of the ex vivo studies, such measurements are severely limited for diagnosis and preclude development of treatment strategies. With the advent of detailed imaging modalities, it is possible to determine the in vivo mechanical properties using inverse finite element (FE) modeling. An inverse modeling approach requires an appropriate objective function for reliable estimation of parameters. In the case of the iris, numerous measurements such as iris chord length (CL) and iris concavity (CV) are made routinely in clinical practice. In this study, we have evaluated five different objective functions chosen based on the iris biometrics (in the presence and absence of clinical measurement errors) to determine the appropriate criterion for inverse modeling. Our results showed that in the absence of experimental measurement error, a combination of iris CL and CV can be used as the objective function. However, with the addition of measurement errors, the objective functions that employ a large number of local displacement values provide more reliable outcomes.

Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element

PubMed Central

Oropeza-Aburto, Araceli; Cruz-Ramírez, Alfredo; Acevedo-Hernández, Gustavo J.; Pérez-Torres, Claudia-Anahí; Caballero-Pérez, Juan; Herrera-Estrella, Luis

2012-01-01

Plants have evolved a plethora of responses to cope with phosphate (Pi) deficiency, including the transcriptional activation of a large set of genes. Among Pi-responsive genes, the expression of the Arabidopsis phospholipase DZ2 (PLDZ2) is activated to participate in the degradation of phospholipids in roots in order to release Pi to support other cellular activities. A deletion analysis was performed to identify the regions determining the strength, tissue-specific expression, and Pi responsiveness of this regulatory region. This study also reports the identification and characterization of a transcriptional enhancer element that is present in the PLDZ2 promoter and able to confer Pi responsiveness to a minimal, inactive 35S promoter. This enhancer also shares the cytokinin and sucrose responsive properties observed for the intact PLDZ2 promoter. The EZ2 element contains two P1BS motifs, each of which is the DNA binding site of transcription factor PHR1. Mutation analysis showed that the P1BS motifs present in EZ2 are necessary but not sufficient for the enhancer function, revealing the importance of adjacent sequences. The structural organization of EZ2 is conserved in the orthologous genes of at least eight families of rosids, suggesting that architectural features such as the distance between the two P1BS motifs are also important for the regulatory properties of this enhancer element. PMID:22210906

Intra-amniotic administration (Gallus gallus) of cicer arietinum and lens culinaris prebiotics extracts and duck egg white peptides affects calcium status and intestinal functionality

USDA-ARS?s Scientific Manuscript database

Calcium (Ca) is one of the most abundant inorganic elements in the human body and has many important physiological roles. Prebiotics and bioactive peptides are two important substances used to promote calcium uptake. However, the difference in mechanisms of the calcium uptake from these two suppleme...

Functional dissection of a napin gene promoter: identification of promoter elements required for embryo and endosperm-specific transcription.

PubMed

Ellerström, M; Stålberg, K; Ezcurra, I; Rask, L

1996-12-01

The promoter region (-309 to +44) of the Brassica napus storage protein gene napA was studied in transgenic tobacco by successive 5' as well as internal deletions fused to the reporter gene GUS (beta-glucuronidase). The expression in the two main tissues of the seed, the endosperm and the embryo, was shown to be differentially regulated. This tissue-specific regulation within the seed was found to affect the developmental expression during seed development. The region between -309 to -152, which has a large effect on quantitative expression, was shown to harbour four elements regulating embryo and one regulating endosperm expression. This region also displayed enhancer activity. Deletion of eight bp from position -152 to position -144 totally abolished the activity of the napA promoter. This deletion disrupted a cis element with similarity to an ABA-responsive element (ABRE) overlapping with an E-box, demonstrating its crucial importance for quantitative expression. An internal deletion of the region -133 to -120, resulted in increased activity in both leaves and endosperm and a decreased activity in the embryo. Within this region, a cis element similar to the (CA)n element, found in other storage protein promoters, was identified. This suggest that the (CA)n element is important for conferring seed specificity by serving both as an activator and a repressor element.

Drainage Adits in Upper Silesia - Industrial Technology Heritage and Important Elements of the Hydrotechnical Infrastructure

NASA Astrophysics Data System (ADS)

Duży, Stanisław; Dyduch, Grzegorz; Preidl, Wojciech; Stacha, Grzegorz

2017-12-01

Adits played an important role in the hydrotechnical infrastructure for centuries. Initially, they were used mainly to drain wetland and supply water to the population. There were also inherent in the conduct of mining activities. They were used as exploratory, development and supply headings. Their usual function was to drain, ventilate and transport, and after the cessation of mining they became important elements of the hydrotechnical infrastructure in the transformed mining areas. The article presents issues related to the revitalization of the Main Key Hereditary Adit and Friedrich Adit as essential for the areas in which they are located. Both are hydraulic structures with the possibility of adaptation for tourism purposes. The need to consider some technical activities to be undertaken in this type of objects was pointed out, not only including aspects related to their proper protection so that they can continue to safely perform their function, but also to the preservation of their historical values. Due to their age and the method of drilling used in them, those headings are often included in the list of monuments and protected by law.

ICP-MS: Analytical Method for Identification and Detection of Elemental Impurities.

PubMed

Mittal, Mohini; Kumar, Kapil; Anghore, Durgadas; Rawal, Ravindra K

2017-01-01

Aim of this article is to review and discuss the currently used quantitative analytical method ICP-MS, which is used for quality control of pharmaceutical products. ICP-MS technique has several applications such as determination of single elements, multi element analysis in synthetic drugs, heavy metals in environmental water, trace element content of selected fertilizers and dairy manures. ICP-MS is also used for determination of toxic and essential elements in different varieties of food samples and metal pollutant present in the environment. The pharmaceuticals may generate impurities at various stages of development, transportation and storage which make them risky to be administered. Thus, it is essential that these impurities must be detected and quantified. ICP-MS plays an important function in the recognition and revealing of elemental impurities. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Performance analysis and material dependence of micro holographic optical elements as couplers for fiber optic communication

NASA Astrophysics Data System (ADS)

Ambadiyil, Sajan; Prasannan, G.; Sathyan, Jithesh; Ajith Kumar, P. T.

2005-01-01

Holographic Optical Elements (HOEs) are gaining much importance and finding newer and better applications in areas of optical fiber communication and optical information processing systems. In contrast to conventional HOEs, optical communication and information systems require smaller and efficient elements of desired characteristics and transfer functions. Such Micro Holographic Optical Elements (MHOEs) can either be an HOE, recorded with two narrow beams of laser light or a segment cut from a larger HOE (SHOEs), and recorded in the conventional manner. In this study, micro holographic couplers, having specific focusing and diffraction characteristics were recorded in different holographic recording media such as silver halide and dichromated gelatin. Wavelength response of the elements was tested at 633 nm and 442 nm. Variation in diffraction efficiency/coupling factor, and insertion loss of the elements were studied. The paper reports in detail about the above results and related design considerations.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications.

PubMed

Etzl, Stefan; Lindner, Robert; Nelson, Matthew D; Winkler, Andreas

2018-06-08

Genetically targeting biological systems to control cellular processes with light is the concept of optogenetics. Despite impressive developments in this field, underlying molecular mechanisms of signal transduction of the employed photoreceptor modules are frequently not sufficiently understood to rationally design new optogenetic tools. Here, we investigate the requirements for functional coupling of red light-sensing phytochromes with non-natural enzymatic effectors by creating a series of constructs featuring the Deinococcus radiodurans bacteriophytochrome linked to a Synechocystis guanylate/adenylate cyclase. Incorporating characteristic structural elements important for cyclase regulation in our designs, we identified several red light-regulated fusions with promising properties. We provide details of one light-activated construct with low dark-state activity and high dynamic range that outperforms previous optogenetic tools in vitro and expands our in vivo toolkit, as demonstrated by manipulation of Caenorhabditis elegans locomotor activity. The full-length crystal structure of this phytochrome-linked cyclase revealed molecular details of photoreceptor-effector coupling, highlighting the importance of the regulatory cyclase element. Analysis of conformational dynamics by hydrogen-deuterium exchange in different functional states enriched our understanding of phytochrome signaling and signal integration by effectors. We found that light-induced conformational changes in the phytochrome destabilize the coiled-coil sensor-effector linker, which releases the cyclase regulatory element from an inhibited conformation, increasing cyclase activity of this artificial system. Future designs of optogenetic functionalities may benefit from our work, indicating that rational considerations for the effector improve the rate of success of initial designs to obtain optogenetic tools with superior properties. © 2018 Etzl et al.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

Vitamin D, Essential Minerals, and Toxic Elements: Exploring Interactions between Nutrients and Toxicants in Clinical Medicine

PubMed Central

Schwalfenberg, Gerry K.; Genuis, Stephen J.

2015-01-01

In clinical medicine, increasing attention is being directed towards the important areas of nutritional biochemistry and toxicant bioaccumulation as they relate to human health and chronic disease. Optimal nutritional status, including healthy levels of vitamin D and essential minerals, is requisite for proper physiological function; conversely, accrual of toxic elements has the potential to impair normal physiology. It is evident that vitamin D intake can facilitate the absorption and assimilation of essential inorganic elements (such as calcium, magnesium, copper, zinc, iron, and selenium) but also the uptake of toxic elements (such as lead, arsenic, aluminum, cobalt, and strontium). Furthermore, sufficiency of essential minerals appears to resist the uptake of toxic metals. This paper explores the literature to determine a suitable clinical approach with regard to vitamin D and essential mineral intake to achieve optimal biological function and to avoid harm in order to prevent and overcome illness. It appears preferable to secure essential mineral status in conjunction with adequate vitamin D, as intake of vitamin D in the absence of mineral sufficiency may result in facilitation of toxic element absorption with potential adverse clinical outcomes. PMID:26347061

Unstructured Adaptive Meshes: Bad for Your Memory?

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Feng, Hui-Yu; VanderWijngaart, Rob

2003-01-01

This viewgraph presentation explores the need for a NASA Advanced Supercomputing (NAS) parallel benchmark for problems with irregular dynamical memory access. This benchmark is important and necessary because: 1) Problems with localized error source benefit from adaptive nonuniform meshes; 2) Certain machines perform poorly on such problems; 3) Parallel implementation may provide further performance improvement but is difficult. Some examples of problems which use irregular dynamical memory access include: 1) Heat transfer problem; 2) Heat source term; 3) Spectral element method; 4) Base functions; 5) Elemental discrete equations; 6) Global discrete equations. Nonconforming Mesh and Mortar Element Method are covered in greater detail in this presentation.

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

PubMed Central

Gogarten, J Peter; Hilario, Elena

2006-01-01

Self splicing introns and inteins that rely on a homing endonuclease for propagation are parasitic genetic elements. Their life-cycle and evolutionary fate has been described through the homing cycle. According to this model the homing endonuclease is selected for function only during the spreading phase of the parasite. This phase ends when the parasitic element is fixed in the population. Upon fixation the homing endonuclease is no longer under selection, and its activity is lost through random processes. Recent analyses of these parasitic elements with functional homing endonucleases suggest that this model in its most simple form is not always applicable. Apparently, functioning homing endonuclease can persist over long evolutionary times in populations and species that are thought to be asexual or nearly asexual. Here we review these recent findings and discuss their implications. Reasons for the long-term persistence of a functional homing endonuclease include: More recombination (sexual and as a result of gene transfer) than previously assumed for these organisms; complex population structures that prevent the element from being fixed; a balance between active spreading of the homing endonuclease and a decrease in fitness caused by the parasite in the host organism; or a function of the homing endonuclease that increases the fitness of the host organism and results in purifying selection for the homing endonuclease activity, even after fixation in a local population. In the future, more detailed studies of the population dynamics of the activity and regulation of homing endonucleases are needed to decide between these possibilities, and to determine their relative contributions to the long term survival of parasitic genes within a population. Two outstanding publications on the amoeba Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6:39) and the PRP8 inteins in ascomycetes (Butler et al.BMC Evol Biol 2006, 6:42) provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts. PMID:17101053

Monitoring and Alerting Congestion at Airports and Sectors under Uncertainty in Traffic Demand Predictions.

DOT National Transportation Integrated Search

2011-04-01

Important functions of the Traffic Flow Management System (TFMS) include prediction air traffic demand for National Air Space (NAS) elements (airports, fixes and enroute sectors) for several hours into the future, and using these predictions to alert...

In-Situ Analysis Of Metal(loid)s In Plants: State Of The Art And Artefacts

EPA Science Inventory

Metals and metalloids play important roles in plant function and metabolism. Likewise, plants subsequently introduce vital dietary nutrition to people and animals. Understanding the transport, localisation and speciation of these elements is critical for understanding availabil...

Preliminary estimates of the quantities of rare-earth elements contained in selected products and in imports of semimanufactured products to the United States, 2010

USGS Publications Warehouse

Bleiwas, Donald I.; Gambogi, Joseph

2013-01-01

Rare-earth elements (REEs) are contained in a wide range of products of economic and strategic importance to the Nation. The REEs may or may not represent a significant component of that product by mass, value, or volume; however, in many cases, the embedded REEs are critical for the device’s function. Domestic sources of primary supply and the manufacturing facilities to produce products are inadequate to meet U.S. requirements; therefore, a significant percentage of the supply of REEs and the products that contain them are imported to the United States. In 2011, mines in China produced roughly 97 percent of the world’s supply of REEs, and the country’s production of these elements will likely dominate global supply until at least 2020. Preliminary estimates of the types and amount of rare-earth elements, reported as oxides, in semimanufactured form and the amounts used for electric vehicle batteries, catalytic converters, computers, and other applications were developed to provide a perspective on the Nation’s use of these elements. The amount of rare-earth metals recovered from recycling, remanufacturing, and reuse is negligible when the tonnage of products that contain REEs deposited in landfills and retained in storage is considered. Under favorable market conditions, the recovery of REEs from obsolete products could potentially displace a portion of the supply from primary sources.

Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins.

PubMed

Schraivogel, Daniel; Meister, Gunter

2014-09-01

Small RNAs are important regulators of gene expression in many different organisms. Nuclear and cytoplasmic biogenesis enzymes generate functional small RNAs from double-stranded (ds) or single-stranded (ss) RNA precursors, and mature small RNAs are loaded into Argonaute proteins. In the cytoplasm, small RNAs guide Argonaute proteins to complementary RNAs leading to cleavage of these targets, translational silencing, or mRNA decay. In the nucleus Argonaute proteins engage in transcriptional silencing processes such as epigenetic silencing of repetitive elements at the chromatin level. During the past few years many novel functions of small RNA-guided gene silencing proteins in the nucleus have been reported. However, their specific import routes are largely unknown. In this review we summarize the current knowledge on nuclear transport routes that Argonaute and other RNA-silencing proteins take to carry out their various functions in the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

The heptanucleotide motif GAGACGC is a key component of a cis-acting promoter element that is critical for SnSAG1 expression in Sarcocystis neurona.

PubMed

Gaji, Rajshekhar Y; Howe, Daniel K

2009-07-01

The apicomplexan parasite Sarcocystis neurona undergoes a complex process of intracellular development, during which many genes are temporally regulated. The described study was undertaken to begin identifying the basic promoter elements that control gene expression in S. neurona. Sequence analysis of the 5'-flanking region of five S. neurona genes revealed a conserved heptanucleotide motif GAGACGC that is similar to the WGAGACG motif described upstream of multiple genes in Toxoplasma gondii. The promoter region for the major surface antigen gene SnSAG1, which contains three heptanucleotide motifs within 135 bases of the transcription start site, was dissected by functional analysis using a dual luciferase reporter assay. These analyses revealed that a minimal promoter fragment containing all three motifs was sufficient to drive reporter molecule expression, with the presence and orientation of the 5'-most heptanucleotide motif being absolutely critical for promoter function. Further studies should help to identify additional sequence elements important for promoter function and for controlling gene expression during intracellular development by this apicomplexan pathogen.

On Orbital Elements of Extrasolar Planetary Candidates and Spectroscopic Binaries

NASA Technical Reports Server (NTRS)

Stepinski, T. F.; Black, D. C.

2001-01-01

We estimate probability densities of orbital elements, periods, and eccentricities, for the population of extrasolar planetary candidates (EPC) and, separately, for the population of spectroscopic binaries (SB) with solar-type primaries. We construct empirical cumulative distribution functions (CDFs) in order to infer probability distribution functions (PDFs) for orbital periods and eccentricities. We also derive a joint probability density for period-eccentricity pairs in each population. Comparison of respective distributions reveals that in all cases EPC and SB populations are, in the context of orbital elements, indistinguishable from each other to a high degree of statistical significance. Probability densities of orbital periods in both populations have P(exp -1) functional form, whereas the PDFs of eccentricities can he best characterized as a Gaussian with a mean of about 0.35 and standard deviation of about 0.2 turning into a flat distribution at small values of eccentricity. These remarkable similarities between EPC and SB must be taken into account by theories aimed at explaining the origin of extrasolar planetary candidates, and constitute an important clue us to their ultimate nature.

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes.

PubMed

Infante, Carlos R; Mihala, Alexandra G; Park, Sungdae; Wang, Jialiang S; Johnson, Kenji K; Lauderdale, James D; Menke, Douglas B

2015-10-12

The amniote phallus and limbs differ dramatically in their morphologies but share patterns of signaling and gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks also share cis-regulatory elements has remained unexplored. We show that many limb enhancers are retained in snake genomes, suggesting that these elements may function in non-limb tissues. Consistent with this, our analysis of cis-regulatory activity in mice and Anolis lizards reveals that patterns of enhancer activity in embryonic limbs and genitalia overlap heavily. In mice, deletion of HLEB, an enhancer of Tbx4, produces defects in hindlimbs and genitalia, establishing the importance of this limb-genital enhancer for development of these different appendages. Further analyses demonstrate that the HLEB of snakes has lost hindlimb enhancer function while retaining genital activity. Our findings identify roles for Tbx4 in genital development and highlight deep similarities in cis-regulatory activity between limbs and genitalia. Copyright © 2015 Elsevier Inc. All rights reserved.

Massive contribution of transposable elements to mammalian regulatory sequences.

PubMed

Rayan, Nirmala Arul; Del Rosario, Ricardo C H; Prabhakar, Shyam

2016-09-01

Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Method for analyzing soil structure according to the size of structural elements

NASA Astrophysics Data System (ADS)

Wieland, Ralf; Rogasik, Helmut

2015-02-01

The soil structure in situ is the result of cropping history and soil development over time. It can be assessed by the size distribution of soil structural elements such as air-filled macro-pores, aggregates and stones, which are responsible for important water and solute transport processes, gas exchange, and the stability of the soil against compacting and shearing forces exerted by agricultural machinery. A method was developed to detect structural elements of the soil in selected horizontal slices of soil core samples with different soil structures in order for them to be implemented accordingly. In the second step, a fitting tool (Eureqa) based on artificial programming was used to find a general function to describe ordered sets of detected structural elements. It was shown that all the samples obey a hyperbolic function: Y(k) = A /(B + k) , k ∈ { 0 , 1 , 2 , … }. This general behavior can be used to develop a classification method based on parameters {A and B}. An open source software program in Python was developed, which can be downloaded together with a selection of soil samples.

Effect of land use change on soil properties and functions

NASA Astrophysics Data System (ADS)

Tonutare, Tonu; Kõlli, Raimo; Köster, Tiina; Rannik, Kaire; Szajdak, Lech; Shanskiy, Merrit

2014-05-01

For good base of sustainable land management and ecologically sound protection of soils are researches on soil properties and functioning. Ecosystem approach to soil properties and functioning is equally important in both natural and cultivated land use conditions. Comparative analysis of natural and agro-ecosystems formed on similar soil types enables to elucidate principal changes caused by land use change (LUC) and to elaborate the best land use practices for local pedo-ecological conditions. Taken for actual analysis mineral soils' catena - rendzina → brown soils → pseudopodzolic soils → gley-podzols - represent ca 1/3 of total area of Estonian normal mineral soils. All soils of this catena differ substantially each from other by calcareousness, acidity, nutrition conditions, fabric and humus cover type. This catena (representative to Estonian pedo-ecological conditions) starts with drought-prone calcareous soils. Brown (distributed in northern and central Estonia) and pseudopodzolic soils (in southern Estonia) are the most broadly acknowledged for agricultural use medium-textured high-quality automorphic soils. Dispersedly distributed gley-podzols are permanently wet and strongly acid, low-productivity sandy soils. In presentation four complex functions of soils are treated: (1) being a suitable soil environment for plant cover productivity (expressed by annual increment, Mg ha-1 yr-1); (2) forming adequate conditions for decomposition, transformation and conversion of fresh falling litter (characterized by humus cover type); (3) deposition of humus, individual organic compounds, plant nutrition elements, air and water, and (4) forming (bio)chemically variegated active space for soil type specific edaphon. Capacity of soil cover as depositor (3) depends on it thickness, texture, calcareousness and moisture conditions. Biological activity of soil (4) is determined by fresh organic matter influx, quality and quantity of biochemical substances and humus, and pedo-ecological conditions. LUC from natural to arable is accompanied by different regulations: (1) regular restoration of plant available nutrition elements' stocks in soil, (2) regulation (if needed) of water regime of gleyed and gley soils, (3) optimizing of soil actual acidity by liming, and (4) forming a suitable for crops seed bed instead of natural epipedon. Principal changes are occurred in fabric and agrochemical properties of topsoil and in soil functioning. The connected with LUC changes in soil functioning are: (1) increase of openness level of chemical elements cycling and nutrition elements concentration in phytomass, and (2) decrease of total phytomass, species diversity, amount of annual falling litter and content of mortmass in soil cover. These changes lead to decreasing of biological control on soil resources, flux of energy and substances to soil processes, and volume of cycling. At the same time the intensity of organic matter decomposition and outflow of nutrition elements are increased. All these changes are resulted by alteration of food chains and exhausting of nutrition elements' stocks. The changes in soil functioning (decrease or increase of productivity) depend much on soil type. The aspects of functioning, which do not changed with LUC are chemical-textural potential of soil cover and functioning character of subsoil. The sound matching of soil and plant cover is of decisive importance for sustainable functioning of ecosystem and in attaining a good environmental status of the area.

KAOS/LIB-V: A library of nuclear response functions generated by KAOS-V code from ENDF/B-V and other data files

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

Farawila, Y.; Gohar, Y.; Maynard, C.

1989-04-01

KAOS/LIB-V: A library of processed nuclear responses for neutronics analyses of nuclear systems has been generated. The library was prepared using the KAOS-V code and nuclear data from ENDF/B-V. The library includes kerma (kinetic energy released in materials) factors and other nuclear response functions for all materials presently of interest in fusion and fission applications for 43 nonfissionable and 15 fissionable isotopes and elements. The nuclear response functions include gas production and tritium-breeding functions, and all important reaction cross sections. KAOS/LIB-V employs the VITAMIN-E weighting function and energy group structure of 174 neutron groups. Auxiliary nuclear data bases, e.g., themore » Japanese evaluated nuclear data library JENDL-2 were used as a source of isotopic cross sections when these data are not provided in ENDF/B-V files for a natural element. These are needed mainly to estimate average quantities such as effective Q-values for the natural element. This analysis of local energy deposition was instrumental in detecting and understanding energy balance deficiencies and other problems in the ENDF/B-V data. Pertinent information about the library and a graphical display of the main nuclear response functions for all materials in the library are given. 35 refs.« less

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements. PMID:26865697

Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory

PubMed Central

Welti, Nina; Striebel, Maren; Ulseth, Amber J.; Cross, Wyatt F.; DeVilbiss, Stephen; Glibert, Patricia M.; Guo, Laodong; Hirst, Andrew G.; Hood, Jim; Kominoski, John S.; MacNeill, Keeley L.; Mehring, Andrew S.; Welter, Jill R.; Hillebrand, Helmut

2017-01-01

Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES) often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1) changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2) changing trophic dynamics influences the transformation and fluxes of matter across environmental boundaries; (3) changing ecosystem metabolism will alter the chemical diversity of the non-living environment. Finally, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment. PMID:28747904

Prediction of Geomagnetic Activity and Key Parameters in High-latitude Ionosphere

NASA Technical Reports Server (NTRS)

Khazanov, George V.; Lyatsky, Wladislaw; Tan, Arjun; Ridley, Aaron

2007-01-01

Prediction of geomagnetic activity and related events in the Earth's magnetosphere and ionosphere are important tasks of US Space Weather Program. Prediction reliability is dependent on the prediction method, and elements included in the prediction scheme. Two of the main elements of such prediction scheme are: an appropriate geomagnetic activity index, and an appropriate coupling function (the combination of solar wind parameters providing the best correlation between upstream solar wind data and geomagnetic activity). We have developed a new index of geomagnetic activity, the Polar Magnetic (PM) index and an improved version of solar wind coupling function. PM index is similar to the existing polar cap PC index but it shows much better correlation with upstream solar wind/IMF data and other events in the magnetosphere and ionosphere. We investigate the correlation of PM index with upstream solar wind/IMF data for 10 years (1995-2004) that include both low and high solar activity. We also have introduced a new prediction function for the predicting of cross-polar-cap voltage and Joule heating based on using both PM index and upstream solar wind/IMF data. As we show such prediction function significantly increase the reliability of prediction of these important parameters. The correlation coefficients between the actual and predicted values of these parameters are approx. 0.9 and higher.

49 CFR 236.526 - Roadway element not functioning properly.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Roadway element not functioning properly. 236.526... element not functioning properly. When a roadway element except track circuit of automatic train stop... roadway element shall be caused manually to display its most restrictive aspect until such element has...

49 CFR 236.526 - Roadway element not functioning properly.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Roadway element not functioning properly. 236.526... element not functioning properly. When a roadway element except track circuit of automatic train stop... roadway element shall be caused manually to display its most restrictive aspect until such element has...

49 CFR 236.526 - Roadway element not functioning properly.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Roadway element not functioning properly. 236.526... element not functioning properly. When a roadway element except track circuit of automatic train stop... roadway element shall be caused manually to display its most restrictive aspect until such element has...

Scattering Properties of Needle-Like and plate-like Ice Spheroids with Moderate Size Parameters

NASA Technical Reports Server (NTRS)

Zakharova, Nadia T.; Mishchenko, Michael I.; Hansen, James E. (Technical Monitor)

2000-01-01

We use the current advanced version of the T-matrix method to compute the optical cross sections, the asymmetry parameter of the phase function, and the scattering matrix elements of ice spheroids with aspect ratios up to 20 and surface-equivalent-sphere size parameters up to 12. We demonstrate that plate-like and needle-like particles with moderate size parameters possess unique scattering properties: their asymmetry parameters and phase functions are similar to those of surface-equivalent spheres, whereas all other elements of the scattering matrix are typical of particles much smaller than the wavelength (Rayleigh scatterers). This result may have important implications for optical particle sizing and remote sensing of the terrestrial and planetary atmospheres.

Mutations that alter a repeated ACCA element located at the 5' end of the Potato virus X genome affect RNA accumulation.

PubMed

Park, Mi-Ri; Kwon, Sun-Jung; Choi, Hong-Soo; Hemenway, Cynthia L; Kim, Kook-Hyung

2008-08-15

The repeated ACCA or AC-rich sequence and structural (SL1) elements in the 5' non-translated region (NTR) of the Potato virus X (PVX) RNA play vital roles in the PVX life cycle by controlling translation, RNA replication, movement, and assembly. It has already been shown that the repeated ACCA or AC-rich sequence affect both gRNA and sgRNA accumulation, while not affecting minus-strand RNA accumulation, and are also required for host protein binding. The functional significance of the repeated ACCA sequence elements in the 5' NTR region was investigated by analyzing the effects of deletion and site-directed mutations on PVX replication in Nicotiana benthamiana plants and NT1 protoplasts. Substitution (ACCA into AAAA or UUUU) mutations introduced in the first (nt 10-13) element in the 5' NTR of the PVX RNA significantly affected viral replication, while mutations introduced in the second (nt 17-20) and third (nt 20-23) elements did not. The fourth (nt 29-32) ACCA element weakly affected virus replication, whereas mutations in the fifth (nt 38-41) significantly reduced virus replication due to the structure disruption of SL1 by AAAA and/or UUUU substitutions. Further characterization of the first ACCA element indicated that duplication of ACCA at nt 10-13 (nt 10-17, ACCAACCA) caused severe symptom development as compared to that of wild type, while deletion of the single element (nt 10-13), DeltaACCA) or tripling of this element caused reduced symptom development. Single- and double-nucleotide substitutions introduced into the first ACCA element revealed the importance of CC located at nt positions 11 and 12. Altogether, these results indicate that the first ACCA element is important for PVX replication.

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis.

PubMed

Koufopanou, Vassiliki; Burt, Austin

2005-07-01

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.

Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.

PubMed

Schrider, Daniel R; Kern, Andrew D

2014-06-09

Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the prioritization of loci when searching for the genetic bases of disease or adaptive phenotypes. Because mutations that disrupt function are disfavored by natural selection, purifying selection leaves a detectable signature within functional elements; accordingly, this signal has been exploited for over a decade through the use of genomic comparisons of distantly related species. While this is so, the functional complement of the genome changes extensively across time and between lineages; therefore, evidence of the current action of purifying selection in humans is essential. Because the removal of deleterious mutations by natural selection also reduces within-species genetic diversity within functional loci, dense population genetic data have the potential to reveal genomic elements that are currently functional. Here, we assess the potential of this approach by examining an ultradeep sample of human mitochondrial genomes (n = 16,411). We show that the high density of polymorphism in this data set precisely delineates regions experiencing purifying selection. Furthermore, we show that the number of segregating alleles at a site is strongly correlated with its divergence across species after accounting for known mutational biases in human mitochondrial DNA (ρ = 0.51; P < 2.2 × 10(-16)). These two measures track one another at a remarkably fine scale across many loci-a correlation that is purely the result of natural selection. Our results demonstrate that genetic variation has the potential to reveal with surprising precision which regions in the genome are currently performing important functions and likely to have deleterious fitness effects when mutated. As more complete human genomes are sequenced, similar power to reveal purifying selection may be achievable in the human nuclear genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The importance of shortleaf pine for wildlife and diversity in mixed oak-pine forests and in pine-grassland woodlands

Treesearch

Ronald E. Masters

2007-01-01

Shortleaf pine, by virtue of its wide distribution and occurrence in many forest types in eastern North America, is an important species that provides high habitat value for many wildlife species. Shortleaf pine functions as a structural habitat element in both mixed oak-pine forests and in pine-grassland woodlands. It also adds diversity throughout all stages of plant...

Designing User-Computer Dialogues: Basic Principles and Guidelines.

ERIC Educational Resources Information Center

Harrell, Thomas H.

This discussion of the design of computerized psychological assessment or testing instruments stresses the importance of the well-designed computer-user interface. The principles underlying the three main functional elements of computer-user dialogue--data entry, data display, and sequential control--are discussed, and basic guidelines derived…

Development of the Integrated Communication Model

ERIC Educational Resources Information Center

Ho, Hua-Kuo

2008-01-01

Human communication is a critical issue in personal life. It also should be the indispensable core element of general education curriculum in universities and colleges. Based on literature analysis and the author's clinical observation, the importance of human communication, functions of model, and often seen human communication models were…

De novo mutations in regulatory elements in neurodevelopmental disorders

PubMed Central

Short, Patrick J.; McRae, Jeremy F.; Gallone, Giuseppe; Sifrim, Alejandro; Won, Hyejung; Geschwind, Daniel H.; Wright, Caroline F.; Firth, Helen V; FitzPatrick, David R.; Barrett, Jeffrey C.; Hurles, Matthew E.

2018-01-01

We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders. PMID:29562236

Finite Element Analysis for Turbine Blades with Contact Problems

NASA Astrophysics Data System (ADS)

Yang, Yuan-Jian; Yang, Liang; Wang, Hai-Kun; Zhu, Shun-Peng; Huang, Hong-Zhong

2016-12-01

Turbine blades are one of the key components in a typical turbofan engine, which plays an important role in flight safety. In this paper, we establish a establishes a three-dimensional finite element model of the turbine blades, then analyses the strength of the blade in complicated conditions under the joint function of temperature load, centrifugal load, and aerodynamic load. Furthermore, contact analysis of blade tenon and dovetail slot is also carried out to study the stress based on the contact elements. Finally, the Von Mises stress-strain distributions are obtained to acquire the several dangerous points and maximum Von Mises stress, which provide the basis for life prediction of turbine blade.

Identifying protein β-turns with vibrational Raman optical activity.

PubMed

Weymuth, Thomas; Jacob, Christoph R; Reiher, Markus

2011-04-18

β-turns belong to the most important secondary structure elements in proteins. On the basis of density functional calculations, vibrational Raman optical activity signatures of different types of β-turns are established and compared as well as related to other signatures proposed in the literature earlier. Our findings indicate that there are much more characteristic ROA signals of β-turns than have been hitherto suggested. These suggested signatures are, however, found to be valid for the most important type of β-turns. Moreover, we compare the influence of different amino acid side chains on these signatures and investigate the discrimination of β-turns from other secondary structure elements, namely α- and 3(10)-helices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Personal reflections on a galvanizing trail.

PubMed

O'Dell, B L

1998-01-01

This article encompasses my perception of, and experience in, an exciting segment of the trace element era in nutrition research: the role of zinc in the nutrition of animals and humans. Zinc has been a major player on the stage of trace element research, and it has left a trail that galvanized the attention of many researchers, including myself. It is ubiquitous in biological systems, and it plays a multitude of physiologic and biochemical functions. A brief historical overview is followed by a discussion of the contributions the work done in my laboratory has made toward understanding the physiological and biochemical functions of zinc. The effort of 40 years has led to the belief that one of zinc's major roles, and perhaps its first limiting role, is to preserve plasma-membrane function as regards ion channels and signal transduction. Although substantial knowledge has been gained relating to the importance of zinc in nutrition, much remains to be discovered.

The importance of 'global meaning' for people rehabilitating from spinal cord injury.

PubMed

Littooij, E; Leget, C J W; Stolwijk-Swüste, J M; Doodeman, S; Widdershoven, G A M; Dekker, J

2016-11-01

Qualitative study. To explore whether aspects of global meaning (that is, fundamental beliefs and life goals concerning core values, relationships, worldview, identity and inner posture) are associated with processes and outcomes in rehabilitation, as experienced by people with spinal cord injury (SCI). People living in the community receiving outpatient rehabilitation in a Dutch rehabilitation center. In-depth semi-structured interviews were conducted with 16 people with SCI. Interviews were analyzed using qualitative research methods: structural and provisional coding. Core values, relationships, worldview, identity and inner posture (that is, the way in which people relate to the facts of life) were associated with various processes and outcomes of rehabilitation. Elements of the rehabilitation process included motivation, regulation of emotion, making decisions and handling stress. Elements of the outcome of rehabilitation included physical functioning, emotional functioning, social functioning and subjective sense of meaning. The influence was positive, with the exception of one case in which worldview and inner posture were negatively associated with motivation. Besides that, respondents emphasized the importance of rehabilitation professionals attuning to their global meaning. All aspects of global meaning were positively associated with various processes and outcomes of rehabilitation. It is recommended that rehabilitation professionals are aware of the importance of global meaning to people with SCI and that they take people's fundamental beliefs and life goals into account.

Transcriptional regulation of ABI3- and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis.

PubMed

Nakashima, Kazuo; Fujita, Yasunari; Katsura, Koji; Maruyama, Kyonoshin; Narusaka, Yoshihiro; Seki, Motoaki; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2006-01-01

ABA-responsive elements (ABREs) are cis-acting elements and basic leucine zipper (bZIP)-type ABRE-binding proteins (AREBs) are transcriptional activators that function in the expression of RD29B in vegetative tissue of Arabidopsis in response to abscisic acid (ABA) treatment. Dehydration-responsive elements (DREs) function as coupling elements of ABRE in the expression of RD29A in response to ABA. Expression analysis using abi3 and abi5 mutants showed that ABI3 and ABI5 play important roles in the expression of RD29B in seeds. Base-substitution analysis showed that two ABREs function strongly and one ABRE coupled with DRE functions weakly in the expression of RD29A in embryos. In a transient transactivation experiment, ABI3, ABI5 and AREB1 activated transcription of a GUS reporter gene driven by the RD29B promoter strongly but these proteins activated the transcription driven by the RD29A promoter weakly. In 35S::ABI3 Arabidopsis plants, the expression of RD29B was up-regulated strongly, but that of RD29A was up-regulated weakly. These results indicate that the expression of RD29B having ABREs in the promoter is up-regulated strongly by ABI3, whereas that of RD29A having one ABRE coupled with DREs in the promoter is up-regulated weakly by ABI3. We compared the expression of 7000 Arabidopsis genes in response to ABA treatment during germination and in the vegetative growth stage, and that in 35S::ABI3 plants using a full-length cDNA microarray. The expression of ABI3- and/or ABA-responsive genes and cis-elements in the promoters are discussed.

C-terminal motifs in promyelocytic leukemia protein isoforms critically regulate PML nuclear body formation.

PubMed

Li, Chuang; Peng, Qiongfang; Wan, Xiao; Sun, Haili; Tang, Jun

2017-10-15

Promyelocytic leukemia protein (PML) nuclear bodies (NBs), which are sub-nuclear protein structures, are involved in a variety of important cellular functions. PML-NBs are assembled by PML isoforms, and contact between small ubiquitin-like modifiers (SUMOs) with the SUMO interaction motif (SIM) are critically involved in this process. PML isoforms contain a common N-terminal region and a variable C-terminus. However, the contribution of the C-terminal regions to PML-NB formation remains poorly defined. Here, using high-resolution microscopy, we show that mutation of the SIM distinctively influences the structure of NBs formed by each individual PML isoform, with that of PML-III and PML-V minimally changed, and PML-I and PML-IV dramatically impaired. We further identify several C-terminal elements that are important in regulating NB structure and provide strong evidence to suggest that the 8b element in PML-IV possesses a strong ability to interact with SUMO-1 and SUMO-2, and critically participates in NB formation. Our findings highlight the importance of PML C-termini in NB assembly and function, and provide molecular insight into the PML-NB assembly of each distinctive isoform. © 2017. Published by The Company of Biologists Ltd.

National Mapping of Wetland Connectivity | Science Inventory ...

EPA Pesticide Factsheets

Connectivity has become a major focus of hydrological and ecological studies. Connectivity influences fluxes between landscape elements, while isolation reduces flows between elements. Thus connectivity can be an important characteristic controlling ecosystem services. Hydrologic connectivity is particularly significant, since movement of chemical constituents and biota flows are often associated with water flow. While wetlands have many important on-site functions, the degree to which they are connected to other ecosystems is a controlling influence on the effect these waters have on the larger landscape. Specifically, wetlands with high connectivity can serve as sources (e.g., net exporters of dissolved carbon), while those with low connectivity can function as sinks (e.g., net importers of suspended sediments). Here we focus on so-called “geographically isolated wetlands” (GIWs), or wetlands that are completely surrounded by uplands. While these wetlands normally lack surface water connections, they can be hydrologically connected to downstream waters through intermittent surface flow or groundwater. To help quantify connectivity of GIWs with downstream waters, we developed a system to classify GIWs based on type, magnitude, and frequency of hydrologic connectivity. We determine type (overland, shallow groundwater, or deep groundwater connectivity) by considering soil and bedrock permeability. For magnitude, we developed indices to represent tra

Individual differences in perceiving and recognizing faces-One element of social cognition.

PubMed

Wilhelm, Oliver; Herzmann, Grit; Kunina, Olga; Danthiir, Vanessa; Schacht, Annekathrin; Sommer, Werner

2010-09-01

Recognizing faces swiftly and accurately is of paramount importance to humans as a social species. Individual differences in the ability to perform these tasks may therefore reflect important aspects of social or emotional intelligence. Although functional models of face cognition based on group and single case studies postulate multiple component processes, little is known about the ability structure underlying individual differences in face cognition. In 2 large individual differences experiments (N = 151 and N = 209), a broad variety of face-cognition tasks were tested and the component abilities of face cognition-face perception, face memory, and the speed of face cognition-were identified and then replicated. Experiment 2 also showed that the 3 face-cognition abilities are clearly distinct from immediate and delayed memory, mental speed, general cognitive ability, and object cognition. These results converge with functional and neuroanatomical models of face cognition by demonstrating the difference between face perception and face memory. The results also underline the importance of distinguishing between speed and accuracy of face cognition. Together our results provide a first step toward establishing face-processing abilities as an independent ability reflecting elements of social intelligence. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

Wetland Hydrological Connectivity: A Classification Approach ...

EPA Pesticide Factsheets

Connectivity has become a major focus of hydrological and ecological studies. Connectivity influences fluxes between landscape elements, while isolation reduces flows between elements. Thus connectivity can be an important characteristic controlling ecosystem services. Hydrologic connectivity is particularly significant, since movement of chemical constituents and biota flows are often associated with water flow. While wetlands have many important on-site functions, the degree to which they are connected to other ecosystems is a controlling influence on the effect these waters have on the larger landscape. Specifically, wetlands with high connectivity can serve as sources (e.g., net exporters of dissolved carbon), while those with low connectivity can function as sinks (e.g., net importers of suspended sediments). Here we focus on so-called “geographically isolated wetlands” (GIWs), or wetlands that are completely surrounded by uplands. While these wetlands normally lack surface water connections, they can be hydrologically connected to downstream waters through intermittent surface flow or groundwater. To help quantify connectivity of GIWs with downstream waters, we developed a system to classify GIWs based on type, magnitude, and frequency of hydrologic connectivity. We determine type (overland, shallow groundwater, or deep groundwater connectivity) by considering soil and bedrock permeability. For magnitude, we developed indices to repre

Influence of surface chemistry of carbon materials on their interactions with inorganic nitrogen contaminants in soil and water.

PubMed

Sumaraj; Padhye, Lokesh P

2017-10-01

Inorganic nitrogen contaminants (INC) (NH 4 + , NO 3 - , NO 2 - , NH 3 , NO, NO 2 , and N 2 O) pose a growing risk to the environment, and their remediation methods are highly sought after. Application of carbon materials (CM), such as biochar and activated carbon, to remediate INC from agricultural fields and wastewater treatment plants has gained a significant interest since past few years. Understanding the role of surface chemistry of CM in adsorption of various INC is highly critical to increase adsorption efficiency as well as to assess the long term impact of using these highly recalcitrant CM for remediation of INC. Critical reviews of adsorption studies related to INC have revealed that carbon surface chemistry (surface functional groups, pH, Eh, elemental composition, and mineral content) has significant influence on adsorption of INC. Compared to basic functional groups, oxygen containing surface functional groups have been found to be more influential for adsorption of INC. However, basic sites on carbon materials still play an important role in chemisorption of anionic INC. Apart from surface functional groups, pH, Eh and pH zpc of CM and elemental and mineral composition of its surface are important properties capable of altering INC interactions with CM. This review summarizes our current understanding of INC interactions with CM's surface through the known chemisorption mechanisms: electrostatic interaction, hydrogen bonding, electron donor-acceptor mechanism, hydrophobic and hydrophilic interaction, chemisorption aided by minerals, and interactions influenced by pH and elemental composition. Change in surface chemistry of CM in soil during aging is also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

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

Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

2003-12-31

Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involvedmore » in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.« less

Generalized multiscale finite-element method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

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

Gao, Kai; Fu, Shubin; Gibson, Richard L.

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both the boundaries and interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale mediummore » property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.« less

Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

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

Gao, Kai, E-mail: kaigao87@gmail.com; Fu, Shubin, E-mail: shubinfu89@gmail.com; Gibson, Richard L., E-mail: gibson@tamu.edu

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both the boundaries and interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale mediummore » property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.« less

Generalized multiscale finite-element method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

DOE PAGES

Gao, Kai; Fu, Shubin; Gibson, Richard L.; ...

2015-04-14

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both the boundaries and interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale mediummore » property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.« less

RAF and Intelligence Warfighting Function

DTIC Science & Technology

2015-02-01

Warfighting Function 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT...meet the CCDR’s need to leverage the entire Intelligence Enterprise. Balancing IWfF RAF “solutions against an ever reducing budget will require...right balance is important. Using DOTMLPF as a framework can assist in seeing how the IWfF can support RAF implementation. Furthermore, identifying gaps

A novel adaptive algorithm for 3D finite element analysis to model extracortical bone growth.

PubMed

Cheong, Vee San; Blunn, Gordon W; Coathup, Melanie J; Fromme, Paul

2018-02-01

Extracortical bone growth with osseointegration of bone onto the shaft of massive bone tumour implants is an important clinical outcome for long-term implant survival. A new computational algorithm combining geometrical shape changes and bone adaptation in 3D Finite Element simulations has been developed, using a soft tissue envelope mesh, a novel concept of osteoconnectivity, and bone remodelling theory. The effects of varying the initial tissue density, spatial influence function and time step were investigated. The methodology demonstrated good correspondence to radiological results for a segmental prosthesis.

