The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context.

PubMed

Cremer, T; Cremer, M; Cremer, C

2018-04-01

4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

A Reference Architecture for Space Information Management

NASA Technical Reports Server (NTRS)

Mattmann, Chris A.; Crichton, Daniel J.; Hughes, J. Steven; Ramirez, Paul M.; Berrios, Daniel C.

2006-01-01

We describe a reference architecture for space information management systems that elegantly overcomes the rigid design of common information systems in many domains. The reference architecture consists of a set of flexible, reusable, independent models and software components that function in unison, but remain separately managed entities. The main guiding principle of the reference architecture is to separate the various models of information (e.g., data, metadata, etc.) from implemented system code, allowing each to evolve independently. System modularity, systems interoperability, and dynamic evolution of information system components are the primary benefits of the design of the architecture. The architecture requires the use of information models that are substantially more advanced than those used by the vast majority of information systems. These models are more expressive and can be more easily modularized, distributed and maintained than simpler models e.g., configuration files and data dictionaries. Our current work focuses on formalizing the architecture within a CCSDS Green Book and evaluating the architecture within the context of the C3I initiative.

Executive control systems in the engineering design environment. M.S. Thesis

NASA Technical Reports Server (NTRS)

Hurst, P. W.

1985-01-01

An executive control system (ECS) is a software structure for unifying various applications codes into a comprehensive system. It provides a library of applications, a uniform access method through a cental user interface, and a data management facility. A survey of twenty-four executive control systems designed to unify various CAD/CAE applications for use in diverse engineering design environments within government and industry was conducted. The goals of this research were to establish system requirements to survey state-of-the-art architectural design approaches, and to provide an overview of the historical evolution of these systems. Foundations for design are presented and include environmental settings, system requirements, major architectural components, and a system classification scheme based on knowledge of the supported engineering domain(s). An overview of the design approaches used in developing the major architectural components of an ECS is presented with examples taken from the surveyed systems. Attention is drawn to four major areas of ECS development: interdisciplinary usage; standardization; knowledge utilization; and computer science technology transfer.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

PubMed

Liu, Bernard A

2017-01-01

Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution.

PubMed

Galupa, Rafael; Heard, Edith

2018-04-23

The packaging of genetic material into chromatin and chromosomes has been recognized for more than a century, thanks to microscopy and biochemical approaches. This was followed by the progressive realization that chromatin organization is critical for genome functions such as transcription and DNA replication and repair. The recent discovery that chromosomes are partitioned at the submegabase scale into topologically associating domains (TADs) has implications for our understanding of gene regulation during developmental processes such as X-chromosome inactivation, as well as for evolution and for the search for disease-associated loci. Here we discuss our current knowledge about this recently recognized level of mammalian chromosome organization, with a special emphasis on the potential role of TADs as a structural basis for the function and evolution of mammalian regulatory landscapes. © 2017 Galupa and Heard; Published by Cold Spring Harbor Laboratory Press.

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Directed evolution of the TALE N-terminal domain for recognition of all 5' bases.

PubMed

Lamb, Brian M; Mercer, Andrew C; Barbas, Carlos F

2013-11-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.

Evolution from Packet Utilisation to Mission Operation Services

NASA Astrophysics Data System (ADS)

Cooper, Sam; Forwell, Stuart D.

2012-08-01

The ECSS Packet Utilisation Standard (PUS) and the forthcoming CCSDS Mission Operations (MO) Services occupy a very similar domain. This paper discusses the history of the two standards, their relationship and how the two can co-exist in the near term and long terms. It also covers implications with implementing MO services in current and future on-board architectures.

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.