Leadership for a Technology-Rich Educational Environment.

ERIC Educational Resources Information Center

Riedl, Richard; Smith, Tracy; Ware, Anita; Wark, Alan; Yount, Peter

This paper emphasizes the importance of exploring the attitudes, skills, and knowledge that will enable individuals in educational leadership positions to function effectively and to provide support to create and maintain technology-rich educational systems. The discussion is guided by the following five elements, the understanding of which are…

Key Elements of the Chemistry of Cytochrome P-450: The Oxygen Rebound Mechanism.

ERIC Educational Resources Information Center

Groves, John T.

1985-01-01

Discusses the structure and function of the liver protein cytochrome P-450, an important catalyst for a variety of detoxification reactions. Diagnostic substracts for this heme-containing monooxygenase, synthetic modes of the active site, and oxidations with synthetic metalloporphyrins are the major topic areas considered. (JN)

Interdisciplinary, Team-Taught, Undergraduate Business Courses: The Impact of Integration

ERIC Educational Resources Information Center

Ducoffe, Sandra J. Smith; Tromley, Cheryl L.; Tucker, Michael

2006-01-01

Given the widespread use and success of cross-functional teams in industry and the American Assembly of Collegiate Schools of Business's focus on the importance of interdisciplinary education, many business schools have incorporated interdisciplinary elements into their curricula. This study examined current student and alumni perceptions of the…

Light, Colour & Air Quality: Important Elements of the Learning Environment?

ERIC Educational Resources Information Center

Hathaway, Warren E.

1987-01-01

Reviews and evaluates studies of the effects of light, color, and air quality on the learning environment. Concludes that studies suggest a role for light in establishing and maintaining physiological functions and balances and a need for improved air quality in airtight, energy efficient buildings. (JHZ)

Moving Particles Through a Finite Element Mesh

PubMed Central

Peskin, Adele P.; Hardin, Gary R.

1998-01-01

We present a new numerical technique for modeling the flow around multiple objects moving in a fluid. The method tracks the dynamic interaction between each particle and the fluid. The movements of the fluid and the object are directly coupled. A background mesh is designed to fit the geometry of the overall domain. The mesh is designed independently of the presence of the particles except in terms of how fine it must be to track particles of a given size. Each particle is represented by a geometric figure that describes its boundary. This figure overlies the mesh. Nodes are added to the mesh where the particle boundaries intersect the background mesh, increasing the number of nodes contained in each element whose boundary is intersected. These additional nodes are then used to describe and track the particle in the numerical scheme. Appropriate element shape functions are defined to approximate the solution on the elements with extra nodes. The particles are moved through the mesh by moving only the overlying nodes defining the particles. The regular finite element grid remains unchanged. In this method, the mesh does not distort as the particles move. Instead, only the placement of particle-defining nodes changes as the particles move. Element shape functions are updated as the nodes move through the elements. This method is especially suited for models of moderate numbers of moderate-size particles, where the details of the fluid-particle coupling are important. Both the complications of creating finite element meshes around appreciable numbers of particles, and extensive remeshing upon movement of the particles are simplified in this method. PMID:28009377

Arabidopsis ACTIN-DEPOLYMERIZING FACTOR3 Is Required for Controlling Aphid Feeding from the Phloem1[OPEN

PubMed Central

Mondal, Hossain A.; Louis, Joe; Archer, Lani; Patel, Monika; Nalam, Vamsi J.; Sarowar, Sujon; Sivapalan, Vishala

2018-01-01

The actin cytoskeleton network has an important role in plant cell growth, division, and stress response. Actin-depolymerizing factors (ADFs) are a group of actin-binding proteins that contribute to reorganization of the actin network. Here, we show that the Arabidopsis (Arabidopsis thaliana) ADF3 is required in the phloem for controlling infestation by Myzus persicae Sülzer, commonly known as the green peach aphid (GPA), which is an important phloem sap-consuming pest of more than fifty plant families. In agreement with a role for the actin-depolymerizing function of ADF3 in defense against the GPA, we show that resistance in adf3 was restored by overexpression of the related ADF4 and the actin cytoskeleton destabilizers, cytochalasin D and latrunculin B. Electrical monitoring of the GPA feeding behavior indicates that the GPA stylets found sieve elements faster when feeding on the adf3 mutant compared to the wild-type plant. In addition, once they found the sieve elements, the GPA fed for a more prolonged period from sieve elements of adf3 compared to the wild-type plant. The longer feeding period correlated with an increase in fecundity and population size of the GPA and a parallel reduction in callose deposition in the adf3 mutant. The adf3-conferred susceptibility to GPA was overcome by expression of the ADF3 coding sequence from the phloem-specific SUC2 promoter, thus confirming the importance of ADF3 function in the phloem. We further demonstrate that the ADF3-dependent defense mechanism is linked to the transcriptional up-regulation of PHYTOALEXIN-DEFICIENT4, which is an important regulator of defenses against the GPA. PMID:29133373

How to quantify conduits in wood?

PubMed

Scholz, Alexander; Klepsch, Matthias; Karimi, Zohreh; Jansen, Steven

2013-01-01

Vessels and tracheids represent the most important xylem cells with respect to long distance water transport in plants. Wood anatomical studies frequently provide several quantitative details of these cells, such as vessel diameter, vessel density, vessel element length, and tracheid length, while important information on the three dimensional structure of the hydraulic network is not considered. This paper aims to provide an overview of various techniques, although there is no standard protocol to quantify conduits due to high anatomical variation and a wide range of techniques available. Despite recent progress in image analysis programs and automated methods for measuring cell dimensions, density, and spatial distribution, various characters remain time-consuming and tedious. Quantification of vessels and tracheids is not only important to better understand functional adaptations of tracheary elements to environment parameters, but will also be essential for linking wood anatomy with other fields such as wood development, xylem physiology, palaeobotany, and dendrochronology.

Analysis of the Duration of Rising Tone Chorus Elements

NASA Astrophysics Data System (ADS)

Teng, S.; Tao, X.; Xie, Y.; Zonca, F.; Chen, L.; Fang, W. B.; Wang, S.

2017-12-01

The duration of chorus elements is an important parameter to understand chorus excitation and to quantify the effects of nonlinear wave-particle interactions on energetic electron dynamics. In this work, we analyze the duration of rising tone chorus elements statistically using Van Allen Probes data. We present the distribution of chorus element duration (τ) as a function of magnetic local time (MLT) and the geomagnetic activity level characterized by auroral electrojet (AE) index. We show that the typical value of τ for nightside and dawnside is about 0.12 s, smaller than that for dayside and duskside by about a factor of 2 to 4. Using a previously developed hybrid code, DAWN, we suggest that the background magnetic field inhomogeneity might be an important factor in controlling the chorus element duration. We also report that τ is larger during quiet times and shorter during moderate and active periods; this result is consistent with the MLT dependence of τ and the occurrence pattern of chorus waves at different levels of geomagnetic activity. We then investigate the correlation between τ and the frequency chirping rate (Γ). We show that, from observation, τ scales with Γ as τ∝Γ-1.1, suggesting that statistically the frequency range of chorus elements (τΓ) should be roughly the same for different elements. These findings should be useful to the further development of a theoretical model of chorus excitation and to the quantification of nonlinear wave-particle interactions on energetic electron dynamics.

Multi-scale Finite Element Modeling of Eustachian Tube Function: Influence of Mucosal Adhesion

PubMed Central

Malik, J.E.; Swarts, J.D.; Ghadiali, S. N.

2017-01-01

The inability to open the collapsible Eustachian tube (ET) leads to the development of chronic Otitis Media (OM). Although mucosal inflammation during OM leads to increased mucin gene expression and elevated adhesion forces within the ET lumen, it is not known how changes in mucosal adhesion alter the biomechanical mechanisms of ET function. In this study, we developed a novel multi-scale finite element model of ET function in adults that utilizes adhesion spring elements to simulate changes in mucosal adhesion. Models were created for six adult subjects and dynamic patterns in muscle contraction were used to simulate the wave-like opening of the ET that occurs during swallowing. Results indicate that ET opening is highly sensitive to the level of mucosal adhesion and that exceeding a critical value of adhesion leads to rapid ET dysfunction. Parameter variation studies and sensitivity analysis indicate that increased mucosal adhesion alters the relative importance of several tissue biomechanical properties. For example, increases in mucosal adhesion reduced the sensitivity of ET function to tensor veli palatini muscle forces but did not alter the insensitivity of ET function to levator veli palatini muscle forces. Interestingly, although changes in cartilage stiffness did not significantly influence ET opening under low adhesion conditions, ET opening was highly sensitive to changes in cartilage stiffness under high adhesion conditions. Therefore, our multi-scale computational models indicate that changes in mucosal adhesion as would occur during inflammatory OM alter the biomechanical mechanisms of ET function. PMID:26891171

[Proposal of new trace elements classification to be used in nutrition, oligotherapy and other therapeutics strategies].

PubMed

Ramírez Hernández, Javier; Bonete Pérez, María José; Martínez Espinosa, Rosa María

2014-12-17

1) to propose a new classification of the trace elements based on a study of the recently reported research; 2) to offer detailed and actualized information about trace elements. the analysis of the research results recently reported reveals that the advances of the molecular analysis techniques point out the importance of certain trace elements in human health. A detailed analysis of the catalytic function related to several elements not considered essential o probably essentials up to now is also offered. To perform the integral analysis of the enzymes containing trace elements informatics tools have been used. Actualized information about physiological role, kinetics, metabolism, dietetic sources and factors promoting trace elements scarcity or toxicity is also presented. Oligotherapy uses catalytic active trace elements with therapeutic proposals. The new trace element classification here presented will be of high interest for different professional sectors: doctors and other professions related to medicine; nutritionist, pharmaceutics, etc. Using this new classification and approaches, new therapeutic strategies could be designed to mitigate symptomatology related to several pathologies, particularly carential and metabolic diseases. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Extrachromosomal genetic elements in Micrococcus.

PubMed

Dib, Julián Rafael; Liebl, Wolfgang; Wagenknecht, Martin; Farías, María Eugenia; Meinhardt, Friedhelm

2013-01-01

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

Functional role of inorganic trace elements in angiogenesis part III: (Ti, Li, Ce, As, Hg, Va, Nb and Pb).

PubMed

Saghiri, Mohammad Ali; Orangi, Jafar; Asatourian, Armen; Sorenson, Christine M; Sheibani, Nader

2016-02-01

Many essential elements exist in nature with significant influence on human health. Angiogenesis is vital in developmental, repair, and regenerative processes, and its aberrant regulation contributes to pathogenesis of many diseases including cancer. Thus, it is of great importance to explore the role of these elements in such a vital process. This is third in a series of reviews that serve as an overview of the role of inorganic elements in regulation of angiogenesis and vascular function. Here we will review the roles of titanium, lithium, cerium, arsenic, mercury, vanadium, niobium, and lead in these processes. The roles of other inorganic elements in angiogenesis were discussed in part I (N, Fe, Se, P, Au, and Ca) and part II (Cr, Si, Zn, Cu, and S) of these series. The methods of exposure, structure, mechanisms, and potential activities of these elements are briefly discussed. An electronic search was performed on the role of these elements in angiogenesis from January 2005 to April 2014. These elements can promote and/or inhibit angiogenesis through different mechanisms. The anti-angiogenic effect of titanium dioxide nanoparticles comes from the inhibition of angiogenic processes, and not from its toxicity. Lithium affects vasculogenesis but not angiogenesis. Nanoceria treatment inhibited tumor growth by inhibiting angiogenesis. Vanadium treatment inhibited cell proliferation and induced cytotoxic effects through interactions with DNA. The negative impact of mercury on endothelial cell migration and tube formation activities was dose and time dependent. Lead induced IL-8 production, which is known to promote tumor angiogenesis. Thus, understanding the impact of these elements on angiogenesis will help in development of new modalities to modulate angiogenesis under various conditions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Continuous quality improvement for the clinical decision unit.

PubMed

Mace, Sharon E

2004-01-01

Clinical decision units (CDUs) are a relatively new and growing area of medicine in which patients undergo rapid evaluation and treatment. Continuous quality improvement (CQI) is important for the establishment and functioning of CDUs. CQI in CDUs has many advantages: better CDU functioning, fulfillment of Joint Commission on Accreditation of Healthcare Organizations mandates, greater efficiency/productivity, increased job satisfaction, better performance improvement, data availability, and benchmarking. Key elements include a database with volume indicators, operational policies, clinical practice protocols (diagnosis specific/condition specific), monitors, benchmarks, and clinical pathways. Examples of these important parameters are given. The CQI process should be individualized for each CDU and hospital.

The Serum Response Factor and a Putative Novel Transcription Factor Regulate Expression of the Immediate-Early Gene Arc/Arg3.1 in Cultured Cortical Neurons

PubMed Central

Pintchovski, Sean A.; Peebles, Carol L.; Kim, Hong Joo; Verdin, Eric; Finkbeiner, Steven

2010-01-01

The immediate-early effector gene Arc/Arg3.1 is robustly upregulated by synaptic activity associated with learning and memory. Here we show in primary cortical neuron culture that diverse stimuli induce Arc expression through new transcription. Searching for regulatory regions important for Arc transcription, we found nine DNaseI-sensitive nucleosome-depleted sites at this genomic locus. A reporter gene encompassing these sites responded to synaptic activity in an NMDA receptor–dependent manner, consistent with endogenous Arc mRNA. Responsiveness mapped to two enhancer regions ∼6.5 kb and ∼1.4 kb upstream of Arc. We dissected these regions further and found that the proximal enhancer contains a functional and conserved “Zeste-like” response element that binds a putative novel nuclear protein in neurons. Therefore, activity regulates Arc transcription partly by a novel signaling pathway. We also found that the distal enhancer has a functional and highly conserved serum response element. This element binds serum response factor, which is recruited by synaptic activity to regulate Arc. Thus, Arc is the first target of serum response factor that functions at synapses to mediate plasticity. PMID:19193899

Physical Therapy Adjuvants to Promote Optimization of Walking Recovery after Stroke

PubMed Central

Bowden, Mark G.; Embry, Aaron E.; Gregory, Chris M.

2011-01-01

Stroke commonly results in substantial and persistent deficits in locomotor function. The majority of scientific inquiries have focused on singular intervention approaches, with recent attention given to task specific therapies. We propose that measurement should indicate the most critical limiting factor(s) to be addressed and that a combination of adjuvant treatments individualized to target accompanying impairment(s) will result in the greatest improvements in locomotor function. We explore training to improve walking performance by addressing a combination of: (1) walking specific motor control; (2) dynamic balance; (3) cardiorespiratory fitness and (4) muscle strength and put forward a theoretical framework to maximize the functional benefits of these strategies as physical adjuvants. The extent to which any of these impairments contribute to locomotor dysfunction is dependent on the individual and will undoubtedly change throughout the rehabilitation intervention. Thus, the ability to identify and measure the relative contributions of these elements will allow for identification of a primary intervention as well as prescription of additional adjuvant approaches. Importantly, we highlight the need for future studies as appropriate dosing of each of these elements is contingent on improving the capacity to measure each element and to titrate the contribution of each to optimal walking performance. PMID:22013549

Capacity for cooperative binding of thyroid hormone (T3) receptor dimers defines wild type T3 response elements.

PubMed

Brent, G A; Williams, G R; Harney, J W; Forman, B M; Samuels, H H; Moore, D D; Larsen, P R

1992-04-01

Thyroid hormone response elements (T3REs) have been identified in a variety of promoters including those directing expression of rat GH (rGH), alpha-myosin heavy chain (rMHC), and malic enzyme (rME). A detailed biochemical and genetic analysis of the rGH element has shown that it consists of three hexamers related to the consensus [(A/G)GGT(C/A)A]. We have extended this analysis to the rMHC and rME elements. Binding of highly purified thyroid hormone receptor (T3R) to T3REs was determined using the gel shift assay, and thyroid hormone (T3) induction was measured in transient tranfections. We show that the wild type version of each of the three elements binds T3R dimers cooperatively. Mutational analysis of the rMHC and rME elements identified domains important for binding T3R dimers and allowed a direct determination of the relationship between T3R binding and function. In each element two hexamers are required for dimer binding, and mutations that interfere with dimer formation significantly reduce T3 induction. Similar to the rGH element, the rMHC T3RE contains three hexameric domains arranged as a direct repeat followed by an inverted copy, although the third domain is weaker than in rGH. All three are required for full function and T3R binding. The rME T3RE is a two-hexamer direct repeat T3RE, which also binds T3R monomer and dimer. Across a series of mutant elements, there was a strong correlation between dimer binding in vitro and function in vivo for rMHC (r = 0.99, P less than 0.01) and rME (r = 0.67, P less than 0.05) T3REs. Our results demonstrate a similar pattern of T3R dimer binding to a diverse array of hexameric sequences and arrangements in three wild type T3REs. Addition of nuclear protein enhanced T3R binding but did not alter the specificity of binding to wild type or mutant elements. Binding of purified T3R to T3REs was highly correlated with function, both with and without the addition of nuclear protein. T3R dimer formation is the common feature which defines the capacity of these elements to confer T3 induction.

A finite element method with overlapping meshes for free-boundary axisymmetric plasma equilibria in realistic geometries

NASA Astrophysics Data System (ADS)

Heumann, Holger; Rapetti, Francesca

2017-04-01

Existing finite element implementations for the computation of free-boundary axisymmetric plasma equilibria approximate the unknown poloidal flux function by standard lowest order continuous finite elements with discontinuous gradients. As a consequence, the location of critical points of the poloidal flux, that are of paramount importance in tokamak engineering, is constrained to nodes of the mesh leading to undesired jumps in transient problems. Moreover, recent numerical results for the self-consistent coupling of equilibrium with resistive diffusion and transport suggest the necessity of higher regularity when approximating the flux map. In this work we propose a mortar element method that employs two overlapping meshes. One mesh with Cartesian quadrilaterals covers the vacuum chamber domain accessible by the plasma and one mesh with triangles discretizes the region outside. The two meshes overlap in a narrow region. This approach gives the flexibility to achieve easily and at low cost higher order regularity for the approximation of the flux function in the domain covered by the plasma, while preserving accurate meshing of the geometric details outside this region. The continuity of the numerical solution in the region of overlap is weakly enforced by a mortar-like mapping.

Stabilised finite-element methods for solving the level set equation with mass conservation

NASA Astrophysics Data System (ADS)

Kabirou Touré, Mamadou; Fahsi, Adil; Soulaïmani, Azzeddine

2016-01-01

Finite-element methods are studied for solving moving interface flow problems using the level set approach and a stabilised variational formulation proposed in Touré and Soulaïmani (2012; Touré and Soulaïmani To appear in 2016), coupled with a level set correction method. The level set correction is intended to enhance the mass conservation satisfaction property. The stabilised variational formulation (Touré and Soulaïmani 2012; Touré and Soulaïmani, To appear in 2016) constrains the level set function to remain close to the signed distance function, while the mass conservation is a correction step which enforces the mass balance. The eXtended finite-element method (XFEM) is used to take into account the discontinuities of the properties within an element. XFEM is applied to solve the Navier-Stokes equations for two-phase flows. The numerical methods are numerically evaluated on several test cases such as time-reversed vortex flow, a rigid-body rotation of Zalesak's disc, sloshing flow in a tank, a dam-break over a bed, and a rising bubble subjected to buoyancy. The numerical results show the importance of satisfying global mass conservation to accurately capture the interface position.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.

PubMed

Lim, Chun Shen; Brown, Chris M

2017-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

PubMed Central

Lim, Chun Shen; Brown, Chris M.

2018-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community. PMID:29354101

Designing added functions in engineered cementitious composites

NASA Astrophysics Data System (ADS)

Yang, En-Hua

In this dissertation, a new and systematic material design approach is developed for ECC with added functions through material microstructures linkage to composite macroscopic behavior. The thesis research embodies theoretical development by building on previous ECC micromechanical models, and experimental investigations into three specific new versions of ECC with added functions aimed at addressing societal demands of our built infrastructure. Specifically, the theoretical study includes three important ECC modeling elements: Steady-state crack propagation analyses and simulation, predictive accuracy of the fiber bridging constitutive model, and development of the rate-dependent strain-hardening criteria. The first element establishes the steady-state cracking criterion as a fundamental requirement for multiple cracking behavior in brittle matrix composites. The second element improves the accuracy of crack-width prediction in ECC. The third element establishes the micromechanics basis for impact-resistant ECC design. Three new ECCs with added functions were developed and experimentally verified in this thesis research through the enhanced theoretical framework. A green ECC incorporating a large volume of industrial waste was demonstrated to possess reduced crack width and drying shrinkage. The self-healing ECC designed with tight crack width was demonstrated to recover transport and mechanical properties after microcrack damage when exposed to wet and dry cycles. The impact-resistant ECC was demonstrated to retain tensile ductility with increased strength under moderately high strain-rate loading. These new versions of ECC with added functions are expected to contribute greatly to enhancing the sustainability, durability, and safety of civil infrastructure built with ECC. This research establishes the effectiveness of micromechanics-based design and material ingredient tailoring for ECC with added new attributes but without losing its basic tensile ductile characteristics.

Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data

PubMed Central

Xu, Shuhua

2015-01-01

Noncoding DNA sequences (NCS) have attracted much attention recently due to their functional potentials. Here we attempted to reveal the functional roles of noncoding sequences from the point of view of natural selection that typically indicates the functional potentials of certain genomic elements. We analyzed nearly 37 million single nucleotide polymorphisms (SNPs) of Phase I data of the 1000 Genomes Project. We estimated a series of key parameters of population genetics and molecular evolution to characterize sequence variations of the noncoding genome within and between populations, and identified the natural selection footprints in NCS in worldwide human populations. Our results showed that purifying selection is prevalent and there is substantial constraint of variations in NCS, while positive selectionis more likely to be specific to some particular genomic regions and regional populations. Intriguingly, we observed larger fraction of non-conserved NCS variants with lower derived allele frequency in the genome, indicating possible functional gain of non-conserved NCS. Notably, NCS elements are enriched for potentially functional markers such as eQTLs, TF motif, and DNase I footprints in the genome. More interestingly, some NCS variants associated with diseases such as Alzheimer's disease, Type 1 diabetes, and immune-related bowel disorder (IBD) showed signatures of positive selection, although the majority of NCS variants, reported as risk alleles by genome-wide association studies, showed signatures of negative selection. Our analyses provided compelling evidence of natural selection forces on noncoding sequences in the human genome and advanced our understanding of their functional potentials that play important roles in disease etiology and human evolution. PMID:26053627

Alternative Pre-mRNA Splicing in Mammals and Teleost Fish: A Effective Strategy for the Regulation of Immune Responses Against Pathogen Infection.

PubMed

Chang, Ming Xian; Zhang, Jie

2017-07-15

Pre-mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre-mRNA splicing provides an important source of transcriptome and proteome complexity through selectively joining different coding elements to form mRNAs, which encode proteins with similar or distinct functions. In mammals, previous studies have shown the role of alternative splicing in regulating the function of the immune system, especially in the regulation of T-cell activation and function. As lower vertebrates, teleost fish mainly rely on a large family of pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs) from various invading pathogens. In this review, we summarize recent advances in our understanding of alternative splicing of piscine PRRs including peptidoglycan recognition proteins (PGRPs), nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and their downstream signaling molecules, compared to splicing in mammals. We also discuss what is known and unknown about the function of splicing isoforms in the innate immune responses against pathogens infection in mammals and teleost fish. Finally, we highlight the consequences of alternative splicing in the innate immune system and give our view of important directions for future studies.

Self supporting heat transfer element

DOEpatents

Story, Grosvenor Cook; Baldonado, Ray Orico

2002-01-01

The present invention provides an improved internal heat exchange element arranged so as to traverse the inside diameter of a container vessel such that it makes good mechanical contact with the interior wall of that vessel. The mechanical element is fabricated from a material having a coefficient of thermal conductivity above about 0.8 W cm.sup.-1.degree. K.sup.-1 and is designed to function as a simple spring member when that member has been cooled to reduce its diameter to just below that of a cylindrical container or vessel into which it is placed and then allowed to warm to room temperature. A particularly important application of this invention is directed to a providing a simple compartmented storage container for accommodating a hydrogen absorbing alloy.

Functional analysis of a WRKY transcription factor involved in transcriptional activation of the DBAT gene in Taxus chinensis.

PubMed

Li, S; Zhang, P; Zhang, M; Fu, C; Yu, L

2013-01-01

Although the regulation of taxol biosynthesis at the transcriptional level remains unclear, 10-deacetylbaccatin III-10 β-O-acetyl transferase (DBAT) is a critical enzyme in the biosynthesis of taxol. The 1740 bp fragment 5'-flanking sequence of the dbat gene was cloned from Taxus chinensis cells. Important regulatory elements needed for activity of the dbat promoter were located by deletion analyses in T. chinensis cells. A novel WRKY transcription factor, TcWRKY1, was isolated with the yeast one-hybrid system from a T. chinensis cell cDNA library using the important regulatory elements as bait. The gene expression of TcWRKY1 in T. chinensis suspension cells was specifically induced by methyl jasmonate (MeJA). Biochemical analysis indicated that TcWRKY1 protein specifically interacts with the two W-box (TGAC) cis-elements among the important regulatory elements. Overexpression of TcWRKY1 enhanced dbat expression in T. chinensis suspension cells, and RNA interference (RNAi) reduced the level of transcripts of dbat. These results suggest that TcWRKY1 participates in regulation of taxol biosynthesis in T. chinensis cells, and that dbat is a target gene of this transcription factor. This research also provides a potential candidate gene for engineering increased taxol accumulation in Taxus cell cultures. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

PubMed

Smith, Robin P; Riesenfeld, Samantha J; Holloway, Alisha K; Li, Qiang; Murphy, Karl K; Feliciano, Natalie M; Orecchia, Lorenzo; Oksenberg, Nir; Pollard, Katherine S; Ahituv, Nadav

2013-07-18

Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.

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

PubMed Central

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

2007-01-01

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

An Ultraconserved Brain-specific Enhancer within ADGRL3 (LPHN3) Underpins ADHD Susceptibility

PubMed Central

Martinez, Ariel F.; Abe, Yu; Hong, Sungkook; Molyneux, Kevin; Yarnell, David; Löhr, Heiko; Driever, Wolfgang; Acosta, Maria T.; Arcos-Burgos, Mauricio; Muenke, Maximilian

2016-01-01

BACKGROUND Genetic factors predispose to attention deficit/hyperactivity disorder (ADHD). Previous studies have reported linkage and association to ADHD of gene variants within ADGRL3. In this study, we functionally analyzed non-coding variants in this gene as likely pathological contributors. METHODS In silico, in vitro and in vivo approaches were used to identify and characterize evolutionary conserved elements within the ADGRL3 linkage region (~207 Kb). Family-based genetic analyses on 838 individuals (372 affected and 466 unaffected) identified ADHD-associated SNPs harbored in some of these conserved elements. Luciferase assays and zebrafish GFP transgenesis tested conserved elements for transcriptional enhancer activity. Electromobility shift assays were used to verify transcription factor binding disruption by ADHD risk alleles. RESULTS An ultraconserved element was discovered (ECR47) that functions as a transcriptional enhancer. A three-variant ADHD risk haplotype in ECR47, formed by rs17226398, rs56038622 and rs2271338, reduced enhancer activity by 40% in neuroblastoma and astrocytoma cells (PBonferroni<0.0001). This enhancer also drove GFP expression in the zebrafish brain in a tissue-specific manner, sharing aspects of endogenous ADGRL3 expression. The rs2271338 risk allele disrupts binding of YY1, an important factor in the development and function of the central nervous system. Expression quantitative trait loci analysis of post-mortem human brain tissues revealed an association between rs2271338 and reduced ADGRL3 expression in the thalamus. CONCLUSIONS These results uncover the first functional evidence of common non-coding variants with potential implications for the pathology of ADHD. PMID:27692237

Evolution and Application of Inteins in Candida species: A Review

PubMed Central

Fernandes, José A. L.; Prandini, Tâmara H. R.; Castro, Maria da Conceiçao A.; Arantes, Thales D.; Giacobino, Juliana; Bagagli, Eduardo; Theodoro, Raquel C.

2016-01-01

Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species-specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic among the different species. Although absent in Candida albicans, these elements are present in different sizes, in some environmental Candida spp. and also in most of the non-albicans Candida spp. considered emergent opportunistic pathogens. Besides, the possible role of these inteins in yeast physiology was also discussed in the light of the recent findings on the importance of these elements as post-translational modulators of gene expression, reinforcing their relevance as alternative therapeutic targets for the treatment of non-albicans Candida infections, because, once the splicing of an intein is inhibited, its host protein, which is usually a housekeeping protein, becomes non-functional. PMID:27777569

Case Studies of Rock Reinforcement Components and Systems Testing

NASA Astrophysics Data System (ADS)

Thompson, A. G.; Villaescusa, E.

2014-09-01

Rock reinforcement is widely used in tunnels and surface and underground mines. A large number of proprietary products are available in various configurations of components. While the mechanical properties of the primary element are available from product brochures, the associated component properties may vary widely and adversely influence the overall performance of the system. Field pull out tests are most commonly used to measure the system response in the toe anchor region. However, the response of the collar region is less commonly considered but may be more important. Several case studies are described in which various components and systems of rock bolts and cable bolts have been subjected to static loading in the laboratory and in the field. The results generally demonstrate the importance of considering the properties of all the components and not simply those of the primary element. In some cases, the internal fixtures have strengths much less than the elements. Often it has also been found that the fixture at the collar has significantly less strength than the element and this will result in complete loss of function in restraining surface support hardware, such as plates, mesh and reinforced shotcrete.

Developing the snow component of a distributed hydrological model: a step-wise approach based on multi-objective analysis

NASA Astrophysics Data System (ADS)

Dunn, S. M.; Colohan, R. J. E.

1999-09-01

A snow component has been developed for the distributed hydrological model, DIY, using an approach that sequentially evaluates the behaviour of different functions as they are implemented in the model. The evaluation is performed using multi-objective functions to ensure that the internal structure of the model is correct. The development of the model, using a sub-catchment in the Cairngorm Mountains in Scotland, demonstrated that the degree-day model can be enhanced for hydroclimatic conditions typical of those found in Scotland, without increasing meteorological data requirements. An important element of the snow model is a function to account for wind re-distribution. This causes large accumulations of snow in small pockets, which are shown to be important in sustaining baseflows in the rivers during the late spring and early summer, long after the snowpack has melted from the bulk of the catchment. The importance of the wind function would not have been identified using a single objective function of total streamflow to evaluate the model behaviour.

A petunia ethylene-responsive element binding factor, PhERF2, plays an important role in antiviral RNA silencing

USDA-ARS?s Scientific Manuscript database

Virus-induced gene silencing (VIGS) is a useful technique for functional characterization of plant genes. However, the silencing efficiency of the VIGS system is variable largely depending on compatibility between the host and the virus. Antiviral RNA silencing is involved in plant antiviral defense...

[The construction of cast removable partial dentures with functional-effective structural elements].

PubMed

Hahn, P P

1977-09-01

In view of caries susceptibility and periodontal condition, oral examination (fig. 1) is of prime importance in treatment planning (fig. 2). Crownings as well as possibilities of direct and indirect stiffenings are explained from the viewpoints of construction and differential indication in connection with the design of the prosthesis.

What Is the Function of a Figurine? Can the Repertory Grid Technique Tell?

ERIC Educational Resources Information Center

Persson, Helena Isakssson

2016-01-01

Teaching design and product development at upper secondary school level in Sweden is a matter of interdisciplinary considerations. Education in product development, at this level, prepares students for further studies and career in engineering or industrial design. Knowledge of artefacts is an important element in the education. In coherence with…

Periodicity in the Acid-Base Behavior of Oxides and Hydroxides.

ERIC Educational Resources Information Center

Rich, Ronald L.

1985-01-01

Aqueous solubilities of many important hydrous oxides and hydroxides are displayed, for the various elements, as functions primarily of pH. These graphs are then arranged in groups to facilitate studies of the effects of oxidation state, electron structure, and position in the periodic table, along with size and coordination number. (JN)

Trust in School Principals: Teachers' Opinions

ERIC Educational Resources Information Center

Balyer, Aydin

2017-01-01

Trust is considered as one of the essential elements at schools. Although it is important, there is relatively little research on trust in educational settings. Research indicate that trust across school affects much of a school's functioning and it is a critical resource as principals embark on improvement plans. In this regard, it is a matter of…

Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers.

PubMed

Rahimi, Amir; Madadkar-Sobhani, Armin; Touserkani, Rouzbeh; Goliaei, Bahram

2013-11-07

Due to the increasing number of protein structures with unknown function originated from structural genomics projects, protein function prediction has become an important subject in bioinformatics. Among diverse function prediction methods, exploring known 3D-motifs, which are associated with functional elements in unknown protein structures is one of the most biologically meaningful methods. Homologous enzymes inherit such motifs in their active sites from common ancestors. However, slight differences in the properties of these motifs, results in variation in the reactions and substrates of the enzymes. In this study, we examined the possibility of discriminating highly related active site patterns according to their EC-numbers by 3D-motifs. For each EC-number, the spatial arrangement of an active site, which has minimum average distance to other active sites with the same function, was selected as a representative 3D-motif. In order to characterize the motifs, various points in active site elements were tested. The results demonstrated the possibility of predicting full EC-number of enzymes by 3D-motifs. However, the discriminating power of 3D-motifs varies among different enzyme families and depends on selecting the appropriate points and features. © 2013 Elsevier Ltd. All rights reserved.

Terminological aspects of data elements

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

Strehlow, R.A.; Kenworthey, W.H. Jr.; Schuldt, R.E.

1991-01-01

The creation and display of data comprise a process that involves a sequence of steps requiring both semantic and systems analysis. An essential early step in this process is the choice, definition, and naming of data element concepts and is followed by the specification of other needed data element concept attributes. The attributes and the values of data element concept remain associated with them from their birth as a concept to a generic data element that serves as a template for final application. Terminology is, therefore, centrally important to the entire data creation process. Smooth mapping from natural language tomore » a database is a critical aspect of database, and consequently, it requires terminology standardization from the outset of database work. In this paper the semantic aspects of data elements are analyzed and discussed. Seven kinds of data element concept information are considered and those that require terminological development and standardization are identified. The four terminological components of a data element are the hierarchical type of a concept, functional dependencies, schematas showing conceptual structures, and definition statements. These constitute the conventional role of terminology in database design. 12 refs., 8 figs., 1 tab.« less

Isolation, characterization and expression analysis of the BABY BOOM (BBM) gene from Larix kaempferi × L. olgensis during adventitious rooting.

PubMed

Li, Kui-Peng; Sun, Xiao-Mei; Han, Hua; Zhang, Shou-Gong

2014-11-10

The full-length cDNA and genomic sequences of the BABY BOOM (BBM) gene, designated LkBBM, were isolated from Larix kaempferi × Larix olgensis. The 3324 bp cDNA was cloned and its open reading frame (ORF) consists of 2370 nucleotides. The deduced 789 amino acid protein contains two AP2 domains and a BBM specific motif. Four conserved motifs between BBM and PLT were identified, which may be conducive to the similar function of BBM and PLT. The three dimensional (3D) structure of LkBBM was predicted and β-sheets in the AP2-R2 domain of LkBBM might recognize the specific base pairs in the major groove. Analysis of the LkBBM gene structure indicates that the gene has eight introns and nine exons. In the 5'-flanking promoter region of LkBBM, many important potential cis-acting elements were identified, such as the TATABOX5 element (a functional TATA element), ROOTMOTIFTAPOX1 element (element of root specificity), AUXREPSIAA4 element (element involved in auxin responsiveness and gene expression in root meristem), MYB1AT element (element involved in MYB recognition), ARR1AT element (element involved in cytokinin responsiveness), GARE1OSREP1 element (element involved in gibberellin responsiveness) and PYRIMIDINEBOXHVEPB1 element (element involved in abscisic acid responsiveness), which all suggested that the expression of LkBBM is highly regulated. Compared with gene expression levels in the stem, stem tip and leaf, LkBBM shows a specific expression in the root, which indicates that LkBBM plays a key role in regulating the development and growth of root in larch. In the processing of larch adventitious root formation, LkBBM started to express on the eighth day after rooting treatment and its transcript level increased continuously afterwards. According to the gene characteristics, LkBBM is proposed as a molecular marker for root primordia of larch, and the initial period of LkBBM expression may be the formation period of root primordia in the processing of adventitious rooting of larch. Copyright © 2014 Elsevier B.V. All rights reserved.

The Financial Sector and Sustainable Development

NASA Astrophysics Data System (ADS)

Rusko, Miroslav; Korauš, Anton

2010-01-01

Growing load and deterioration of the environment can be interpreted as a result of some external effects interventions. While the positive externalities influence the positive productional and utilizational functions of other subjects, the negative externalities influence the negative ones. Both types of external effects can act as parcial or global externalities. Linking the environmental issues to economy and finance is an important sphere. Coimplementation of both marketing and environmental audits is an important element of this sphere too.

Investigation of proton induced reactions on niobium at low and medium energies

NASA Astrophysics Data System (ADS)

Ditrói, F.; Hermanne, A.; Corniani, E.; Takács, S.; Tárkányi, F.; Csikai, J.; Shubin, Yu. N.

2009-10-01

Niobium is a metal with important technological applications: use as alloying element to increase strength of super alloys, as thin layer for tribological applications, as superconductive material, in high temperature engineering systems, etc. In the frame of a systematic study of activation cross-sections of charged particle induced reactions on structural materials proton induced excitation functions on Nb targets were determined with the aim of applications in accelerator and reactor technology and for thin layer activation (TLA). The charged particle activation cross-sections on this element are also important for yield calculation of medical isotope production ( 88,89Zr, 86,87,88Y) and for dose estimation in PET targetry. As niobium is a monoisotopic element it is an ideal target material to test nuclear reaction theories. We present here the experimental excitation functions of 93Nb(p,x) 90,93mMo, 92m,91m,90Nb, 88,89Zr and 88Y in the energy range 0-37 MeV. The results were compared with the theoretical cross-sections calculated by means of the code ALICE-IPPE, EMPIRE-3, TALYS and with the literature data. The theory reproduces the shape of the measured results well and magnitude is also acceptable. Thick target yields calculated from our fitted cross-section give reliable estimations for production of medically relevant radioisotopes and for dose estimation in accelerator technology.

Fetal cerebrovascular acclimatization responses to high-altitude, long-term hypoxia: a model for prenatal programming of adult disease?

PubMed

Longo, Lawrence D; Pearce, William J

2005-01-01

During the past several decades, many risk factors for cerebrovascular and cardiovascular disease have been identified. More recently, it has been appreciated that inadequate nutrition and/or other intrauterine factors during fetal development may play an important role in the genesis of these conditions. An additional stress factor that may "program" the fetus for disease later in life is chronic hypoxia. In studies originally designed to examine the function of developing cerebral arterial function in response to long-term hypoxia (LTH), it has become clear that many cellular and subcellular changes may have important implications for later life. Here we review some of the significant alterations in fetal cerebral artery structure and function induced by high-altitude (3,820 m, 12,470 ft) LTH ( approximately 110 days). LTH is associated with augmentation or upregulation of presynaptic functions, including responses to perivascular (i.e., sympathetic) nerve stimulation, and structural maturational changes. In contrast, many postsynaptic functions related to the Ca(2+)-dependent contractile pathway tend to be downregulated, whereas elements of the Ca(2+)-independent contraction pathway are upregulated. The results emphasize the role of high-altitude LTH in modulating many aspects of electromechanical and pharmacomechanical coupling in the developing cerebral vasculature. A complicating factor is that the regulation of cerebrovascular tone by Ca(2+)-dependent and Ca(2+)-independent pathways changes significantly as a function of maturational age. In addition to highlighting independent regulation of various elements of the signal transduction cascade, the studies demonstrate the potential for LTH to program the fetus for cerebrovascular and other disease as an adult.

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems

PubMed Central

Burmistrz, Michał; Dudek, Bartosz; Staniec, Dominika; Rodriguez Martinez, Jose Ignacio; Bochtler, Matthias; Potempa, Jan

2015-01-01

ABSTRACT The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and transposons. It is present in the majority of Archaea and almost half of species of Bacteria. Porphyromonas gingivalis is an important human pathogen that has been proven to be an etiological agent of periodontitis and has been linked to systemic conditions, such as rheumatoid arthritis and cardiovascular disease. At least 95% of clinical strains of P. gingivalis carry CRISPR arrays, suggesting that these arrays play an important function in vivo. Here we show that all four CRISPR arrays present in the P. gingivalis W83 genome are transcribed. For one of the arrays, we demonstrate in vivo activity against double-stranded DNA constructs containing protospacer sequences accompanied at the 3′ end by an NGG protospacer-adjacent motif (PAM). Most of the 44 spacers present in the genome of P. gingivalis W83 share no significant similarity with any known sequences, although 4 spacers are similar to sequences from bacteria found in the oral cavity and the gastrointestinal tract. Four spacers match genomic sequences of the host; however, none of these is flanked at its 3′ terminus by the appropriate PAM element. IMPORTANCE The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression. PMID:26013482

Targeting and assembly of components of the TOC protein import complex at the chloroplast outer envelope membrane

PubMed Central

Richardson, Lynn G. L.; Paila, Yamuna D.; Siman, Steven R.; Chen, Yi; Smith, Matthew D.; Schnell, Danny J.

2014-01-01

The translocon at the outer envelope membrane of chloroplasts (TOC) initiates the import of thousands of nuclear encoded preproteins required for chloroplast biogenesis and function. The multimeric TOC complex contains two GTP-regulated receptors, Toc34 and Toc159, which recognize the transit peptides of preproteins and initiate protein import through a β–barrel membrane channel, Toc75. Different isoforms of Toc34 and Toc159 assemble with Toc75 to form structurally and functionally diverse translocons, and the composition and levels of TOC translocons is required for the import of specific subsets of coordinately expressed proteins during plant growth and development. Consequently, the proper assembly of the TOC complexes is key to ensuring organelle homeostasis. This review will focus on our current knowledge of the targeting and assembly of TOC components to form functional translocons at the outer membrane. Our analyses reveal that the targeting of TOC components involves elements common to the targeting of other outer membrane proteins, but also include unique features that appear to have evolved to specifically facilitate assembly of the import apparatus. PMID:24966864

Targeting and assembly of components of the TOC protein import complex at the chloroplast outer envelope membrane.

PubMed

Richardson, Lynn G L; Paila, Yamuna D; Siman, Steven R; Chen, Yi; Smith, Matthew D; Schnell, Danny J

2014-01-01

The translocon at the outer envelope membrane of chloroplasts (TOC) initiates the import of thousands of nuclear encoded preproteins required for chloroplast biogenesis and function. The multimeric TOC complex contains two GTP-regulated receptors, Toc34 and Toc159, which recognize the transit peptides of preproteins and initiate protein import through a β-barrel membrane channel, Toc75. Different isoforms of Toc34 and Toc159 assemble with Toc75 to form structurally and functionally diverse translocons, and the composition and levels of TOC translocons is required for the import of specific subsets of coordinately expressed proteins during plant growth and development. Consequently, the proper assembly of the TOC complexes is key to ensuring organelle homeostasis. This review will focus on our current knowledge of the targeting and assembly of TOC components to form functional translocons at the outer membrane. Our analyses reveal that the targeting of TOC components involves elements common to the targeting of other outer membrane proteins, but also include unique features that appear to have evolved to specifically facilitate assembly of the import apparatus.

Contributions of individual domains to function of the HIV-1 Rev response element.

PubMed

O'Carroll, Ina P; Thappeta, Yashna; Fan, Lixin; Ramirez-Valdez, Edric A; Smith, Sean; Wang, Yun-Xing; Rein, Alan

2017-08-16

The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an "A" shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using SAXS and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other. IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev Response Element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is "A"-shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains, and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function. Copyright © 2017 American Society for Microbiology.

Contributions of Individual Domains to Function of the HIV-1 Rev Response Element

PubMed Central

O'Carroll, Ina P.; Thappeta, Yashna; Fan, Lixin; Ramirez-Valdez, Edric A.; Smith, Sean; Wang, Yun-Xing

2017-01-01

ABSTRACT The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an “A” shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using small-angle X-ray scattering (SAXS) and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other. IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev response element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is “A” shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function. PMID:28814520

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

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

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE PAGES

Deng, Junjing; Vine, David J.; Chen, Si; ...

2015-02-24

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

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

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and similar to 90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.« less

Important factors of perceiving and memorizing the city during the process of vehicle and pedestrian traffic

NASA Astrophysics Data System (ADS)

Alihodžić, Rifat; Butyrin, Andrey; Makhov, Dmitry

2017-10-01

Moving within the city, both by vehicle and pedestrian, is a prerequisite of creating visual sequences. A variety of factors should be taken into consideration when planning cities, not only of functional nature, but also of the aesthetic one. A particular problem lies in complex cities having a compound identification matrix as a consequence of a boisterous development during long period of time. Considering that the city follows the needs of its user, inevitably moving along it, one of the most important factors required is easy orientation in the complex urban area. Some research has been carried out on the condition of easy orientation and moving in the city, and on appearance of urban elements that provide remembering of the city. This work deals with defining important factors effecting perceiving and memorizing, by inhabitants and also of those visiting it for the first time, regardless they are walking or using a vehicle. Physical structures, topography and a climate and a range of other elements are implied to create a clear idea of some urban area. Many elements were considered - not only being of fixed nature (streets, squares, topography and morphology), but also elements that make the essence of the urban image - elements that can also be some specific public transportation means, such as double-deckers in London, bicycles in Amsterdam or Beijing or gondolas in Venice. The purpose of this work is to notice the rules helping the urban planning process and contribute to reading and memorizing the image of the city.

Heme oxygenase/carbon monoxide in the female reproductive system: an overlooked signalling pathway

PubMed Central

Němeček, David; Dvořáková, Markéta; Sedmíková, Markéta

2017-01-01

For a long time, carbon monoxide (CO) was known for its toxic effect on organisms. But there are still many things left to discover on that molecule. CO is formed directly in the body by the enzymatic activity of heme oxygenase (HO). CO plays an important role in many physiological processes, such as cell protections (against various stress factors), and the regulation of metabolic processes. Recent research proves that CO also operates in the female reproductive system. At the centre of interest is the importance of CO for gestation. During the gestation period, CO is an important element affecting the proper function of the feto-placental unit and generally affects fetal survivability rates. Gestation is one of the most important processes of successful reproduction, although there are more relevant processes that need to be researched. While already proven that CO influences steroidogenesis and the corpus luteum survivability rate, our knowledge concerning the function and importance of CO in the reproductive system is still relatively limited. As an example, our knowledge of CO function in an oocyte, the most important cell for reproduction, is almost non-existent. The aim of this review is to summarize our current knowledge concerning the function of CO in the female reproductive system. PMID:28123837

French Cooperative Passive Payload (FRECOPA)

NASA Technical Reports Server (NTRS)

Durin, Christian

1992-01-01

The fact that the LDEF satellite mission was extended resulted in a study of FRECOPA system elements. These tests were run on materials, electronics, wiring, and motor drives. It is worthwhile studying these elements as they have been exposed to the low earth orbit for nearly six years, whereas the experimental specimens were exposed for ten months. No functional damage was observed which was induced by impacts or erosion. A decrease in thermal, optical, and mechanical properties for DELRIN and teflon glass fabric induced by erosion and thermal environment was observed. The most important damage parameters are UV radiation and thermal cycling.

NETWORK SYNTHESIS OF CASCADED THRESHOLD ELEMENTS.

DTIC Science & Technology

A threshold function is a switching function which can be stimulated by a single, simplified, idealized neuron, or threshold element. In this report... threshold functions are examined in the context of abstract set theory and linear algebra for the purpose of obtaining practical synthesis procedures...for networks of threshold elements. A procedure is described by which, for any given switching function, a cascade network of these elements can be

[Introduction of Functional Foods--Types, Manufacturing Methods and Quality Assurance].

PubMed

Budai, Kinga Anna; Hankó, Balázs; AntalL, István; Zelkó, Romána

2015-01-01

Because of the beneficial effects to health functional foods are important elements of health promotion. The positive effect of the functional components should be based on scientific evidence-based. In addition to the traditional food processing technology new technologies have appeared, e.g. microencapsulation, edible coatings and orodispersible films, nano-technology, vacuum impregnation. In the present study, probiotics and the structure, the production and the impact of prebiotic functional cereals are discussed in more detail. In addition to their numerous advantages in connection with the safe application, several questions arise because of inadequate quality control measures prior to coming onto the market.

Loss of astrocyte cholesterol synthesis disrupts neuronal function and alters whole-body metabolism.

PubMed

Ferris, Heather A; Perry, Rachel J; Moreira, Gabriela V; Shulman, Gerald I; Horton, Jay D; Kahn, C Ronald

2017-01-31

Cholesterol is important for normal brain function. The brain synthesizes its own cholesterol, presumably in astrocytes. We have previously shown that diabetes results in decreased brain cholesterol synthesis by a reduction in sterol regulatory element-binding protein 2 (SREBP2)-regulated transcription. Here we show that coculture of control astrocytes with neurons enhances neurite outgrowth, and this is reduced with SREBP2 knockdown astrocytes. In vivo, mice with knockout of SREBP2 in astrocytes have impaired brain development and behavioral and motor defects. These mice also have altered energy balance, altered body composition, and a shift in metabolism toward carbohydrate oxidation driven by increased glucose oxidation by the brain. Thus, SREBP2-mediated cholesterol synthesis in astrocytes plays an important role in brain and neuronal development and function, and altered brain cholesterol synthesis may contribute to the interaction between metabolic diseases, such as diabetes and altered brain function.

Loss of astrocyte cholesterol synthesis disrupts neuronal function and alters whole-body metabolism

PubMed Central

Ferris, Heather A.; Perry, Rachel J.; Moreira, Gabriela V.; Shulman, Gerald I.; Horton, Jay D.; Kahn, C. Ronald

2017-01-01

Cholesterol is important for normal brain function. The brain synthesizes its own cholesterol, presumably in astrocytes. We have previously shown that diabetes results in decreased brain cholesterol synthesis by a reduction in sterol regulatory element-binding protein 2 (SREBP2)-regulated transcription. Here we show that coculture of control astrocytes with neurons enhances neurite outgrowth, and this is reduced with SREBP2 knockdown astrocytes. In vivo, mice with knockout of SREBP2 in astrocytes have impaired brain development and behavioral and motor defects. These mice also have altered energy balance, altered body composition, and a shift in metabolism toward carbohydrate oxidation driven by increased glucose oxidation by the brain. Thus, SREBP2-mediated cholesterol synthesis in astrocytes plays an important role in brain and neuronal development and function, and altered brain cholesterol synthesis may contribute to the interaction between metabolic diseases, such as diabetes and altered brain function. PMID:28096339

Synergistic effect of alloying elements doping and external pressure on the elastic property of Ni{sub 3}Al: A first-principles study

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

Li, C., E-mail: lichun@nwpu.edu.cn; Shang, J.; Yue, Z.

2015-07-15

In this paper, the basic electronic structures and elastic properties of Ni{sub 3}Al doping with alloying elements (Re, Cr, and Mo) under different pressures have been investigated using first-principles calculations based on density functional theory. It is shown that both alloying elements and external applied pressure contribute positively to the elastic properties of Ni{sub 3}Al, and the configurations of the compounds remain almost unchanged. The calculated elastic constants and moduli increase linearly with the pressure increasing from 0 and 40 GPa. Among the alloying elements studied in the present work, Re exhibits the most significant effect compared with the othermore » elements, showing its practical importance. Especially, if both alloying elements doping and pressure effects are considered simultaneously, which has not been considered previously, the studied compounds exhibit an even better elastic property than the simple superposition of the two influences. Such synergistic effect demonstrates promising applications of Ni-based single crystal superalloys in possible extreme mechanical environments.« less

Compilation of 1987 Annual Reports of the Navy ELF (Extremely Low Frequency) Communications System Ecological Monitoring Program. Volume 1

DTIC Science & Technology

1988-08-01

was used to: 1) develop functions using species importance values from pretreatment years (1985 and 1986) and 2) determine if discriminant functions...degrade lignocellulose . L -7- During 1988, this work element will focus on two objec- tives: 1) obtaining the first year’s data on streptomycete...cellulose, and lignin/ lignocellulose in both coniferous and deci- duous litter systems (Graustein gt &. 1977, Crawford 1978, Knut- son &I jL. 1980

Experts' opinions on the management of medically unexplained symptoms in primary care. A qualitative analysis of narrative reviews and scientific editorials.

PubMed

Heijmans, Mieke; Olde Hartman, Tim C; van Weel-Baumgarten, Evelyn; Dowrick, Christopher; Lucassen, Peter L B J; van Weel, Chris

2011-08-01

The feasibility as well as the suitability of several therapies for medically unexplained symptoms (MUS) in primary care applied by the family physician (FP) appeared to be low. FPs need effective and acceptable strategies to manage these functionally impaired patients. To review important and effective elements in the treatment of patients with MUS in primary care according to experts in MUS research. We performed a systematic search of narrative reviews and scientific editorials in Medline and PsycINFO and triangulated our findings by conducting a focus group with MUS experts. We included 7 scientific editorials and 23 narrative reviews. According to MUS experts, the most important elements in the treatment of MUS are creating a safe therapeutic environment, generic interventions (such as motivational interviewing, giving tangible explanations, reassurance and regularly scheduled appointments) and specific interventions (such as cognitive approaches and pharmacotherapy). Furthermore, MUS experts indicate that a multi-component approach in which these three important elements are combined are most helpful for patients with MUS. In contrast to most specific interventions, opinions of MUS experts regarding generic interventions and creating a safe therapeutic relationship seem to be more based on theory and experience than on quantitative research. MUS experts highlight the importance of generic interventions and doctor-patient communication and relationship. However, studies showing the effectiveness of these elements in the management of MUS in primary care is still scarce. Research as well as medical practice should focus more on these non-specific aspects of the medical consultation.

Multi-scale finite element modeling of Eustachian tube function: influence of mucosal adhesion.

PubMed

Malik, J E; Swarts, J D; Ghadiali, S N

2016-12-01

The inability to open the collapsible Eustachian tube (ET) leads to the development of chronic Otitis Media (OM). Although mucosal inflammation during OM leads to increased mucin gene expression and elevated adhesion forces within the ET lumen, it is not known how changes in mucosal adhesion alter the biomechanical mechanisms of ET function. In this study, we developed a novel multi-scale finite element model of ET function in adults that utilizes adhesion spring elements to simulate changes in mucosal adhesion. Models were created for six adult subjects, and dynamic patterns in muscle contraction were used to simulate the wave-like opening of the ET that occurs during swallowing. Results indicate that ET opening is highly sensitive to the level of mucosal adhesion and that exceeding a critical value of adhesion leads to rapid ET dysfunction. Parameter variation studies and sensitivity analysis indicate that increased mucosal adhesion alters the relative importance of several tissue biomechanical properties. For example, increases in mucosal adhesion reduced the sensitivity of ET function to tensor veli palatini muscle forces but did not alter the insensitivity of ET function to levator veli palatini muscle forces. Interestingly, although changes in cartilage stiffness did not significantly influence ET opening under low adhesion conditions, ET opening was highly sensitive to changes in cartilage stiffness under high adhesion conditions. Therefore, our multi-scale computational models indicate that changes in mucosal adhesion as would occur during inflammatory OM alter the biomechanical mechanisms of ET function. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Design Through Manufacturing: The Solid Model-Finite Element Analysis Interface

NASA Technical Reports Server (NTRS)

Rubin, Carol

2002-01-01

State-of-the-art computer aided design (CAD) presently affords engineers the opportunity to create solid models of machine parts reflecting every detail of the finished product. Ideally, in the aerospace industry, these models should fulfill two very important functions: (1) provide numerical. control information for automated manufacturing of precision parts, and (2) enable analysts to easily evaluate the stress levels (using finite element analysis - FEA) for all structurally significant parts used in aircraft and space vehicles. Today's state-of-the-art CAD programs perform function (1) very well, providing an excellent model for precision manufacturing. But they do not provide a straightforward and simple means of automating the translation from CAD to FEA models, especially for aircraft-type structures. Presently, the process of preparing CAD models for FEA consumes a great deal of the analyst's time.

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

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

Konopka, Allan

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbesmore » possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered a community property.« less

Functional Data Approximation on Bounded Domains using Polygonal Finite Elements.

PubMed

Cao, Juan; Xiao, Yanyang; Chen, Zhonggui; Wang, Wenping; Bajaj, Chandrajit

2018-07-01

We construct and analyze piecewise approximations of functional data on arbitrary 2D bounded domains using generalized barycentric finite elements, and particularly quadratic serendipity elements for planar polygons. We compare approximation qualities (precision/convergence) of these partition-of-unity finite elements through numerical experiments, using Wachspress coordinates, natural neighbor coordinates, Poisson coordinates, mean value coordinates, and quadratic serendipity bases over polygonal meshes on the domain. For a convex n -sided polygon, the quadratic serendipity elements have 2 n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, rather than the usual n ( n + 1)/2 basis functions to achieve quadratic convergence. Two greedy algorithms are proposed to generate Voronoi meshes for adaptive functional/scattered data approximations. Experimental results show space/accuracy advantages for these quadratic serendipity finite elements on polygonal domains versus traditional finite elements over simplicial meshes. Polygonal meshes and parameter coefficients of the quadratic serendipity finite elements obtained by our greedy algorithms can be further refined using an L 2 -optimization to improve the piecewise functional approximation. We conduct several experiments to demonstrate the efficacy of our algorithm for modeling features/discontinuities in functional data/image approximation.

BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements.

PubMed

Bhagwat, Anand S; Roe, Jae-Seok; Mok, Beverly Y L; Hohmann, Anja F; Shi, Junwei; Vakoc, Christopher R

2016-04-19

The bromodomain and extraterminal (BET) protein BRD4 can physically interact with the Mediator complex, but the relevance of this association to the therapeutic effects of BET inhibitors in cancer is unclear. Here, we show that BET inhibition causes a rapid release of Mediator from a subset of cis-regulatory elements in the genome of acute myeloid leukemia (AML) cells. These sites of Mediator eviction were highly correlated with transcriptional suppression of neighboring genes, which are enriched for targets of the transcription factor MYB and for functions related to leukemogenesis. A shRNA screen of Mediator in AML cells identified the MED12, MED13, MED23, and MED24 subunits as performing a similar regulatory function to BRD4 in this context, including a shared role in sustaining a block in myeloid maturation. These findings suggest that the interaction between BRD4 and Mediator has functional importance for gene-specific transcriptional activation and for AML maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Exploring the Reduction of Fuel Consumption for Ship-to-Shore Connectors of the Marine Expeditionary Brigade

DTIC Science & Technology

2013-12-01

include the Command Element (CE), the Aviation Combat Element (ACE), the Ground Combat Element ( GCE ), and the Combat Service Support Element (CSSE) (from...35 Figure 9. The upper level functional architecture for EW12 shows the three primary functions of F1-Assemble the Seabase, F2...Function F2-Perform Assault is decomposed to obtain the lower level specific functions. From this decomposition, the sub-function of F2.2- Gain Entry

Discrimination of lichen genera and species using element concentrations

USGS Publications Warehouse

Bennett, James P.

2008-01-01

The importance of organic chemistry in the classification of lichens is well established, but inorganic chemistry has been largely overlooked. Six lichen species were studied over a period of 23 years that were growing in 11 protected areas of the northern Great Lakes ecoregion, which were not greatly influenced by anthropogenic particulates or gaseous air pollutants. The elemental data from these studies were aggregated in order to test the hypothesis that differences among species in tissue element concentrations were large enough to discriminate between taxa faithfully. Concentrations of 16 chemical elements that were found in tissue samples from Cladonia rangiferina, Evernia mesomorpha, Flavopunctelia flaventior, Hypogymnia physodes, Parmelia sulcata, and Punctelia rudecta were analyzed statistically using multivariate discriminant functions and CART analyses, as well as t-tests. Genera and species were clearly separated in element space, and elemental discriminant functions were able to classify 91-100 of the samples correctly into species. At the broadest level, a Zn concentration of 51 ppm in tissues of four of the lichen species effectively discriminated foliose from fruticose species. Similarly, a S concentration of 680 ppm discriminated C. rangiferina and E. mesomorpha, and a Ca concentration of 10 436 ppm discriminated H. physodes from P. sulcata. For the three parmelioid species, a Ca concentration >32 837 ppm discriminated Punctelia rudecta from the other two species, while a Zn concentration of 56 ppm discriminated Parmelia sulcata from F. flaventior. Foliose species also had higher concentrations than did fruticose species of all elements except Na. Elemental signatures for each of the six species were developed using standardized means. Twenty-four mechanisms explaining the differences among species are summarized. Finally, the relationships of four species based on element concentrations, using additive-trees clustering of a Euclidean-distance matrix, produced identical relationships as did analyses based on secondary product chemistry that used additive-trees clustering of a Jaccard similarity matrix. At least for these six species, element composition has taxonomic significance, and may be useful for discriminating other taxa.

Iodized salt sales in the United States.

PubMed

Maalouf, Joyce; Barron, Jessica; Gunn, Janelle P; Yuan, Keming; Perrine, Cria G; Cogswell, Mary E

2015-03-10

Iodized salt has been an important source of dietary iodine, a trace element important for regulating human growth, development, and metabolic functions. This analysis identified iodized table salt sales as a percentage of retail salt sales using Nielsen ScanTrack. We identified 1117 salt products, including 701 salt blends and 416 other salt products, 57 of which were iodized. When weighted by sales volume in ounces or per item, 53% contained iodized salt. These findings may provide a baseline for future monitoring of sales of iodized salt.

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

PubMed Central

Marreiros, Bruno C.; Sena, Filipa V.; Sousa, Filipe M.; Oliveira, A. Sofia F.; Soares, Cláudio M.; Batista, Ana P.; Pereira, Manuela M.

2017-01-01

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains. These proteins contribute indirectly to the establishment of the transmembrane difference of electrochemical potential by catalyzing the reduction of quinone by oxidation of NAD(P)H. NDH-2s are widespread enzymes being present in the three domains of life. In this work, we explored the catalytic mechanism of NDH-2 by investigating the common elements of all NDH-2s, based on the rationale that conservation of such elements reflects their structural/functional importance. We observed conserved sequence motifs and structural elements among 1762 NDH-2s. We identified two proton pathways possibly involved in the protonation of the quinone. Our results led us to propose the first catalytic mechanism for NDH-2 family, in which a conserved glutamate residue, E172 (in NDH-2 from Staphylococcus aureus) plays a key role in proton transfer to the quinone pocket. This catalytic mechanism may also be extended to the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, such as sulfide:quinone oxidoreductases. PMID:28181562

A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

PubMed Central

McMurchy, Alicia N; Stempor, Przemyslaw; Gaarenstroom, Tessa; Wysolmerski, Brian; Dong, Yan; Aussianikava, Darya; Appert, Alex; Huang, Ni; Kolasinska-Zwierz, Paulina; Sapetschnig, Alexandra; Miska, Eric A; Ahringer, Julie

2017-01-01

Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways. Remarkably, fertility of heterochromatin mutants could be partially restored by inhibiting cep-1/p53, endogenous meiotic double strand breaks, or the expression of MIRAGE1 DNA transposons. Functional redundancy among factors and pathways underlies the importance of safeguarding the genome through multiple means. DOI: http://dx.doi.org/10.7554/eLife.21666.001 PMID:28294943

Persuasibility--A Reception-yielding Process: A Nonmonotonic Theory of Man's Reception Distortion Behaviors as a Function of Environmental Fluctuations.

ERIC Educational Resources Information Center

Crawford, John E.; Reinard, John C., Jr.

Three environmental elements--messages, events, and perceived consequences of choices--cause varying amounts of stress on an individual and affect his capacity to deal with his environment. There is a nonmonotonic relationship between environmental pressures ("event press") and persuasibility in that the number and importance of…

Problematic Internet Use, Loneliness and Dating Anxiety among Young Adult University Students

ERIC Educational Resources Information Center

Odaci, Hatice; Kalkan, Melek

2010-01-01

The Internet, an important modern means of obtaining information and establishing communication with others, has become an increasingly essential element of human life. Although Internet use makes life easier, it can become problematic in the event of non-functional use. Debate and research into whether Internet addiction is a cause or an effect…

The Effect of Hidden Curriculum on Character Education Process of Primary School Students

ERIC Educational Resources Information Center

Cubukcu, Zuhal

2012-01-01

Character education is defined as a planned and systematical approach in terms of self- respect, responsibility and honesty etc. for being a good citizen. The elements of hidden curriculum possessed in schools are values, beliefs, attitudes, and norms and values which are important parts of school function, ceremonies and the quality of…

A Worthy Function for Music in Education

ERIC Educational Resources Information Center

Walker, Robert

2005-01-01

The evidence from many sources is unambiguous in that music is one of the most important elements in the life of all humans. Most people listen to music as opposed to performing music. Although there are societies where everyone participates in singing and dancing, music is mostly performed by a small elite often for the pleasure and enjoyment of…

Spatial and Temporal Episodic Memory Retrieval Recruit Dissociable Functional Networks in the Human Brain

ERIC Educational Resources Information Center

Ekstrom, Arne D.; Bookheimer, Susan Y.

2007-01-01

Imaging, electrophysiological studies, and lesion work have shown that the medial temporal lobe (MTL) is important for episodic memory; however, it is unclear whether different MTL regions support the spatial, temporal, and item elements of episodic memory. In this study we used fMRI to examine retrieval performance emphasizing different aspects…

Lightweight In-Plane Actuated Deformable Mirrors for Space Telescopes

DTIC Science & Technology

2006-09-01

dimensional beam-string and axisymmetric plate-membrane. The beam-string (a clamped beam simultaneously under an axial load ) is an important...Tensile load versus radius. . . . . . . . . . . . . . . . . . . . . . 175 7.4. Actuation voltage functions. . . . . . . . . . . . . . . . . . . . 179...membrane Asymptotic finite element Flint and De- noyer [45] 2003 In-plane Circular membrane Numerical least squares fit Actuators modelled as line loads

Divergent Task Performance in Older Adults: Declarative Memory or Creative Potential?

ERIC Educational Resources Information Center

Leon, Susan A.; Altmann, Lori J. P.; Abrams, Lise; Gonzalez Rothi, Leslie J.; Heilman, Kenneth M.

2014-01-01

Divergent thinking is a process or method used to generate creative ideas by exploring many possible solutions or responses, and is a critical element of creativity. Lesion and imaging studies have shown that the frontal lobes are important in mediating divergent thinking, and frontal lobe function is highly dependent on white matter connections…

Enhanced Deployment Strategy for Role-Based Hierarchical Application Agents in Wireless Sensor Networks with Established Clusterheads

ERIC Educational Resources Information Center

Gendreau, Audrey

2014-01-01

Efficient self-organizing virtual clusterheads that supervise data collection based on their wireless connectivity, risk, and overhead costs, are an important element of Wireless Sensor Networks (WSNs). This function is especially critical during deployment when system resources are allocated to a subsequent application. In the presented research,…

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Diffractometric measurement of the temperature dependence of piezoelectric tensor in GMO monocrystal

NASA Astrophysics Data System (ADS)

Breczko, Teodor; Lempaszek, Andrzej

2007-04-01

Functional materials, of which an example is ferroelectric, ferroelastic monocrystal of molybdate (III) gadolinium (VI), are often used in the micro-motor operators (micro-servo motors) working in changeable environment conditions. Most frequently this change refers to temperature. That is why the important practical problem is the precise measurement of the value of piezoelectric tensor elements in dependence on the temperature of a particular monocrystal. In the presented article for this kind of measurements, the use of X-ray diffractometer has been shown. The advantage of the method presented is that, apart from precise dependence measurement between the temperature of a monocrystal and the value of piezoelectric tensor elements, it enables synchronous measurement of the value of thermal expansion tensor elements for a monocrystal.

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

PubMed Central

Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

2015-01-01

Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

A novel VLSI processor architecture for supercomputing arrays

NASA Technical Reports Server (NTRS)

Venkateswaran, N.; Pattabiraman, S.; Devanathan, R.; Ahmed, Ashaf; Venkataraman, S.; Ganesh, N.

1993-01-01

Design of the processor element for general purpose massively parallel supercomputing arrays is highly complex and cost ineffective. To overcome this, the architecture and organization of the functional units of the processor element should be such as to suit the diverse computational structures and simplify mapping of complex communication structures of different classes of algorithms. This demands that the computation and communication structures of different class of algorithms be unified. While unifying the different communication structures is a difficult process, analysis of a wide class of algorithms reveals that their computation structures can be expressed in terms of basic IP,IP,OP,CM,R,SM, and MAA operations. The execution of these operations is unified on the PAcube macro-cell array. Based on this PAcube macro-cell array, we present a novel processor element called the GIPOP processor, which has dedicated functional units to perform the above operations. The architecture and organization of these functional units are such to satisfy the two important criteria mentioned above. The structure of the macro-cell and the unification process has led to a very regular and simpler design of the GIPOP processor. The production cost of the GIPOP processor is drastically reduced as it is designed on high performance mask programmable PAcube arrays.

The discriminative stimulus effects of a nicotine-ethanol compound in rats: Extinction with the parts differs from the whole.

PubMed

Troisi, Joseph R; Dooley, Thomas F; Craig, Elizabeth M

2013-12-01

Nicotine and ethyl alcohol (EtOH) interact neurophysiologically and induce internal sensory states that contribute to their coabuse. Evaluating the combined internal sensory effects of nicotine and alcohol may be important for understanding this nexus. With rats, this investigation used an operant drug discrimination procedure to establish discriminative stimulus control with a mixture of nicotine plus EtOH (NE) at doses of nicotine (0.3 mg/kg) and EtOH (1.0 g/kg) that have previously been shown to be equally salient (Gauvin & Holloway, 1993). In Experiment (Exp) 1 the NE compound mixture continued to evoke responding despite extinction of responding with nicotine and EtOH alone. In Exp 2 the NE mixture was reliably discriminated from the nicotine and EtOH elements. Experiment 3 showed that the discriminative functions of the NE mixture emerged when the nicotine and EtOH elements were combined following their initial establishment as separate discriminative stimuli; however, nicotine evoked more control than EtOH. Extinction of responding with the NE mixture impacted rates of responding with nicotine and EtOH alone. The results of the all three studies parallel findings with exteroceptive Pavlovian literature in showing that extinction of responding with the elemental parts does not appear to impact the whole-but, extinction with the whole appears to affect its parts. The multielement discriminative function of a NE mixture appears to be a "unique cue" that differs qualitatively from nicotine or EtOH alone. Associative factors related to compound conditioning (i.e., configural learning) play an important role in mediating the discriminative functions of drug mixtures.

Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements.

PubMed

Schartl, Manfred; Schories, Susanne; Wakamatsu, Yuko; Nagao, Yusuke; Hashimoto, Hisashi; Bertin, Chloé; Mourot, Brigitte; Schmidt, Cornelia; Wilhelm, Dagmar; Centanin, Lazaro; Guiguen, Yann; Herpin, Amaury

2018-01-29

Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network. This rewiring was brought about by the exaptation of a transposable element (TE) called Izanagi, which is co-opted to act as a silencer to turn off the dmrt1bY gene after it performed its function in sex determination. We now show that a second TE, Rex1, has been incorporated into Izanagi. The insertion of Rex1 brought in a preformed regulatory element for the transcription factor Sox5, which here functions in establishing the temporal and cell-type-specific expression pattern of dmrt1bY. Mutant analysis demonstrates the importance of Sox5 in the gonadal development of medaka, and possibly in mice, in a dmrt1bY-independent manner. Moreover, Sox5 medaka mutants have complete female-to-male sex reversal. Our work reveals an unexpected complexity in TE-mediated transcriptional rewiring, with the exaptation of a second TE into a network already rewired by a TE. We also show a dual role for Sox5 during sex determination: first, as an evolutionarily conserved regulator of germ-cell number in medaka, and second, by de novo regulation of dmrt1 transcriptional activity during primary sex determination due to exaptation of the Rex1 transposable element.

Diffusion of Redox-Sensitive Elements in Basalt at Different Oxygen Fugacities

NASA Technical Reports Server (NTRS)

Szumila, I.; Trail, D.; Danielson, L. R.

2017-01-01

The terrestrial planets and moons of our solar system have differentiated over a range of oxygen fugacity conditions. Basalts formed from magmas on the Earth cover a range of more oxidized states (from approximately IW (iron wustite) plus 2 to approximately FMQ (fayalite-magnetite-quartz) plus 3) than crustal rocks from Mars (IW to approximately IW plus 3), and basalts from the Moon are more reduced than both, ranging from IW to IW minus 2. The small body Vesta differentiated around IW minus 4. Characterization of redox sensitive elements' diffusivities will offer insight into behavior of these elements as a function of f (fugacity of) O2 for these planetary bodies. Here, we report a systematic study of the diffusion of redox-sensitive elements in basaltic melts with varying oxygen fugacities (fO2) for trace elements, V, Nb, W, Mo, La, Ce, Pr, Sm, Eu, Gd, Ta, and W. Since fO2 is an intensive variable that is different for the reservoirs of various planets and moons in our solar system, it is important to characterize how changes in redox states will affect diffusion. We conducted experiments in a piston cylinder device at 1300 degrees Centigrade and 1 gigapascal, at the University of Rochester and NASA Johnson Space Center. We buffered some experiments at Ru-RuO2 (FMQ plus 6.00), and conducted other experiments within either a graphite or Mo capsule, which corresponds to fO2s of either FMQ minus1.2, or FMQ minus 3.00, respectively. Characterizing the diffusivities of redox sensitive elements at different fO2s is important because some elements, like Eu, have varying valence states, such as Eu (sup 2 plus) and Eu (sup 3 plus). Differences in charge and ion radii may lead to differences in diffusivities within silicate melts. This could, lead to formation of a Eu anomaly by diffusion, the magnitude of which may be controlled by the fO2. Characterization of trace element diffusion is also important in understanding trace element fractionation. We found, during the course of our investigation, that not only did the diffusivities of the redox sensitive elements change with fO2, but that the diffusivities of all other analyzed elements also changed. This indicates that not only do changes in valence influence trace elements diffusivities but that the structure of melt may have changed with varying oxygen fugacity, probably due to changes in the speciation of the major element Fe.

Lessons on RNA Silencing Mechanisms in Plants from Eukaryotic Argonaute Structures[W

PubMed Central

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed. PMID:23303917

Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures.

PubMed

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed.

Mutational analysis of three predicted 5'-proximal stem-loop structures in the genome of tick-borne encephalitis virus indicates different roles in RNA replication and translation

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

Rouha, Harald; Hoenninger, Verena M.; Thurner, Caroline

2011-08-15

Flavivirus gene expression is modulated by RNA secondary structure elements at the terminal ends of the viral RNA molecule. For tick-borne encephalitis virus (TBEV), four stem-loop (SL) elements have been predicted in the first 180 nucleotides of the viral genome: 5'-SL1, 5'-SL2, 5'-SL3 and 5'-SL4. The last three of these appear to be unique to tick-borne flaviviruses. Here, we report their characterization by mutagenesis in a TBEV luciferase reporter system. By manipulating their thermodynamic properties, we found that an optimal stability of the 5'-SL2 is required for efficient RNA replication. 5'-SL3 formation is also important for viral RNA replication, butmore » although it contains the viral start codon, its formation is dispensable for RNA translation. 5'-SL4 appears to facilitate both RNA translation and replication. Our data suggest that maintenance of the balanced thermodynamic stability of these SL elements is important for temporal regulation of its different functions.« less

In-circuit-measurement of parasitic elements in high gain high bandwidth low noise transimpedance amplifiers.

PubMed

Cochems, P; Kirk, A; Zimmermann, S

2014-12-01

Parasitic elements play an important role in the development of every high performance circuit. In the case of high gain, high bandwidth transimpedance amplifiers, the most important parasitic elements are parasitic capacitances at the input and in the feedback path, which significantly influence the stability, the frequency response, and the noise of the amplifier. As these parasitic capacitances range from a few picofarads down to only a few femtofarads, it is nearly impossible to measure them accurately using traditional LCR meters. Unfortunately, they also cannot be easily determined from the transfer function of the transimpedance amplifier, as it contains several overlapping effects and its measurement is only possible when the circuit is already stable. Therefore, we developed an in-circuit measurement method utilizing minimal modifications to the input stage in order to measure its parasitic capacitances directly and with unconditional stability. Furthermore, using the data acquired with this measurement technique, we both proposed a model for the complicated frequency response of high value thick film resistors as they are used in high gain transimpedance amplifiers and optimized our transimpedance amplifier design.

Path Integral Monte Carlo Simulations of Warm Dense Matter and Plasmas

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

Militzer, Burkhard

2018-01-13

New path integral Monte Carlo simulation (PIMC) techniques will be developed and applied to derive the equation of state (EOS) for the regime of warm dense matter and dense plasmas where existing first-principles methods cannot be applied. While standard density functional theory has been used to accurately predict the structure of many solids and liquids up to temperatures on the order of 10,000 K, this method is not applicable at much higher temperature where electronic excitations become important because the number of partially occupied electronic orbitals reaches intractably large numbers and, more importantly, the use of zero-temperature exchange-correlation functionals introducesmore » an uncontrolled approximation. Here we focus on PIMC methods that become more and more efficient with increasing temperatures and still include all electronic correlation effects. In this approach, electronic excitations increase the efficiency rather than reduce it. While it has commonly been assumed such methods can only be applied to elements without core electrons like hydrogen and helium, we recently showed how to extend PIMC to heavier elements by performing the first PIMC simulations of carbon and water plasmas [Driver, Militzer, Phys. Rev. Lett. 108 (2012) 115502]. Here we propose to continue this important development to extend the reach of PIMC simulations to yet heavier elements and also lower temperatures. The goal is to provide a robust first-principles simulation method that can accurately and efficiently study materials with excited electrons at solid-state densities in order to access parts of the phase diagram such the regime of warm dense matter and plasmas where so far only more approximate, semi-analytical methods could be applied.« less

Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics.

PubMed

Culumber, Zachary W

2014-02-01

The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.

Interaction of root exudates with the mineral soil constituents and their effect on mineral weathering

NASA Astrophysics Data System (ADS)

Mimmo, T.; Terzano, R.; Medici, L.; Lettino, A.; Fiore, S.; Tomasi, N.; Pinton, R.; Cesco, S.

2012-04-01

Plants release significant amounts of high and low molecular weight organic compounds into the rhizosphere. Among these exudates organic acids (e.g. citric acid, malic acid, oxalic acid), phenolic compounds (e.g. flavonoids), amino acids and siderophores of microbial and/or plant origin strongly influence and modify the biogeochemical cycles of several elements, thus causing changes in their availability for plant nutrition. One class of these elements is composed by the trace elements; some of them are essential for plants even if in small concentrations and are considered micronutrients, such as Fe, Zn, Mn. Their solubility and bioavailability can be influenced, among other factors, by the presence in soil solution of low molecular weight root exudates acting as organic complexing agents that can contribute to the mineral weathering and therefore, to their mobilization in the soil solution. The mobilized elements, in function of the element and of its concentration, can be either important nutrients or toxic elements for plants. The objective of this study was to assess the influence of several root exudates (citric acid, malic acid, oxalic acid, genistein, quercetin and siderophores) on the mineralogy of two different soils (an agricultural calcareous soil and an acidic polluted soil) and to evaluate possible synergic or competitive behaviors. X-ray diffraction (XRD) coupled with Electron Probe Micro Analysis (EPMA) was used to identify the crystalline and amorphous phases which were subjected to mineral alteration when exposed to the action of root exudates. Solubilization of trace metals such as Cu, Zn, Ni, Cr, Pb, Cd as well as of major elements such as Si, Al, Fe and Mn was assessed by means of Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Soil microorganisms have proven to decrease mineral weathering by reducing the concentration of active root exudates in solution. Results obtained are an important cornerstone to better understand the biogeochemical processes acting in the rhizosphere which can play an important role in the availability of trace elements (either nutrient or toxic) for plant uptake. Research is supported by MIUR - FIRB "Futuro in ricerca", internal grant of Unibz (TN5031 & TN5046) and the Autonomous Province of Bolzano (Rhizotyr TN5218).

Comparing geological and statistical approaches for element selection in sediment tracing research

NASA Astrophysics Data System (ADS)

Laceby, J. Patrick; McMahon, Joe; Evrard, Olivier; Olley, Jon

2015-04-01

Elevated suspended sediment loads reduce reservoir capacity and significantly increase the cost of operating water treatment infrastructure, making the management of sediment supply to reservoirs of increasingly importance. Sediment fingerprinting techniques can be used to determine the relative contributions of different sources of sediment accumulating in reservoirs. The objective of this research is to compare geological and statistical approaches to element selection for sediment fingerprinting modelling. Time-integrated samplers (n=45) were used to obtain source samples from four major subcatchments flowing into the Baroon Pocket Dam in South East Queensland, Australia. The geochemistry of potential sources were compared to the geochemistry of sediment cores (n=12) sampled in the reservoir. The geochemical approach selected elements for modelling that provided expected, observed and statistical discrimination between sediment sources. Two statistical approaches selected elements for modelling with the Kruskal-Wallis H-test and Discriminatory Function Analysis (DFA). In particular, two different significance levels (0.05 & 0.35) for the DFA were included to investigate the importance of element selection on modelling results. A distribution model determined the relative contributions of different sources to sediment sampled in the Baroon Pocket Dam. Elemental discrimination was expected between one subcatchment (Obi Obi Creek) and the remaining subcatchments (Lexys, Falls and Bridge Creek). Six major elements were expected to provide discrimination. Of these six, only Fe2O3 and SiO2 provided expected, observed and statistical discrimination. Modelling results with this geological approach indicated 36% (+/- 9%) of sediment sampled in the reservoir cores were from mafic-derived sources and 64% (+/- 9%) were from felsic-derived sources. The geological and the first statistical approach (DFA0.05) differed by only 1% (σ 5%) for 5 out of 6 model groupings with only the Lexys Creek modelling results differing significantly (35%). The statistical model with expanded elemental selection (DFA0.35) differed from the geological model by an average of 30% for all 6 models. Elemental selection for sediment fingerprinting therefore has the potential to impact modeling results. Accordingly is important to incorporate both robust geological and statistical approaches when selecting elements for sediment fingerprinting. For the Baroon Pocket Dam, management should focus on reducing the supply of sediments derived from felsic sources in each of the subcatchments.

Integrated command, control, communications and computation system functional architecture

NASA Technical Reports Server (NTRS)

Cooley, C. G.; Gilbert, L. E.

1981-01-01

The functional architecture for an integrated command, control, communications, and computation system applicable to the command and control portion of the NASA End-to-End Data. System is described including the downlink data processing and analysis functions required to support the uplink processes. The functional architecture is composed of four elements: (1) the functional hierarchy which provides the decomposition and allocation of the command and control functions to the system elements; (2) the key system features which summarize the major system capabilities; (3) the operational activity threads which illustrate the interrelationahip between the system elements; and (4) the interfaces which illustrate those elements that originate or generate data and those elements that use the data. The interfaces also provide a description of the data and the data utilization and access techniques.

Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

PubMed Central

Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

2015-01-01

Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state. PMID:26630011

The Overshoot Phenomenon in Geodynamics Codes

NASA Astrophysics Data System (ADS)

Kommu, R. K.; Heien, E. M.; Kellogg, L. H.; Bangerth, W.; Heister, T.; Studley, E. H.

2013-12-01

The overshoot phenomenon is a common occurrence in numerical software when a continuous function on a finite dimensional discretized space is used to approximate a discontinuous jump, in temperature and material concentration, for example. The resulting solution overshoots, and undershoots, the discontinuous jump. Numerical simulations play an extremely important role in mantle convection research. This is both due to the strong temperature and stress dependence of viscosity and also due to the inaccessibility of deep earth. Under these circumstances, it is essential that mantle convection simulations be extremely accurate and reliable. CitcomS and ASPECT are two finite element based mantle convection simulations developed and maintained by the Computational Infrastructure for Geodynamics. CitcomS is a finite element based mantle convection code that is designed to run on multiple high-performance computing platforms. ASPECT, an adaptive mesh refinement (AMR) code built on the Deal.II library, is also a finite element based mantle convection code that scales well on various HPC platforms. CitcomS and ASPECT both exhibit the overshoot phenomenon. One attempt at controlling the overshoot uses the Entropy Viscosity method, which introduces an artificial diffusion term in the energy equation of mantle convection. This artificial diffusion term is small where the temperature field is smooth. We present results from CitcomS and ASPECT that quantify the effect of the Entropy Viscosity method in reducing the overshoot phenomenon. In the discontinuous Galerkin (DG) finite element method, the test functions used in the method are continuous within each element but are discontinuous across inter-element boundaries. The solution space in the DG method is discontinuous. FEniCS is a collection of free software tools that automate the solution of differential equations using finite element methods. In this work we also present results from a finite element mantle convection simulation implemented in FEniCS that investigates the effect of using DG elements in reducing the overshoot problem.

Adaptive Shape Functions and Internal Mesh Adaptation for Modelling Progressive Failure in Adhesively Bonded Joints

NASA Technical Reports Server (NTRS)

Stapleton, Scott; Gries, Thomas; Waas, Anthony M.; Pineda, Evan J.

2014-01-01

Enhanced finite elements are elements with an embedded analytical solution that can capture detailed local fields, enabling more efficient, mesh independent finite element analysis. The shape functions are determined based on the analytical model rather than prescribed. This method was applied to adhesively bonded joints to model joint behavior with one element through the thickness. This study demonstrates two methods of maintaining the fidelity of such elements during adhesive non-linearity and cracking without increasing the mesh needed for an accurate solution. The first method uses adaptive shape functions, where the shape functions are recalculated at each load step based on the softening of the adhesive. The second method is internal mesh adaption, where cracking of the adhesive within an element is captured by further discretizing the element internally to represent the partially cracked geometry. By keeping mesh adaptations within an element, a finer mesh can be used during the analysis without affecting the global finite element model mesh. Examples are shown which highlight when each method is most effective in reducing the number of elements needed to capture adhesive nonlinearity and cracking. These methods are validated against analogous finite element models utilizing cohesive zone elements.

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes

PubMed Central

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B.; Blanc, Hervé; Verdier, Yann; Vinh, Joelle

2017-01-01

ABSTRACT Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo. The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. PMID:28539440

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes.

PubMed

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B; Blanc, Hervé; Verdier, Yann; Vinh, Joelle; Lambrechts, Louis; Saleh, Maria-Carla

2017-08-01

Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. Copyright © 2017 Suzuki et al.

Ergonomic Redesign of an Industrial Control Panel.

PubMed

Raeisi, S; Osqueizadeh, R; Maghsoudipour, M; Jafarpisheh, A S

2016-07-01

Operator's role in industrial control centers takes place in time, which is one of the most important determinants of whether an expected action is going to be successful or not. In certain situations, due to the complex nature of the work, the existing interfaces and already prepared procedures do not meet the dynamic requirements of operator's cognitive demands, making the control tasks unnecessarily difficult. This study was conducted to identify ergonomic issues with a specific industrial control panel, and redesign its layout and elements to enhance its usability. Task and link analysis methodologies were implemented. All essential functions and supporting operations were identified at the required trivial levels. Next, the weight of any possible link between the elements of the panel was computed as a composite index of frequency and importance. Finally, all components were rearranged within a new layout, and a computerized mockup was generated. A total of 8 primary tasks was identified, including 4 system failure handling tasks, switching between manual and automated modes, and 3 types of routine vigilance and control tasks. These tasks were broken down into 28 functions and 145 supporting operations, accordingly. Higher link values were observed between hand rest position and 2 elements. Also, 6 other components showed robust linkages. In conclusion, computer modeling can reduce the likelihood of accidents and near misses in industrial control rooms by considering the operators' misperception or mental burden and correcting poor design of the panels and inappropriate task allocation.

Mountain torrents: Quantifying vulnerability and assessing uncertainties

PubMed Central

Totschnig, Reinhold; Fuchs, Sven

2013-01-01

Vulnerability assessment for elements at risk is an important component in the framework of risk assessment. The vulnerability of buildings affected by torrent processes can be quantified by vulnerability functions that express a mathematical relationship between the degree of loss of individual elements at risk and the intensity of the impacting process. Based on data from the Austrian Alps, we extended a vulnerability curve for residential buildings affected by fluvial sediment transport processes to other torrent processes and other building types. With respect to this goal to merge different data based on different processes and building types, several statistical tests were conducted. The calculation of vulnerability functions was based on a nonlinear regression approach applying cumulative distribution functions. The results suggest that there is no need to distinguish between different sediment-laden torrent processes when assessing vulnerability of residential buildings towards torrent processes. The final vulnerability functions were further validated with data from the Italian Alps and different vulnerability functions presented in the literature. This comparison showed the wider applicability of the derived vulnerability functions. The uncertainty inherent to regression functions was quantified by the calculation of confidence bands. The derived vulnerability functions may be applied within the framework of risk management for mountain hazards within the European Alps. The method is transferable to other mountain regions if the input data needed are available. PMID:27087696

A Surrogate Approach to Study the Evolution of Noncoding DNA Elements That Organize Eukaryotic Genomes

PubMed Central

Vermaak, Danielle; Bayes, Joshua J.