PubMed

Dias, Raquel; Manny, Austin; Kolaczkowski, Oralia; Kolaczkowski, Bryan

2017-06-01

Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution in thermodynamics

NASA Astrophysics Data System (ADS)

Bejan, Adrian

2017-03-01

This review covers two aspects of "evolution" in thermodynamics. First, with the constructal law, thermodynamics is becoming the domain of physics that accounts for the phenomenon of evolution in nature, in general. Second, thermodynamics (and science generally) is the evolving add-on that empowers humans to predict the future and move more easily on earth, farther and longer in time. The part of nature that thermodynamics represents is this: nothing moves by itself unless it is driven by power, which is then destroyed (dissipated) during movement. Nothing evolves unless it flows and has the freedom to change its architecture such that it provides greater and easier access to the available space. Thermodynamics is the modern science of heat and work and their usefulness, which comes from converting the work (power) into movement (life) in flow architectures that evolve over time to facilitate movement. I also review the rich history of the science, and I clarify misconceptions regarding the second law, entropy, disorder, and the arrow of time, and the supposed analogy between heat and work.

Evolution and Conservation of Plant NLR Functions

PubMed Central

Jacob, Florence; Vernaldi, Saskia; Maekawa, Takaki

2013-01-01

In plants and animals, nucleotide-binding domain and leucine-rich repeats (NLR)-containing proteins play pivotal roles in innate immunity. Despite their similar biological functions and protein architecture, comparative genome-wide analyses of NLRs and genes encoding NLR-like proteins suggest that plant and animal NLRs have independently arisen in evolution. Furthermore, the demonstration of interfamily transfer of plant NLR functions from their original species to phylogenetically distant species implies evolutionary conservation of the underlying immune principle across plant taxonomy. In this review we discuss plant NLR evolution and summarize recent insights into plant NLR-signaling mechanisms, which might constitute evolutionarily conserved NLR-mediated immune mechanisms. PMID:24093022

Military Cyberspace: From Evolution to Revolution

DTIC Science & Technology

2012-02-08

support the GCCs and enable USCYBERCOM to accomplish its mission? 15. SUBJECT TERMS Network Operations, Global Information Grid ( GIG ), Network...DATE: 08 February 2012 WORD COUNT: 5,405 PAGES: 30 KEY TERMS: Network Operations, Global Information Grid ( GIG ), Network Architecture...defense of the DOD global information grid ( GIG ). The DOD must pursue an enterprise approach to network management in the cyberspace domain to

Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases

PubMed Central

Lamb, Brian M.; Mercer, Andrew C.; Barbas, Carlos F.

2013-01-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5′-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5′ T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5′ T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes. PMID:23980031

Domain architecture conservation in orthologs

PubMed Central

2011-01-01

Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the notion that orthologs are functionally more similar than other types of homologs at the same evolutionary distance. PMID:21819573

Crustal-Scale Fault Interaction at Rifted Margins and the Formation of Domain-Bounding Breakaway Complexes: Insights From Offshore Norway

NASA Astrophysics Data System (ADS)

Osmundsen, P. T.; Péron-Pinvidic, G.

2018-03-01

The large-magnitude faults that control crustal thinning and excision at rifted margins combine into laterally persistent structural boundaries that separate margin domains of contrasting morphology and structure. We term them breakaway complexes. At the Mid-Norwegian margin, we identify five principal breakaway complexes that separate the proximal, necking, distal, and outer margin domains. Downdip and lateral interactions between the faults that constitute breakaway complexes became fundamental to the evolution of the 3-D margin architecture. Different types of fault interaction are observed along and between these faults, but simple models for fault growth will not fully describe their evolution. These structures operate on the crustal scale, cut large thicknesses of heterogeneously layered lithosphere, and facilitate fundamental margin processes such as deformation coupling and exhumation. Variations in large-magnitude fault geometry, erosional footwall incision, and subsequent differential subsidence along the main breakaway complexes likely record the variable efficiency of these processes.

The SOAPS project - Spin-orbit alignment of planetary systems. Exoplanets' evolution histories in systems with different architectures

NASA Astrophysics Data System (ADS)

Faedi, F.; Gómez Maqueo Chew, Y.; Fossati, L.; Pollacco, D.; McQuillan, A.; Hebb, L.; Chaplin, W. J.; Aigrain, S.