2009-01-01

Comparative genomics provides a facile way to address issues of evolutionary constraint acting on different elements of the genome. However, several important DNA elements have not reaped the benefits of this new approach. Some have proved intractable to current day sequencing technology. These include centromeric and heterochromatic DNA, which are essential for chromosome segregation as well as gene regulation, but the highly repetitive nature of the DNA sequences in these regions make them difficult to assemble into longer contigs. Other sequences, like dosage compensation X chromosomal sites, origins of DNA replication, or heterochromatic sequences that encode piwi-associated RNAs, have proved difficult to study because they do not have recognizable DNA features that allow them to be described functionally or computationally. We have employed an alternate approach to the direct study of these DNA elements. By using proteins that specifically bind these noncoding DNAs as surrogates, we can indirectly assay the evolutionary constraints acting on these important DNA elements. We review the impact that such “surrogate strategies” have had on our understanding of the evolutionary constraints shaping centromeres, origins of DNA replication, and dosage compensation X chromosomal sites. These have begun to reveal that in contrast to the view that such structural DNA elements are either highly constrained (under purifying selection) or free to drift (under neutral evolution), some of them may instead be shaped by adaptive evolution and genetic conflicts (these are not mutually exclusive). These insights also help to explain why the same elements (e.g., centromeres and replication origins), which are so complex in some eukaryotic genomes, can be simple and well defined in other where similar conflicts do not exist. PMID:19635763

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems.

PubMed

Burmistrz, Michał; Dudek, Bartosz; Staniec, Dominika; Rodriguez Martinez, Jose Ignacio; Bochtler, Matthias; Potempa, Jan; Pyrc, Krzysztof

2015-08-01

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and transposons. It is present in the majority of Archaea and almost half of species of Bacteria. Porphyromonas gingivalis is an important human pathogen that has been proven to be an etiological agent of periodontitis and has been linked to systemic conditions, such as rheumatoid arthritis and cardiovascular disease. At least 95% of clinical strains of P. gingivalis carry CRISPR arrays, suggesting that these arrays play an important function in vivo. Here we show that all four CRISPR arrays present in the P. gingivalis W83 genome are transcribed. For one of the arrays, we demonstrate in vivo activity against double-stranded DNA constructs containing protospacer sequences accompanied at the 3' end by an NGG protospacer-adjacent motif (PAM). Most of the 44 spacers present in the genome of P. gingivalis W83 share no significant similarity with any known sequences, although 4 spacers are similar to sequences from bacteria found in the oral cavity and the gastrointestinal tract. Four spacers match genomic sequences of the host; however, none of these is flanked at its 3' terminus by the appropriate PAM element. The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

New insights into globoids of protein storage vacuoles in wheat aleurone using synchrotron soft X-ray microscopy

PubMed Central

Regvar, Marjana; Eichert, Diane; Kaulich, Burkhard; Gianoncelli, Alessandra; Pongrac, Paula; Vogel-Mikuš, Katarina; Kreft, Ivan

2011-01-01

Mature developed seeds are physiologically and biochemically committed to store nutrients, principally as starch, protein, oils, and minerals. The composition and distribution of elements inside the aleurone cell layer reflect their biogenesis, structural characteristics, and physiological functions. It is therefore of primary importance to understand the mechanisms underlying metal ion accumulation, distribution, storage, and bioavailability in aleurone subcellular organelles for seed fortification purposes. Synchrotron radiation soft X-ray full-field imaging mode (FFIM) and low-energy X-ray fluorescence (LEXRF) spectromicroscopy were applied to characterize major structural features and the subcellular distribution of physiologically important elements (Zn, Fe, Na, Mg, Al, Si, and P). These direct imaging methods reveal the accumulation patterns between the apoplast and symplast, and highlight the importance of globoids with phytic acid mineral salts and walls as preferential storage structures. C, N, and O chemical topographies are directly linked to the structural backbone of plant substructures. Zn, Fe, Na, Mg, Al, and P were linked to globoid structures within protein storage vacuoles with variable levels of co-localization. Si distribution was atypical, being contained in the aleurone apoplast and symplast, supporting a physiological role for Si in addition to its structural function. These results reveal that the immobilization of metals within the observed endomembrane structures presents a structural and functional barrier and affects bioavailability. The combination of high spatial and chemical X-ray microscopy techniques highlights how in situ analysis can yield new insights into the complexity of the wheat aleurone layer, whose precise biochemical composition, morphology, and structural characteristics are still not unequivocally resolved. PMID:21447756

Enhancer Analysis Unveils Genetic Interactions between TLX and SOX2 in Neural Stem Cells and In Vivo Reprogramming.

PubMed

Islam, Mohammed M; Smith, Derek K; Niu, Wenze; Fang, Sanhua; Iqbal, Nida; Sun, Guoqiang; Shi, Yanhong; Zhang, Chun-Li

2015-11-10

The orphan nuclear receptor TLX is a master regulator of postnatal neural stem cell (NSC) self-renewal and neurogenesis; however, it remains unclear how TLX expression is precisely regulated in these tissue-specific stem cells. Here, we show that a highly conserved cis-element within the Tlx locus functions to drive gene expression in NSCs. We demonstrate that the transcription factors SOX2 and MYT1 specifically interact with this genomic element to directly regulate Tlx enhancer activity in vivo. Knockdown experiments further reveal that SOX2 dominantly controls endogenous expression of TLX, whereas MYT1 only plays a modulatory role. Importantly, TLX is essential for SOX2-mediated in vivo reprogramming of astrocytes and itself is also sufficient to induce neurogenesis in the adult striatum. Together, these findings unveil functional genetic interactions among transcription factors that are critical to NSCs and in vivo cell reprogramming.

High-Payoff Space Transportation Design Approach with a Technology Integration Strategy

NASA Technical Reports Server (NTRS)

McCleskey, C. M.; Rhodes, R. E.; Chen, T.; Robinson, J.

2011-01-01

A general architectural design sequence is described to create a highly efficient, operable, and supportable design that achieves an affordable, repeatable, and sustainable transportation function. The paper covers the following aspects of this approach in more detail: (1) vehicle architectural concept considerations (including important strategies for greater reusability); (2) vehicle element propulsion system packaging considerations; (3) vehicle element functional definition; (4) external ground servicing and access considerations; and, (5) simplified guidance, navigation, flight control and avionics communications considerations. Additionally, a technology integration strategy is forwarded that includes: (a) ground and flight test prior to production commitments; (b) parallel stage propellant storage, such as concentric-nested tanks; (c) high thrust, LOX-rich, LOX-cooled first stage earth-to-orbit main engine; (d) non-toxic, day-of-launch-loaded propellants for upper stages and in-space propulsion; (e) electric propulsion and aero stage control.

In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa

PubMed Central

Kaur, Amritpreet; Pati, Pratap Kumar; Pati, Aparna Maitra; Nagpal, Avinash Kaur

2017-01-01

Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5’ UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants. PMID:28910327

Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation

PubMed Central

Chatterjee, Aniruddha; Stockwell, Peter A.; Rodger, Euan J.; Duncan, Elizabeth J.; Parry, Matthew F.; Weeks, Robert J.; Morison, Ian M.

2015-01-01

The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript. PMID:26612583

Determination of the core promoter regions of the Saccharomyces cerevisiae RPS3 gene.

PubMed

Joo, Yoo Jin; Kim, Jin-Ha; Baek, Joung Hee; Seong, Ki Moon; Lee, Jae Yung; Kim, Joon

2009-01-01

Ribosomal protein genes (RPG), which are scattered throughout the genomes of all eukaryotes, are subjected to coordinated expression. In yeast, the expression of RPGs is highly regulated, mainly at the transcriptional level. Recent research has found that many ribosomal proteins (RPs) function in multiple processes in addition to protein synthesis. Therefore, detailed knowledge of promoter architecture as well as gene regulation is important in understanding the multiple cellular processes mediated by RPGs. In this study, we investigated the functional architecture of the yeast RPS3 promoter and identified many putative cis-elements. Using beta-galactosidase reporter analysis and EMSA, the core promoter of RPS3 containing UASrpg and T-rich regions was corroborated. Moreover, the promoter occupancy of RPS3 by three transcription factors was confirmed. Taken together, our results further the current understanding of the promoter architecture and trans-elements of the Saccharomyces cerevisiae RPS3 gene.

In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa.

PubMed

Kaur, Amritpreet; Pati, Pratap Kumar; Pati, Aparna Maitra; Nagpal, Avinash Kaur

2017-01-01

Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.

Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

PubMed

Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

2017-07-01

Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10 -8 ) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits. SNPs were annotated using HaploReg for the eight functional elements across any tissue: DNase sites, expression quantitative trait loci (eQTL), sequence conservation, enhancers, promoters, missense variants, sequence motifs, and protein binding sites. In addition, tissue-specific annotations were considered for brain vs. blood. Disease/trait SNPs were compared to a control set of 4809 SNPs matched to the GWAS SNPs (N = 1639) on allele frequency, gene density, distance to nearest gene, and linkage disequilibrium at ~3:1 ratio. Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

Spectroscopic Analyses of Neutron Capture Elements in Open Clusters

NASA Astrophysics Data System (ADS)

O'Connell, Julia E.

The evolution of elements as a function or age throughout the Milky Way disk provides strong constraints for galaxy evolution models, and on star formation epochs. In an effort to provide such constraints, we conducted an investigation into r- and s-process elemental abundances for a large sample of open clusters as part of an optical follow-up to the SDSS-III/APOGEE-1 near infrared survey. To obtain data for neutron capture abundance analysis, we conducted a long-term observing campaign spanning three years (2013-2016) using the McDonald Observatory Otto Struve 2.1-meter telescope and Sandiford Cass Echelle Spectrograph (SES, R(lambda/Deltalambda) ˜60,000). The SES provides a wavelength range of ˜1400 A, making it uniquely suited to investigate a number of other important chemical abundances as well as the neutron capture elements. For this study, we derive abundances for 18 elements covering four nucleosynthetic families- light, iron-peak, neutron capture and alpha-elements- for ˜30 open clusters within 6 kpc of the Sun with ages ranging from ˜80 Myr to ˜10 Gyr. Both equivalent width (EW) measurements and spectral synthesis methods were employed to derive abundances for all elements. Initial estimates for model stellar atmospheres- effective temperature and surface gravity- were provided by the APOGEE data set, and then re-derived for our optical spectra by removing abundance trends as a function of excitation potential and reduced width log(EW/lambda). With the exception of Ba II and Zr I, abundance analyses for all neutron capture elements were performed by generating synthetic spectra from the new stellar parameters. In order to remove molecular contamination, or blending from nearby atomic features, the synthetic spectra were modeled by a best-fit Gaussian to the observed data. Nd II shows a slight enhancement in all cluster stars, while other neutron capture elements follow solar abundance trends. Ba II shows a large cluster-to-cluster abundance spread, consistent with other open cluster abundance studies. From log(Age) ˜8.5, this large spread as a function of age appears to replicate the findings from an earlier, much debated study by Orazi et al. (2009) which found a linear trend of decreasing barium abundance with increasing age.

A Study on Design-Oriented Demands of VR via ZMET-QFD Model for Industrial Design Education and Students' Learning

ERIC Educational Resources Information Center

Liang, Yo-Wen; Lee, An-Sheng; Liu, Shuo-Fang

2016-01-01

The difficulty of Virtual Reality application in industrial design education and learning is VR engineers cannot comprehend what the important functions or elements are for students. In addition, a general-purpose VR usually confuses the students and provides neither good manipulation means nor useful toolkits. To solve these problems, the…

Commentary: The Development of Hippocampal-Dependent Memory Functions: Theoretical Comments on Jabès and Nelson Review (2015)

ERIC Educational Resources Information Center

Bachevalier, Jocelyne

2015-01-01

Studies investigating the development of memory processes and their neural substrates have flourished over the past two decades. The review by Jabès and Nelson (2015) adds an important piece to our understanding of the maturation of different elements and circuits within the hippocampal system and their association with the progressive development…

A Viral (Arc)hive for Metazoan Memory.

PubMed

Parrish, Nicholas F; Tomonaga, Keizo

2018-01-11

Arc, a master regulator of synaptic plasticity, contains sequence elements that are evolutionarily related to retrotransposon Gag genes. Two related papers in this issue of Cell show that Arc retains retroviral-like capsid-forming ability and can transmit mRNA between cells in the nervous system, a process that may be important for synaptic function. Copyright © 2017 Elsevier Inc. All rights reserved.

Parent-Child Agreement of Anxiety Symptoms in Youth with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Blakeley-Smith, Audrey; Reaven, Judy; Ridge, Katherine; Hepburn, Susan

2012-01-01

Best practice for assessment of anxiety symptoms in children suggests that child self-report is an important element to consider. Yet, it is not known if it is a reliable assessment method for children with high-functioning autism spectrum disorders (ASDs). The present study examines the extent to which verbally fluent children with ASD and their…

Advanced Numerical-Algebraic Thinking: Constructing the Concept of Covariation as a Prelude to the Concept of Function

ERIC Educational Resources Information Center

Hitt, Fernando; Morasse, Christian

2009-01-01

Introduction: In this document we stress the importance of developing in children a structure for advanced numerical-algebraic thinking that can provide an element of control when solving mathematical situations. We analyze pupils' conceptions that induce errors in algebra due to a lack of control in connection with their numerical thinking. We…

A Framework for Wetlands Research: Development of a Wetlands Data Base

NASA Technical Reports Server (NTRS)

1983-01-01

Issues related to the assembly of a comprehensive global wetlands data base are presented. A strategy to collect relevant data for wetland ecosystems through remote sensing inventories of wetland distribution was discussed. Elements of a research program on biogenic gas fluxes were identified. The major wetland parameters and their functional importance to material exchange mechanisms are summarized.

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

PubMed Central

De la Fuente, Ildefonso M.; Cortes, Jesus M.; Perez-Pinilla, Martin B.; Ruiz-Rodriguez, Vicente; Veguillas, Juan

2011-01-01

Background Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms. Methodology/Principal Findings In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows. Conclusions/Significance We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub –with a high degree of effective connectivity- exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic Metabolic Structure. PMID:22125607

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

PubMed Central

Ogilvie, Lesley A.; Firouzmand, Sepinoud; Jones, Brian V.

2012-01-01

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed. PMID:22126801

Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis.

PubMed

Kuwabara, Tomoko; Hsieh, Jenny; Muotri, Alysson; Yeo, Gene; Warashina, Masaki; Lie, Dieter Chichung; Moore, Lynne; Nakashima, Kinichi; Asashima, Makoto; Gage, Fred H

2009-09-01

In adult hippocampus, new neurons are continuously generated from neural stem cells (NSCs), but the molecular mechanisms regulating adult neurogenesis remain elusive. We found that Wnt signaling, together with the removal of Sox2, triggered the expression of NeuroD1 in mice. This transcriptional regulatory mechanism was dependent on a DNA element containing overlapping Sox2 and T-cell factor/lymphoid enhancer factor (TCF/LEF)-binding sites (Sox/LEF) in the promoter. Notably, Sox/LEF sites were also found in long interspersed nuclear element 1 (LINE-1) elements, consistent with their critical roles in the transition of NSCs to proliferating neuronal progenitors. Our results describe a previously unknown Wnt-mediated regulatory mechanism that simultaneously coordinates activation of NeuroD1 and LINE-1, which is important for adult neurogenesis and survival of neuronal progenitors. Moreover, the discovery that LINE-1 retro-elements embedded in the mammalian genome can function as bi-directional promoters suggests that Sox/LEF regulatory sites may represent a general mechanism, at least in part, for relaying environmental signals to other nearby loci to promote adult hippocampal neurogenesis.

A parameterization scheme for the x-ray linear attenuation coefficient and energy absorption coefficient.

PubMed

Midgley, S M

2004-01-21

A novel parameterization of x-ray interaction cross-sections is developed, and employed to describe the x-ray linear attenuation coefficient and mass energy absorption coefficient for both elements and mixtures. The new parameterization scheme addresses the Z-dependence of elemental cross-sections (per electron) using a simple function of atomic number, Z. This obviates the need for a complicated mathematical formalism. Energy dependent coefficients describe the Z-direction curvature of the cross-sections. The composition dependent quantities are the electron density and statistical moments describing the elemental distribution. We show that it is possible to describe elemental cross-sections for the entire periodic table and at energies above the K-edge (from 6 keV to 125 MeV), with an accuracy of better than 2% using a parameterization containing not more than five coefficients. For the biologically important elements 1 < or = Z < or = 20, and the energy range 30-150 keV, the parameterization utilizes four coefficients. At higher energies, the parameterization uses fewer coefficients with only two coefficients needed at megavoltage energies.

High time-resolved elemental components in fine and coarse particles in the Pearl River Delta region of Southern China: Dynamic variations and effects of meteorology.

PubMed

Zhou, Shengzhen; Davy, Perry K; Wang, Xuemei; Cohen, Jason Blake; Liang, Jiaquan; Huang, Minjuan; Fan, Qi; Chen, Weihua; Chang, Ming; Ancelet, Travis; Trompetter, William J

2016-12-01

Hourly-resolved PM 2.5 and PM 10-2.5 samples were collected in the industrial city Foshan in the Pearl River Delta region, China. The samples were subsequently analyzed for elemental components and black carbon (BC). A key purpose of the study was to understand the composition of particulate matter (PM) at high-time resolution in a polluted urban atmosphere to identify key components contributing to extreme PM concentration events and examine the diurnal chemical concentration patterns for air quality management purposes. It was found that BC and S concentrations dominated in the fine mode, while elements with mostly crustal and oceanic origins such as Si, Ca, Al and Cl were found in the coarse size fraction. Most of the elements showed strong diurnal variations. S did not show clear diurnal variations, suggesting regional rather than local origin. Based on empirical orthogonal functions (EOF) method, 3 forcing factors were identified contributing to the extreme events of PM 2.5 and selected elements, i.e., urban direct emissions, wet deposition and a combination of coarse mode sources. Conditional probability functions (CPF) were performed using wind profiles and elemental concentrations. The CPF results showed that BC and elemental Cl, K, Fe, Cu and Zn in the fine mode were mostly from the northwest, indicating that industrial emissions and combustion were the main sources. For elements in the coarse mode, Si, Al, K, Ca, Fe and Ti showed similar patterns, suggesting same sources such as local soil dust/construction activities. Coarse elemental Cl was mostly from the south and southeast, implying the influence of marine aerosol sources. For other trace elements, we found vanadium (V) in fine PM was mainly from the sources located to the southeast of the measuring site. Combined with CPF results of S and V in fine PM, we concluded shipping emissions were likely an important elemental emission source. Copyright © 2016. Published by Elsevier B.V.

Modular assembly of optical nanocircuits.

PubMed

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-29

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic 'lumped' circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

Modular assembly of optical nanocircuits

NASA Astrophysics Data System (ADS)

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-01

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic ‘lumped’ circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

A finite element simulation of sound attenuation in a finite duct with a peripherally variable liner

NASA Technical Reports Server (NTRS)

Watson, W. R.

1977-01-01

Using multimodal analysis, a variational finite element method is presented for analyzing sound attenuation in a three-dimensional finite duct with a peripherally variable liner in the absence of flow. A rectangular element, with cubic shaped functions, is employed. Once a small portion of a peripheral liner is removed, the attenuation rate near the frequency where maximum attenuation occurs drops significantly. The positioning of the liner segments affects the attenuation characteristics of the liner. Effects of the duct termination are important in the low frequency ranges. The main effect of peripheral variation of the liner is a broadening of the attenuation characteristics in the midfrequency range. Because of matrix size limitations of the presently available computer program, the eigenvalue equations should be solved out of core in order to handle realistic sources.

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities.

PubMed

Rauscher, S; Flamm, C; Mandl, C W; Heinz, F X; Stadler, P F

1997-07-01

The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure elements, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organization, but exhibit a significant degree of RNA sequence diversity in the functionally important 3'-NCR. We demonstrate the presence of secondary structures shared by all flaviviruses, as well as structural features that are characteristic for groups of viruses within the genus reflecting the established classification scheme. The significance of most of the predicted structures is corroborated by compensatory mutations. The availability of infectious clones for several flaviviruses will allow the assessment of these structural elements in processes of the viral life cycle, such as replication and assembly.

Nanoparticles of barium induce apoptosis in human phagocytes

PubMed Central

Mores, Luana; França, Eduardo Luzia; Silva, Núbia Andrade; Suchara, Eliane Aparecida; Honorio-França, Adenilda Cristina

2015-01-01

Purpose Nutrients and immunological factors of breast milk are essential for newborn growth and the development of their immune system, but this secretion can contain organic and inorganic toxins such as barium. Colostrum contamination with barium is an important issue to investigate because this naturally occurring element is also associated with human activity and industrial pollution. The study evaluated the administration of barium nanoparticles to colostrum, assessing the viability and functional activity of colostral mononuclear phagocytes. Methods Colostrum was collected from 24 clinically healthy women (aged 18–35 years). Cell viability, superoxide release, intracellular Ca2+ release, and phagocyte apoptosis were analyzed in the samples. Results Treatment with barium lowered mononuclear phagocyte viability, increased superoxide release, and reduced intracellular calcium release. In addition, barium increased cell death by apoptosis. Conclusion These data suggest that nanoparticles of barium in colostrum are toxic to cells, showing the importance of avoiding exposure to this element. PMID:26451108

Preliminary Identification of Urban Park Infrastructure Resilience in Semarang Central Java

NASA Astrophysics Data System (ADS)

Muzdalifah, Aji Uhfatun; Maryono

2018-02-01

Park is one of the spot green infrastructure. There are two major characteristic of park, first Active parks and second passive park. Those of two open spaces have been significant on the fulfillment of urban environment. To maintenance the urban park, it is very importance to identify the characteristic of active and passive park. The identification also needs to fostering stakeholder effort to increase quality of urban park infrastructure. This study aims to explore and assess the characteristic of urban park infrastructure in Semarang City, Central Java. Data collection methods conduct by review formal document, field observation and interview with key government officer. The study founded that urban active parks infrastructure resilience could be defined by; Park Location, Garden Shape, Vegetation, Support Element, Park Function, and Expected Benefit from Park Existence. Moreover, the vegetation aspect and the supporting elements are the most importance urban park infrastructure in Semarang.

Synthetic-lattice enabled all-optical devices based on orbital angular momentum of light.

PubMed

Luo, Xi-Wang; Zhou, Xingxiang; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can; Zhang, Chuanwei; Zhou, Zheng-Wei

2017-07-14

All-optical photonic devices are crucial for many important photonic technologies and applications, ranging from optical communication to quantum information processing. Conventional design of all-optical devices is based on photon propagation and interference in real space, which may rely on large numbers of optical elements, and the requirement of precise control makes this approach challenging. Here we propose an unconventional route for engineering all-optical devices using the photon's internal degrees of freedom, which form photonic crystals in such synthetic dimensions for photon propagation and interference. We demonstrate this design concept by showing how important optical devices such as quantum memory and optical filters can be realized using synthetic orbital angular momentum (OAM) lattices in degenerate cavities. The design route utilizing synthetic photonic lattices may significantly reduce the requirement for numerous optical elements and their fine tuning in conventional design, paving the way for realistic all-optical photonic devices with novel functionalities.

Nanoparticles of barium induce apoptosis in human phagocytes.

PubMed

Mores, Luana; França, Eduardo Luzia; Silva, Núbia Andrade; Suchara, Eliane Aparecida; Honorio-França, Adenilda Cristina

2015-01-01

Nutrients and immunological factors of breast milk are essential for newborn growth and the development of their immune system, but this secretion can contain organic and inorganic toxins such as barium. Colostrum contamination with barium is an important issue to investigate because this naturally occurring element is also associated with human activity and industrial pollution. The study evaluated the administration of barium nanoparticles to colostrum, assessing the viability and functional activity of colostral mononuclear phagocytes. Colostrum was collected from 24 clinically healthy women (aged 18-35 years). Cell viability, superoxide release, intracellular Ca(2+) release, and phagocyte apoptosis were analyzed in the samples. Treatment with barium lowered mononuclear phagocyte viability, increased superoxide release, and reduced intracellular calcium release. In addition, barium increased cell death by apoptosis. These data suggest that nanoparticles of barium in colostrum are toxic to cells, showing the importance of avoiding exposure to this element.

Development of the IBD Disk: A Visual Self-administered Tool for Assessing Disability in Inflammatory Bowel Diseases.

PubMed

Ghosh, Subrata; Louis, Edouard; Beaugerie, Laurent; Bossuyt, Peter; Bouguen, Guillaume; Bourreille, Arnaud; Ferrante, Marc; Franchimont, Denis; Frost, Karen; Hebuterne, Xavier; Marshall, John K; OʼShea, Ciara; Rosenfeld, Greg; Williams, Chadwick; Peyrin-Biroulet, Laurent

2017-03-01

The Inflammatory bowel disease (IBD) Disability Index is a validated tool that evaluates functional status; however, it is used mainly in the clinical trial setting. We describe the use of an iterative Delphi consensus process to develop the IBD Disk-a shortened, self-administered adaption of the validated IBD Disability Index-to give immediate visual representation of patient-reported IBD-related disability. In the preparatory phase, the IBD CONNECT group (30 health care professionals) ranked IBD Disability Index items in the perceived order of importance. The Steering Committee then selected 10 items from the IBD Disability Index to take forward for inclusion in the IBD Disk. In the consensus phase, the items were refined and agreed by the IBD Disk Working Group (14 gastroenterologists) using an online iterative Delphi consensus process. Members could also suggest new element(s) or recommend changes to included elements. The final items for the IBD Disk were agreed in February 2016. After 4 rounds of voting, the following 10 items were agreed for inclusion in the IBD Disk: abdominal pain, body image, education and work, emotions, energy, interpersonal interactions, joint pain, regulating defecation, sexual functions, and sleep. All elements, except sexual functions, were included in the validated IBD Disability Index. The IBD Disk has the potential to be a valuable tool for use at a clinical visit. It can facilitate assessment of inflammatory bowel disease-related disability relevant to both patients and physicians, discussion on specific disability-related issues, and tracking changes in disease burden over time.

Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity

PubMed Central

Kienesberger, Sabine; Sprenger, Hanna; Wolfgruber, Stella; Halwachs, Bettina; Thallinger, Gerhard G.; Perez-Perez, Guillermo I.; Blaser, Martin J.; Zechner, Ellen L.; Gorkiewicz, Gregor

2014-01-01

Campylobacter fetus are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of C. fetus subsp. venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40. Functional analysis of genes predicted to be involved in C. fetus virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of C. fetus pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens. PMID:24416416

Exact finite elements for conduction and convection

NASA Technical Reports Server (NTRS)

Thornton, E. A.; Dechaumphai, P.; Tamma, K. K.

1981-01-01

An approach for developing exact one dimensional conduction-convection finite elements is presented. Exact interpolation functions are derived based on solutions to the governing differential equations by employing a nodeless parameter. Exact interpolation functions are presented for combined heat transfer in several solids of different shapes, and for combined heat transfer in a flow passage. Numerical results demonstrate that exact one dimensional elements offer advantages over elements based on approximate interpolation functions.

Towards bio monitoring of toxic (lead) and essential elements in whole blood from 1- to 72-month old children: a cross-sectional study.

PubMed

Kang-Sheng, Liu; Xiao-Dong, Mao; Juan, Shi; Chun-Fan, Dai; Pingqing, Gu

2015-06-01

Minerals such as zinc, copper, selenium, calcium, and magnesium are essential for normal human development and functioning of the body. They have been found to play important roles in immuno-physiologic functions. The study is to evaluate the distribution and correlation of nonessential (lead) and essential elements in whole blood from 1- to 72-month old children. The cross-sectional study was performed in 1551 children. Six element concentrations, including copper (Cu), zinc (Zn), calcium (Ca), magnesium (Mg), iron (Fe) and lead (Pb) in the blood were determined by atomic absorption spectrometry. Distributions and correlations of trace elements in different age groups were analyzed and compared. A Pearson correlation controlled for age and gender was used to assess the relationship of non essential (lead) and essential elements. Levels of copper and magnesium were 18.09 ± 4.42 µmol/L and 1.42 ± 0.12 mmol/L, respectively. 6.04% of all children showed copper levels below the normal threshold, the levels of Magnesium were stable in different age groups. Though the overall mean blood zinc and iron concentrations (61.19 ± 11.30 µmol/L and 8.24 ± 0.59 mmol/L, respectively) gradually increased with age and the overall deficiency levels (24.1% and 36.0%, respectively) decreased with age, zinc and iron deficiencies were still very stable. Controlling for gender and age, significant positive correlations were found when comparing copper to zinc, calcium, magnesium, and iron ((r = 0.333, 0.241, 0.417, 0.314 ,p < 0.01); zinc to magnesium and iron (r = 0.440, 0.497p < 0.01); and magnesium to Calcium and iron (r = 0.349, 0.645, p < 0.01). The overall mean blood lead levels (41.16 ± 16.10) were relatively unstable among different age groups. The prevalence of lead intoxication in all children was 1.3% .Calcium levels decreased gradually with age, with an overall concentration of 1.78 ± 0.13 mmol/L. Significant negative correlations were also noted between Pb and Zn, Fe (r = -0.179, -0.124.p < 0.01) .The importance of calcium deficiency and supplementation is well realized, but the severity of iron and zinc deficiency is not well recorded. The degree of lead intoxication in all the children studied was low; The established reference intervals for Cu, Zn, Ca and Mg provide an important guidance for the reasonable supplementation of essential elements during different age groups.

X-ray fluorescence microscopy reveals the role of selenium in spermatogenesis

PubMed Central

Kehr, Sebastian; Malinouski, Mikalai; Finney, Lydia; Vogt, Stefan; Labunskyy, Vyacheslav M.; Kasaikina, Marina V.; Carlson, Bradley A.; Zhou, You; Hatfield, Dolph L.; Gladyshev, Vadim N.

2009-01-01

Selenium (Se) is a trace element with important roles in human health. Several selenoproteins have essential functions in development. However, the cellular and tissue distribution of Se remains largely unknown because of the lack of analytical techniques that image this element with sufficient sensitivity and resolution. Herein, we report that X-ray fluorescence microscopy (XFM) can be used to visualize and quantify the tissue, cellular and subcellular topography of Se. We applied this technique to characterize the role of Se in spermatogenesis and identified a dramatic Se enrichment specifically in late spermatids, a pattern that was not seen in any other elemental maps. This enrichment was due to elevated levels of the mitochondrial form of glutathione peroxidase 4 and was fully dependent on the supplies of Se by Selenoprotein P. High-resolution scans revealed that Se concentrated near the lumen side of elongating spermatids, where structural components of sperm are formed. During spermatogenesis, maximal Se associated with decreased phosphorus, whereas Zn did not change. In sperm, Se was primarily in the midpiece and co-localized with Cu and Fe. XFM allowed quantification of Se in the midpiece (0.8 fg) and head (0.14 fg) of individual sperm cells, revealing the ability of sperm cells to handle the amounts of this element well above its toxic levels. Overall, the use of XFM allowed visualization of tissue and cellular Se and provided important insights in the role of this and other trace elements in spermatogenesis. PMID:19379757

Biomechanical Analysis of Hearing in Whales Using Nanoindentation and the Finite Element Method

NASA Astrophysics Data System (ADS)

Tubelli, Andrew A.; Zosuls, Aleks; Ketten, Darlene R.; Mountain, David C.

2011-11-01

The detailed biomechanics of hearing in baleen whales are almost entirely unknown. As a first step to predicting the audiogram for these species, a linear three-dimensional finite-element model of the minke whale (Balaenoptera acutorostrata) middle ear was developed. A reconstruction of the ear was made from CT scans and imported into a finite element solver. Young's modulus of the bone was estimated via nanoindentation. The middle-ear transfer function was estimated by applying a pressure to the glove finger (the thick, everted equivalent of the tympanic membrane) with velocity calculated at the stapes footplate. It was found that the most sensitive frequencies corresponded with vocalization frequencies. For all frequencies tested, the malleus-incus complex flexed about the anterior process of the malleus and the stapes rotated within the oval window. Results indictae that finite element modeling is a useful approach for studying the mechanics of hearing in species that are difficult to study in vivo.

Evolutionary interaction between W/Y chromosome and transposable elements.

PubMed

Śliwińska, Ewa B; Martyka, Rafał; Tryjanowski, Piotr

2016-06-01

The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

In Vitro and Ex Vivo Approaches to Evaluate Next-Generation Tobacco and Non-Tobacco Products on Human Blood Platelets

PubMed Central

Spinelli, Sherry L.; Lannan, Katie L.; Loelius, Shannon G.

2017-01-01

Abstract Human blood platelets are major hemostatic regulators in the circulation and important in the mediation of chronic inflammation and immunomodulation. They are key elements that promote cardiovascular pathogenesis that leads to atherosclerosis, thrombosis, myocardial infarction, and stroke. New information on tobacco use and platelet dysregulation shows that these highly understudied vascular cells are dysregulated by tobacco smoke. Thus, platelet function studies should be an important consideration for the evaluation of existing and next-generation tobacco and non-tobacco products. Novel in vitro approaches are being sought to investigate these products and their influence on platelet function. Platelets are ideally suited for product assessment, as robust and novel in vitro translational methods are available to assess platelet function. Furthermore, the use of human biological systems has the advantage that risk predictions will better reflect the human condition. PMID:28337466

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Super-enhancers: Asset management in immune cell genomes.

PubMed

Witte, Steven; O'Shea, John J; Vahedi, Golnaz

2015-09-01

Super-enhancers (SEs) are regions of the genome consisting of clusters of regulatory elements bound with very high amounts of transcription factors, and this architecture appears to be the hallmark of genes and noncoding RNAs linked with cell identity. Recent studies have identified SEs in CD4(+) T cells and have further linked these regions to single nucleotide polymorphisms (SNPs) associated with immune-mediated disorders, pointing to an important role for these structures in the T cell differentiation and function. Here we review the features that define SEs, and discuss their function within the broader understanding of the mechanisms that define immune cell identity and function. We propose that SEs present crucial regulatory hubs, coordinating intrinsic and extrinsic differentiation signals, and argue that delineating these regions will provide important insight into the factors and mechanisms that define immune cell identity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Divergent variations in concentrations of chemical elements among shrub organs in a temperate desert

PubMed Central

He, Mingzhu; Song, Xin; Tian, Fuping; Zhang, Ke; Zhang, Zhishan; Chen, Ning; Li, Xinrong

2016-01-01

Desert shrubs, a dominant component of desert ecosystems, need to maintain sufficient levels of nutrients in their different organs to ensure operation of various physiological functions for the purpose of survival and reproduction. In the present study, we analyzed 10 elements in leaves, stems, and roots of 24 dominant shrub species from 52 sites across a temperate desert ecosystem in northwestern China. We found that concentrations of all 10 elements were higher in leaves than in stems and roots, that non-legumes had higher levels of leaf Na and Mg than did legumes, and that Na was more concentrated in C4 leaves than in C3 leaves. Scaling relationships of elements between the photosynthetic organ (leaf) and non-photosynthetic organs (stem and root) were allometric. Results of principal components analysis (PCA) highlighted the important role of the elements responsible for osmoregulation (K and Na) in water utilization of desert shrubs. Soil properties and taxonomy explained most variation of element concentrations in desert shrubs. Desert shrubs may not be particularly susceptible to future change in climate factors, because most elements (including N, P, K, Ca, Mn, Zn, and Cu) associated with photosynthesis, osmoregulation, enzyme activity, and water use efficiency primarily depend on soil conditions. PMID:26818575

Divergent variations in concentrations of chemical elements among shrub organs in a temperate desert.

PubMed

He, Mingzhu; Song, Xin; Tian, Fuping; Zhang, Ke; Zhang, Zhishan; Chen, Ning; Li, Xinrong

2016-01-28

Desert shrubs, a dominant component of desert ecosystems, need to maintain sufficient levels of nutrients in their different organs to ensure operation of various physiological functions for the purpose of survival and reproduction. In the present study, we analyzed 10 elements in leaves, stems, and roots of 24 dominant shrub species from 52 sites across a temperate desert ecosystem in northwestern China. We found that concentrations of all 10 elements were higher in leaves than in stems and roots, that non-legumes had higher levels of leaf Na and Mg than did legumes, and that Na was more concentrated in C4 leaves than in C3 leaves. Scaling relationships of elements between the photosynthetic organ (leaf) and non-photosynthetic organs (stem and root) were allometric. Results of principal components analysis (PCA) highlighted the important role of the elements responsible for osmoregulation (K and Na) in water utilization of desert shrubs. Soil properties and taxonomy explained most variation of element concentrations in desert shrubs. Desert shrubs may not be particularly susceptible to future change in climate factors, because most elements (including N, P, K, Ca, Mn, Zn, and Cu) associated with photosynthesis, osmoregulation, enzyme activity, and water use efficiency primarily depend on soil conditions.

A parallel finite element procedure for contact-impact problems using edge-based smooth triangular element and GPU

NASA Astrophysics Data System (ADS)

Cai, Yong; Cui, Xiangyang; Li, Guangyao; Liu, Wenyang

2018-04-01

The edge-smooth finite element method (ES-FEM) can improve the computational accuracy of triangular shell elements and the mesh partition efficiency of complex models. In this paper, an approach is developed to perform explicit finite element simulations of contact-impact problems with a graphical processing unit (GPU) using a special edge-smooth triangular shell element based on ES-FEM. Of critical importance for this problem is achieving finer-grained parallelism to enable efficient data loading and to minimize communication between the device and host. Four kinds of parallel strategies are then developed to efficiently solve these ES-FEM based shell element formulas, and various optimization methods are adopted to ensure aligned memory access. Special focus is dedicated to developing an approach for the parallel construction of edge systems. A parallel hierarchy-territory contact-searching algorithm (HITA) and a parallel penalty function calculation method are embedded in this parallel explicit algorithm. Finally, the program flow is well designed, and a GPU-based simulation system is developed, using Nvidia's CUDA. Several numerical examples are presented to illustrate the high quality of the results obtained with the proposed methods. In addition, the GPU-based parallel computation is shown to significantly reduce the computing time.

How should spin-weighted spherical functions be defined?

NASA Astrophysics Data System (ADS)

Boyle, Michael

2016-09-01

Spin-weighted spherical functions provide a useful tool for analyzing tensor-valued functions on the sphere. A tensor field can be decomposed into complex-valued functions by taking contractions with tangent vectors on the sphere and the normal to the sphere. These component functions are usually presented as functions on the sphere itself, but this requires an implicit choice of distinguished tangent vectors with which to contract. Thus, we may more accurately say that spin-weighted spherical functions are functions of both a point on the sphere and a choice of frame in the tangent space at that point. The distinction becomes extremely important when transforming the coordinates in which these functions are expressed, because the implicit choice of frame will also transform. Here, it is proposed that spin-weighted spherical functions should be treated as functions on the spin or rotation groups, which simultaneously tracks the point on the sphere and the choice of tangent frame by rotating elements of an orthonormal basis. In practice, the functions simply take a quaternion argument and produce a complex value. This approach more cleanly reflects the geometry involved, and allows for a more elegant description of the behavior of spin-weighted functions. In this form, the spin-weighted spherical harmonics have simple expressions as elements of the Wigner 𝔇 representations, and transformations under rotation are simple. Two variants of the angular-momentum operator are defined directly in terms of the spin group; one is the standard angular-momentum operator L, while the other is shown to be related to the spin-raising operator ð.

THE ROLES OF METAL IONS IN REGULATION BY RIBOSWITCHES

PubMed Central

2012-01-01

Metal ions are required by all organisms in order to execute an array of essential molecular functions. They play a critical role in many catalytic mechanisms and structural properties. Proper homeostasis of ions is critical; levels that are aberrantly low or high are deleterious to cellular physiology. To maintain stable intracellular pools, metal ion-sensing regulatory (metalloregulatory) proteins couple metal ion concentration fluctuations with expression of genes encoding for cation transport or sequestration. However, these transcriptional-based regulatory strategies are not the only mechanisms by which organisms coordinate metal ions with gene expression. Intriguingly, a few classes of signal-responsive RNA elements have also been discovered to function as metalloregulatory agents. This suggests that RNA-based regulatory strategies can be precisely tuned to intracellular metal ion pools, functionally akin to metalloregulatory proteins. In addition to these metal-sensing regulatory RNAs, there is a yet broader role for metal ions in directly assisting the structural integrity of other signal-responsive regulatory RNA elements. In this chapter, we discuss how the intimate physicochemical relationship between metal ions and nucleic acids is important for the structure and function of metal ion- and metabolite-sensing regulatory RNAs. PMID:22010271

Association between social contact frequency and negative symptoms, psychosocial functioning and quality of life in patients with schizophrenia.

PubMed

Siegrist, Karin; Millier, Aurelie; Amri, Ikbal; Aballéa, Samuel; Toumi, Mondher

2015-12-30

The lack of social contacts may be an important element in the presumed vicious circle aggravating, or at least stabilising negative symptoms in patients with schizophrenia. A European 2-year cohort study collected negative symptom scores, psychosocial functioning scores, objective social contact frequency scores and quality of life scores every 6 months. Bivariate analyses, correlation analyses, multivariate regressions and random effects regressions were conducted to describe relations between social contact and outcomes of interest and to gain a better understanding of this relation over time. Using data from 1208 patients with schizophrenia, a link between social contact frequency and negative symptom scores, functioning and quality of life at baseline was established. Regression models confirmed the significant association between social contact and negative symptoms as well as psychosocial functioning. This study aimed at demonstrating the importance of social contact for deficient behavioural aspects of schizophrenia. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site.

PubMed

Means, A L; Farnham, P J

1990-02-01

We have identified a sequence element that specifies the position of transcription initiation for the dihydrofolate reductase gene. Unlike the functionally analogous TATA box that directs RNA polymerase II to initiate transcription 30 nucleotides downstream, the positioning element of the dihydrofolate reductase promoter is located directly at the site of transcription initiation. By using DNase I footprint analysis, we have shown that a protein binds to this initiator element. Transcription initiated at the dihydrofolate reductase initiator element when 28 nucleotides were inserted between it and all other upstream sequences, or when it was placed on either side of the DNA helix, suggesting that there is no strict spatial requirement between the initiator and an upstream element. Although neither a single Sp1-binding site nor a single initiator element was sufficient for transcriptional activity, the combination of one Sp1-binding site and the dihydrofolate reductase initiator element cloned into a plasmid vector resulted in transcription starting at the initiator element. We have also shown that the simian virus 40 late major initiation site has striking sequence homology to the dihydrofolate reductase initiation site and that the same, or a similar, protein binds to both sites. Examination of the sequences at other RNA polymerase II initiation sites suggests that we have identified an element that is important in the transcription of other housekeeping genes. We have thus named the protein that binds to the initiator element HIP1 (Housekeeping Initiator Protein 1).

The role of selenium in thyroid gland pathophysiology.

PubMed

Stuss, Michał; Michalska-Kasiczak, Marta; Sewerynek, Ewa

2017-01-01

It is now assumed that proper functioning of the thyroid gland (TG), beside iodine, requires also a number of elements, including selenium, iron, zinc, copper, and calcium. In many cases, only an adequate supply of one of these microelements (e.g. iodine) may reveal symptoms resulting from deficits of other microelements (e.g. iron or selenium). Selenium is accounted to the trace elements of key importance for homeostasis of the human system, in particular, for the proper functioning of the immune system and the TG. Results of epidemiological studies have demonstrated that selenium deficit may affect as many as one billion people in many countries all over the world. A proper sequence of particular supplementations is also worth emphasising for the significant correlations among the supplemented microelements. For example, it has been demonstrated that an excessive supplementation of selenium may enhance the effects of iodine deficit in endemic regions, while proper supplementation of selenium in studied animals may alleviate the consequences of iodine excess, preventing destructive-inflammatory lesions in the TG. This paper is a summary of the current knowledge on the role of selenium in the functionality of the TG.

Functional analysis of LDLR promoter and 5' UTR mutations in subjects with clinical diagnosis of familial hypercholesterolemia.

PubMed

De Castro-Orós, Isabel; Pampín, Sandra; Bolado-Carrancio, Alfonso; De Cubas, Aguirre; Palacios, Lourdes; Plana, Nuria; Puzo, Jose; Martorell, Esperanza; Stef, Marianne; Masana, Luis; Civeira, Fernando; Rodríguez-Rey, Jose Carlos; Pocoví, Miguel

2011-08-01

Familial hypercholesterolemia (FH) is a dominant disorder due to mutations in the LDLR gene. Several mutations in the LDLR promoter are associated with FH. Screening of 3,705 Spanish FH patients identified 10 variants in the promoter and 5' UTR. Here, we analyse the functionality of six newly identified LDLR variants. Mutations located in the LDLR promoter regulatory elements R2 and R3 (c.-155_-150delACCCCinsTTCTGCAAACTCCTCCC, c.-136C>G, c.-140C>G, and c.-140C>T) resulted in 6 to 15% residual activity in reporter expression experiments and changes in nuclear protein binding affinity compared to wild type. No reduction was observed when cells were transfected with c.-208T, c.-88A, and c.-36G mutant fragments. Our results indicate that mutations localized in R2 and R3 are associated with hypercholesterolemia, whereas mutations outside the LDLR response elements are not a cause of FH. This data emphasizes the importance of functional analysis of variants in the LDLR promoter to determine their association with the FH phenotype. © 2011 Wiley-Liss, Inc.

Resolving rates of mutation in the brain using single-neuron genomics

PubMed Central

Evrony, Gilad D; Lee, Eunjung; Park, Peter J; Walsh, Christopher A

2016-01-01

Whether somatic mutations contribute functional diversity to brain cells is a long-standing question. Single-neuron genomics enables direct measurement of somatic mutation rates in human brain and promises to answer this question. A recent study (Upton et al., 2015) reported high rates of somatic LINE-1 element (L1) retrotransposition in the hippocampus and cerebral cortex that would have major implications for normal brain function, and suggested that these events preferentially impact genes important for neuronal function. We identify aspects of the single-cell sequencing approach, bioinformatic analysis, and validation methods that led to thousands of artifacts being interpreted as somatic mutation events. Our reanalysis supports a mutation frequency of approximately 0.2 events per cell, which is about fifty-fold lower than reported, confirming that L1 elements mobilize in some human neurons but indicating that L1 mosaicism is not ubiquitous. Through consideration of the challenges identified, we provide a foundation and framework for designing single-cell genomics studies. DOI: http://dx.doi.org/10.7554/eLife.12966.001 PMID:26901440

Trace element levels in drinking water and cognitive function among elderly Chinese.

PubMed

Emsley, C L; Gao, S; Li, Y; Liang, C; Ji, R; Hall, K S; Cao, J; Ma, F; Wu, Y; Ying, P; Zhang, Y; Sun, S; Unverzagt, F W; Slemenda, C W; Hendrie, H C

2000-05-01

The relation between trace element levels in drinking water and cognitive function was investigated in a population-based study of elderly residents (n = 1,016) in rural China in 1996-1997. Cognitive function was measured using a Chinese translation of the Community Screening Interview for Dementia. A mixed effects model was used to evaluate the effect of each of the elements on cognitive function while adjusting for age, sex, and educational level. Several of the elements examined had a significant effect on cognitive function when they were assessed in a univariate context. However, after adjustment for other elements, many of these results were not significant. There was a significant quadratic effect for calcium and a significant zinc-cadmium interaction. Cognitive function increased with calcium level up to a certain point and then decreased as calcium continued to increase. Zinc showed a positive relation with cognitive function at low cadmium levels but a negative relation at high levels.

Synthesis of antiviral tetrahydrocarbazole derivatives by photochemical and acid-catalyzed C-H functionalization via intermediate peroxides (CHIPS).

PubMed

Gulzar, Naeem; Klussmann, Martin

2014-06-20

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order to streamline synthesis by saving steps, time and material compared to conventional methods that require the introduction and removal of activating or directing groups. Therefore, the functionalization of C-H bonds is also attractive for green chemistry. Under oxidative conditions, two C-H bonds or one C-H and one heteroatom-H bond can be transformed to C-C and C-heteroatom bonds, respectively. Often these oxidative coupling reactions require synthetic oxidants, expensive catalysts or high temperatures. Here, we describe a two-step procedure to functionalize indole derivatives, more specifically tetrahydrocarbazoles, by C-H amination using only elemental oxygen as oxidant. The reaction uses the principle of C-H functionalization via Intermediate PeroxideS (CHIPS). In the first step, a hydroperoxide is generated oxidatively using visible light, a photosensitizer and elemental oxygen. In the second step, the N-nucleophile, an aniline, is introduced by Brønsted-acid catalyzed activation of the hydroperoxide leaving group. The products of the first and second step often precipitate and can be conveniently filtered off. The synthesis of a biologically active compound is shown.

Identification of two novel functional p53 responsive elements in the Herpes Simplex Virus-1 genome

PubMed Central

Hsieh, Jui-Cheng; Kuta, Ryan; Armour, Courtney R.; Boehmer, Paul E.

2014-01-01

Analysis of the herpes simplex virus-1 (HSV-1) genome reveals two candidate p53 responsive elements (p53RE), located in proximity to the replication origins oriL and oriS, referred to as p53RE-L and p53RE-S, respectively. The sequences of p53RE-L and p53RE-S conform to the p53 consensus site and are present in HSV-1 strains KOS, 17, and F. p53 binds to both elements in vitro and in virus-infected cells. Both p53RE-L and p53RE-S are capable of conferring p53-dependent transcriptional activation onto a heterologous reporter gene. Importantly, expression of the essential immediate early viral transactivator ICP4 and the essential DNA replication protein ICP8, that are adjacent to p53RE-S and p53RE-L, are repressed in a p53-dependent manner. Taken together, this study identifies two novel functional p53RE in the HSV-1 genome and suggests a complex mechanism of viral gene regulation by p53 which may determine progression of the lytic viral replication cycle or the establishment of latency. PMID:25010269

DNA methylation induced changes in chromatin conformation of the promoter of the vitellogenin II gene of Japanese quail during aging.

PubMed

Gupta, Sanjay; Pathak, Rashmi U; Kanungo, Madhu S

2006-08-01

One approach to the understanding of the molecular basis of aging in higher organisms may be to use genes whose timing and rate of expression during the life span run parallel with specific functions that can be monitored. The genes for egg proteins, such as vitellogenin (VTG), which is expressed in the liver, and ovalbumin, lysozyme etc. that are expressed in the oviduct of birds, meet these requirements. Egg laying function is dependent on the production of these proteins, which, in turn, depends on the expression of their genes. In this communication we present the age-related studies on the VTG II gene of the bird, Japanese quail. The gene is expressed only in the liver and its expression is considerably lower in old birds that do not lay eggs. Comparison of the promoter region of the gene carrying the two important cis-acting elements, estrogen responsive element (ERE) and progesterone responsive element (PRE), shows it to be 100% homologous to the corresponding region of the chicken VTG II gene. Methylation of DNA and conformation of chromatin of this region were studied, as they are known to be important for regulation of expression of genes. Our studies show that in the liver of adult female quails which lay eggs, a -CCGG- sequence located in this region is hypomethylated, and the chromatin encompassing this region of the gene is relaxed. In the old, the -CCGG- sequence is hypermethylated and the chromatin is compact. This is correlated with a decrease in the expression of the gene and decrease in egg production. Further, electrophoretic mobility shift assay (EMSA) shows that the levels/affinity of specific trans-acting factors that bind to ERE and PRE present in the region, are not different in adult and old birds. Hence the methylation status of the -CCGG- sequence that is located in-between the ERE and the PRE may be crucial for the conformation of chromatin and availability of these two important cis-acting elements for the binding of the trans-acting factors. This, in turn, may downregulate the expression of the gene in old birds.

Balancing aggregation and smoothing errors in inverse models

DOE PAGES

Turner, A. J.; Jacob, D. J.

2015-06-30

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function ofmore » state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.« less

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-01-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-06-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.

Studies on the mechanism of functional cooperativity between progesterone and estrogen receptors.

PubMed

Bradshaw, M S; Tsai, S Y; Leng, X H; Dobson, A D; Conneely, O M; O'Malley, B W; Tsai, M J

1991-09-05

Steroid response elements (SREs) cooperate with many different cis-acting elements including NF-1 sites, CACCC boxes, and other SREs to induce target gene expression (Schule, R., Muller, M., Otsuka-Murakami, H., and Renkawitz, R. (1988) Nature 332, 87-90; Strahle, U., Schmid, W., and Schutz, G. (1988) EMBO J. 7, 3389-3395). Induction of gene expression can be additive or synergistic with respect to the level of activation by either transactivators. Two mechanisms have been proposed for how synergism occurs: 1) cooperative binding of transcriptional activators to DNA or 2) simultaneous interaction of individually bound activators with a common target protein. We have shown previously that cooperative binding of receptors is important for synergism between two progesterone response elements (PREs). Here we showed that an estrogen response element (ERE) and a PRE can also functionally cooperate and this synergism between an ERE and a PRE is not contributed by cooperative DNA binding. Furthermore, we have demonstrated that the activation domains of the progesterone receptor (PR) (C1Act) are required for synergism between two PREs and sufficient for confirming cooperative binding. However these two activation domains of PR are not sufficient for synergism between an ERE and a PRE. Additional regions within the NH2-terminal and COOH-terminal domains are also required for synergistic interaction between two heterologous SREs.

Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs

PubMed Central

Guzina, Jelena

2016-01-01

ABSTRACT Extracytoplasmic function (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both −35 and −10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended −10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ2, which is responsible for the interaction with the identified extension of the −10 element. Interestingly, a similar protein motif is found C-terminal of domain σ2 in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the −10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable −35 element and σ4 domain, which we identify in a homologous phage, 7-11, indicating that the extended −10 element can compensate for the lack of −35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested. IMPORTANCE ECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors. PMID:27137497

Heterogeneity of reward mechanisms.

PubMed

Lajtha, A; Sershen, H

2010-06-01

The finding that many drugs that have abuse potential and other natural stimuli such as food or sexual activity cause similar chemical changes in the brain, an increase in extracellular dopamine (DA) in the shell of the nucleus accumbens (NAccS), indicated some time ago that the reward mechanism is at least very similar for all stimuli and that the mechanism is relatively simple. The presently available information shows that the mechanisms involved are more complex and have multiple elements. Multiple brain regions, multiple receptors, multiple distinct neurons, multiple transmitters, multiple transporters, circuits, peptides, proteins, metabolism of transmitters, and phosphorylation, all participate in reward mechanisms. The system is variable, is changed during development, is sex-dependent, and is influenced by genetic differences. Not all of the elements participate in the reward of all stimuli. Different set of mechanisms are involved in the reward of different drugs of abuse, yet different mechanisms in the reward of natural stimuli such as food or sexual activity; thus there are different systems that distinguish different stimuli. Separate functions of the reward system such as anticipation, evaluation, consummation and identification; all contain function-specific elements. The level of the stimulus also influences the participation of the elements of the reward system, there are possible reactions to even below threshold stimuli, and excessive stimuli can change reward to aversion involving parts of the system. Learning and memory of past reward is an important integral element of reward and addictive behavior. Many of the reward elements are altered by repeated or chronic stimuli, and chronic exposure to one drug is likely to alter the response to another stimulus. To evaluate and identify the reward stimulus thus requires heterogeneity of the reward components in the brain.

The Effects of Mother Education Programs on the Functionality, Anger Management and Conflict Solution Levels of Families

ERIC Educational Resources Information Center

Kabasakal, Zekavet

2013-01-01

Problem Statement: Studies carried out in recent years both in Turkey and abroad indicate that child and teenage violence has increased and become widespread. Annually, 91.1% of deaths due to violence in the world occur in low and middle-income countries. Family life is an important element in understanding violent behavior as it relates to family…

[Genome organization and life cycle of the hepatitis c virus].

PubMed

Kalinina, O V; Dmitriev, A V

2015-01-01

The review summarizes the current data about the hepatitis C viral genome and polyprotein organization. The functional role of the structural and non-structural viral proteins including their interaction with cellular regulatory proteins and cell structural elements is discussed. Specific peculiarities of the life cycle of the hepatitis C virus important for the understanding of the viral hepatitis C pathogenesis are summarized.

Identifying Cytochrome P450 Functional Networks and Their Allosteric Regulatory Elements

DTIC Science & Technology

2013-12-03

drug alters the metabolism of another drug, potentially altering the pharmacological properties of either drug and leading to adverse toxic effects ...Despite extensive efforts in past decades to understand the mechanism behind these effects , drug metabolism and drug-drug interactions remain...important isoforms that is responsible for >50% of all drug metabolism, exhibits atypical kinetics due to allosteric effects [6]. Recently, Woods et al

Discrimination of lichen genera and species using element concentrations

USGS Publications Warehouse

Bennett, J.P.

2008-01-01

The importance of organic chemistry in the classification of lichens is well established, but inorganic chemistry has been largely overlooked. Six lichen species were studied over a period of 23 years that were growing in 11 protected areas of the northern Great Lakes ecoregion, which were not greatly influenced by anthropogenic particulates or gaseous air pollutants. The elemental data from these studies were aggregated in order to test the hypothesis that differences among species in tissue element concentrations were large enough to discriminate between taxa faithfully. Concentrations of 16 chemical elements that were found in tissue samples from Cladonia rangiferina, Evernia mesomorpha, Flavopunctelia flaventior, Hypogymnia physodes, Parmelia sulcata, and Punctelia rudecta were analyzed statistically using multivariate discriminant functions and CART analyses, as well as t-tests. Genera and species were clearly separated in element space, and elemental discriminant functions were able to classify 91-100 of the samples correctly into species. At the broadest level, a Zn concentration of 51 ppm in tissues of four of the lichen species effectively discriminated foliose from fruticose species. Similarly, a S concentration of 680 ppm discriminated C. rangiferina and E. mesomorpha, and a Ca concentration of 10 436 ppm discriminated H. physodes from P. sulcata. For the three parmelioid species, a Ca concentration >32 837 ppm discriminated Punctelia rudecta from the other two species, while a Zn concentration of 56 ppm discriminated Parmelia sulcata from F. flaventior. Foliose species also had higher concentrations than did fruticose species of all elements except Na. Elemental signatures for each of the six species were developed using standardized means. Twenty-four mechanisms explaining the differences among species are summarized. Finally, the relationships of four species based on element concentrations, using additive-trees clustering of a Euclidean-distance matrix, produced identical relationships as did analyses based on secondary product chemistry that used additive-trees clustering of a Jaccard similarity matrix. At least for these six species, element composition has taxonomic significance, and may be useful for discriminating other taxa. ?? 2008 British Lichen Society.

Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs).

PubMed

Szuplewska, Magdalena; Ludwiczak, Marta; Lyzwa, Katarzyna; Czarnecki, Jakub; Bartosik, Dariusz

2014-01-01

Functional transposable elements (TEs) of several Pseudomonas spp. strains isolated from black shale ore of Lubin mine and from post-flotation tailings of Zelazny Most in Poland, were identified using a positive selection trap plasmid strategy. This approach led to the capture and characterization of (i) 13 insertion sequences from 5 IS families (IS3, IS5, ISL3, IS30 and IS1380), (ii) isoforms of two Tn3-family transposons--Tn5563a and Tn4662a (the latter contains a toxin-antitoxin system), as well as (iii) non-autonomous TEs of diverse structure, ranging in size from 262 to 3892 bp. The non-autonomous elements transposed into AT-rich DNA regions and generated 5- or 6-bp sequence duplications at the target site of transposition. Although these TEs lack a transposase gene, they contain homologous 38-bp-long terminal inverted repeat sequences (IRs), highly conserved in Tn5563a and many other Tn3-family transposons. The simplest elements of this type, designated TIMEs (Tn3 family-derived Inverted-repeat Miniature Elements) (262 bp), were identified within two natural plasmids (pZM1P1 and pLM8P2) of Pseudomonas spp. It was demonstrated that TIMEs are able to mobilize segments of plasmid DNA for transposition, which results in the generation of more complex non-autonomous elements, resembling IS-driven composite transposons in structure. Such transposon-like elements may contain different functional genetic modules in their core regions, including plasmid replication systems. Another non-autonomous element "captured" with a trap plasmid was a TIME derivative containing a predicted resolvase gene and a res site typical for many Tn3-family transposons. The identification of a portable site-specific recombination system is another intriguing example confirming the important role of non-autonomous TEs of the TIME family in shuffling genetic information in bacterial genomes. Transposition of such mosaic elements may have a significant impact on diversity and evolution, not only of transposons and plasmids, but also of other types of mobile genetic elements.

Decomposition of New Woody Inputs as a Dry Tropical Forest Regenerates

NASA Astrophysics Data System (ADS)

Schilling, J. S.; Powers, J. S.; Ayres, A.; Kaffenberger, J. T.

2015-12-01

Modeling deadwood dynamics is limited by our empirical understanding of decomposition patterns and drivers. This gap is significant in dry tropical forests (and in the tropics, broadly) where forest regeneration is a management priority but where decision-making lacks resources. Our goal was to track decomposition and its biological drivers in tree boles added to the forest floor of a regenerating dry forest. We cut and then placed logs (~18 cm dia) of eight representative tree species in ground contact at two different sites (n=8, per site). We tracked density loss and element import/export in both sapwood and heartwood each 6 months over two years. We measured initial and final lignin, structural carbohydrates, nitrogen, and extractives. We also quantified insect gallery volumes, and used two residue 'signatures' to determine dominant fungal rot type: 1) dilute alkali solubility (DAS) and lignin:glucan loss. By year 2, mean density losses in sapwood were 11.6 - 44.4% among tree species, excluding one species that decomposed completely. The best predictor of density loss in sapwood was initial pH, but the correlation was negative rather than positive, as has been reported in temperate systems. Decay was consistently more advanced in sapwood than in heartwood, and although extractives were as high as 16.4% in heartwood, trait-density loss correlations were insignificant. Insects contributed little at this stage to density loss (<3%), and both lignin:glucan loss and DAS confirmed that white rot fungi dominated decomposition. Although element import dynamics broadly resembled those from temperate studies (e.g., Ca gain, P, K loss), there was high spatial variability. This perhaps related to zone line (spalting) complexity, suggesting intense competition among fungi colonizing small territories within the wood. Estimated CO2 fluxes from the test logs ranged from ~25 to 75% of the annual fluxes from litter fall at these sites. Collectively, these results implicate wood decomposition as an important component of dry forest carbon cycling. Emergent patterns from decomposers are also interesting in this case, where fungi assigned as a single functional group (white rot type) produced little variability in decay rates (Function 1) but high variability in element translocation (Function 2).

Exact finite elements for conduction and convection

NASA Technical Reports Server (NTRS)

Thornton, E. A.; Dechaumphai, P.; Tamma, K. K.

1981-01-01

An appproach for developing exact one dimensional conduction-convection finite elements is presented. Exact interpolation functions are derived based on solutions to the governing differential equations by employing a nodeless parameter. Exact interpolation functions are presented for combined heat transfer in several solids of different shapes, and for combined heat transfer in a flow passage. Numerical results demonstrate that exact one dimensional elements offer advantages over elements based on approximate interpolation functions. Previously announced in STAR as N81-31507

Automatic Assembly of Combined Checkingfixture for Auto-Body Components Based Onfixture Elements Libraries

NASA Astrophysics Data System (ADS)

Jiang, Jingtao; Sui, Rendong; Shi, Yan; Li, Furong; Hu, Caiqi

In this paper 3-D models of combined fixture elements are designed, classified by their functions, and saved in computer as supporting elements library, jointing elements library, basic elements library, localization elements library, clamping elements library, and adjusting elements library etc. Then automatic assembly of 3-D combined checking fixture for auto-body part is presented based on modularization theory. And in virtual auto-body assembly space, Locating constraint mapping technique and assembly rule-based reasoning technique are used to calculate the position of modular elements according to localization points and clamp points of auto-body part. Auto-body part model is transformed from itself coordinate system space to virtual assembly space by homogeneous transformation matrix. Automatic assembly of different functional fixture elements and auto-body part is implemented with API function based on the second development of UG. It is proven in practice that the method in this paper is feasible and high efficiency.

MILAMIN 2 - Fast MATLAB FEM solver

NASA Astrophysics Data System (ADS)

Dabrowski, Marcin; Krotkiewski, Marcin; Schmid, Daniel W.

2013-04-01

MILAMIN is a free and efficient MATLAB-based two-dimensional FEM solver utilizing unstructured meshes [Dabrowski et al., G-cubed (2008)]. The code consists of steady-state thermal diffusion and incompressible Stokes flow solvers implemented in approximately 200 lines of native MATLAB code. The brevity makes the code easily customizable. An important quality of MILAMIN is speed - it can handle millions of nodes within minutes on one CPU core of a standard desktop computer, and is faster than many commercial solutions. The new MILAMIN 2 allows three-dimensional modeling. It is designed as a set of functional modules that can be used as building blocks for efficient FEM simulations using MATLAB. The utilities are largely implemented as native MATLAB functions. For performance critical parts we use MUTILS - a suite of compiled MEX functions optimized for shared memory multi-core computers. The most important features of MILAMIN 2 are: 1. Modular approach to defining, tracking, and discretizing the geometry of the model 2. Interfaces to external mesh generators (e.g., Triangle, Fade2d, T3D) and mesh utilities (e.g., element type conversion, fast point location, boundary extraction) 3. Efficient computation of the stiffness matrix for a wide range of element types, anisotropic materials and three-dimensional problems 4. Fast global matrix assembly using a dedicated MEX function 5. Automatic integration rules 6. Flexible prescription (spatial, temporal, and field functions) and efficient application of Dirichlet, Neuman, and periodic boundary conditions 7. Treatment of transient and non-linear problems 8. Various iterative and multi-level solution strategies 9. Post-processing tools (e.g., numerical integration) 10. Visualization primitives using MATLAB, and VTK export functions We provide a large number of examples that show how to implement a custom FEM solver using the MILAMIN 2 framework. The examples are MATLAB scripts of increasing complexity that address a given technical topic (e.g., creating meshes, reordering nodes, applying boundary conditions), a given numerical topic (e.g., using various solution strategies, non-linear iterations), or that present a fully-developed solver designed to address a scientific topic (e.g., performing Stokes flow simulations in synthetic porous medium). References: Dabrowski, M., M. Krotkiewski, and D. W. Schmid MILAMIN: MATLAB-based finite element method solver for large problems, Geochem. Geophys. Geosyst., 9, Q04030, 2008

Changes in the location of biodiversity-ecosystem function hot spots across the seafloor landscape with increasing sediment nutrient loading.

PubMed

Thrush, Simon F; Hewitt, Judi E; Kraan, Casper; Lohrer, A M; Pilditch, Conrad A; Douglas, Emily

2017-04-12

Declining biodiversity and loss of ecosystem function threatens the ability of habitats to contribute ecosystem services. However, the form of the relationship between biodiversity and ecosystem function (BEF) and how relationships change with environmental change is poorly understood. This limits our ability to predict the consequences of biodiversity loss on ecosystem function, particularly in real-world marine ecosystems that are species rich, and where multiple ecosystem functions are represented by multiple indicators. We investigated spatial variation in BEF relationships across a 300 000 m 2 intertidal sandflat by nesting experimental manipulations of sediment pore water nitrogen concentration into sites with contrasting macrobenthic community composition. Our results highlight the significance of many different elements of biodiversity associated with environmental characteristics, community structure, functional diversity, ecological traits or particular species (ecosystem engineers) to important functions of coastal marine sediments (benthic oxygen consumption, ammonium pore water concentrations and flux across the sediment-water interface). Using the BEF relationships developed from our experiment, we demonstrate patchiness across a landscape in functional performance and the potential for changes in the location of functional hot and cold spots with increasing nutrient loading that have important implications for mapping and predicating change in functionality and the concomitant delivery of ecosystem services. © 2017 The Author(s).

Methods and circuitry for reconfigurable SEU/SET tolerance

NASA Technical Reports Server (NTRS)

Shuler, Jr., Robert L. (Inventor)

2010-01-01

A device is disclosed in one embodiment that has multiple identical sets of programmable functional elements, programmable routing resources, and majority voters that correct errors. The voters accept a mode input for a redundancy mode and a split mode. In the redundancy mode, the programmable functional elements are identical and are programmed identically so the voters produce an output corresponding to the majority of inputs that agree. In a split mode, each voter selects a particular programmable functional element output as the output of the voter. Therefore, in the split mode, the programmable functional elements can perform different functions, operate independently, and/or be connected together to process different parts of the same problem.

DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements.

PubMed

Osypov, Alexander A; Krutinin, Gleb G; Krutinina, Eugenia A; Kamzolova, Svetlana G

2012-04-01

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.

[Finite Element Analysis of Intravascular Stent Based on ANSYS Software].

PubMed

Shi, Gengqiang; Song, Xiaobing

2015-10-01

This paper adopted UG8.0 to bulid the stent and blood vessel models. The models were then imported into the finite element analysis software ANSYS. The simulation results of ANSYS software showed that after endothelial stent implantation, the velocity of the blood was slow and the fluctuation of velocity was small, which meant the flow was relatively stable. When blood flowed through the endothelial stent, the pressure gradually became smaller, and the range of the pressure was not wide. The endothelial shear stress basically unchanged. In general, it can be concluded that the endothelial stents have little impact on the flow of blood and can fully realize its function.

Auger spectroscopy analysis of lubrication with zinc dialkyldithiophosphate of several metal combinations in sliding contact

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1979-01-01

Sliding friction experiments were conducted with aluminum and other riders rubbing on disks of various elemental metals in the presence of a thin film of zinc dialkyldithiophosphate (ZDP). Auger emission spectroscopy was used to in situ monitor the changes in surface chemistry with rubbing under various loads. The metal disks examined included iron, titanium, rhodium, tungsten, molybdenum, and copper. For equivalent films of ZDP the film is a more effective lubricant for some metals than it is for others. The important active element in the compound varies with the metal lubricated and is a function of metal chemistry. The zinc in the ZDP is susceptible to electron beam induced desorption.

Average M shell fluorescence yields for elements with 70≤Z≤92

NASA Astrophysics Data System (ADS)

Kahoul, A.; Deghfel, B.; Aylikci, V.; Aylikci, N. K.; Nekkab, M.

2015-03-01

The theoretical, experimental and analytical methods for the calculation of average M-shell fluorescence yield (ω¯M ) of different elements are very important because of the large number of their applications in various areas of physical chemistry and medical research. In this paper, the bulk of the average M-shell fluorescence yield measurements reported in the literature, covering the period 1955 to 2005 are interpolated by using an analytical function to deduce the empirical average M-shell fluorescence yield in the atomic range of 70≤Z≤92. The results were compared with the theoretical and fitted values reported by other authors. Reasonable agreement was typically obtained between our result and other works.

Stress and the Hair Growth Cycle: Cortisol-Induced Hair Growth Disruption.

PubMed

Thom, Erling

2016-08-01

The stress hormone, cortisol, is known to affect the function and cyclic regulation of the hair follicle. When cortisol is present at high levels it has been demonstrated to reduce the synthesis and accelerate the degradation of important skin elements, namely hyaluronan and proteoglycans by approximately 40%. The following discussion outlines the relationship between stress, cortisol, and the effect on the normal function of the hair follicle. As a result of this connection, important correlations have been established in the literature to form a basis for novel, effective treatments of stress-related hair growth disorders.
Amongst various treatment methods and substances, oral supplementation with a specific bioavailable proteoglycan stands out as a promising new therapeutic treatment method.

J Drugs Dermatol. 2016;15(8):1001-1004.

Application of an ecosystem model to evaluate the importance of different processes and food web structure for transfer of 13 elements in a shallow lake.

PubMed

Konovalenko, L; Bradshaw, C; Andersson, E; Kautsky, U

2017-04-01

In environmental risk assessments of nuclear waste, there is need to estimate the potential risks of a large number of radionuclides over a long time period during which the environment is likely to change. Usually concentration ratios (CRs) are used to calculate the activity concentrations in organisms. However, CRs are not available for all radionuclides and they are not easily scalable to the varying environment. Here, an ecosystem transport model of elements, which estimates concentrations in organisms using carbon flows and food transfer instead of CR is presented. It is a stochastic compartment model developed for Lake Eckarfjärden at Forsmark in Sweden. The model was based on available data on carbon circulation, physical and biological processes from the site and identifies 11 functional groups of organisms. The ecosystem model was used to estimate the environmental transfer of 13 elements (Al, Ca, Cd, Cl, Cs, I, Ni, Nb, Pb, Se, Sr, Th, U) to various aquatic organisms, using element-specific distribution coefficients for suspended particles (K d PM ) and upper sediment (K d sed ), and subsequent transfer in the foodweb. The modelled CRs for different organism groups were compared with measured CRs from the lake and literature data, and showed good agreement for many elements and organisms, particularly for lower trophic levels. The model is, therefore, proposed as an alternative to measured CR, though it is suggested to further explore active uptake, assimilation and elimination processes to get better correspondence for some of the elements. The benthic organisms (i.e. bacteria, microphytobenthos and macroalgae) were identified as more important than pelagic organisms for transfer of elements to top predators. The element transfer model revealed that most of the radionuclides were channelled through the microbial loop, despite the fact that macroalgae dominated the carbon fluxes in this lake. Thus, element-specific adsorption of elements to the surface of aquatic species, that may be food sources for organisms at higher trophic levels, needs to be considered in combination with generic processes described by carbon fluxes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Processing of extraterrestrial materials by high temperature vacuum vaporization

NASA Technical Reports Server (NTRS)

Grimley, R. T.; Lipschutz, M. E.

1983-01-01

It is noted that problems associated with the extraction and concentration of elements and commpounds important for the construction and operation of space habitats have received little attention. High temperature vacuum vaporization is considered a promising approach; this is a technique for which the space environment offers advantages in the form of low ambient pressures and temperatures and the possibility of sustained high temperatures via solar thermal energy. To establish and refine this new technology, experimental determinations must be made of the material release profiles as a function of temperature, of the release kinetics and chemical forms of material being transported, and of the various means of altering release kinetics. Trace element data determined by neutron activation analysis of meteorites heated to 1400 C in vacuum is summarized. The principal tool, high temperature spectrometry, is used to examine the vaporization thermodynamics and kinetics of major and minor elements from complex multicomponent extraterrestrial materials.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

PubMed

Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar; Ruan, Yijun; Menghi, Francesca; Shin, Dong-Guk; Stitzel, Michael L; Vera-Licona, Paola; Ucar, Duygu

2016-06-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

Study of proton induced reactions on niobium targets up to 70 MeV

NASA Astrophysics Data System (ADS)

Ditrói, F.; Takács, S.; Tárkányi, F.; Baba, M.; Corniani, E.; Shubin, Yu. N.

2008-12-01

Niobium is a metal with important technological applications: use as alloying element to increase strength of super alloys, as thin layer for tribological applications, as superconductive material, in high temperature engineering systems, etc. In the frame of a systematic study of activation cross-sections of charged particle induced reactions on structural materials proton induced excitation functions on Nb targets were determined with the aim of applications in accelerator and reactor technology and for thin layer activation (TLA). The charged particle activation cross-sections on this element are also important for yield calculation of medical isotope production ( 88,89Zr, 86,87,88Y) and for dose estimation in PET targetry. As Niobium is a monoisotopic element it is an ideal target material to test nuclear reaction theories. We present here the integral excitation functions of 93Nb(p,x) 90,93mMo, 92m,91m,90Nb, 86,88,89Zr, 86,87mg,88Y and 85Sr in the energy range 30-70 MeV, some measured for the first time at this energy range. The results were compared with the theoretical cross-sections calculated by means of the code ALICE-IPPE and with the literature data. The calculations have been carried out without any parameter adjustment. The theory reproduces the shape of the measured results well and magnitude is also acceptable. Thick target yields calculated from our fitted cross-section give reliable estimations for production of medically relevant radioisotopes and for dose estimation in accelerator technology.

Gemitis : an integrated and participative risk reduction strategy for the sustainable development of cities

NASA Astrophysics Data System (ADS)

Masure, P.

2003-04-01

The GEMITIS method has been implemented since 1995 into a global and integrated Risk Reduction Strategy for improving the seismic risk-assessment effectiveness in urban areas, including the generation of crisis scenarios and mid- to long term- seismic impact assessment. GEMITIS required us to provide more precise definitions of notions in common use by natural-hazard specialists, such as elements at risk and vulnerability. Until then, only the physical and human elements had been considered, and analysis of their vulnerability referred to their fragility in the face of aggression by nature. We have completed this approach by also characterizing the social and cultural vulnerability of a city and its inhabitants, and, with a wider scope, the functional vulnerability of the "urban system". This functional vulnerability depends upon the relations between the system elements (weak links in chains, functional relays, and defense systems) and upon the city's relations with the outside world (interdependence). Though well developed in methods for evaluating industrial risk (fault-tree analysis, event-tree analysis, multiple defense barriers, etc.), this aspect had until now been ignored by the "hard-science" specialists working on natural hazards. Based on the implementation of an Urban System Exposure methodology, we were able to identify specific human, institutional, or functional vulnerability factors for each urban system, which until had been very little discussed by risk-analysis and civil-protection specialists. In addition, we have defined the new concept of "main stakes" of the urban system, ranked by order of social value (or collective utility). Obviously, vital or strategic issues must be better resistant or protected against natural hazards than issues of secondary importance. The ranking of exposed elements of a city in terms of "main stakes" provides a very useful guide for adapting vulnerability studies and for orienting preventive actions. For this, GEMITIS is based on a systemic approach of the city and on value analysis of exposed elements. It facilitates a collective expertise for the definition of a preventive action plan based on the participation of the main urban actors (crisis preparedness, construction, land-use, etc.).

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

PubMed Central

2013-01-01

Background Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers' targets. Results We discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs. Conclusions We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders. PMID:23628424

Understanding how prevocational training on care farms can lead to functioning, motivation and well-being.

PubMed

Ellingsen-Dalskau, Lina H; Berget, Bente; Pedersen, Ingeborg; Tellnes, Gunnar; Ihlebæk, Camilla

2016-12-01

Prevocational training aims to improve basic vocational and social skills, supporting return to work for people who have been out of work for a long time. Care farms provide prevocational training; the aim of the study was to use the self-determination theory to gain an understanding of how these programmes can lead to healthy functioning and motivation for clients. A total of 194 participants in prevocational training on care farms answered questions about demographic information, their perception of being a colleague, the social community on the farm, experiencing nature and animals and need satisfaction. A cross-sectional design resulting in a structural equation model was used to understand how elements of the care farm context influence satisfaction of three psychological needs. The results showed that a feeling of being a useful colleague led to competence, experiencing a sense of group belonging led to relatedness and autonomy, while receiving social support from the farmer led to satisfaction of all three needs for the participants. The results explain how prevocational training can stimulate participants' functionality, motivation and well-being. This understanding enables initiators and managers of prevocational training to understand and further strengthen the need-supportive elements of such programmes. Implications for Rehabilitation Prevocational training on care farms can facilitate motivation, functioning and well-being for clients. Making clients feel like useful colleagues that belong to a client group will strengthen the positive qualities of these programmes. Support, understanding and acknowledgement from the farmer are the most important elements for a positive development for the clients.

Design methodology and results evaluation of a heating functionality in modular lab-on-chip systems

NASA Astrophysics Data System (ADS)

Streit, Petra; Nestler, Joerg; Shaporin, Alexey; Graunitz, Jenny; Otto, Thomas

2018-06-01

Lab-on-a-chip (LoC) systems offer the opportunity of fast and customized biological analyses executed at the ‘point-of-need’ without expensive lab equipment. Some biological processes need a temperature treatment. Therefore, it is important to ensure a defined and stable temperature distribution in the biosensor area. An integrated heating functionality is realized with discrete resistive heating elements including temperature measurement. The focus of this contribution is a design methodology and evaluation technique of the temperature distribution in the biosensor area with regard to the thermal-electrical behaviour of the heat sources. Furthermore, a sophisticated control of the biosensor temperature is proposed. A finite element (FE) model with one and more integrated heat sources in a polymer-based LoC system is used to investigate the impact of the number and arrangement of heating elements on the temperature distribution around the heating elements and in the biosensor area. Based on this model, various LOC systems are designed and fabricated. Electrical characterization of the heat sources and independent temperature measurements with infrared technique are performed to verify the model parameters and prove the simulation approach. The FE model and the proposed methodology is the foundation for optimization and evaluation of new designs with regard to temperature requirements of the biosensor. Furthermore, a linear dependency of the heater temperature on the electric current is demonstrated in the targeted temperature range of 20 °C to 70 °C enabling the usage of the heating functionality for biological reactions requiring a steady-state temperature up to 70 °C. The correlation between heater and biosensor area temperature is derived for a direct control through the heating current.

Highly Accurate Beam Torsion Solutions Using the p-Version Finite Element Method

NASA Technical Reports Server (NTRS)

Smith, James P.

1996-01-01

A new treatment of the classical beam torsion boundary value problem is applied. Using the p-version finite element method with shape functions based on Legendre polynomials, torsion solutions for generic cross-sections comprised of isotropic materials are developed. Element shape functions for quadrilateral and triangular elements are discussed, and numerical examples are provided.

COMPUTING MEDIUM USING THRESHOLD ELEMENTS WITH COMBINED FUNCTIONS,

DTIC Science & Technology

by grouping a number of elements to perform the desired functions. In the pulsed threshold system, a refractory period exists when the elements do not...disjunction, storage, and interaction. The level threshold elements, on the other hand do not have a refractory property but nevertheless they are able to perform signal branching, NOR operation, negation, and storage. (Author)

Weight-lattice discretization of Weyl-orbit functions

NASA Astrophysics Data System (ADS)

Hrivnák, Jiří; Walton, Mark A.

2016-08-01

Weyl-orbit functions have been defined for each simple Lie algebra, and permit Fourier-like analysis on the fundamental region of the corresponding affine Weyl group. They have also been discretized, using a refinement of the coweight lattice, so that digitized data on the fundamental region can be Fourier-analyzed. The discretized orbit function has arguments that are redundant if related by the affine Weyl group, while its labels, the Weyl-orbit representatives, invoke the dual affine Weyl group. Here we discretize the orbit functions in a novel way, by using the weight lattice. A cleaner theory results with symmetry between the arguments and labels of the discretized orbit functions. Orthogonality of the new discretized orbit functions is proved, and leads to the construction of unitary, symmetric matrices with Weyl-orbit-valued elements. For one type of orbit function, the matrix coincides with the Kac-Peterson modular S matrix, important for Wess-Zumino-Novikov-Witten conformal field theory.

CONSTRUCTION OF SCALAR AND VECTOR FINITE ELEMENT FAMILIES ON POLYGONAL AND POLYHEDRAL MESHES

PubMed Central

GILLETTE, ANDREW; RAND, ALEXANDER; BAJAJ, CHANDRAJIT

2016-01-01

We combine theoretical results from polytope domain meshing, generalized barycentric coordinates, and finite element exterior calculus to construct scalar- and vector-valued basis functions for conforming finite element methods on generic convex polytope meshes in dimensions 2 and 3. Our construction recovers well-known bases for the lowest order Nédélec, Raviart-Thomas, and Brezzi-Douglas-Marini elements on simplicial meshes and generalizes the notion of Whitney forms to non-simplicial convex polygons and polyhedra. We show that our basis functions lie in the correct function space with regards to global continuity and that they reproduce the requisite polynomial differential forms described by finite element exterior calculus. We present a method to count the number of basis functions required to ensure these two key properties. PMID:28077939

CONSTRUCTION OF SCALAR AND VECTOR FINITE ELEMENT FAMILIES ON POLYGONAL AND POLYHEDRAL MESHES.

PubMed

Gillette, Andrew; Rand, Alexander; Bajaj, Chandrajit

2016-10-01

We combine theoretical results from polytope domain meshing, generalized barycentric coordinates, and finite element exterior calculus to construct scalar- and vector-valued basis functions for conforming finite element methods on generic convex polytope meshes in dimensions 2 and 3. Our construction recovers well-known bases for the lowest order Nédélec, Raviart-Thomas, and Brezzi-Douglas-Marini elements on simplicial meshes and generalizes the notion of Whitney forms to non-simplicial convex polygons and polyhedra. We show that our basis functions lie in the correct function space with regards to global continuity and that they reproduce the requisite polynomial differential forms described by finite element exterior calculus. We present a method to count the number of basis functions required to ensure these two key properties.

[Postoperative management of partial or reconstructive pharyngo-laryngectomies].

PubMed

Monziols, F; Verhulst, J; Lenoir, J L; Alix, M; Larricque, J; Krispel, N

1995-01-01

The multidisciplinary management of patients following pharyngolaryngeal surgery is an essential condition for its functional and socio-professional success. Early, overall rehabilitation, geared to each type of exeresis and to the personality of each patient, will enable both the voice and swallowing to regain their autonomy. A series of 195 patients after partial or reconstructive laryngectomy or pharyngectomy is analysed. The maintenance of a functional crico-arytenoid unity, the preservation of the mucosal sensitivity, the establishment of a facilitating posture and the dynamisation of the neoglottic sphincter are all equally important elements requiring the mobilisation of the entire health care team.

Analysis of sDMA modifications of PIWI proteins

PubMed Central

Honda, Shozo; Kirino, Yoriko; Kirino, Yohei

2015-01-01

Summary Arginine methylation is an important post-translational protein modification that modulates protein function for a wide range of biological processes. PIWI proteins, a subclade of the Argonaute family proteins, contain evolutionarily conserved symmetrical dimethylarginines (sDMAs). It has become increasingly apparent that the sDMAs of PIWI proteins serve as binding elements for TUDOR-domain containing proteins and that sDMA-dependent protein interactions play crucial roles in the biogenesis and function of PIWI-interacting RNAs (piRNAs). We describe a method for detecting PIWI sDMAs and purifying PIWI/piRNA complexes using anti-sDMA antibodies. PMID:24178562

Ecosystem function and services provided by the deep sea

NASA Astrophysics Data System (ADS)

Thurber, A. R.; Sweetman, A. K.; Narayanaswamy, B. E.; Jones, D. O. B.; Ingels, J.; Hansman, R. L.

2014-07-01

The deep sea is often viewed as a vast, dark, remote, and inhospitable environment, yet the deep ocean and seafloor are crucial to our lives through the services that they provide. Our understanding of how the deep sea functions remains limited, but when treated synoptically, a diversity of supporting, provisioning, regulating and cultural services becomes apparent. The biological pump transports carbon from the atmosphere into deep-ocean water masses that are separated over prolonged periods, reducing the impact of anthropogenic carbon release. Microbial oxidation of methane keeps another potent greenhouse gas out of the atmosphere while trapping carbon in authigenic carbonates. Nutrient regeneration by all faunal size classes provides the elements necessary for fueling surface productivity and fisheries, and microbial processes detoxify a diversity of compounds. Each of these processes occur on a very small scale, yet considering the vast area over which they occur they become important for the global functioning of the ocean. The deep sea also provides a wealth of resources, including fish stocks, enormous bioprospecting potential, and elements and energy reserves that are currently being extracted and will be increasingly important in the near future. Society benefits from the intrigue and mystery, the strange life forms, and the great unknown that has acted as a muse for inspiration and imagination since near the beginning of civilization. While many functions occur on the scale of microns to meters and timescales up to years, the derived services that result are only useful after centuries of integrated activity. This vast dark habitat, which covers the majority of the globe, harbors processes that directly impact humans in a variety of ways; however, the same traits that differentiate it from terrestrial or shallow marine systems also result in a greater need for integrated spatial and temporal understanding as it experiences increased use by society. In this manuscript we aim to provide a foundation for informed conservation and management of the deep sea by summarizing the important role of the deep sea in society.

The E7 Open Reading Frame Acts in cis and in trans To Mediate Differentiation-Dependent Activities in the Human Papillomavirus Type 16 Life Cycle▿†

PubMed Central

Bodily, Jason M.; Mehta, Kavi P. M.; Cruz, Linda; Meyers, Craig; Laimins, Laimonis A.

2011-01-01

Human papillomaviruses (HPVs) are the causative agents of several important genital and other mucosal cancers. The HPV16 E7 gene encodes a viral oncogene that is necessary for the continued growth of cancer cells, but its role in the normal, differentiation-dependent life cycle of the virus is not fully understood. The function of E7 in the viral life cycle was examined using a series of mutations of E7 created in the context of the complete HPV16 genome. The effect of these E7 mutations on key events of the viral life cycle, including immortalization, episomal maintenance, late promoter activation, and infectious virion synthesis, was examined. Our studies show that the pRb binding domain is indispensable for early viral activities, whereas the C-terminal zinc finger domain contributed primarily to very late events. Mutations of the casein kinase II phosphorylation site caused a complex phenotype involving both the function of E7 protein and a cis element necessary for the activation of the late promoter, identifying for the first time a promoter element important for late promoter function in the context of the viral genome. All mutant genomes tested showed reduced viral titers following growth in organotypic raft cultures. These studies clarify the role of E7 as a regulator of late events in the differentiation-dependent HPV life cycle. PMID:21697473

Structure of MRDI Explains its Dual Function as a Metabolic Enzyme and a Mediator of Cell Invasion

PubMed Central

Templeton, Paul D.; Litman, Elizabeth S.; Metzner, Sandra I.; Ahn, Natalie G.; Sousa, Marcelo C.