2013-04-01

The wealth of information rendered by Kepler planets and planet candidates is indispensable for statistically significant studies of distinct planet populations, in both single and multiple systems. Empirical evidences suggest that Kepler's planet population shows different physical properties as compared to the bulk of known exoplanets. The SOAPS project, aims to shed light on Kepler's planets formation, their migration and architecture. By measuring v sini accurately for Kepler hosts with rotation periods measured from their high-precision light curves, we will assess the alignment of the planetary orbit with respect to the stellar spin axis. This degree of alignment traces the formation history and evolution of the planetary systems, and thus, allows to distinguish between different proposed migration theories. SOAPS will increase by a factor of 2 the number of spin-orbit alignment measurements pushing the parameters space down to the SuperEarth domain. Here we present our preliminary results.

A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution

PubMed Central

Heinz, Eva; Lithgow, Trevor

2014-01-01

Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071

An incoherent feedforward loop facilitates adaptive tuning of gene expression.

PubMed

Hong, Jungeui; Brandt, Nathan; Abdul-Rahman, Farah; Yang, Ally; Hughes, Tim; Gresham, David

2018-04-05

We studied adaptive evolution of gene expression using long-term experimental evolution of Saccharomyces cerevisiae in ammonium-limited chemostats. We found repeated selection for non-synonymous variation in the DNA binding domain of the transcriptional activator, GAT1, which functions with the repressor, DAL80 in an incoherent type-1 feedforward loop (I1-FFL) to control expression of the high affinity ammonium transporter gene, MEP2. Missense mutations in the DNA binding domain of GAT1 reduce its binding to the GATAA consensus sequence. However, we show experimentally, and using mathematical modeling, that decreases in GAT1 binding result in increased expression of MEP2 as a consequence of properties of I1-FFLs. Our results show that I1-FFLs, one of the most commonly occurring network motifs in transcriptional networks, can facilitate adaptive tuning of gene expression through modulation of transcription factor binding affinities. Our findings highlight the importance of gene regulatory architectures in the evolution of gene expression. © 2018, Hong et al.

Insulator function and topological domain border strength scale with architectural protein occupancy

PubMed Central

2014-01-01

Background Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions. Results By mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals. Conclusions We identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains. PMID:24981874

ELISA, a demonstrator environment for information systems architecture design

NASA Technical Reports Server (NTRS)

Panem, Chantal

1994-01-01

This paper describes an approach of reusability of software engineering technology in the area of ground space system design. System engineers have lots of needs similar to software developers: sharing of a common data base, capitalization of knowledge, definition of a common design process, communication between different technical domains. Moreover system designers need to simulate dynamically their system as early as possible. Software development environments, methods and tools now become operational and widely used. Their architecture is based on a unique object base, a set of common management services and they host a family of tools for each life cycle activity. In late '92, CNES decided to develop a demonstrative software environment supporting some system activities. The design of ground space data processing systems was chosen as the application domain. ELISA (Integrated Software Environment for Architectures Specification) was specified as a 'demonstrator', i.e. a sufficient basis for demonstrations, evaluation and future operational enhancements. A process with three phases was implemented: system requirements definition, design of system architectures models, and selection of physical architectures. Each phase is composed of several activities that can be performed in parallel, with the provision of Commercial Off the Shelves Tools. ELISA has been delivered to CNES in January 94, currently used for demonstrations and evaluations on real projects (e.g. SPOT4 Satellite Control Center). It is on the way of new evolutions.

The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer

PubMed Central

Enkhmandakh, Badam; Makeyev, Alexandr V.; Bayarsaihan, Dashzeveg

2006-01-01

Lim1, Ssdp1, and Ldb1 proteins are components of the Ldb1-associated transcriptional complex, which is important in the head-organizing activity during early mouse development. Depletion of each individual protein alone causes a headless phenotype. To explore in more detail the modular architecture of the complex, we have generated two different gene-trapped mouse lines that express truncated forms of Ssdp1. Embryos derived from the gene-trapped line that encodes a truncated Ssdp1 lacking the proline-rich sequence exhibit a lethal abnormal head-development phenotype, resembling mouse embryos deficient for Lim1, Ssdp1, or Otx2 genes. Embryos derived from the second gene-trapped line, in which most of the proline-rich domain of Ssdp1 is retained, did not show abnormalities in head development. Our data demonstrate that components of the Ldb1-dependent module can be subdivided further into discrete functional domains and that the proline-rich stretch of Ssdp1 is critical for embryonic head development. Furthermore, phylogenetic comparisons revealed that in Caenorhabditis elegans, a similar proline-rich sequence is absent in Ssdp but present in Ldb1. We conclude that although the overall architecture of the Ldb1-dependent module has been preserved, the genetic specification of its individual components has diversified during evolution, without compromising the function of the module. PMID:16864769

The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer.