2013-01-01

Metastatic melanoma is among the most intractable cancers to treat, where patients show resistance to therapy and limited survival time. A critical step in the development of metastatic melanoma is the acquisition of invasion and transition from thin to thick tumors on the skin, followed by invasion to lymph nodes. Prior studies have shown that metastatic melanoma is associated with dysregulation of RhoA and enhanced expression of a protein named “mediator of RhoA-dependent invasion (MRDI)”. Importantly, MRDI is a “moonlighting” enzyme, with two distinct functions in melanoma cells. First, MRDI acts as a methylthioribose-1-phosphate (MTR-1-P) isomerase, catalyzing a critical step in methionine salvage. Second, MRDI promotes and is necessary for melanoma cell invasion, independent of its catalytic activity. Here, we demonstrate that MtnA, a bacterial MTR-1-P isomerase, rescues the methionine salvage function of MRDI, but is unable to rescue its role in invasion. We then solve the crystal structure of MRDI to a resolution of 2.5 Å, in order to identify structural elements important for its invasion activity. We present this structure and its comparison with other MTR-1-P isomerases, and identify mutations within a region separate from the MTR-1-P binding site which interfere with invasion. Thus, structural elements in MRDI distal from the MTR-1-P catalytic site are responsible for the invasion phenotype. PMID:23859498

A post-publication analysis of the idealized upper reference value of 2.5 mIU/L for TSH: Time to support the thyroid axis with magnesium and iron especially in the setting of reproduction medicine.

PubMed

Moncayo, Roy; Moncayo, Helga

2017-06-01

Laboratory medicine approaches the evaluation of thyroid function mostly through the single determination of the blood level of thyroid stimulating hormone (TSH). Some authors have suggested an upper reference value for TSH of 2.5 mIU/L. This suggestion has not been confirmed by recent clinical studies. These studies have delivered a clinically valid reference range going from 0.3 to 3.5 mIU/L. These values are valid for both for the general population as well as in the setting of fertility and pregnancy. Current biochemical evidence about the elements required to maintain thyroid function shows that these not only include dietary iodine but also magnesium, iron, selenium and coenzyme Q10. Iron is important for the synthesis of thyroid peroxidase; magnesium-ATP contributes to the active process of iodine uptake; iodine has to be sufficiently present in the diet; selenium acts through selenoproteins to protect the thyroid cell during hormone synthesis and in deiodination of thyroxine; coenzyme Q10 influences thyroid vascularity. As a consequence, good clinical practice requires additional biochemical information on the blood levels of magnesium, selenium, coenzyme Q10 as well as iron status. Since these elements are also important for the maintenance of reproductive function, we postulate that they constitute the connecting link between both endocrine systems.

Fitness landscapes, heuristics and technological paradigms: A critique on random search models in evolutionary economics

NASA Astrophysics Data System (ADS)

Frenken, Koen

2001-06-01

The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analyzed as "hill-climbing" on NK fitness landscapes through random mutation and natural selection. In evolutionary economics, NK fitness landscapes have been used to simulate the evolution of complex technological systems containing elements that are interdependent in their functioning. In these models, economic agents randomly search for new technological design by trial-and-error and run the risk of ending up in sub-optimal solutions due to interdependencies between the elements in a complex system. These models of random search are legitimate for reasons of modeling simplicity, but remain limited as these models ignore the fact that agents can apply heuristics. A specific heuristic is one that sequentially optimises functions according to their ranking by users of the system. To model this heuristic, a generalized NK-model is developed. In this model, core elements that influence many functions can be distinguished from peripheral elements that affect few functions. The concept of paradigmatic search can then be analytically defined as search that leaves core elements in tact while concentrating on improving functions by mutation of peripheral elements.

Superluminal antenna

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

Singleton, John; Earley, Lawrence M.; Krawczyk, Frank L.

A superluminal antenna element integrates a balun element to better impedance match an input cable or waveguide to a dielectric radiator element, thus preventing stray reflections and consequent undesirable radiation. For example, a dielectric housing material can be used that has a cutout area. A cable can extend into the cutout area. A triangular conductor can function as an impedance transition. An additional cylindrical element functions as a sleeve balun to better impedance match the radiator element to the cable.

Superluminal antenna

DOEpatents

Singleton, John; Earley, Lawrence M.; Krawczyk, Frank L.; Potter, James M.; Romero, William P.; Wang, Zhi-Fu

2018-04-17

A superluminal antenna element integrates a balun element to better impedance match an input cable or waveguide to a dielectric radiator element, thus preventing stray reflections and consequent undesirable radiation. For example, a dielectric housing material can be used that has a cutout area. A cable can extend into the cutout area. A triangular conductor can function as an impedance transition. An additional cylindrical element functions as a sleeve balun to better impedance match the radiator element to the cable.

Application of finite element approach to transonic flow problems

NASA Technical Reports Server (NTRS)

Hafez, M. M.; Murman, E. M.; Wellford, L. C., Jr.

1976-01-01

A variational finite element model for transonic small disturbance calculations is described. Different strategy is adopted in subsonic and supersonic regions, and blending elements are introduced between different regions. In the supersonic region, no upstream effect is allowed. If rectangular elements with linear shape functions are used, the model is similar to Murman's finite difference operators. Higher order shape functions, nonrectangular elements, and discontinuous approximation of shock waves are also discussed.

Reduce beam hardening artifacts of polychromatic X-ray computed tomography by an iterative approximation approach.

PubMed

Shi, Hongli; Yang, Zhi; Luo, Shuqian

2017-01-01

The beam hardening artifact is one of most important modalities of metal artifact for polychromatic X-ray computed tomography (CT), which can impair the image quality seriously. An iterative approach is proposed to reduce beam hardening artifact caused by metallic components in polychromatic X-ray CT. According to Lambert-Beer law, the (detected) projections can be expressed as monotonic nonlinear functions of element geometry projections, which are the theoretical projections produced only by the pixel intensities (image grayscale) of certain element (component). With help of a prior knowledge on spectrum distribution of X-ray beam source and energy-dependent attenuation coefficients, the functions have explicit expressions. Newton-Raphson algorithm is employed to solve the functions. The solutions are named as the synthetical geometry projections, which are the nearly linear weighted sum of element geometry projections with respect to mean of each attenuation coefficient. In this process, the attenuation coefficients are modified to make Newton-Raphson iterative functions satisfy the convergence conditions of fixed pointed iteration(FPI) so that the solutions will approach the true synthetical geometry projections stably. The underlying images are obtained using the projections by general reconstruction algorithms such as the filtered back projection (FBP). The image gray values are adjusted according to the attenuation coefficient means to obtain proper CT numbers. Several examples demonstrate the proposed approach is efficient in reducing beam hardening artifacts and has satisfactory performance in the term of some general criteria. In a simulation example, the normalized root mean square difference (NRMSD) can be reduced 17.52% compared to a newest algorithm. Since the element geometry projections are free from the effect of beam hardening, the nearly linear weighted sum of them, the synthetical geometry projections, are almost free from the effect of beam hardening. By working out the synthetical geometry projections, the proposed approach becomes quite efficient in reducing beam hardening artifacts.

Design strategies of sea urchin teeth: structure, composition and micromechanical relations to function.

PubMed

Wang, R Z; Addadi, L; Weiner, S

1997-04-29

The teeth of sea urchins comprise a variety of different structural entities, all of which are composed of magnesium-bearing calcite together with a small amount of organic material. The teeth are worn down continuously, but in such a way that they remain sharp and functional. Here we describe aspects of the structural, compositional and micromechanical properties of the teeth of Paracentrotus lividus using scanning electron microscopy, infrared spectrometry, atomic absorption. X-ray diffraction and microindentation. The S-shaped single crystalline calcitic fibres are one of the main structural elements of the tooth. They extend from the stone part to the keel. The diameter of the fibres increases gradually from less than 1 micron at the stone tip to about 20 microns at the keel end, while their MgCO3 contents decrease from about 13 mol% to about 4.5 mol%. Each fibre is coated by a thin organic sheath and surrounded by polycrystalline calcitic discs containing as much as 35 mol% MgCO3. This structure constitutes a unique kind of gradient fibre-reinforced ceramic matrix composite, whose microhardness and toughness decrease gradually from the stone part to the keel. Primary plates are also important structural elements of the tooth. Each primary plate has a very unusual sandwich-like structure with a calcitic envelope surrounding a thin apparently amorphous CaCO3 layer. This central layer, together with the primary plate/disc interface, improves the toughness of this zone by stopping and blunting cracks. The self-sharpening function of the teeth is believed to result from the combination of the geometrical shape of the main structural elements and their spatial arrangement, the interfacial strength between structural elements, and the hardness gradient extending from the working stone part to the surrounding zones. The sea urchin tooth structure possesses an array of interesting functional design features, some of which may possibly be applicable to materials science.

The Lorentzian distance formula in noncommutative geometry

NASA Astrophysics Data System (ADS)

Franco, Nicolas

2018-02-01

For almost twenty years, a search for a Lorentzian version of the well-known Connes’ distance formula has been undertaken. Several authors have contributed to this search, providing important milestones, and the time has now come to put those elements together in order to get a valid and functional formula. This paper presents a historical review of the construction and the proof of a Lorentzian distance formula suitable for noncommutative geometry.

Matrix Management in DoD: An Annotated Bibliography

DTIC Science & Technology

1984-04-01

ADDRESS 10 PROGRAM ELEMENT. PROJECT, TASK AREA & WORK UNIT NUMBERS ACSC/EDCC, MAXWELL AFB AL 36112 1 1. CONTROLLING OFFICE NAME AND ADDRESS 12 ...completes their message that matrix orga- nization is the likely format of the multiprogram Program Office. 12 The text’s discussion of matrix is...manager, and functional specialist are of vital importance to the effective operation of the matrix .... Matrix management will not achieve its

Economic value of ecosystem conservation in Japan: Reduction of starting point bias by bid effect function

Treesearch

Mitsuyasu Yabe

2007-01-01

Over 18 million people visit and enjoy the view of the world’s largest class caldera topography, which forms the important landscape element of National Park Aso. Aso grassland spreads and rare plants exist in the harmony of nature and human activities. This study was a Contingent Valuation (CV) survey to estimate the conservation value of Aso grassland. We...

Preliminary Component Integration Using Rapid Prototyping Techniques

NASA Technical Reports Server (NTRS)

Cooper, Ken; Salvail, Pat; Gordon, Gail (Technical Monitor)

2001-01-01

Rapid prototyping is a very important tool that should be used by both design and manufacturing disciplines during the development of elements for the aerospace industry. It helps prevent lack of adequate communication between design and manufacturing engineers (which could lead to costly errors) through mutual consideration of functional models generated from drawings. Rapid prototyping techniques are used to test hardware for design and material compatibility at Marshall Space Flight Center.

A Generic Expert Scheduling System Architecture and Toolkit: GUESS (Generically Used Expert Scheduling System)

NASA Technical Reports Server (NTRS)

Liebowitz, Jay; Krishnamurthy, Vijaya; Rodens, Ira; Houston, Chapman; Liebowitz, Alisa; Baek, Seung; Radko, Joe; Zeide, Janet

1996-01-01

Scheduling has become an increasingly important element in today's society and workplace. Within the NASA environment, scheduling is one of the most frequently performed and challenging functions. Towards meeting NASA's scheduling needs, a research version of a generic expert scheduling system architecture and toolkit has been developed. This final report describes the development and testing of GUESS (Generically Used Expert Scheduling System).

Simultaneous shifts in elemental stoichiometry and fatty acids of Emiliania huxleyi in response to environmental changes

NASA Astrophysics Data System (ADS)

Bi, Rong; Ismar, Stefanie M. H.; Sommer, Ulrich; Zhao, Meixun

2018-02-01

Climate-driven changes in environmental conditions have significant and complex effects on marine ecosystems. Variability in phytoplankton elements and biochemicals can be important for global ocean biogeochemistry and ecological functions, while there is currently limited understanding on how elements and biochemicals respond to the changing environments in key coccolithophore species such as Emiliania huxleyi. We investigated responses of elemental stoichiometry and fatty acids (FAs) in a strain of E. huxleyi under three temperatures (12, 18 and 24 °C), three N : P supply ratios (molar ratios 10:1, 24:1 and 63:1) and two pCO2 levels (560 and 2400 µatm). Overall, C : N : P stoichiometry showed the most pronounced response to N : P supply ratios, with high ratios of particulate organic carbon vs. particulate organic nitrogen (POC : PON) and low ratios of PON vs. particulate organic phosphorus (PON : POP) in low-N media, and high POC : POP and PON : POP in low-P media. The ratio of particulate inorganic carbon vs. POC (PIC : POC) and polyunsaturated fatty acid proportions strongly responded to temperature and pCO2, both being lower under high pCO2 and higher with warming. We observed synergistic interactions between warming and nutrient deficiency (and high pCO2) on elemental cellular contents and docosahexaenoic acid (DHA) proportion in most cases, indicating the enhanced effect of warming under nutrient deficiency (and high pCO2). Our results suggest differential sensitivity of elements and FAs to the changes in temperature, nutrient availability and pCO2 in E. huxleyi, which is to some extent unique compared to non-calcifying algal classes. Thus, simultaneous changes of elements and FAs should be considered when predicting future roles of E. huxleyi in the biotic-mediated connection between biogeochemical cycles, ecological functions and climate change.

Cloning and functional analysis of 5'-upstream region of the Pokemon gene.

PubMed

Yang, Yutao; Zhou, Xiaowei; Zhu, Xudong; Zhang, Chuanfu; Yang, Zhixin; Xu, Long; Huang, Peitang

2008-04-01

Pokemon, the POK erythroid myeloid ontogenic factor, not only regulates the expression of many genes, but also plays an important role in cell tumorigenesis. To investigate the molecular mechanism regulating expression of the Pokemon gene in humans, its 5'-upstream region was cloned and analyzed. Transient analysis revealed that the Pokemon promoter is constitutive. Deletion analysis and a DNA decoy assay indicated that the NEG-U and NEG-D elements were involved in negative regulation of the Pokemon promoter, whereas the POS-D element was mainly responsible for its strong activity. Electrophoretic mobility shift assays suggested that the NEG-U, NEG-D and POS-D elements were specifically bound by the nuclear extract from A549 cells in vitro. Mutation analysis demonstrated that cooperation of the NEG-U and NEG-D elements led to negative regulation of the Pokemon promoter. Moreover, the NEG-U and NEG-D elements needed to be an appropriate distance apart in the Pokemon promoter in order to cooperate. Taken together, our results elucidate the mechanism underlying the regulation of Pokemon gene transcription, and also define a novel regulatory sequence that may be used to decrease expression of the Pokemon gene in cancer gene therapy.

Robust Translation of the Nucleoid Protein Fis Requires a Remote Upstream AU Element and Is Enhanced by RNA Secondary Structure

PubMed Central

Nafissi, Maryam; Chau, Jeannette; Xu, Jimin

2012-01-01

Synthesis of the Fis nucleoid protein rapidly increases in response to nutrient upshifts, and Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions. Previous work has shown that control of Fis synthesis occurs at transcription initiation of the dusB-fis operon. We show here that while translation of the dihydrouridine synthase gene dusB is low, unusual mechanisms operate to enable robust translation of fis. At least two RNA sequence elements located within the dusB coding region are responsible for high fis translation. The most important is an AU element centered 35 nucleotides (nt) upstream of the fis AUG, which may function as a binding site for ribosomal protein S1. In addition, a 44-nt segment located upstream of the AU element and predicted to form a stem-loop secondary structure plays a prominent role in enhancing fis translation. On the other hand, mutations close to the AUG, including over a potential Shine-Dalgarno sequence, have little effect on Fis protein levels. The AU element and stem-loop regions are phylogenetically conserved within dusB-fis operons of representative enteric bacteria. PMID:22389479

Proteomics technique opens new frontiers in mobilome research.

PubMed

Davidson, Andrew D; Matthews, David A; Maringer, Kevin

2017-01-01

A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons. In a recent paper, we overcame these technical hurdles using a technique called "proteomics informed by transcriptomics" (PIT), and thus published the first unbiased global mobilome-derived proteome for any organism (using cell lines derived from the mosquito Aedes aegypti ). In this commentary, we describe our methods in more detail, and summarise our major findings. We also use new genome sequencing data to show that, in many cases, the specific genomic element expressing a given protein can be identified using PIT. This proteomic technique therefore represents an important technological advance that will open new avenues of research into the role that proteins derived from transposons and other repetitive and sequence diverse genetic elements, such as endogenous retroviruses, play in health and disease.

Soybean DREB1/CBF-type transcription factors function in heat and drought as well as cold stress-responsive gene expression.

PubMed

Kidokoro, Satoshi; Watanabe, Keitaro; Ohori, Teppei; Moriwaki, Takashi; Maruyama, Kyonoshin; Mizoi, Junya; Myint Phyu Sin Htwe, Nang; Fujita, Yasunari; Sekita, Sachiko; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2015-02-01

Soybean (Glycine max) is a globally important crop, and its growth and yield are severely reduced by abiotic stresses, such as drought, heat, and cold. The cis-acting element DRE (dehydration-responsive element)/CRT plays an important role in activating gene expression in response to these stresses. The Arabidopsis DREB1/CBF genes that encode DRE-binding proteins function as transcriptional activators in the cold stress responsive gene expression. In this study, we identified 14 DREB1-type transcription factors (GmDREB1s) from a soybean genome database. The expression of most GmDREB1 genes in soybean was strongly induced by a variety of abiotic stresses, such as cold, drought, high salt, and heat. The GmDREB1 proteins activated transcription via DREs (dehydration-responsive element) in Arabidopsis and soybean protoplasts. Transcriptome analyses using transgenic Arabidopsis plants overexpressing GmDREB1s indicated that many of the downstream genes are cold-inducible and overlap with those of Arabidopsis DREB1A. We then comprehensively analyzed the downstream genes of GmDREB1B;1, which is closely related to DREB1A, using a transient expression system in soybean protoplasts. The expression of numerous genes induced by various abiotic stresses were increased by overexpressing GmDREB1B;1 in soybean, and DREs were the most conserved element in the promoters of these genes. The downstream genes of GmDREB1B;1 included numerous soybean-specific stress-inducible genes that encode an ABA receptor family protein, GmPYL21, and translation-related genes, such as ribosomal proteins. We confirmed that GmDREB1B;1 directly activates GmPYL21 expression and enhances ABRE-mediated gene expression in an ABA-independent manner. These results suggest that GmDREB1 proteins activate the expression of numerous soybean-specific stress-responsive genes under diverse abiotic stress conditions. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

The Drosophila Translational Control Element (TCE) Is Required for High-Level Transcription of Many Genes That Are Specifically Expressed in Testes

PubMed Central

Anderson, Ashley K.; Ohler, Uwe; Wassarman, David A.

2012-01-01

To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5′ untranslated region of Mst(3)CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300–400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the dual role of the TCE in translational and transcriptional regulation. PMID:22984601

The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.

PubMed

Katzenberger, Rebeccah J; Rach, Elizabeth A; Anderson, Ashley K; Ohler, Uwe; Wassarman, David A

2012-01-01

To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5' untranslated region of Mst(3)CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300-400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the dual role of the TCE in translational and transcriptional regulation.

Convergence of the transcriptional responses to heat shock and singlet oxygen stresses.

PubMed

Dufour, Yann S; Imam, Saheed; Koo, Byoung-Mo; Green, Heather A; Donohue, Timothy J

2012-09-01

Cells often mount transcriptional responses and activate specific sets of genes in response to stress-inducing signals such as heat or reactive oxygen species. Transcription factors in the RpoH family of bacterial alternative σ factors usually control gene expression during a heat shock response. Interestingly, several α-proteobacteria possess two or more paralogs of RpoH, suggesting some functional distinction. We investigated the target promoters of Rhodobacter sphaeroides RpoH(I) and RpoH(II) using genome-scale data derived from gene expression profiling and the direct interactions of each protein with DNA in vivo. We found that the RpoH(I) and RpoH(II) regulons have both distinct and overlapping gene sets. We predicted DNA sequence elements that dictate promoter recognition specificity by each RpoH paralog. We found that several bases in the highly conserved TTG in the -35 element are important for activity with both RpoH homologs; that the T-9 position, which is over-represented in the RpoH(I) promoter sequence logo, is critical for RpoH(I)-dependent transcription; and that several bases in the predicted -10 element were important for activity with either RpoH(II) or both RpoH homologs. Genes that are transcribed by both RpoH(I) and RpoH(II) are predicted to encode for functions involved in general cell maintenance. The functions specific to the RpoH(I) regulon are associated with a classic heat shock response, while those specific to RpoH(II) are associated with the response to the reactive oxygen species, singlet oxygen. We propose that a gene duplication event followed by changes in promoter recognition by RpoH(I) and RpoH(II) allowed convergence of the transcriptional responses to heat and singlet oxygen stress in R. sphaeroides and possibly other bacteria.

The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster

PubMed Central

Lee, Yuh Chwen G.

2015-01-01

The piwi-interacting RNAs (piRNA) are small RNAs that target selfish transposable elements (TEs) in many animal genomes. Until now, piRNAs’ role in TE population dynamics has only been discussed in the context of their suppression of TE transposition, which alone is not sufficient to account for the skewed frequency spectrum and stable containment of TEs. On the other hand, euchromatic TEs can be epigenetically silenced via piRNA-dependent heterochromatin formation and, similar to the widely known “Position-effect variegation”, heterochromatin induced by TEs can “spread” into nearby genes. We hypothesized that the piRNA-mediated spread of heterochromatin from TEs into adjacent genes has deleterious functional effects and leads to selection against individual TEs. Unlike previously identified deleterious effects of TEs due to the physical disruption of DNA, the functional effect we investigated here is mediated through the epigenetic influences of TEs. We found that the repressive chromatin mark, H3K9me, is elevated in sequences adjacent to euchromatic TEs at multiple developmental stages in Drosophila melanogaster. Furthermore, the heterochromatic states of genes depend not only on the number of and distance from adjacent TEs, but also on the likelihood that their nearest TEs are targeted by piRNAs. These variations in chromatin status probably have functional consequences, causing genes near TEs to have lower expression. Importantly, we found stronger selection against TEs that lead to higher H3K9me enrichment of adjacent genes, demonstrating the pervasive evolutionary consequences of TE-induced epigenetic silencing. Because of the intrinsic biological mechanism of piRNA amplification, spread of TE heterochromatin could result in the theoretically required synergistic deleterious effects of TE insertions for stable containment of TE copy number. The indirect deleterious impact of piRNA-mediated epigenetic silencing of TEs is a previously unexplored, yet important, element for the evolutionary dynamics of TEs. PMID:26042931

Local Burn-Up Effects in the NBSR Fuel Element

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

Brown N. R.; Hanson A.; Diamond, D.

2013-01-31

This study addresses the over-prediction of local power when the burn-up distribution in each half-element of the NBSR is assumed to be uniform. A single-element model was utilized to quantify the impact of axial and plate-wise burn-up on the power distribution within the NBSR fuel elements for both high-enriched uranium (HEU) and low-enriched uranium (LEU) fuel. To validate this approach, key parameters in the single-element model were compared to parameters from an equilibrium core model, including neutron energy spectrum, power distribution, and integral U-235 vector. The power distribution changes significantly when incorporating local burn-up effects and has lower power peakingmore » relative to the uniform burn-up case. In the uniform burn-up case, the axial relative power peaking is over-predicted by as much as 59% in the HEU single-element and 46% in the LEU single-element with uniform burn-up. In the uniform burn-up case, the plate-wise power peaking is over-predicted by as much as 23% in the HEU single-element and 18% in the LEU single-element. The degree of over-prediction increases as a function of burn-up cycle, with the greatest over-prediction at the end of Cycle 8. The thermal flux peak is always in the mid-plane gap; this causes the local cumulative burn-up near the mid-plane gap to be significantly higher than the fuel element average. Uniform burn-up distribution throughout a half-element also causes a bias in fuel element reactivity worth, due primarily to the neutronic importance of the fissile inventory in the mid-plane gap region.« less

Kinesin and Dynein Mechanics: Measurement Methods and Research Applications.

PubMed

Abraham, Zachary; Hawley, Emma; Hayosh, Daniel; Webster-Wood, Victoria A; Akkus, Ozan

2018-02-01

Motor proteins play critical roles in the normal function of cells and proper development of organisms. Among motor proteins, failings in the normal function of two types of proteins, kinesin and dynein, have been shown to lead many pathologies, including neurodegenerative diseases and cancers. As such, it is critical to researchers to understand the underlying mechanics and behaviors of these proteins, not only to shed light on how failures may lead to disease, but also to guide research toward novel treatment and nano-engineering solutions. To this end, many experimental techniques have been developed to measure the force and motility capabilities of these proteins. This review will (a) discuss such techniques, specifically microscopy, atomic force microscopy (AFM), optical trapping, and magnetic tweezers, and (b) the resulting nanomechanical properties of motor protein functions such as stalling force, velocity, and dependence on adenosine triphosophate (ATP) concentrations will be comparatively discussed. Additionally, this review will highlight the clinical importance of these proteins. Furthermore, as the understanding of the structure and function of motor proteins improves, novel applications are emerging in the field. Specifically, researchers have begun to modify the structure of existing proteins, thereby engineering novel elements to alter and improve native motor protein function, or even allow the motor proteins to perform entirely new tasks as parts of nanomachines. Kinesin and dynein are vital elements for the proper function of cells. While many exciting experiments have shed light on their function, mechanics, and applications, additional research is needed to completely understand their behavior.

The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties

PubMed Central

Gaillard, Muriel; Vallaeys, Tatiana; Vorhölter, Frank Jörg; Minoia, Marco; Werlen, Christoph; Sentchilo, Vladimir; Pühler, Alfred; van der Meer, Jan Roelof

2006-01-01

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties. PMID:16484212

Elemental Concentrations in Urban Green Stormwater Infrastructure Soils.

PubMed

Kondo, Michelle C; Sharma, Raghav; Plante, Alain F; Yang, Yunwen; Burstyn, Igor

2016-01-01

Green stormwater infrastructure (GSI) is designed to capture stormwater for infiltration, detention, evapotranspiration, or reuse. Soils play a key role in stormwater interception at these facilities. It is important to assess whether contamination is occurring in GSI soils because urban stormwater drainage areas often accumulate elements of concern. Soil contamination could affect hydrologic and ecosystem functions. Maintenance workers and the public may also be exposed to GSI soils. We investigated soil elemental concentrations, categorized as macro- and micronutrients, heavy metals, and other elements, at 59 GSI sites in the city of Philadelphia. Non-GSI soil samples 3 to 5 m upland of GSI sites were used for comparison. We evaluated differences in elemental composition in GSI and non-GSI soils; the comparisons were corrected for the age of GSI facility, underlying soil type, street drainage, and surrounding land use. Concentrations of Ca and I were greater than background levels at GSI sites. Although GSI facilities appear to accumulate Ca and I, these elements do not pose a significant human health risk. Elements of concern to human health, including Cd, Hg, and Pb, were either no different or were lower in GSI soils compared with non-GSI soils. However, mean values found across GSI sites were up to four times greater than soil cleanup objectives for residential use. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Trace element levels and cognitive function in rural elderly Chinese.

PubMed

Gao, Sujuan; Jin, Yinlong; Unverzagt, Frederick W; Ma, Feng; Hall, Kathleen S; Murrell, Jill R; Cheng, Yibin; Shen, Jianzhao; Ying, Bo; Ji, Rongdi; Matesan, Janetta; Liang, Chaoke; Hendrie, Hugh C

2008-06-01

Trace elements are involved in metabolic processes and oxidation-reduction reactions in the central nervous system and could have a possible effect on cognitive function. The relationship between trace elements measured in individual biological samples and cognitive function in an elderly population had not been investigated extensively. The participant population is part of a large cohort study of 2000 rural elderly Chinese persons. Six cognitive assessment tests were used to evaluate cognitive function in this population, and a composite score was created to represent global cognitive function. Trace element levels of aluminum, calcium, cadmium, copper, iron, lead, and zinc were analyzed in plasma samples of 188 individuals who were randomly selected and consented to donating fasting blood. Analysis of covariance models were used to assess the association between each trace element and the composite cognitive score adjusting for demographics, medical history of chronic diseases, and the apolipoprotein E (APOE) genotype. Three trace elements-calcium, cadmium, and copper-were found to be significantly related to the composite cognitive score. Increasing plasma calcium level was associated with higher cognitive score (p <.0001). Increasing cadmium and copper, in contrast, were significantly associated with lower composite score (p =.0044 and p =.0121, respectively). Other trace elements did not show significant association with the composite cognitive score. Our results suggest that calcium, cadmium, and copper may be associated with cognitive function in the elderly population.

Enhancer Analysis Unveils Genetic Interactions between TLX and SOX2 in Neural Stem Cells and In Vivo Reprogramming

PubMed Central

Islam, Mohammed M.; Smith, Derek K.; Niu, Wenze; Fang, Sanhua; Iqbal, Nida; Sun, Guoqiang; Shi, Yanhong; Zhang, Chun-Li

2015-01-01

Summary The orphan nuclear receptor TLX is a master regulator of postnatal neural stem cell (NSC) self-renewal and neurogenesis; however, it remains unclear how TLX expression is precisely regulated in these tissue-specific stem cells. Here, we show that a highly conserved cis-element within the Tlx locus functions to drive gene expression in NSCs. We demonstrate that the transcription factors SOX2 and MYT1 specifically interact with this genomic element to directly regulate Tlx enhancer activity in vivo. Knockdown experiments further reveal that SOX2 dominantly controls endogenous expression of TLX, whereas MYT1 only plays a modulatory role. Importantly, TLX is essential for SOX2-mediated in vivo reprogramming of astrocytes and itself is also sufficient to induce neurogenesis in the adult striatum. Together, these findings unveil functional genetic interactions among transcription factors that are critical to NSCs and in vivo cell reprogramming. PMID:26607952

Charge-transfer contributions to the excitonic coupling matrix element in BODIPY-based energy transfer cassettes

NASA Astrophysics Data System (ADS)

Spiegel, J. Dominik; Lyskov, Igor; Kleinschmidt, Martin; Marian, Christel M.

2017-01-01

BODIPY-based dyads serve as model systems for the investigation of excitation energy transfer (EET). Through-space EET is brought about by direct and exchange interactions between the transition densities of donor and acceptor localized states. The presence of a molecular linker gives rise to additional charge transfer (CT) contributions. Here, we present a novel approach for the calculation of the excitonic coupling matrix element (ECME) including CT contributions which is based on supermolecular one-electron transition density matrices (STD). The validity of the approach is assessed for a model system of two π -stacked ethylene molecules at varying intermolecular separation. Wave functions and electronic excitation energies of five EET cassettes comprising anthracene as exciton donor and BODIPY as exciton acceptor are obtained by the redesigned combined density functional theory and multireference configuration interaction (DFT/MRCI-R) method. CT contributions to the ECME are shown to be important in the covalently linked EET cassettes.

UV Radiation–Sensitive Norin 1 Rice Contains Defective Cyclobutane Pyrimidine Dimer Photolyase

PubMed Central

Hidema, Jun; Kumagai, Tadashi; Sutherland, Betsy M.

2000-01-01

Norin 1, a progenitor of many economically important Japanese rice strains, is highly sensitive to the damaging effects of UVB radiation (wavelengths 290 to 320 nm). Norin 1 seedlings are deficient in photorepair of cyclobutane pyrimidine dimers. However, the molecular origin of this deficiency was not known and, because rice photolyase genes have not been cloned and sequenced, could not be determined by examining photolyase structural genes or upstream regulatory elements for mutations. We therefore used a photoflash approach, which showed that the deficiency in photorepair in vivo resulted from a functionally altered photolyase. These results were confirmed by studies with extracts, which showed that the Norin 1 photolyase–dimer complex was highly thermolabile relative to the wild-type Sasanishiki photolyase. This deficiency results from a structure/function alteration of photolyase rather than of nonspecific repair, photolytic, or regulatory elements. Thus, the molecular origin of this plant DNA repair deficiency, resulting from a spontaneously occurring mutation to UV radiation sensitivity, is defective photolyase. PMID:11006332

A case study examination of structure and function in a state health department chronic disease unit.

PubMed

Alongi, Jeanne

2015-04-01

I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness.

Verbal play as a discourse resource in the social interactions of older and younger communication pairs.

PubMed

Shune, Samantha; Duff, Melissa Collins

2014-01-01

Verbal play, or the playful manipulation of elements of language, is a pervasive component of social interaction, serving important interpersonal functions. We analyzed verbal play in the interactional discourse of ten healthy younger pairs and ten healthy older pairs as they completed a collaborative referencing task. A total of 1,893 verbal play episodes were coded. While there were no group differences in verbal play frequency, age-related differences in the quality and function of these episodes emerged. While older participants engaged in more complex, extended, and reciprocal episodes that supported the social nature of communicative interactions (e.g., teasing), younger participants were more likely to engage in verbal play episodes for the purpose of successful task completion. Despite these age-related variations in the deployment of verbal play, verbal play is a robust interactional discourse resource in healthy aging, highlighting an element of human cognition that does not appear to decline with age.

Verbal play as a discourse resource in the social interactions of older and younger communication pairs

PubMed Central

Shune, Samantha; Duff, Melissa Collins

2014-01-01

Verbal play, or the playful manipulation of elements of language, is a pervasive component of social interaction, serving important interpersonal functions. We analyzed verbal play in the interactional discourse of ten healthy younger pairs and ten healthy older pairs as they completed a collaborative referencing task. A total of 1,893 verbal play episodes were coded. While there were no group differences in verbal play frequency, age-related differences in the quality and function of these episodes emerged. While older participants engaged in more complex, extended, and reciprocal episodes that supported the social nature of communicative interactions (e.g., teasing), younger participants were more likely to engage in verbal play episodes for the purpose of successful task completion. Despite these age-related variations in the deployment of verbal play, verbal play is a robust interactional discourse resource in healthy aging, highlighting an element of human cognition that does not appear to decline with age. PMID:25485072

Cognitive impairment, genomic instability and trace elements.

PubMed

Meramat, A; Rajab, N F; Shahar, S; Sharif, R

2015-01-01

Cognitive impairments are often related to aging and micronutrient deficiencies. Various essential micronutrients in the diet are involved in age-altered biological functions such as, zinc, copper, iron, and selenium that play pivotal roles either in maintaining and reinforcing the antioxidant performances or in affecting the complex network of genes (nutrigenomic approach) involved in encoding proteins for biological functions. Genomic stability is one of the leading causes of cognitive decline and deficiencies or excess in trace elements are two of the factors relating to it. In this review, we report and discuss the role of micronutrients in cognitive impairment in relation to genomic stability in an aging population. Telomere integrity will also be discussed in relation to aging and cognitive impairment, as well as, the micronutrients related to these events. This review will provide an understanding on how these three aspects can relate with each other and why it is important to keep a homeostasis of micronutrients in relation to healthy aging. Micronutrient deficiencies and aging process can lead to genomic instability.

Bromine is an essential trace element for assembly of collagen IV scaffolds in tissue development and architecture

PubMed Central

McCall, A. Scott; Cummings, Christopher F.; Bhave, Gautam; Vanacore, Roberto; Page-McCaw, Andrea; Hudson, Billy G.

2014-01-01

Summary Bromine is ubiquitously present in animals as ionic bromide (Br−) yet has no known essential function. Herein, we demonstrate that Br− is a required cofactor for peroxidasin-catalyzed formation of sulfilimine crosslinks, a post-translational modification essential for tissue development and architecture found within the collagen IV scaffold of basement membranes (BMs). Bromide, converted to hypobromous acid, forms a bromosulfonium-ion intermediate that energetically selects for sulfilimine formation. Dietary Br-deficiency is lethal in Drosophila while Br-replenishment restores viability, demonstrating its physiologic requirement. Importantly, Br-deficient flies phenocopy the developmental and BM defects observed in peroxidasin mutants and indicate a functional connection between Br−, collagen IV, and peroxidasin. We establish that Br− is required for sulfilimine formation within collagen IV, an event critical for BM assembly and tissue development. Thus, bromine is an essential trace element for all animals and its deficiency may be relevant to BM alterations observed in nutritional and smoking related disease. PMID:24906154

Ethane-xenon mixtures under shock conditions

DOE PAGES

Magyar, Rudolph J.; Root, Seth; Mattsson, Thomas; ...

2015-04-22

Mixtures of light elements with heavy elements are important in inertial confinement fusion. We explore the physics of molecular scale mixing through a validation study of equation of state (EOS) properties. Density functional theory molecular dynamics (DFT-MD) at elevated temperature and pressure is used to obtain the thermodynamic state properties of pure xenon, ethane, and various compressed mixture compositions along their principal Hugoniots. In order to validate these simulations, we have performed shock compression experiments using the Sandia Z-Machine. A bond tracking analysis correlates the sharp rise in the Hugoniot curve with the completion of dissociation in ethane. Furthermore, themore » DFT-based simulation results compare well with the experimental data along the principal Hugoniots and are used to provide insight into the dissociation and temperature along the Hugoniots as a function of mixture composition. Interestingly, we find that the compression ratio for complete dissociation is similar for several compositions suggesting a limiting compression for C-C bonded systems.« less

Ethnicity, Social Support, and Depression Among Elderly Chilean People.

PubMed

Gallardo-Peralta, Lorena P; Sánchez-Moreno, Esteban; López De Roda, Ana Barrón; Arias Astray, Andrés

2015-01-01

Recent evidence regarding the relationship between social support and depression in elderly people shows the important role of ethnicity. This research describes the characteristics of social support in a sample of elderly people aged 60 and above living in northern Chile (n = 493), and analyzes the differences in the relationship between social support and depression between an indigenous group (Aymara population, n = 147) and a nonindigenous group (white, Caucasian, mestizo, n = 346). Various dimensions of social support were considered: structural elements, functional social support according to source, and community participation. The results show the existence of significant differences in the characteristics and dimensions of social support depending on sex, ethnicity, and marital status. Further, the central role of the family group is observed for both Aymara and nonindigenous elderly people. The hierarchical regression models obtained result in notable differences in the role of the structural, functional, and community elements of support in explaining depression for the ethnic groups considered.

Atomically flat single-crystalline gold nanostructures for plasmonic nanocircuitry.

PubMed

Huang, Jer-Shing; Callegari, Victor; Geisler, Peter; Brüning, Christoph; Kern, Johannes; Prangsma, Jord C; Wu, Xiaofei; Feichtner, Thorsten; Ziegler, Johannes; Weinmann, Pia; Kamp, Martin; Forchel, Alfred; Biagioni, Paolo; Sennhauser, Urs; Hecht, Bert

2010-01-01

Deep subwavelength integration of high-definition plasmonic nanostructures is of key importance in the development of future optical nanocircuitry for high-speed communication, quantum computation and lab-on-a-chip applications. To date, the experimental realization of proposed extended plasmonic networks consisting of multiple functional elements remains challenging, mainly because of the multi-crystallinity of commonly used thermally evaporated gold layers. This can produce structural imperfections in individual circuit elements that drastically reduce the yield of functional integrated nanocircuits. In this paper we demonstrate the use of large (>100 μm(2)) but thin (<80 nm) chemically grown single-crystalline gold flakes that, after immobilization, serve as an ideal basis for focused ion beam milling and other top-down nanofabrication techniques on any desired substrate. Using this methodology we obtain high-definition ultrasmooth gold nanostructures with superior optical properties and reproducible nano-sized features over micrometre-length scales. Our approach provides a possible solution to overcome the current fabrication bottleneck and realize high-definition plasmonic nanocircuitry.

Characterization of a Smad motif similar to Drosophila mad in the mouse Msx 1 promoter.

PubMed

Alvarez Martinez, Cristina E; Binato, Renata; Gonzalez, Sayonara; Pereira, Monica; Robert, Benoit; Abdelhay, Eliana

2002-03-01

Mouse Msx 1 gene, orthologous of the Drosophila msh, is involved in several developmental processes. BMP family members are major proteins in the regulation of Msx 1 expression. BMP signaling activates Smad 1/5/8 proteins, which associate to Smad 4 before translocating to the nucleus. Analysis of Msx 1 promoter revealed the presence of three elements similar to the consensus established for Mad, the Smad 1 Drosophila counterpart. Notably, such an element was identified in an enhancer important for Msx 1 regulation. Gel shift analysis demonstrated that proteins from 13.5 dpc embryo associate to this enhancer. Remarkably, supershift assays showed that Smad proteins are present in the complex. Purified Smad 1 and 4 also bind to this fragment. We demonstrate that functional binding sites in this enhancer are confined to the Mad motif and flanking region. Our data suggest that this Mad motif may be functional in response to BMP signaling. ©2002 Elsevier Science (USA).

A Case Study Examination of Structure and Function in a State Health Department Chronic Disease Unit

PubMed Central

2015-01-01

Objectives. I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. Methods. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Results. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Conclusions. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness. PMID:25689211

Investigation on energy conversion technology using biochemical reaction elements, 2

NASA Astrophysics Data System (ADS)

1994-03-01

For measures taken for resource/energy and environmental issues, a study is made on utilization of microbial biochemical reaction. As a reaction system using chemical energy, cited is production of petroleum substitution substances and food/feed by CO2 fixation using hydrogen energy and hydrogen bacteria. As to photo energy utilization, regarded as promising are CO2 fixation using photo energy and microalgae, and production of hydrogen and useful carbon compound using photosynthetic organisms. As living organism/electric energy interconversion, cited is the culture of chemoautotrophic bacteria which fix CO2 using electric energy. For enhancing its conversion efficiency, it is important to develop a technology of gene manipulation of the bacteria and a system to use functional biochemical elements adaptable to the electrode reaction. With regard to utilization of the microorganism metabolic function, the paper presents emission of soluble nitrogen in the hydrosphere into the atmosphere using denitrifying bacteria, removal of phosphorus, reduction in environmental pollution caused by heavy metal dilute solutions, and recovery as resources, etc.

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

PubMed

Canver, Matthew C; Lessard, Samuel; Pinello, Luca; Wu, Yuxuan; Ilboudo, Yann; Stern, Emily N; Needleman, Austen J; Galactéros, Frédéric; Brugnara, Carlo; Kutlar, Abdullah; McKenzie, Colin; Reid, Marvin; Chen, Diane D; Das, Partha Pratim; A Cole, Mitchel; Zeng, Jing; Kurita, Ryo; Nakamura, Yukio; Yuan, Guo-Cheng; Lettre, Guillaume; Bauer, Daniel E; Orkin, Stuart H

2017-04-01

Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

A biochemical framework for eIF4E-dependent mRNA export and nuclear recycling of the export machinery.

PubMed

Volpon, Laurent; Culjkovic-Kraljacic, Biljana; Sohn, Hye Seon; Blanchet-Cohen, Alexis; Osborne, Michael J; Borden, Katherine L B

2017-06-01

The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date, over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ∼50-nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end. While eIF4E associates with the cap, an unknown factor recognizes the 4ESE element. We previously identified cofactors that functionally interacted with eIF4E in mammalian cell nuclei including the leucine-rich pentatricopeptide repeat protein LRPPRC and the export receptor CRM1/XPO1. LRPPRC simultaneously interacts with both eIF4E bound to the 5' mRNA cap and the 4ESE element in the 3' UTR. In this way, LRPPRC serves as a specificity factor to recruit 4ESE-containing RNAs within the nucleus. Further, we show that CRM1 directly binds LRPPRC likely acting as the export receptor for the LRPPRC-eIF4E-4ESE RNA complex. We also found that Importin 8, the nuclear importer for cap-free eIF4E, imports RNA-free LRPPRC, potentially providing both coordinated nuclear recycling of the export machinery and an important surveillance mechanism to prevent futile export cycles. Our studies provide the first biochemical framework for the eIF4E-dependent mRNA export pathway. © 2017 Volpon et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The Metals in the Biological Periodic System of the Elements: Concepts and Conjectures

PubMed Central

Maret, Wolfgang

2016-01-01

A significant number of chemical elements are either essential for life with known functions, or present in organisms with poorly defined functional outcomes. We do not know all the essential elements with certainty and we know even less about the functions of apparently non-essential elements. In this article, I discuss a basis for a biological periodic system of the elements and that biochemistry should include the elements that are traditionally part of inorganic chemistry and not only those that are in the purview of organic chemistry. A biological periodic system of the elements needs to specify what “essential” means and to which biological species it refers. It represents a snapshot of our present knowledge and is expected to undergo further modifications in the future. An integrated approach of biometal sciences called metallomics is required to understand the interactions of metal ions, the biological functions that their chemical structures acquire in the biological system, and how their usage is fine-tuned in biological species and in populations of species with genetic variations (the variome). PMID:26742035

The Effect of Volumetric Porosity on Roughness Element Drag

NASA Astrophysics Data System (ADS)

Gillies, John; Nickling, William; Nikolich, George; Etyemezian, Vicken

2016-04-01

Much attention has been given to understanding how the porosity of two dimensional structures affects the drag force exerted by boundary-layer flow on these flow obstructions. Porous structures such as wind breaks and fences are typically used to control the sedimentation of sand and snow particles or create micro-habitats in their lee. Vegetation in drylands also exerts control on sediment transport by wind due to aerodynamic effects and interaction with particles in transport. Recent research has also demonstrated that large spatial arrays of solid three dimensional roughness elements can be used to reduce sand transport to specified targets for control of wind erosion through the effect of drag partitioning and interaction of the moving sand with the large (>0.3 m high) roughness elements, but porous elements may improve the effectiveness of this approach. A thorough understanding of the role porosity plays in affecting the drag force on three-dimensional forms is lacking. To provide basic understanding of the relationship between the porosity of roughness elements and the force of drag exerted on them by fluid flow, we undertook a wind tunnel study that systematically altered the porosity of roughness elements of defined geometry (cubes, rectangular cylinders, and round cylinders) and measured the associated change in the drag force on the elements under similar Reynolds number conditions. The elements tested were of four basic forms: 1) same sized cubes with tubes of known diameter milled through them creating three volumetric porosity values and increasing connectivity between the tubes, 2) cubes and rectangular cylinders constructed of brass screen that nested within each other, and 3) round cylinders constructed of brass screen that nested within each other. The two-dimensional porosity, defined as the ratio of total surface area of the empty space to the solid surface area of the side of the element presented to the fluid flow was conserved at 0.519 for the cubes and 0.525 for the mesh forms. Results from the study indicate that as volumetric porosity increases, the force of drag on an element increases although the 2-dimensional porosity remains unchanged for the case of the cube forms. The mesh forms show a similar result that with increasing number of internal forms present, drag increases, but the drag curves are different, suggesting the kind of porosity has an effect on drag. An important scaling parameter that controls drag on the cubes is the permeability (K) of the element, which is a function of the diameter of the tubes and the porosity. K seems to be of lesser importance for controlling drag on the mesh forms. We hypothesize that the drag force data do not universally collapse as a function of permeability due to Reynolds number dependency on flow conditions within the elements that can be laminar, transitional, or turbulent even though flow exterior to the forms is fully turbulent. For the mesh forms, the greatest effect on drag occurs with the addition of the first internal form with subsequent additions showing very little additional effect.

Importance of mental performance in parental choice of food for children aged 4-10 years: a study in four European countries.

PubMed

Gage, Heather; Egan, Bernadette; Williams, Peter; Brands, Brigitte; Györei, Eszter; López-Robles, Juan-Carlos; Campoy, Cristina; Decsi, Tamas; Koletzko, Berthold; Raats, Monique

2017-04-01

Typically, attention focuses on how nutrition affects physical health. The present study investigated the importance that parents attach to the impact of diet on mental performance when choosing food for their child. Questionnaire. Four European countries. Parents of children aged 4-10 years (n 1574): England (n 397), Germany (n 389), Hungary (n 398) and Spain (n 390). Most parents (80-85 %) considered the effect of food on four elements of mental performance (child's ability to learn, attention, behaviour, mood) to be moderately, very, extremely (v. slightly, not at all) important in food choices; over 90 % considered healthiness of food and making food appealing to their child important; 79·8 % cost; 76·8 % convenience. Belief that food affects mental performance was 57·4 % (ability to learn), 60·5 % (attention); less than 40 % of parents agreed they were aware which foods had an effect. Parents with lower general interest in healthy eating were less likely to consider the effect of food on mental performance elements as important. Respondents from Germany were more likely to rate mental performance as important (except behaviour); those in Hungary less likely. The most important influence on parents' decisions about feeding their child was their own experience, except Spain, where family/friends/health professionals were more important. Nutrition affects brain development and cognitive functioning. Low prioritisation of the effect of food on mental performance indicates potential for educating parents.

Optically intraconnected computer employing dynamically reconfigurable holographic optical element

NASA Technical Reports Server (NTRS)

Bergman, Larry A. (Inventor)

1992-01-01

An optically intraconnected computer and a reconfigurable holographic optical element employed therein. The basic computer comprises a memory for holding a sequence of instructions to be executed; logic for accessing the instructions in sequence; logic for determining for each the instruction the function to be performed and the effective address thereof; a plurality of individual elements on a common support substrate optimized to perform certain logical sequences employed in executing the instructions; and, element selection logic connected to the logic determining the function to be performed for each the instruction for determining the class of each function and for causing the instruction to be executed by those the elements which perform those associated the logical sequences affecting the instruction execution in an optimum manner. In the optically intraconnected version, the element selection logic is adapted for transmitting and switching signals to the elements optically.

Beta-globin locus activation regions: conservation of organization, structure, and function.

PubMed Central

Li, Q L; Zhou, B; Powers, P; Enver, T; Stamatoyannopoulos, G

1990-01-01

The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function. Images PMID:2236034

Imprinting high-gradient topographical structures onto optical surfaces using magnetorheological finishing: manufacturing corrective optical elements for high-power laser applications.

PubMed

Menapace, Joseph A; Ehrmann, Paul E; Bayramian, Andrew J; Bullington, Amber; Di Nicola, Jean-Michel G; Haefner, Constantin; Jarboe, Jeffrey; Marshall, Christopher; Schaffers, Kathleen I; Smith, Cal

2016-07-01

Corrective optical elements form an important part of high-precision optical systems. We have developed a method to manufacture high-gradient corrective optical elements for high-power laser systems using deterministic magnetorheological finishing (MRF) imprinting technology. Several process factors need to be considered for polishing ultraprecise topographical structures onto optical surfaces using MRF. They include proper selection of MRF removal function and wheel sizes, detailed MRF tool and interferometry alignment, and optimized MRF polishing schedules. Dependable interferometry also is a key factor in high-gradient component manufacture. A wavefront attenuating cell, which enables reliable measurement of gradients beyond what is attainable using conventional interferometry, is discussed. The results of MRF imprinting a 23 μm deep structure containing gradients over 1.6 μm / mm onto a fused-silica window are presented as an example of the technique's capabilities. This high-gradient element serves as a thermal correction plate in the high-repetition-rate advanced petawatt laser system currently being built at Lawrence Livermore National Laboratory.

Emotion and interior space design: an ergonomic perspective.

PubMed

Reddy, Swathi Matta; Chakrabarti, Debkumar; Karmakar, Sougata

2012-01-01

Interaction between the users and their environment is spontaneous and unavoidable. This interaction can be positive or negative. A good interior space is about considering all the physical, environmental and cognitive elements and harmonizing them to make it a space that feels right, functionally and emotionally. The important element that has to be considered the most in an interior space is the "user". Balancing all these elements is a challenging job and results in a perfect interior space design. This paper intends to bring to light the necessity of designing an optimum interior space, which is a balance of the user's choice and the mandatory standards that ought to be followed for user safety and convenience. There has to be an intervening domain of ergonomics which will guide to bring out a balance between the personal choice of the user and the usual standards followed. It should also provide a step-by-step information, guidance and direction to act to the specifications and standards systematically to adapt an integrated approach of handling all the elements holistically which will indeed result in a good interior space.

Imprinting high-gradient topographical structures onto optical surfaces using magnetorheological finishing: Manufacturing corrective optical elements for high-power laser applications

DOE PAGES

Menapace, Joseph A.; Ehrmann, Paul E.; Bayramian, Andrew J.; ...

2016-03-15

Corrective optical elements form an important part of high-precision optical systems. We have developed a method to manufacture high-gradient corrective optical elements for high-power laser systems using deterministic magnetorheological finishing (MRF) imprinting technology. Several process factors need to be considered for polishing ultraprecise topographical structures onto optical surfaces using MRF. They include proper selection of MRF removal function and wheel sizes, detailed MRF tool and interferometry alignment, and optimized MRF polishing schedules. Dependable interferometry also is a key factor in high-gradient component manufacture. A wavefront attenuating cell, which enables reliable measurement of gradients beyond what is attainable using conventional interferometry,more » is discussed. The results of MRF imprinting a 23 μm deep structure containing gradients over 1.6 μm / mm onto a fused-silica window are presented as an example of the technique’s capabilities. As a result, this high-gradient element serves as a thermal correction plate in the high-repetition-rate advanced petawatt laser system currently being built at Lawrence Livermore National Laboratory.« less

Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

PubMed

Kim, K H; Hemenway, C

1997-05-26

The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy

PubMed Central

Cartault, François; Munier, Patrick; Benko, Edgar; Desguerre, Isabelle; Hanein, Sylvain; Boddaert, Nathalie; Bandiera, Simonetta; Vellayoudom, Jeanine; Krejbich-Trotot, Pascale; Bintner, Marc; Hoarau, Jean-Jacques; Girard, Muriel; Génin, Emmanuelle; de Lonlay, Pascale; Fourmaintraux, Alain; Naville, Magali; Rodriguez, Diana; Feingold, Josué; Renouil, Michel; Munnich, Arnold; Westhof, Eric; Fähling, Michael; Lyonnet, Stanislas; Henrion-Caude, Alexandra

2012-01-01

The human genome is densely populated with transposons and transposon-like repetitive elements. Although the impact of these transposons and elements on human genome evolution is recognized, the significance of subtle variations in their sequence remains mostly unexplored. Here we report homozygosity mapping of an infantile neurodegenerative disease locus in a genetic isolate. Complete DNA sequencing of the 400-kb linkage locus revealed a point mutation in a primate-specific retrotransposon that was transcribed as part of a unique noncoding RNA, which was expressed in the brain. In vitro knockdown of this RNA increased neuronal apoptosis, consistent with the inappropriate dosage of this RNA in vivo and with the phenotype. Moreover, structural analysis of the sequence revealed a small RNA-like hairpin that was consistent with the putative gain of a functional site when mutated. We show here that a mutation in a unique transposable element-containing RNA is associated with lethal encephalopathy, and we suggest that RNAs that harbor evolutionarily recent repetitive elements may play important roles in human brain development. PMID:22411793

Chemical patterning on preformed porous silicon photonic crystals: towards multiplex detection of protease activity at precise positions†Electronic supplementary information (ESI) available: SEM images, XPS result and more optical reflectivity data. See DOI: 10.1039/c4tb00281dClick here for additional data file.

PubMed

Zhu, Ying; Soeriyadi, Alexander H; Parker, Stephen G; Reece, Peter J; Gooding, J Justin

2014-06-21

Porous silicon (PSi) rugate filters modified with alkyne-terminated monolayers were chemically patterned using a combination of photolithography of photoresist and click chemistry. Two chemical functionalities were obtained by conjugating, via click reactions, ethylene glycol moieties containing two different terminal groups to discrete areas towards the exterior of a PSi rugate filter. The patterning of biological species to the functionalized surface was demonstrated through the conjugation of fluorescein isothiocyanate labelled bovine serum albumin (FITC-BSA). Fluorescence microscopy showed selective positioning of FITC-BSA at discretely functionalized areas. Meanwhile, the optical information from precisely defined positions on the patterned surface was monitored by optical reflectivity measurements. The optical measurements revealed successful step-wise chemical functionalization followed by immobilization of gelatin. Multiplex detection of protease activity from different array elements on the patterned surface was demonstrated by monitoring the blue shifts in the reflectivity spectra resulted from the digestion of gelatin by subtilisin. Precise information from both individual elements and average population was acquired. This technique is important for the development of PSi into a microarray platform for highly parallel biosensing applications, especially for cell-based assays.

The local matrix distribution and the functional development of tissue engineered cartilage, a finite element study.

PubMed

Sengers, B G; Van Donkelaar, C C; Oomens, C W J; Baaijens, F P T

2004-12-01

Assessment of the functionality of tissue engineered cartilage constructs is hampered by the lack of correlation between global measurements of extra cellular matrix constituents and the global mechanical properties. Based on patterns of matrix deposition around individual cells, it has been hypothesized previously, that mechanical functionality arises when contact occurs between zones of matrix associated with individual cells. The objective of this study is to determine whether the local distribution of newly synthesized extracellular matrix components contributes to the evolution of the mechanical properties of tissue engineered cartilage constructs. A computational homogenization approach was adopted, based on the concept of a periodic representative volume element. Local transport and immobilization of newly synthesized matrix components were described. Mechanical properties were taken dependent on the local matrix concentration and subsequently the global aggregate modulus and hydraulic permeability were derived. The transport parameters were varied to assess the effect of the evolving matrix distribution during culture. The results indicate that the overall stiffness and permeability are to a large extent insensitive to differences in local matrix distribution. This emphasizes the need for caution in the visual interpretation of tissue functionality from histology and underlines the importance of complementary measurements of the matrix's intrinsic molecular organization.

Possible involvement of SINEs in mammalian-specific brain formation

PubMed Central

Sasaki, Takeshi; Nishihara, Hidenori; Hirakawa, Mika; Fujimura, Koji; Tanaka, Mikiko; Kokubo, Nobuhiro; Kimura-Yoshida, Chiharu; Matsuo, Isao; Sumiyama, Kenta; Saitou, Naruya; Shimogori, Tomomi; Okada, Norihiro

2008-01-01

Retroposons, such as short interspersed elements (SINEs) and long interspersed elements (LINEs), are the major constituents of higher vertebrate genomes. Although there are many examples of retroposons' acquiring function, none has been implicated in the morphological innovations specific to a certain taxonomic group. We previously characterized a SINE family, AmnSINE1, members of which constitute a part of conserved noncoding elements (CNEs) in mammalian genomes. We proposed that this family acquired genomic functionality or was exapted after retropositioning in a mammalian ancestor. Here we identified 53 new AmnSINE1 loci and refined 124 total loci, two of which were further analyzed. Using a mouse enhancer assay, we demonstrate that one SINE locus, AS071, 178 kbp from the gene FGF8 (fibroblast growth factor 8), is an enhancer that recapitulates FGF8 expression in two regions of the developing forebrain, namely the diencephalon and the hypothalamus. Our gain-of-function analysis revealed that FGF8 expression in the diencephalon controls patterning of thalamic nuclei, which act as a relay center of the neocortex, suggesting a role for FGF8 in mammalian-specific forebrain patterning. Furthermore, we demonstrated that the locus, AS021, 392 kbp from the gene SATB2, controls gene expression in the lateral telencephalon, which is thought to be a signaling center during development. These results suggest important roles for SINEs in the development of the mammalian neuronal network, a part of which was initiated with the exaptation of AmnSINE1 in a common mammalian ancestor. PMID:18334644

Possible involvement of SINEs in mammalian-specific brain formation.

PubMed

Sasaki, Takeshi; Nishihara, Hidenori; Hirakawa, Mika; Fujimura, Koji; Tanaka, Mikiko; Kokubo, Nobuhiro; Kimura-Yoshida, Chiharu; Matsuo, Isao; Sumiyama, Kenta; Saitou, Naruya; Shimogori, Tomomi; Okada, Norihiro

2008-03-18

Retroposons, such as short interspersed elements (SINEs) and long interspersed elements (LINEs), are the major constituents of higher vertebrate genomes. Although there are many examples of retroposons' acquiring function, none has been implicated in the morphological innovations specific to a certain taxonomic group. We previously characterized a SINE family, AmnSINE1, members of which constitute a part of conserved noncoding elements (CNEs) in mammalian genomes. We proposed that this family acquired genomic functionality or was exapted after retropositioning in a mammalian ancestor. Here we identified 53 new AmnSINE1 loci and refined 124 total loci, two of which were further analyzed. Using a mouse enhancer assay, we demonstrate that one SINE locus, AS071, 178 kbp from the gene FGF8 (fibroblast growth factor 8), is an enhancer that recapitulates FGF8 expression in two regions of the developing forebrain, namely the diencephalon and the hypothalamus. Our gain-of-function analysis revealed that FGF8 expression in the diencephalon controls patterning of thalamic nuclei, which act as a relay center of the neocortex, suggesting a role for FGF8 in mammalian-specific forebrain patterning. Furthermore, we demonstrated that the locus, AS021, 392 kbp from the gene SATB2, controls gene expression in the lateral telencephalon, which is thought to be a signaling center during development. These results suggest important roles for SINEs in the development of the mammalian neuronal network, a part of which was initiated with the exaptation of AmnSINE1 in a common mammalian ancestor.

A viscoelastic model for dielectric elastomers based on a continuum mechanical formulation and its finite element implementation

NASA Astrophysics Data System (ADS)

Bueschel, A.; Klinkel, S.; Wagner, W.

2011-04-01

Smart materials are active and multifunctional materials, which play an important part for sensor and actuator applications. These materials have the potential to transform passive structures into adaptive systems. However, a prerequisite for the design and the optimization of these materials is, that reliable models exist, which incorporate the interaction between the different combinations of thermal, electrical, magnetic, optical and mechanical effects. Polymeric electroelastic materials, so-called electroactive polymer (EAP), own the characteristic to deform if an electric field is applied. EAP's possesses the benefit that they share the characteristic of polymers, these are lightweight, inexpensive, fracture tolerant, elastic, and the chemical and physical structure is well understood. However, the description "electroactive polymer" is a generic term for many kinds of different microscopic mechanisms and polymeric materials. Based on the laws of electromagnetism and elasticity, a visco-electroelastic model is developed and implemented into the finite element method (FEM). The presented three-dimensional solid element has eight nodes and trilinear interpolation functions for the displacement and the electric potential. The continuum mechanics model contains finite deformations, the time dependency and the nearly incompressible behavior of the material. To describe the possible, large time dependent deformations, a finite viscoelastic model with a split of the deformation gradient is used. Thereby the time dependent characteristic of polymeric materials is incorporated through the free energy function. The electromechanical interactions are considered by the electrostatic forces and inside the energy function.

A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer.

PubMed

Takeda, David Y; Spisák, Sándor; Seo, Ji-Heui; Bell, Connor; O'Connor, Edward; Korthauer, Keegan; Ribli, Dezső; Csabai, István; Solymosi, Norbert; Szállási, Zoltán; Stillman, David R; Cejas, Paloma; Qiu, Xintao; Long, Henry W; Tisza, Viktória; Nuzzo, Pier Vitale; Rohanizadegan, Mersedeh; Pomerantz, Mark M; Hahn, William C; Freedman, Matthew L

2018-06-09

Increased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of this locus presumably targeting the AR gene. Here, we identify and characterize a somatically acquired AR enhancer located 650 kb centromeric to the AR. Systematic perturbation of this enhancer using genome editing decreased proliferation by suppressing AR levels. Insertion of an additional copy of this region sufficed to increase proliferation under low androgen conditions and to decrease sensitivity to enzalutamide. Epigenetic data generated in localized prostate tumors and benign specimens support the notion that this region is a developmental enhancer. Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers. Copyright © 2018 Elsevier Inc. All rights reserved.

Synthetic-lattice enabled all-optical devices based on orbital angular momentum of light

PubMed Central

Luo, Xi-Wang; Zhou, Xingxiang; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can; Zhang, Chuanwei; Zhou, Zheng-Wei

2017-01-01

All-optical photonic devices are crucial for many important photonic technologies and applications, ranging from optical communication to quantum information processing. Conventional design of all-optical devices is based on photon propagation and interference in real space, which may rely on large numbers of optical elements, and the requirement of precise control makes this approach challenging. Here we propose an unconventional route for engineering all-optical devices using the photon’s internal degrees of freedom, which form photonic crystals in such synthetic dimensions for photon propagation and interference. We demonstrate this design concept by showing how important optical devices such as quantum memory and optical filters can be realized using synthetic orbital angular momentum (OAM) lattices in degenerate cavities. The design route utilizing synthetic photonic lattices may significantly reduce the requirement for numerous optical elements and their fine tuning in conventional design, paving the way for realistic all-optical photonic devices with novel functionalities. PMID:28706215

Nuclear localization and transactivation by Vitis CBF transcription factors are regulated by combinations of conserved amino acid domains.

PubMed

Carlow, Chevonne E; Faultless, J Trent; Lee, Christine; Siddiqua, Mahbuba; Edge, Alison; Nassuth, Annette

2017-09-01

The highly conserved CBF pathway is crucial in the regulation of plant responses to low temperatures. Extensive analysis of Arabidopsis CBF proteins revealed that their functions rely on several conserved amino acid domains although the exact function of each domain is disputed. The question was what functions similar domains have in CBFs from other, overwintering woody plants such as Vitis, which likely have a more involved regulation than the model plant Arabidopsis. A total of seven CBF genes were cloned and sequenced from V. riparia and the less frost tolerant V. vinifera. The deduced species-specific amino acid sequences differ in only a few amino acids, mostly in non-conserved regions. Amino acid sequence comparison and phylogenetic analysis showed two distinct groups of Vitis CBFs. One group contains CBF1, CBF2, CBF3 and CBF8 and the other group contains CBF4, CBF5 and CBF6. Transient transactivation assays showed that all Vitis CBFs except CBF5 activate via a CRT or DRE promoter element, whereby Vitis CBF3 and 4 prefer a CRT element. The hydrophobic domains in the C-terminal end of VrCBF6 were shown to be important for how well it activates. The putative nuclear localization domain of Vitis CBF1 was shown to be sufficient for nuclear localization, in contrast to previous reports for AtCBF1, and also important for transactivation. The latter highlights the value of careful analysis of domain functions instead of reliance on computer predictions and published data for other related proteins. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reusable rocket engine intelligent control system framework design, phase 2

NASA Technical Reports Server (NTRS)

Nemeth, ED; Anderson, Ron; Ols, Joe; Olsasky, Mark

1991-01-01

Elements of an advanced functional framework for reusable rocket engine propulsion system control are presented for the Space Shuttle Main Engine (SSME) demonstration case. Functional elements of the baseline functional framework are defined in detail. The SSME failure modes are evaluated and specific failure modes identified for inclusion in the advanced functional framework diagnostic system. Active control of the SSME start transient is investigated, leading to the identification of a promising approach to mitigating start transient excursions. Key elements of the functional framework are simulated and demonstration cases are provided. Finally, the advanced function framework for control of reusable rocket engines is presented.

A finite element boundary integral formulation for radiation and scattering by cavity antennas using tetrahedral elements

NASA Technical Reports Server (NTRS)

Gong, J.; Volakis, J. L.; Chatterjee, A.; Jin, J. M.

1992-01-01

A hybrid finite element boundary integral formulation is developed using tetrahedral and/or triangular elements for discretizing the cavity and/or aperture of microstrip antenna arrays. The tetrahedral elements with edge based linear expansion functions are chosen for modeling the volume region and triangular elements are used for discretizing the aperture. The edge based expansion functions are divergenceless thus removing the requirement to introduce a penalty term and the tetrahedral elements permit greater geometrical adaptability than the rectangular bricks. The underlying theory and resulting expressions are discussed in detail together with some numerical scattering examples for comparison and demonstration.

The domain organization of the bacterial intermediate filament-like protein crescentin is important for assembly and function

PubMed Central

Cabeen, Matthew T; Herrmann, Harald; Jacobs-Wagner, Christine

2011-01-01

Crescentin is a bacterial filament-forming protein that exhibits domain organization features found in metazoan intermediate filament (IF) proteins. Structure-function studies of eukaryotic IFs have been hindered by a lack of simple genetic systems and easily quantifiable phenotypes. Here we exploit the characteristic localization of the crescentin structure along the inner curvature of Caulobacter crescentus cells and the loss of cell curvature associated with impaired crescentin function to analyze the importance of the domain organization of crescentin. By combining biochemistry and ultrastructural analysis in vitro with cellular localization and functional studies, we show that crescentin requires its distinctive domain organization, and furthermore that different structural elements have distinct structural and functional contributions. The head domain can be functionally subdivided into two subdomains; the first (amino-terminal) is required for function but not assembly, while the second is necessary for structure assembly. The rod domain is similarly required for structure assembly, and the linker L1 appears important to prevent runaway assembly into nonfunctional aggregates. The data also suggest that the stutter and the tail domain have critical functional roles in stabilizing crescentin structures against disassembly by monovalent cations in the cytoplasm. This study suggests that the IF-like behavior of crescentin is a consequence of its domain organization, implying that the IF protein layout is an adaptable cytoskeletal motif, much like the actin and tubulin folds, that is broadly exploited for various functions throughout life from bacteria to humans. © 2011 Wiley-Liss, Inc. PMID:21360832

Particle Swarm-Based Translation Control for Immersed Tunnel Element in the Hong Kong-Zhuhai-Macao Bridge Project

NASA Astrophysics Data System (ADS)

Li, Jun-jun; Yang, Xiao-jun; Xiao, Ying-jie; Xu, Bo-wei; Wu, Hua-feng

2018-03-01

Immersed tunnel is an important part of the Hong Kong-Zhuhai-Macao Bridge (HZMB) project. In immersed tunnel floating, translation which includes straight and transverse movements is the main working mode. To decide the magnitude and direction of the towing force for each tug, a particle swarm-based translation control method is presented for non-power immersed tunnel element. A sort of linear weighted logarithmic function is exploited to avoid weak subgoals. In simulation, the particle swarm-based control method is evaluated and compared with traditional empirical method in the case of the HZMB project. Simulation results show that the presented method delivers performance improvement in terms of the enhanced surplus towing force.

Average M shell fluorescence yields for elements with 70≤Z≤92

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

Kahoul, A., E-mail: ka-abdelhalim@yahoo.fr; LPMRN laboratory, Department of Materials Science, Faculty of Sciences and Technology, Mohamed El Bachir El Ibrahimi University, Bordj-Bou-Arreridj 34030; Deghfel, B.

2015-03-30

The theoretical, experimental and analytical methods for the calculation of average M-shell fluorescence yield (ω{sup ¯}{sub M}) of different elements are very important because of the large number of their applications in various areas of physical chemistry and medical research. In this paper, the bulk of the average M-shell fluorescence yield measurements reported in the literature, covering the period 1955 to 2005 are interpolated by using an analytical function to deduce the empirical average M-shell fluorescence yield in the atomic range of 70≤Z≤92. The results were compared with the theoretical and fitted values reported by other authors. Reasonable agreement wasmore » typically obtained between our result and other works.« less

Puberty and adolescent sexuality.

PubMed

Fortenberry, J Dennis

2013-07-01

This article is part of a Special Issue "Puberty and Adolescence". Sexuality emerges as a major developmental element of puberty and the adolescent years that follow. However, connecting the sexuality that emerges with puberty and elements of adult sexuality is difficult because much adolescent sexuality research addresses the transition to partnered sexual behaviors (primarily coitus) and consequences such as unplanned pregnancy and sexually transmitted infections. This review proposes a framework of an expanded understanding of puberty and adolescent sexuality from the perspective of four hallmarks of adult sexuality: sexual desire; sexual arousal; sexual behaviors; and, sexual function. This approach thus addresses important gaps in understanding of the ontogeny of sex and the continuum of sexuality development from adolescence through the adult lifespan. Copyright © 2013 Elsevier Inc. All rights reserved.

Current Conveyor All-Pass Sections: Brief Review and Novel Solution

PubMed Central

Maheshwari, Sudhanshu

2013-01-01

This study relates to the review of an important analog electronic function in form of all-pass filter's realization using assorted current conveyor types and their relative performances, which resulted in a novel solution based on a new proposed active element. The study encompasses notable proposals during last the decade or more, and provides a platform for a broader future survey on the topic for enhancing the knowledge penetration amongst the researchers in the specified field. A new active element named EXCCII (Extra-X second generation current conveyor) with buffered output is found in the study along with its use in a new first-order all-pass section, with possible realization using commercially available IC (AD-844) and results. PMID:24379741

Visual search and segregation as a function of display complexity.

PubMed

Scharroo, J; Stalmeier, P F; Boselie, F

1994-01-01

Complexity is proposed as an important psychological factor in search and segregation tasks. Displays were presented with target and nontarget areas that were each built up of one type of randomly rotated micropatterns. We manipulated experimentally (a) the complexity of the target elements, as measured by Garner's (1970) invariance criterion; (b) the complexity of the target region; (c) the complexity of the nontargets; and (d) the number of elements within a target region. The main result is that detectability increases when the within-region complexity of the target and the nontarget regions decreases. Furthermore, interactions between the target and nontarget areas affect detectability too: We found that search asymmetry is produced by the asymmetrical effect of complexity when target and nontarget areas are interchanged.

Cis-regulatory Elements and Human Evolution

PubMed Central

Siepel, Adam

2014-01-01

Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider “new frontiers” in this field stemming from recent research on transcriptional regulation. PMID:25218861

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

Epitope mapping of the domains of human angiotensin converting enzyme.

PubMed

Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

2006-06-01

Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

Identification of two novel functional p53 responsive elements in the herpes simplex virus-1 genome.

PubMed

Hsieh, Jui-Cheng; Kuta, Ryan; Armour, Courtney R; Boehmer, Paul E

2014-07-01

Analysis of the herpes simplex virus-1 (HSV-1) genome reveals two candidate p53 responsive elements (p53RE), located in proximity to the replication origins oriL and oriS, referred to as p53RE-L and p53RE-S, respectively. The sequences of p53RE-L and p53RE-S conform to the p53 consensus site and are present in HSV-1 strains KOS, 17, and F. p53 binds to both elements in vitro and in virus-infected cells. Both p53RE-L and p53RE-S are capable of conferring p53-dependent transcriptional activation onto a heterologous reporter gene. Importantly, expression of the essential immediate early viral transactivator ICP4 and the essential DNA replication protein ICP8, that are adjacent to p53RE-S and p53RE-L, are repressed in a p53-dependent manner. Taken together, this study identifies two novel functional p53RE in the HSV-1 genome and suggests a complex mechanism of viral gene regulation by p53 which may determine progression of the lytic viral replication cycle or the establishment of latency. Copyright © 2014 Elsevier Inc. All rights reserved.

Leaky gut and diabetes mellitus: what is the link?

PubMed

de Kort, S; Keszthelyi, D; Masclee, A A M

2011-06-01

Diabetes mellitus is a chronic disease requiring lifelong medical attention. With hundreds of millions suffering worldwide, and a rapidly rising incidence, diabetes mellitus poses a great burden on healthcare systems. Recent studies investigating the underlying mechanisms involved in disease development in diabetes point to the role of the dys-regulation of the intestinal barrier. Via alterations in the intestinal permeability, intestinal barrier function becomes compromised whereby access of infectious agents and dietary antigens to mucosal immune elements is facilitated, which may eventually lead to immune reactions with damage to pancreatic beta cells and can lead to increased cytokine production with consequent insulin resistance. Understanding the factors regulating the intestinal barrier function will provide important insight into the interactions between luminal antigens and immune response elements. This review analyses recent advances in the mechanistic understanding of the role of the intestinal epithelial barrier function in the development of type 1 and type 2 diabetes. Given our current knowledge, we may assume that reinforcing the intestinal barrier can offer and open new therapeutic horizons in the treatment of type 1 and type 2 diabetes. © 2011 The Authors. obesity reviews © 2011 International Association for the Study of Obesity.

Environmental Testing and Thermal Analysis of the NPS Solar Cell Array Tester (NPS-SCAT) CubeSat

DTIC Science & Technology

2011-06-01

BCR Battery Charge Regulator C&DH Command and Data Handling CAD Computer Aided Design CDR Critical Design Review CFT Comprehensive Functional Test ...CPT Comprehensive Performance Test CoM Center of Mass COTS Commercial Off-the-Shelf CTB Cargo Transfer Bag EDU Engineering Design Unit EPS...and inexpensive solution. 2 C. ENVIRONMENTAL TESTING Environmental testing is an important element of the design and testing of a satellite. By

Helium 3/Helium 4 dilution cryocooler for space

NASA Technical Reports Server (NTRS)

Hendricks, John B.; Dingus, Michael L.

1991-01-01

Prototype dilution cryocoolers based on dilution refrigeration and adiabatic demagnetization refrigeration (ADR) cycles were designed, constructed, and tested. Although devices the devices did not operate as fully functional dilution cryocoolers, important information was gathered. The porous metal phase separator was demonstrated to operate in the -1-g configuration; this phase separation is the critical element in the He-3 circulation dilution cryocooler. Improvements in instrumentation needed for additional tests and development were identified.

The NASA role in major areas of human concern: Communication

NASA Technical Reports Server (NTRS)

1973-01-01

After introducing some of the general factors that have affected progress in the area of communication, NASA program elements are examined to illustrate relevant points of contact. Interpretive steps are taken throughout the report to show a few of the more important ways people's lives have been affected as a result of the work of NASA and other organizations functioning in this area. The principal documents used and interviews conducted are identified.

Nanometric summation architecture based on optical near-field interaction between quantum dots.

PubMed

Naruse, Makoto; Miyazaki, Tetsuya; Kubota, Fumito; Kawazoe, Tadashi; Kobayashi, Kiyoshi; Sangu, Suguru; Ohtsu, Motoichi

2005-01-15

A nanoscale data summation architecture is proposed and experimentally demonstrated based on the optical near-field interaction between quantum dots. Based on local electromagnetic interactions between a few nanometric elements via optical near fields, we can combine multiple excitations at a certain quantum dot, which allows construction of a summation architecture. Summation plays a key role for content-addressable memory, which is one of the most important functions in optical networks.

Orbital construction support equipment

NASA Technical Reports Server (NTRS)

1977-01-01

Approximately 200 separate construction steps were defined for the three solar power satellite (SPS) concepts. Detailed construction scenarios were developed which describe the specific tasks to be accomplished, and identify general equipment requirements. The scenarios were used to perform a functional analysis, which resulted in the definition of 100 distinct SPS elements. These elements are the components, parts, subsystems, or assemblies upon which construction activities take place. The major SPS elements for each configuration are shown. For those elements, 300 functional requirements were identified in seven generic processes. Cumulatively, these processes encompass all functions required during SPS construction/assembly. Individually each process is defined such that it includes a specific type of activity. Each SPS element may involve activities relating to any or all of the generic processes. The processes are listed, and examples of the requirements defined for a typical element are given.

Use of chemical mechanical polishing in micromachining

DOEpatents

Nasby, Robert D.; Hetherington, Dale L.; Sniegowski, Jeffry J.; McWhorter, Paul J.; Apblett, Christopher A.

1998-01-01

A process for removing topography effects during fabrication of micromachines. A sacrificial oxide layer is deposited over a level containing functional elements with etched valleys between the elements such that the sacrificial layer has sufficient thickness to fill the valleys and extend in thickness upwards to the extent that the lowest point on the upper surface of the oxide layer is at least as high as the top surface of the functional elements in the covered level. The sacrificial oxide layer is then polished down and planarized by chemical-mechanical polishing. Another layer of functional elements is then formed upon this new planarized surface.

Application of wall-models to discontinuous Galerkin LES

NASA Astrophysics Data System (ADS)

Frère, Ariane; Carton de Wiart, Corentin; Hillewaert, Koen; Chatelain, Philippe; Winckelmans, Grégoire

2017-08-01

Wall-resolved Large-Eddy Simulations (LES) are still limited to moderate Reynolds number flows due to the high computational cost required to capture the inner part of the boundary layer. Wall-modeled LES (WMLES) provide more affordable LES by modeling the near-wall layer. Wall function-based WMLES solve LES equations up to the wall, where the coarse mesh resolution essentially renders the calculation under-resolved. This makes the accuracy of WMLES very sensitive to the behavior of the numerical method. Therefore, best practice rules regarding the use and implementation of WMLES cannot be directly transferred from one methodology to another regardless of the type of discretization approach. Whilst numerous studies present guidelines on the use of WMLES, there is a lack of knowledge for discontinuous finite-element-like high-order methods. Incidentally, these methods are increasingly used on the account of their high accuracy on unstructured meshes and their strong computational efficiency. The present paper proposes best practice guidelines for the use of WMLES in these methods. The study is based on sensitivity analyses of turbulent channel flow simulations by means of a Discontinuous Galerkin approach. It appears that good results can be obtained without the use of a spatial or temporal averaging. The study confirms the importance of the wall function input data location and suggests to take it at the bottom of the second off-wall element. These data being available through the ghost element, the suggested method prevents the loss of computational scalability experienced in unstructured WMLES. The study also highlights the influence of the polynomial degree used in the wall-adjacent element. It should preferably be of even degree as using polynomials of degree two in the first off-wall element provides, surprisingly, better results than using polynomials of degree three.

Predicting Epidemic Risk from Past Temporal Contact Data

PubMed Central

Valdano, Eugenio; Poletto, Chiara; Giovannini, Armando; Palma, Diana; Savini, Lara; Colizza, Vittoria

2015-01-01

Understanding how epidemics spread in a system is a crucial step to prevent and control outbreaks, with broad implications on the system’s functioning, health, and associated costs. This can be achieved by identifying the elements at higher risk of infection and implementing targeted surveillance and control measures. One important ingredient to consider is the pattern of disease-transmission contacts among the elements, however lack of data or delays in providing updated records may hinder its use, especially for time-varying patterns. Here we explore to what extent it is possible to use past temporal data of a system’s pattern of contacts to predict the risk of infection of its elements during an emerging outbreak, in absence of updated data. We focus on two real-world temporal systems; a livestock displacements trade network among animal holdings, and a network of sexual encounters in high-end prostitution. We define the node’s loyalty as a local measure of its tendency to maintain contacts with the same elements over time, and uncover important non-trivial correlations with the node’s epidemic risk. We show that a risk assessment analysis incorporating this knowledge and based on past structural and temporal pattern properties provides accurate predictions for both systems. Its generalizability is tested by introducing a theoretical model for generating synthetic temporal networks. High accuracy of our predictions is recovered across different settings, while the amount of possible predictions is system-specific. The proposed method can provide crucial information for the setup of targeted intervention strategies. PMID:25763816

Mechanisms of radiation-induced gene responses

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

Woloschak, G.E.; Paunesku, T.

1996-10-01

In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts;more » however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.« less

Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park

PubMed Central

Jay, Z. J.; Beam, J. P.; Dohnalkova, A.; Lohmayer, R.; Bodle, B.; Planer-Friedrich, B.; Romine, M.

2015-01-01

Thermoproteales (phylum Crenarchaeota) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurring in situ. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the de novo synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of P. yellowstonensis and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to in situ populations. The physiological attributes and metabolic capabilities of P. yellowstonensis provide an important foundation for developing an understanding of the distribution and function of these populations in YNP. PMID:26092468

Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication.

PubMed

Ren, Xiaodi; Siegel, Rachael; Kim, Unkyu; Roeder, Robert G

2011-05-06

B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in Igh promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated Igh promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3' enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3' enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism. Copyright © 2011 Elsevier Inc. All rights reserved.

Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication

PubMed Central

Ren, Xiaodi; Siegel, Rachael; Kim, Unkyu; Roeder, Robert G.

2011-01-01

Summary B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in IgH promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated IgH promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3′enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3′enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism. PMID:21549311

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

PubMed Central

Thibodeau, Asa; Márquez, Eladio J.; Luo, Oscar; Ruan, Yijun; Shin, Dong-Guk; Stitzel, Michael L.; Ucar, Duygu

2016-01-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/. PMID:27336171

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

PubMed Central

Schrider, Daniel R.; Kern, Andrew D.

2015-01-01

The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods. PMID:26590212

Desmosomes in acquired disease

PubMed Central

Stahley, Sara N.; Kowalczyk, Andrew P.

2015-01-01

Desmosomes are cell-cell junctions that mediate adhesion and couple the intermediate filament cytoskeleton to sites of cell-cell contact. This architectural arrangement functions to integrate adhesion and cytoskeletal elements of adjacent cells. The importance of this robust adhesion system is evident in numerous human diseases, both inherited and acquired, that occur when desmosome function is compromised. This review focuses on autoimmune and infectious diseases that impair desmosome function. In addition, we discuss emerging evidence that desmosomal genes are often misregulated in cancer. The emphasis of our discussion is placed on how human diseases inform our understanding of basic desmosome biology, and in turn, how fundamental advances in the cell biology of desmosomes may lead to new treatments for acquired diseases of the desmosome. PMID:25795143

Representation of the Coulomb Matrix Elements by Means of Appell Hypergeometric Function F 2

NASA Astrophysics Data System (ADS)

Bentalha, Zine el abidine

2018-06-01

Exact analytical representation for the Coulomb matrix elements by means of Appell's double series F 2 is derived. The finite sum obtained for the Appell function F 2 allows us to evaluate explicitly the matrix elements of the two-body Coulomb interaction in the lowest Landau level. An application requiring the matrix elements of Coulomb potential in quantum Hall effect regime is presented.

Checkpoints to the Brain: Directing Myeloid Cell Migration to the Central Nervous System

PubMed Central

Harrison-Brown, Meredith; Liu, Guo-Jun; Banati, Richard

2016-01-01

Myeloid cells are a unique subset of leukocytes with a diverse array of functions within the central nervous system during health and disease. Advances in understanding of the unique properties of these cells have inspired interest in their use as delivery vehicles for therapeutic genes, proteins, and drugs, or as “assistants” in the clean-up of aggregated proteins and other molecules when existing drainage systems are no longer adequate. The trafficking of myeloid cells from the periphery to the central nervous system is subject to complex cellular and molecular controls with several ‘checkpoints’ from the blood to their destination in the brain parenchyma. As important components of the neurovascular unit, the functional state changes associated with lineage heterogeneity of myeloid cells are increasingly recognized as important for disease progression. In this review, we discuss some of the cellular elements associated with formation and function of the neurovascular unit, and present an update on the impact of myeloid cells on central nervous system (CNS) diseases in the laboratory and the clinic. We then discuss emerging strategies for harnessing the potential of site-directed myeloid cell homing to the CNS, and identify promising avenues for future research, with particular emphasis on the importance of untangling the functional heterogeneity within existing myeloid subsets. PMID:27918464

Assessment and management of nutrition in older people and its importance to health.

PubMed

Ahmed, Tanvir; Haboubi, Nadim

2010-08-09

Nutrition is an important element of health in the older population and affects the aging process. The prevalence of malnutrition is increasing in this population and is associated with a decline in: functional status, impaired muscle function, decreased bone mass, immune dysfunction, anemia, reduced cognitive function, poor wound healing, delayed recovery from surgery, higher hospital readmission rates, and mortality. Older people often have reduced appetite and energy expenditure, which, coupled with a decline in biological and physiological functions such as reduced lean body mass, changes in cytokine and hormonal level, and changes in fluid electrolyte regulation, delay gastric emptying and diminish senses of smell and taste. In addition pathologic changes of aging such as chronic diseases and psychological illness all play a role in the complex etiology of malnutrition in older people. Nutritional assessment is important to identify and treat patients at risk, the Malnutrition Universal Screening Tool being commonly used in clinical practice. Management requires a holistic approach, and underlying causes such as chronic illness, depression, medication and social isolation must be treated. Patients with physical or cognitive impairment require special care and attention. Oral supplements or enteral feeding should be considered in patients at high risk or in patients unable to meet daily requirements.

New surgical concepts: nasal tip function.

PubMed

Galli, J J; Zavalla, C A; Vivas, D G; Prado, C; Zanetta, G C

1997-01-01

Since the birth of plastic surgery, rhinoplasty has been an outstanding chapter. Facial balance has been endeavoured with two parameters: size and shape. Now, however, the criterion for harmony has involved two more parameters; position and function. Position is related to other facial elements, such as, upper maxilla, upper lip, forehead, and frontonasal sulcus. Function is important because nasal superficial musculoaponeurotic system (SMAS) muscles are important for Nasal tip movement. To understand this better, we must analyze the nasal SMAS, which consists of primary or intrinsic and secondary or extrinsic muscles. When the extrinsics contract, they allow function of the intrinsics. They are the ala nasalis dilator, the ala nasalis elevator, the tranversus, and the tip depressor. Obvious hypertrophies of the dilator and the elevator has been observed in young athletes. Our method combines conventional, new, and modern aspects. It is conventional because the alar cartilages have been completely freed by intercartilaginous and marginal approaches, and the upper or lower border trimmed according to the case. It is more important to measure how much cartilage is left, than how much is removed. The new aspect is consideration of nasal SMAS to treat short noses that display a tendency to descend with laughter, and the modern aspect is the evaluation of dynamic surgical results, apart from the static.

Cartilaginous Epiphyses in Extant Archosaurs and Their Implications for Reconstructing Limb Function in Dinosaurs

PubMed Central

Holliday, Casey M.; Ridgely, Ryan C.; Sedlmayr, Jayc C.; Witmer, Lawrence M.

2010-01-01

Extinct archosaurs, including many non-avian dinosaurs, exhibit relatively simply shaped condylar regions in their appendicular bones, suggesting potentially large amounts of unpreserved epiphyseal (articular) cartilage. This “lost anatomy” is often underappreciated such that the ends of bones are typically considered to be the joint surfaces, potentially having a major impact on functional interpretation. Extant alligators and birds were used to establish an objective basis for inferences about cartilaginous articular structures in such extinct archosaur clades as non-avian dinosaurs. Limb elements of alligators, ostriches, and other birds were dissected, disarticulated, and defleshed. Lengths and condylar shapes of elements with intact epiphyses were measured. Limbs were subsequently completely skeletonized and the measurements repeated. Removal of cartilaginous condylar regions resulted in statistically significant changes in element length and condylar breadth. Moreover, there was marked loss of those cartilaginous structures responsible for joint architecture and congruence. Compared to alligators, birds showed less dramatic, but still significant changes. Condylar morphologies of dinosaur limb bones suggest that most non-coelurosaurian clades possessed large cartilaginous epiphyses that relied on the maintenance of vascular channels that are otherwise eliminated early in ontogeny in smaller-bodied tetrapods. A sensitivity analysis using cartilage correction factors (CCFs) obtained from extant taxa indicates that whereas the presence of cartilaginous epiphyses only moderately increases estimates of dinosaur height and speed, it has important implications for our ability to infer joint morphology, posture, and the complicated functional movements in the limbs of many extinct archosaurs. Evidence suggests that the sizes of sauropod epiphyseal cartilages surpassed those of alligators, which account for at least 10% of hindlimb length. These data suggest that large cartilaginous epiphyses were widely distributed among non-avian archosaurs and must be considered when making inferences about locomotor functional morphology in fossil taxa. PMID:20927347

Early-life adversity programs emotional functions and the neuroendocrine stress system: the contribution of nutrition, metabolic hormones and epigenetic mechanisms.

PubMed

Yam, Kit-Yi; Naninck, Eva F G; Schmidt, Mathias V; Lucassen, Paul J; Korosi, Aniko

2015-01-01

Clinical and pre-clinical studies have shown that early-life adversities, such as abuse or neglect, can increase the vulnerability to develop psychopathologies and cognitive decline later in life. Remarkably, the lasting consequences of stress during this sensitive period on the hypothalamic-pituitary-adrenal axis and emotional function closely resemble the long-term effects of early malnutrition and suggest a possible common pathway mediating these effects. During early-life, brain development is affected by both exogenous factors, like nutrition and maternal care as well as by endogenous modulators including stress hormones. These elements, while mostly considered for their independent actions, clearly do not act alone but rather in a synergistic manner. In order to better understand how the programming by early-life stress takes place, it is important to gain further insight into the exact interplay of these key elements, the possible common pathways as well as the underlying molecular mechanisms that mediate their effects. We here review evidence that exposure to both early-life stress and early-life under-/malnutrition similarly lead to life-long alterations on the neuroendocrine stress system and modify emotional functions. We further discuss how the different key elements of the early-life environment interact and affect one another and next suggest a possible role for the early-life adversity induced alterations in metabolic hormones and nutrient availability in shaping later stress responses and emotional function throughout life, possibly via epigenetic mechanisms. Such knowledge will help to develop intervention strategies, which gives the advantage of viewing the synergistic action of a more complete set of changes induced by early-life adversity.

Cartilaginous epiphyses in extant archosaurs and their implications for reconstructing limb function in dinosaurs.

PubMed

Holliday, Casey M; Ridgely, Ryan C; Sedlmayr, Jayc C; Witmer, Lawrence M

2010-09-30

Extinct archosaurs, including many non-avian dinosaurs, exhibit relatively simply shaped condylar regions in their appendicular bones, suggesting potentially large amounts of unpreserved epiphyseal (articular) cartilage. This "lost anatomy" is often underappreciated such that the ends of bones are typically considered to be the joint surfaces, potentially having a major impact on functional interpretation. Extant alligators and birds were used to establish an objective basis for inferences about cartilaginous articular structures in such extinct archosaur clades as non-avian dinosaurs. Limb elements of alligators, ostriches, and other birds were dissected, disarticulated, and defleshed. Lengths and condylar shapes of elements with intact epiphyses were measured. Limbs were subsequently completely skeletonized and the measurements repeated. Removal of cartilaginous condylar regions resulted in statistically significant changes in element length and condylar breadth. Moreover, there was marked loss of those cartilaginous structures responsible for joint architecture and congruence. Compared to alligators, birds showed less dramatic, but still significant changes. Condylar morphologies of dinosaur limb bones suggest that most non-coelurosaurian clades possessed large cartilaginous epiphyses that relied on the maintenance of vascular channels that are otherwise eliminated early in ontogeny in smaller-bodied tetrapods. A sensitivity analysis using cartilage correction factors (CCFs) obtained from extant taxa indicates that whereas the presence of cartilaginous epiphyses only moderately increases estimates of dinosaur height and speed, it has important implications for our ability to infer joint morphology, posture, and the complicated functional movements in the limbs of many extinct archosaurs. Evidence suggests that the sizes of sauropod epiphyseal cartilages surpassed those of alligators, which account for at least 10% of hindlimb length. These data suggest that large cartilaginous epiphyses were widely distributed among non-avian archosaurs and must be considered when making inferences about locomotor functional morphology in fossil taxa.

Modeling statistics and kinetics of the natural aggregation structures and processes with the solution of generalized logistic equation

NASA Astrophysics Data System (ADS)

Maslov, Lev A.; Chebotarev, Vladimir I.

2017-02-01

The generalized logistic equation is proposed to model kinetics and statistics of natural processes such as earthquakes, forest fires, floods, landslides, and many others. This equation has the form dN(A)/dA = s dot (1-N(A)) dot N(A)q dot A-α, q>0q>0 and A>0A>0 is the size of an element of a structure, and α≥0. The equation contains two exponents α and q taking into account two important properties of elements of a system: their fractal geometry, and their ability to interact either to enhance or to damp the process of aggregation. The function N(A)N(A) can be understood as an approximation to the number of elements the size of which is less than AA. The function dN(A)/dAdN(A)/dA where N(A)N(A) is the general solution of this equation for q=1 is a product of an increasing bounded function and power-law function with stretched exponential cut-off. The relation with Tsallis non-extensive statistics is demonstrated by solving the generalized logistic equation for q>0q>0. In the case 01q>1 it models sub-additive structures. The Gutenberg-Richter (G-R) formula results from interpretation of empirical data as a straight line in the area of stretched exponent with small α. The solution is applied for modeling distribution of foreshocks and aftershocks in the regions of Napa Valley 2014, and Sumatra 2004 earthquakes fitting the observed data well, both qualitatively and quantitatively.

Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

PubMed

Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

2015-01-01

Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

Frequency response function (FRF) based updating of a laser spot welded structure

NASA Astrophysics Data System (ADS)

Zin, M. S. Mohd; Rani, M. N. Abdul; Yunus, M. A.; Sani, M. S. M.; Wan Iskandar Mirza, W. I. I.; Mat Isa, A. A.

2018-04-01

The objective of this paper is to present frequency response function (FRF) based updating as a method for matching the finite element (FE) model of a laser spot welded structure with a physical test structure. The FE model of the welded structure was developed using CQUAD4 and CWELD element connectors, and NASTRAN was used to calculate the natural frequencies, mode shapes and FRF. Minimization of the discrepancies between the finite element and experimental FRFs was carried out using the exceptional numerical capability of NASTRAN Sol 200. The experimental work was performed under free-free boundary conditions using LMS SCADAS. Avast improvement in the finite element FRF was achieved using the frequency response function (FRF) based updating with two different objective functions proposed.

Distractor ratio and grouping processes in visual conjunction search.

PubMed

Poisson, M E; Wilkinson, F

1992-01-01

According to feature integration theory, conjunction search is conducted via a serial self-terminating search. However, effects attributed to search processes operating on the entire display may actually reflect search restricted to elements defined by a single feature. In experiment 1 this question is addressed in a reaction-time (RT) paradigm by varying distractor ratios within an array of fixed size. For trials in which the target was present in the array, RT functions were roughly symmetric, the shortest RTs being for extreme distractor ratios, and the longest RTs being for arrays in which there were an equal number of each distractor type. This result is superficially consistent with Zohary and Hochstein's interpretation that subjects search for only one distractor type and are able to switch search strategy from trial to trial. However, negative-trial data from experiment 1 case doubt on this interpretation. In experiment 2 the possible role of 'pop out' and of distractor grouping in visual conjunction search is investigated. Results of experiment 2 suggest that grouping may play a more important role than does distractor ratio, and point to the importance of the spatial layout of the target and of the distractor elements in visual conjunction search. Results of experiment 2 also provide clear evidence that groups of spatially adjacent homogeneous elements may be processed as a unit.

Endangered Species Hold Clues to Human Evolution

PubMed Central

Bejerano, Gill; Salama, Sofie R.; Haussler, David

2010-01-01

We report that 18 conserved, and by extension functional, elements in the human genome are the result of retroposon insertions that are evolving under purifying selection in mammals. We show evidence that 1 of the 18 elements regulates the expression of ASXL3 during development by encoding an alternatively spliced exon that causes nonsense-mediated decay of the transcript. The retroposon that gave rise to these functional elements was quickly inactivated in the mammalian ancestor, and all traces of it have been lost due to neutral decay. However, the tuatara has maintained a near-ancestral version of this retroposon in its extant genome, which allows us to connect the 18 human elements to the evolutionary events that created them. We propose that conservation efforts over more than 100 years may not have only prevented the tuatara from going extinct but could have preserved our ability to understand the evolutionary history of functional elements in the human genome. Through simulations, we argue that species with historically low population sizes are more likely to harbor ancient mobile elements for long periods of time and in near-ancestral states, making these species indispensable in understanding the evolutionary origin of functional elements in the human genome. PMID:20332163

Specialty functions singularity mechanics problems

NASA Technical Reports Server (NTRS)

Sarigul, Nesrin

1989-01-01

The focus is in the development of more accurate and efficient advanced methods for solution of singular problems encountered in mechanics. At present, finite element methods in conjunction with special functions, boolean sum and blending interpolations are being considered. In dealing with systems which contain a singularity, special finite elements are being formulated to be used in singular regions. Further, special transition elements are being formulated to couple the special element to the mesh that models the rest of the system, and to be used in conjunction with 1-D, 2-D and 3-D elements within the same mesh. Computational simulation with a least squares fit is being utilized to construct special elements, if there is an unknown singularity in the system. A novel approach is taken in formulation of the elements in that: (1) the material properties are modified to include time, temperature, coordinate and stress dependant behavior within the element; (2) material properties vary at nodal points of the elements; (3) a hidden-symbolic computation scheme is developed and utilized in formulating the elements; and (4) special functions and boolean sum are utilized in order to interpolate the field variables and their derivatives along the boundary of the elements. It may be noted that the proposed methods are also applicable to fluids and coupled problems.

A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks.

PubMed

Le, Duc-Hau

2015-01-01

Protein complexes formed by non-covalent interaction among proteins play important roles in cellular functions. Computational and purification methods have been used to identify many protein complexes and their cellular functions. However, their roles in terms of causing disease have not been well discovered yet. There exist only a few studies for the identification of disease-associated protein complexes. However, they mostly utilize complicated heterogeneous networks which are constructed based on an out-of-date database of phenotype similarity network collected from literature. In addition, they only apply for diseases for which tissue-specific data exist. In this study, we propose a method to identify novel disease-protein complex associations. First, we introduce a framework to construct functional similarity protein complex networks where two protein complexes are functionally connected by either shared protein elements, shared annotating GO terms or based on protein interactions between elements in each protein complex. Second, we propose a simple but effective neighborhood-based algorithm, which yields a local similarity measure, to rank disease candidate protein complexes. Comparing the predictive performance of our proposed algorithm with that of two state-of-the-art network propagation algorithms including one we used in our previous study, we found that it performed statistically significantly better than that of these two algorithms for all the constructed functional similarity protein complex networks. In addition, it ran about 32 times faster than these two algorithms. Moreover, our proposed method always achieved high performance in terms of AUC values irrespective of the ways to construct the functional similarity protein complex networks and the used algorithms. The performance of our method was also higher than that reported in some existing methods which were based on complicated heterogeneous networks. Finally, we also tested our method with prostate cancer and selected the top 100 highly ranked candidate protein complexes. Interestingly, 69 of them were evidenced since at least one of their protein elements are known to be associated with prostate cancer. Our proposed method, including the framework to construct functional similarity protein complex networks and the neighborhood-based algorithm on these networks, could be used for identification of novel disease-protein complex associations.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. PMID:27697855

5. Interrelationships, functional packages and priorities.

PubMed

2014-05-01

The basic societal functions (BSFs) do not exist in isolation. Many of the functions are dependent and/or interdependent on one another and/or on the components that comprise the BSFs. Dependency occurs when goods and/or services are required for a function, subfunction, or a component of a function. Interdependency occurs when the same component (commodity, service, or process) is required by more than one BSF or component(s) of a BSF. Insufficiencies of functions that are interdependent are more likely to render a society dysfunctional than are those that are not interdependent. Combinations of functions from different BSF form functional packages. In times of disaster and limited resources, subfunctions, elements, and subelements, etc. must be prioritised in terms of their relative importance for the continuation of the most essential services. Priorities must be established so that when resources are scarce, nonessential services may be temporarily discontinued and similarly, priorities must be determined for re-establishment of services as needed resources become available.

Identification of the Intragenomic Promoter Controlling Hepatitis E Virus Subgenomic RNA Transcription.

PubMed

Ding, Qiang; Nimgaonkar, Ila; Archer, Nicholas F; Bram, Yaron; Heller, Brigitte; Schwartz, Robert E; Ploss, Alexander

2018-05-08

Approximately 20 million hepatitis E virus (HEV) infections occur annually in both developing and industrialized countries. Most infections are self-limiting, but they can lead to chronic infections and cirrhosis in immunocompromised patients, and death in pregnant women. The mechanisms of HEV replication remain incompletely understood due to scarcity of adequate experimental platforms. HEV undergoes asymmetric genome replication, but it produces an additional subgenomic (SG) RNA encoding the viral capsid and a viroporin in partially overlapping open reading frames. Using a novel transcomplementation system, we mapped the intragenomic subgenomic promoter regulating SG RNA synthesis. This cis -acting element is highly conserved across all eight HEV genotypes, and when the element is mutated, it abrogates particle assembly and release. Our work defines previously unappreciated viral regulatory elements and provides the first in-depth view of the intracellular genome dynamics of this emerging human pathogen. IMPORTANCE HEV is an emerging pathogen causing severe liver disease. The genetic information of HEV is encoded in RNA. The genomic RNA is initially copied into a complementary, antigenomic RNA that is a template for synthesis of more genomic RNA and for so-called subgenomic RNA. In this study, we identified the precise region within the HEV genome at which the synthesis of the subgenomic RNA is initiated. The nucleotides within this region are conserved across genetically distinct variants of HEV, highlighting the general importance of this segment for the virus. To identify this regulatory element, we developed a new experimental system that is a powerful tool with broad utility to mechanistically dissect many other poorly understood functional elements of HEV. Copyright © 2018 Ding et al.

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

Hanson-Heine, Magnus W. D.; George, Michael W.; Besley, Nicholas A.

2018-05-01

Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

Noncoding sequence classification based on wavelet transform analysis: part I

NASA Astrophysics Data System (ADS)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

Employer evaluations of nurse graduates: a critical program assessment element.

PubMed

Ryan, M E; Hodson, K E

1992-05-01

Accountability in higher education dictates implementation of a comprehensive evaluation plan. Employer evaluation of graduates is an important component of program evaluation and contributes a different view that is rarely reported in the literature. The purpose of this study was to establish a database by surveying employers of baccalaureate-prepared nurses, postgraduation, over a five-year period. Employer surveys measured perceptions of graduates' functioning. Findings indicated that graduates function above expected levels for leadership skills, nursing skills, communication skills, and professionalism. Systematic program evaluation by employers is recommended at one and five years after graduation. A tool for employer evaluation of baccalaureate graduates is discussed.

The Functional Breakdown Structure (FBS) and Its Relationship to Life Cycle Cost

NASA Technical Reports Server (NTRS)

DeHoff, Bryan; Levack, Danie J. H.; Rhodes, Russell E.

2009-01-01

The Functional Breakdown Structure (FBS) is a structured, modular breakdown of every function that must be addressed to perform a generic mission. It is also usable for any subset of the mission. Unlike a Work Breakdown Structure (WBS), the FBS is a function-oriented tree, not a product-oriented tree. The FBS details not products, but operations or activities that should be performed. The FBS is not tied to any particular architectural implementation because it is a listing of the needed functions, not the elements, of the architecture. The FBS for Space Transportation Systems provides a universal hierarchy of required functions, which include ground and space operations as well as infrastructure - it provides total visibility of the entire mission. By approaching the systems engineering problem from the functional view, instead of the element or hardware view, the SPST has created an exhaustive list of potential requirements which the architecture designers can use to evaluate the completeness of their designs. This is a new approach that will provide full accountability of all functions required to perform the planned mission. It serves as a giant check list to be sure that no functions are omitted, especially in the early architectural design phase. A significant characteristic of a FBS is that if architecture options are compared using this approach, then any missing or redundant elements of each option will be ' identified. Consequently, valid Life Cycle Costs (LCC) comparisons can be made. For example, one architecture option might not need a particular function while another option does. One option may have individual elements to perform each of three functions while another option needs only one element to perform the three functions. Once an architecture has been selected, the FBS will serve as a guide in development of the work breakdown structure, provide visibility of those technologies that need to be further developed to perform required functions, and help identify the personnel skills required to develop and operate the architecture. It also wifi allow the systems engineering activities to totally integrate each discipline to the maximum extent possible and optimize at the total system level, thus avoiding optimizing at the element level (stove-piping). In addition, it furnishes a framework that wifi help prevent over or under specifying requirements because all functions are identified and all elements are aligned to functions.

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

PubMed Central

2009-01-01

Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences. PMID:19821996

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.

PubMed

Förster, Frank; Liang, Chunguang; Shkumatov, Alexander; Beisser, Daniela; Engelmann, Julia C; Schnölzer, Martina; Frohme, Marcus; Müller, Tobias; Schill, Ralph O; Dandekar, Thomas

2009-10-12

Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.

Parts function as perceptual organizational entities in infancy.

PubMed

Kangas, Ashley; Zieber, Nicole; Hayden, Angela; Bhatt, Ramesh S

2013-08-01

Both objects and parts function as organizational entities in adult perception. Prior research has indicated that objects affect organization early in life: Infants grouped elements located within object boundaries and segregated them from those located on different objects. Here, we examined whether parts also induce grouping in infancy. Five- and 6.5-month-olds were habituated to two-part objects containing element pairs. In a subsequent test, infants treated groupings of elements that crossed part boundaries as novel, in comparison with groupings that had shared a common part during habituation. In contrast, the same arrangement of elements failed to elicit evidence of grouping in control conditions in which the elements were not surrounded by closed part boundaries. Thus, infants grouped and segregated elements on the basis of part structure. Part-based processing is a key aspect of many theories of perception. The present research adds to this literature by indicating that parts function as organizational entities early in life.

Characterization of "cis"-regulatory elements ("c"RE) associated with mammary gland function

USDA-ARS?s Scientific Manuscript database

The Bos taurus genome assembly has propelled dairy science into a new era; still, most of the information encoded in the genome has not yet been decoded. The human Encyclopedia of DNA Elements (ENCODE) project has spearheaded the identification and annotation of functional genomic elements in the hu...

Integrative and conjugative elements and their hosts: composition, distribution and organization

PubMed Central

Touchon, Marie; Rocha, Eduardo P. C.

2017-01-01

Abstract Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes. PMID:28911112

Trace Element Levels and Cognitive Function in Rural Elderly Chinese

PubMed Central

Gao, Sujuan; Jin, Yinlong; Unverzagt, Frederick W.; Ma, Feng; Hall, Kathleen S.; Murrell, Jill R.; Cheng, Yibin; Shen, Jianzhao; Ying, Bo; Ji, Rongdi; Matesan, Janetta; Liang, Chaoke; Hendrie, Hugh C.

2009-01-01

Background Trace elements are involved in metabolic processes and oxidation-reduction reactions in the central nervous system and could have a possible effect on cognitive function. The relationship between trace elements measured in individual biological samples and cognitive function in an elderly population had not been investigated extensively. Methods The participant population is part of a large cohort study of 2000 rural elderly Chinese persons. Six cognitive assessment tests were used to evaluate cognitive function in this population, and a composite score was created to represent global cognitive function. Trace element levels of aluminum, calcium, cadmium, copper, iron, lead, and zinc were analyzed in plasma samples of 188 individuals who were randomly selected and consented to donating fasting blood. Analysis of covariance models were used to assess the association between each trace element and the composite cognitive score adjusting for demographics, medical history of chronic diseases, and the apolipoprotein E (APOE) genotype. Results Three trace elements—calcium, cadmium, and copper—were found to be significantly related to the composite cognitive score. Increasing plasma calcium level was associated with higher cognitive score (p < .0001). Increasing cadmium and copper, in contrast, were significantly associated with lower composite score (p = .0044 and p = .0121, respectively). Other trace elements did not show significant association with the composite cognitive score. Conclusions Our results suggest that calcium, cadmium, and copper may be associated with cognitive function in the elderly population. PMID:18559640

On the role of inter-basin surface salinity contrasts in global ocean circulation

NASA Astrophysics Data System (ADS)

Seidov, D.; Haupt, B. J.

2002-08-01

The role of sea surface salinity (SSS) contrasts in maintaining vigorous global ocean thermohaline circulation (TOC) is revisited. Relative importance of different generalizations of sea surface conditions in climate studies is explored. Ocean-wide inter-basin SSS contrasts serve as the major controlling element in global TOC. These contrasts are shown to be at least as important as high-latitudinal freshwater impacts. It is also shown that intra-basin longitudinal distribution of sea surface salinity, as well as intra- and inter-basin longitudinal distribution of sea surface temperature, is not crucial to conveyor functionality if only inter-basin contrasts in sea surface salinity are retained. This is especially important for paleoclimate and future climate simulations.

A Deluge of Complex Repeats: The Solanum Genome

PubMed Central

Mehra, Mrigaya; Gangwar, Indu; Shankar, Ravi

2015-01-01

Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50–60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats. PMID:26241045

Cast Iron in The 19th Century Building Equipment

NASA Astrophysics Data System (ADS)

Kwasek, Michał; Piwek, Aleksander

2017-10-01

Cast iron is a material, characteristics of which enable to receive extremely artistic elements. It maintains good strength properties at the same time. That combination of these seemingly contrary traits makes it a commodity that was widely used in the 19th century industry and architecture. These usages were not only as decorative elements, technical and structural ones. The production of new household utilities started, which made people’s lives more comfortable. Cast iron allowed for fast and cheap production while maintaining high aesthetic qualities. Useful elements, which often were ornamental parts of buildings were created. The aim of the article is to characterise elements of interior equipment of the 19th century building that are made of cast iron. As it appears from performed bibliography, archival and field studies, the ways of exploitation are very broad. Some were mounted into the building; the others were a mobile equipment. As it occurred they were most commonly used as functional items. Cast iron was used to produce the minor elements, which were only parts of the bigger wooden or stone items. Notwithstanding, there were also bigger ones casted as a whole, and frequently ones that were assembled from many elements. Nowadays, elements of an interior feature are one of the subjects of study during the restoration work of the buildings. They can provide important information about the building and the way people lived and are considered as the essential part of historical objects.

Use of chemical mechanical polishing in micromachining

DOEpatents

Nasby, R.D.; Hetherington, D.L.; Sniegowski, J.J.; McWhorter, P.J.; Apblett, C.A.

1998-09-08

A process for removing topography effects during fabrication of micromachines. A sacrificial oxide layer is deposited over a level containing functional elements with etched valleys between the elements such that the sacrificial layer has sufficient thickness to fill the valleys and extend in thickness upwards to the extent that the lowest point on the upper surface of the oxide layer is at least as high as the top surface of the functional elements in the covered level. The sacrificial oxide layer is then polished down and planarized by chemical-mechanical polishing. Another layer of functional elements is then formed upon this new planarized surface. 4 figs.

Epigenetic control of transposon transcription and mobility in Arabidopsis.

PubMed

Bucher, Etienne; Reinders, Jon; Mirouze, Marie

2012-11-01

The mobility of genetic elements called transposable elements (TEs) was discovered half a century ago by Barbara McClintock. Although she had recognized them as chromosomal controlling elements, for much of the consequent time TEs were primarily considered as parasites of the host genome. However the recent explosion of discoveries in the fields of genomics and epigenetics have unambiguously shown the importance of TEs in genome function and evolution. Bursts of endogenous TEs have been reported in plants with epigenetic misregulation, revealing the molecular mechanisms underlying their control. We review here the different steps in TE invasion of the host genome involving epigenetic control and environmental stress responses. As TEs propagate in plant genomes and attract epigenetic marks, their neo-insertions can lead to the formation of new, heritable epigenetic variants (epialleles) of genes in their vicinity and impact on host gene regulatory networks. The epigenetic interplay between TE and genes thus plays a crucial role in the TE-host co-evolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

The impact of transposable elements in environmental adaptation.

PubMed

Casacuberta, Elena; González, Josefa

2013-03-01

Transposable elements (TEs) play an important role in the responsive capacity of their hosts in the face of environmental challenges. The variety of mechanisms by which TEs influence the capacity of adaptation of the host is as large as the variety of TEs and host genomes. For example, TEs might directly affect the function of individual genes, provide a mechanism for rapidly acquiring new genetic material and disseminate regulatory elements that can lead to the creation of stress-inducible regulatory networks. In this review, we summarize recent examples that are part of an increasing body of evidence suggesting a significant role of TEs in the host response to an ever-changing environment, both in prokaryote and in eukaryote organisms. We argue that in the near future, the increasing availability of genome sequences and the development of new tools to discover and analyse TE insertions will further show the relevant role of TEs in environmental adaptation. © 2013 Blackwell Publishing Ltd.

STATs shape the active enhancer landscape of T cell populations.

PubMed

Vahedi, Golnaz; Takahashi, Hayato; Nakayamada, Shingo; Sun, Hong-Wei; Sartorelli, Vittorio; Kanno, Yuka; O'Shea, John J

2012-11-21

Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. Although enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4(+) T cells as a model of differentiation, mapping the activity of cell-type-specific enhancer elements in T helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the activation of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells. Copyright © 2012 Elsevier Inc. All rights reserved.

STATs Shape the Active Enhancer Landscape of T Cell Populations

PubMed Central

Vahedi, Golnaz; Takahashi, Hayato; Nakayamada, Shingo; Sun, Hong-wei; Sartorelli, Vittorio; Kanno, Yuka; O’Shea, John J.

2012-01-01

SUMMARY Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. While enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4+ T cells as a model of differentiation, mapping the acquisition of cell-type-specific enhancer elements in T-helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the acquisition of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells. PMID:23178119

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

Delpassand, M.S.

The power section of a mud driven progressing cavity drill motors consists of a steel rotor shaped with an external helix rotating within a stationary tube with a molded helical elastomeric lining (stator). Operating temperature of the elastomer lining is an important parameter that affects the stator life. Motor operating conditions such as down hole temperature, torque, differential pressure, and speed determine the elastomer temperature. This paper presents an analysis technique to predict stator elastomer temperature as a function of the motor`s operating parameters. A non-linear finite element analysis technique is used to predict the stator temperature. Physical and mechanicalmore » properties of the elastomer are measured, using laboratory equipment such as Monsanto`s RPA2000 dynamic analyzer and BFGoodrich model (II) flexometer. Boundary conditions of the finite element model are defined based on the down hole temperature, differential pressure, and the motor`s speed. Results of the finite element analysis are compared with laboratory test data to verify the accuracy of the analysis.« less

Analysis of the Duration of Lower Band Rising Tone Chorus Elements Using Van Allen Probes Data

NASA Astrophysics Data System (ADS)

Teng, S.; Tao, X.

2017-12-01

The duration of lower band rising tone chorus elements is an important parameter to understand chorus excitation mechanism, and is analyzed statistically in this work using Van Allen Probes data. The distribution of chorus element duration (τ) as a function of magnetic local time, L shell, and geomagnetic activity level characterized by the AE index are presented. We show that the typical value of τ for the nightside (0.15s) is smaller than that for the dayside (0.25s), and τ increases with increasing L-shell and decreasing geomagnetic level. We also investigate the correlation between τ and the frequency sweep rate (Γ). The observed relation between the duration (τ) scales and the frequency sweep rate (Γ) is found to be as τ ∝ Γ(-0.9). Future work is needed to explain this relation theoretically. Our results should be helpful to the further development of the theoretical model of chorus excitation.

Finite element 3D modeling of mechanical behavior of mineralized collagen microfibrils.

PubMed

Barkaoui, Abdelwahed; Hambli, Ridha

2011-01-01

The aim of this work is to develop a 3D finite elements model to study the nanomechanical behavior of mineralized collagen microfibrils, which consists of three phases, (i) collagen phase formed by five tropocollagen (TC) molecules linked together with cross-links, (ii) a mineral phase (Hydroxyapatite), and (iii) impure mineral phase, and to investigate the important role of individual properties of every constituent. The mechanical and geometric properties (TC molecule diameter) of both tropocollagen and mineral were taken into consideration as well as cross-links, which was represented by spring elements with adjusted properties based on experimental data. In this paper an equivalent homogenized model was developed to assess the whole microfibril mechanical properties (Young's modulus and Poisson's ratio) under varying mechanical properties of each phase. In this study, both equivalent Young's modulus and Poisson's ratio, which were expressed as functions of Young's modulus of each phase, were obtained under tensile load with symmetric and periodic boundary conditions.

Influence of Silicate Melt Composition on Metal/Silicate Partitioning of W, Ge, Ga and Ni

NASA Technical Reports Server (NTRS)

Singletary, S. J.; Domanik, K.; Drake, M. J.

2005-01-01

The depletion of the siderophile elements in the Earth's upper mantle relative to the chondritic meteorites is a geochemical imprint of core segregation. Therefore, metal/silicate partition coefficients (Dm/s) for siderophile elements are essential to investigations of core formation when used in conjunction with the pattern of elemental abundances in the Earth's mantle. The partitioning of siderophile elements is controlled by temperature, pressure, oxygen fugacity, and by the compositions of the metal and silicate phases. Several recent studies have shown the importance of silicate melt composition on the partitioning of siderophile elements between silicate and metallic liquids. It has been demonstrated that many elements display increased solubility in less polymerized (mafic) melts. However, the importance of silicate melt composition was believed to be minor compared to the influence of oxygen fugacity until studies showed that melt composition is an important factor at high pressures and temperatures. It was found that melt composition is also important for partitioning of high valency siderophile elements. Atmospheric experiments were conducted, varying only silicate melt composition, to assess the importance of silicate melt composition for the partitioning of W, Co and Ga and found that the valence of the dissolving species plays an important role in determining the effect of composition on solubility. In this study, we extend the data set to higher pressures and investigate the role of silicate melt composition on the partitioning of the siderophile elements W, Ge, Ga and Ni between metallic and silicate liquid.

Nonlinear dynamics based digital logic and circuits.

PubMed

Kia, Behnam; Lindner, John F; Ditto, William L

2015-01-01

We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two.

Molecular characterization of the short interspersed repetitive element SIRE in the six discrete typing units (DTUs) of Trypanosoma cruzi.

PubMed

Pavia, Paula X; Thomas, M Carmen; López, Manuel C; Puerta, Concepción J

2012-10-01

Repetitive sequences constitute an important proportion of the Trypanosoma cruzi genome; hence, they have been used as molecular markers and as amplification targets to identify the parasite presence via PCR. In this study, a molecular characterization of the SIRE repetitive element was performed in the six discrete typing units (DTUs) of T. cruzi. The results evidenced that this element, located in multiple chromosomes, was interspersed in the genome of all DTUs of the parasite. The presence of several motifs implicated in element insertion, duplication, and functionality suggests that SIRE could be an active element in the parasite genome. Of interest, there were SIRE specific Alu I fragments that allowed to discriminate DTU I from the others DTUs. Moreover, an UPGMA phenetic tree constructed from fragment sharing Southern blot data showed that T. cruzi I isolates conform a cluster separated from the T. cruzi II-VI isolates. When the relative number of SIRE copies was determined, a variation from 105 to 2,000 copies per haploid genome was observed among the different isolates without kept a DTU-relationship. In all, these findings suggest that SIRE sequence is a good target for parasite DNA amplification. Copyright © 2012 Elsevier Inc. All rights reserved.

Preceptors' perceptions of the elements of a successful and an unsuccessful orientation period for newly graduated nurses.

PubMed

Lindfors, Kirsi; Meretoja, Riitta; Kaunonen, Marja; Paavilainen, Eija

2018-04-01

To identify existing orientation patterns and to find elements that may enhance or impede successful orientation of newly graduated nurses. Preceptors have first-hand information concerning orientation and their opinions should not be forgotten when organisations develop their orientation processes. An open-ended questionnaire was undertaken to collect data from preceptors (n = 172) about the current orientation patterns. Data were analysed by using deductive content analysis and by quantifying the phrases. Communal commitment to the orientation process, strong professional orientation know-how and supportive leadership were the enhancing elements of successful orientation. Complex interpersonal relationship problems during orientation, inadequate orientation resources and the organisation's structural and functional problems were the impeding elements of successful orientation. With the elements of successful orientation we ensure a supportive transition to practice for newly graduate nurses and possibilities to focus on good orientation practices for preceptors. Nurse leaders play an important part in ensuring newly graduated nurses have a safe nursing career starting point and, for preceptors, opportunities to provide orientation that is as good as possible. Supportive leadership, sufficient resources and good interpersonal relationships should be the leading principles during newly graduated nurses' orientation period. © 2017 John Wiley & Sons Ltd.

Proteomics technique opens new frontiers in mobilome research

PubMed Central

Davidson, Andrew D.; Matthews, David A.

2017-01-01

ABSTRACT A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the “mobilome,” which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the “domestication” of transposon proteins for cellular functions. Although ‘omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons. In a recent paper, we overcame these technical hurdles using a technique called “proteomics informed by transcriptomics” (PIT), and thus published the first unbiased global mobilome-derived proteome for any organism (using cell lines derived from the mosquito Aedes aegypti). In this commentary, we describe our methods in more detail, and summarise our major findings. We also use new genome sequencing data to show that, in many cases, the specific genomic element expressing a given protein can be identified using PIT. This proteomic technique therefore represents an important technological advance that will open new avenues of research into the role that proteins derived from transposons and other repetitive and sequence diverse genetic elements, such as endogenous retroviruses, play in health and disease. PMID:28932623

Cross-organizational workflow in radiology: an empirical study of the quality of shared metadata elements in Region Västra Götaland, Sweden.

PubMed

Lindsköld, Lars; Wintell, Mikael; Edgren, Lars; Aspelin, Peter; Lundberg, Nina

2013-07-01

Challenges related to the cross-organizational access of accurate and timely information about a patient's condition has become a critical issue in healthcare. Interoperability of different local sources is necessary. To identify and present missing and semantically incorrect data elements of metadata in the radiology enterprise service that supports cross-organizational sharing of dynamic information about patients' visits, in the Region Västra Götaland, Sweden. Quantitative data elements of metadata were collected yearly from the first Wednesday in March from 2006 to 2011 from the 24 in-house radiology departments in Region Västra Götaland. These radiology departments were organized into four hospital groups and three stand-alone hospitals. Included data elements of metadata were the patient name, patient ID, institutional department name, referring physician's name, and examination description. The majority of missing data elements of metadata was related to the institutional department name for Hospital 2, from 87% in 2007 to 25% in 2011. All data elements of metadata except the patient ID contained semantic errors. For example, for the data element "patient name", only three names out of 3537 were semantically correct. This study shows that the semantics of metadata elements are poorly structured and inconsistently used. Although a cross-organizational solution may technically be fully functional, semantic errors may prevent it from serving as an information infrastructure for collaboration between all departments and hospitals in the region. For interoperability, it is important that the agreed semantic models are implemented in vendor systems using the information infrastructure.

Characterization of carotenoid hydroxylase gene promoter in Haematococcus pluvialis.

PubMed

Meng, C X; Wei, W; Su, Z- L; Qin, S

2006-10-01

Astaxanthin, a high-value ketocarotenoid is mainly used in fish aquaculture. It also has potential in human health due to its higher antioxidant capacity than beta-carotene and vitamin E. The unicellular green alga Haematococcus pluvialis is known to accumulate astaxanthin in response to environmental stresses, such as high light intensity and salt stress. Carotenoid hydroxylase plays a key role in astaxanthin biosynthesis in H. pluvialis. In this paper, we report the characterization of a promoter-like region (-378 to -22 bp) of carotenoid hydroxylase gene by cloning, sequence analysis and functional verification of its 919 bp 5'-flanking region in H. pluvialis. The 5'-flanking region was characterized using micro-particle bombardment method and transient expression of LacZ reporter gene. Results of sequence analysis showed that the 5'-flanking region might have putative cis-acting elements, such as ABA (abscisic acid)-responsive element (ABRE), C-repeat/dehydration responsive element (C-repeat/DRE), ethylene-responsive element (ERE), heat-shock element (HSE), wound-responsive element (WUN-motif), gibberellin-responsive element (P-box), MYB-binding site (MBS) etc., except for typical TATA and CCAAT boxes. Results of 5' deletions construct and beta-galactosidase assays revealed that a highest promoter-like region might exist from -378 to -22 bp and some negative regulatory elements might lie in the region from -919 to -378 bp. Results of site-directed mutagenesis of a putative C-repeat/DRE and an ABRE-like motif in the promoter-like region (-378 to -22 bp) indicated that the putative C-repeat/DRE and ABRE-like motif might be important for expression of carotenoid hydroxylase gene.

Horizon state, Hawking radiation, and boundary Liouville model.

PubMed

Solodukhin, Sergey N

2004-02-13

We demonstrate that the near-horizon physics, the Hawking radiation, and the reflection off the radial potential barrier can be understood entirely within a conformal field theory picture in terms of one- and two-point functions in the boundary Liouville theory. An important element in this demonstration is the notion of horizon state, the Hawking radiation being interpreted as a result of the transition of horizon state to the ordinary states propagating outside the black hole horizon.

The NASA role in major areas of human concern: Environmental quality

NASA Technical Reports Server (NTRS)

1973-01-01

After introducing some of the general factors that have affected progress in the area of environmental quality, NASA program elements are examined to illustrate relevant points of contact. Interpretive steps are taken throughout the report to show a few of the more important ways people's lives have been affected as a result of the work of NASA and other organizations functioning in this area. The principal documents used and interviews conducted are identified.

Characterization of Steroid Receptor RNA Activator Protein Function in Modulating the Estrogen Signaling Pathway

DTIC Science & Technology

2007-05-01

Signaling Pathway 5b. GRANT NUMBER W81XWH-05-1-0245 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Yi Yan 5e. TASK NUMBER...negative control to identify proteins non-specifically precipitated. Tandem mass spectrometric analysis of immunoprecipitated samples identified a...immunoprecipitated sample and negative control. It is important to note that, SRAP was present among the remaining specifically precipitated 87 proteins. Using the

Integrated Parallel Processes: The Elements of Meaning in Language. Volume IV.

DTIC Science & Technology

1981-11-01

times linguistics and psychology have sought them. Religion is deeply involved, and anthropology and sociology are in important ways relevant. The...quite cir’rly. No matter what heights the human mind can at- tain, it can work only with the organs it has and the functions peculiar to them. Eyes that...is speci- fied. If a neighborhood is specified with respect to outline, colour and texture, then all objects in a sufficiently small neighborhood will

Coalition, partnership, and constituency building by a state public health agency: a retrospective.

PubMed

Kimbrell, J D

2000-03-01

This article is a retrospective that traces the development of an evolutionary process for a state health agency in addressing the challenge of implementing core public health functions and the provision of essential services. Coalition, partnership, and constituency building were critical elements in the process. Various initiatives are described and their importance as building blocks to a larger process of organizational change is explained. Key lessons from the process are outlined.

Envisioning an oral healthcare workforce for the future.

PubMed

Nash, David A

2012-10-01

Health is critical to human well-being. Oral health is an integral component of health. One is not healthy without oral health. As health is essential to human flourishing, it is important that an oral healthcare delivery system and workforce be developed and deployed which can help ensure all citizens have the potential to access oral health care. As such access does not generally exist today, it is imperative to advance the realization of this goal and to develop a vision of an oral healthcare workforce to functionally support access. Public funding of basic oral health care is an important element to improving access. However, funding is only economically feasible if a workforce exists that is structured in a manner such that duties are assigned to individuals who have been uniquely trained to fulfill specific clinical responsibilities. An essential element of any cost-effective organizational system must be the shared responsibility of duties. Delegation must occur in the oral health workforce if competent, cost-effective care is to be provided. Desirable members of the oral health team in an efficient and effective system are as follows: generalist dentists who are educated as physicians of the stomatognathic system (oral physicians), specialist dentists, dental therapists, dental hygienists, dually trained hygienists/therapists (oral health therapists), oral prosthetists (denturists), and expanded function dental assistants (dental nurses). © 2012 John Wiley & Sons A/S.

The importance, impact and influence of group clinical supervision for graduate entry nursing students.

PubMed

Sheppard, Fiona; Stacey, Gemma; Aubeeluck, Aimee

2018-01-01

This paper will report on an evaluation of group clinical supervision (CS) facilitated for graduate entry nursing (GEN) students whilst on clinical placement. The literature suggests educational forums which enable GEN students to engage in critical dialogue, promote reflective practice and ongoing support are an essential element of GEN curricula. The model of supervision employed was informed by Proctor's three function interactive CS model and Inskipp and Proctor's Supervision Alliance. Both emphasise the normative, formative and restorative functions of CS as task areas within an overarching humanistic supervisory approach. The three-function model informed the design of a questionnaire which intended to measure their importance, impact and influence through both structured and open-ended questions. Findings suggest the restorative function of supervision is most valued and is facilitated in an environment where humanistic principles of non-judgement, empathy and trust are clearly present. Also the opportunity to learn from others, consider alternative perspectives and question personal assumptions regarding capability and confidence are a priority for this student group. It is suggested that the restorative function of CS should be prioritised within future developments and models which view this function as a key purpose of CS should be explored. Copyright © 2017 Elsevier Ltd. All rights reserved.

The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs

PubMed Central

Kim, Eugene Z.; Wespiser, Adam R.; Caffrey, Daniel R.

2016-01-01

Approximately 75% of the human genome is transcribed and many of these spliced transcripts contain primate-specific Alu elements, the most abundant mobile element in the human genome. The majority of exonized Alu elements are located in long noncoding RNAs (lncRNAs) and the untranslated regions of mRNA, with some performing molecular functions. To further assess the potential for Alu elements to be repurposed as functional RNA domains, we investigated the distribution and evolution of Alu elements in spliced transcripts. Our analysis revealed that Alu elements are underrepresented in mRNAs and lncRNAs, suggesting that most exonized Alu elements arising in the population are rare or deleterious to RNA function. When mRNAs and lncRNAs retain exonized Alu elements, they have a clear preference for Alu dimers, left monomers, and right monomers. mRNAs often acquire Alu elements when their genes are duplicated within Alu-rich regions. In lncRNAs, reverse-oriented Alu elements are significantly enriched and are not restricted to the 3′ and 5′ ends. Both lncRNAs and mRNAs primarily contain the Alu J and S subfamilies that were amplified relatively early in primate evolution. Alu J subfamilies are typically overrepresented in lncRNAs, whereas the Alu S dimer is overrepresented in mRNAs. The sequences of Alu dimers tend to be constrained in both lncRNAs and mRNAs, whereas the left and right monomers are constrained within particular Alu subfamilies and classes of RNA. Collectively, these findings suggest that Alu-containing RNAs are capable of forming stable structures and that some of these Alu domains might have novel biological functions. PMID:26654912

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Material efficiency: rare and critical metals.

PubMed

Ayres, Robert U; Peiró, Laura Talens

2013-03-13

In the last few decades, progress in electronics, especially, has resulted in important new uses for a number of geologically rare metals, some of which were mere curiosities in the past. Most of them are not mined for their own sake (gold, the platinum group metals and the rare Earth elements are exceptions) but are found mainly in the ores of the major industrial metals, such as aluminium, copper, zinc and nickel. We call these major metals 'attractors' and the rare accompanying metals 'hitch-hikers'. The key implication is that rising prices do not necessarily call forth greater output because that would normally require greater output of the attractor metal. We trace the geological relationships and the functional uses of these metals. Some of these metals appear to be irreplaceable in the sense that there are no known substitutes for them in their current functional uses. Recycling is going to be increasingly important, notwithstanding a number of barriers.

Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein

PubMed Central

van Anken, Eelco; Sanders, Rogier W.; Liscaljet, I. Marije; Land, Aafke; Bontjer, Ilja; Tillemans, Sonja; Nabatov, Alexey A.; Paxton, William A.; Berkhout, Ben

2008-01-01

Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein's folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins. PMID:18653472

Prediction of interface residue based on the features of residue interaction network.

PubMed

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.