PubMed

Enkhmandakh, Badam; Makeyev, Alexandr V; Bayarsaihan, Dashzeveg

2006-08-01

Lim1, Ssdp1, and Ldb1 proteins are components of the Ldb1-associated transcriptional complex, which is important in the head-organizing activity during early mouse development. Depletion of each individual protein alone causes a headless phenotype. To explore in more detail the modular architecture of the complex, we have generated two different gene-trapped mouse lines that express truncated forms of Ssdp1. Embryos derived from the gene-trapped line that encodes a truncated Ssdp1 lacking the proline-rich sequence exhibit a lethal abnormal head-development phenotype, resembling mouse embryos deficient for Lim1, Ssdp1, or Otx2 genes. Embryos derived from the second gene-trapped line, in which most of the proline-rich domain of Ssdp1 is retained, did not show abnormalities in head development. Our data demonstrate that components of the Ldb1-dependent module can be subdivided further into discrete functional domains and that the proline-rich stretch of Ssdp1 is critical for embryonic head development. Furthermore, phylogenetic comparisons revealed that in Caenorhabditis elegans, a similar proline-rich sequence is absent in Ssdp but present in Ldb1. We conclude that although the overall architecture of the Ldb1-dependent module has been preserved, the genetic specification of its individual components has diversified during evolution, without compromising the function of the module.

Enabling Communication and Navigation Technologies for Future Near Earth Science Missions

NASA Technical Reports Server (NTRS)

Israel, David J.; Heckler, Gregory; Menrad, Robert; Hudiburg, John; Boroson, Don; Robinson, Bryan; Cornwell, Donald

2016-01-01

In 2015, the Earth Regimes Network Evolution Study (ERNESt) proposed an architectural concept and technologies that evolve to enable space science and exploration missions out to the 2040 timeframe. The architectural concept evolves the current instantiations of the Near Earth Network and Space Network with new technologies to provide a global communication and navigation network that provides communication and navigation services to a wide range of space users in the near Earth domain. The technologies included High Rate Optical Communications, Optical Multiple Access (OMA), Delay Tolerant Networking (DTN), User Initiated Services (UIS), and advanced Position, Navigation, and Timing technology. This paper describes the key technologies and their current technology readiness levels. Examples of science missions that could be enabled by the technologies and the projected operational benefits of the architecture concept to missions are also described.

Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes

PubMed Central

Fischbach, Michael A.; Lai, Jonathan R.; Roche, Eric D.; Walsh, Christopher T.; Liu, David R.

2007-01-01

Nonribosomal peptides (NRPs) are produced by NRP synthetase (NRPS) enzymes that function as molecular assembly lines. The modular architecture of NRPSs suggests that a domain responsible for activating a building block could be replaced with a domain from a foreign NRPS to create a chimeric assembly line that produces a new variant of a natural NRP. However, such chimeric NRPS modules are often heavily impaired, impeding efforts to create novel NRP variants by swapping domains from different modules or organisms. Here we show that impaired chimeric NRPSs can be functionally restored by directed evolution. Using rounds of mutagenesis coupled with in vivo screens for NRP production, we rapidly isolated variants of two different chimeric NRPSs with ≈10-fold improvements in enzyme activity and product yield, including one that produces new derivatives of the potent NRP/polyketide antibiotic andrimid. Because functional restoration in these examples required only modest library sizes (103 to 104 clones) and three or fewer rounds of screening, our approach may be widely applicable even for NRPSs from genetically challenging hosts. PMID:17620609

Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD.

PubMed

Grande-García, Araceli; Lallous, Nada; Díaz-Tejada, Celsa; Ramón-Maiques, Santiago

2014-02-04

Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usage as an antitumoral target. However, there is no detailed structural information about CAD other than that it self-assembles into hexamers of ∼1.5 MDa. Here we report the crystal structure and functional characterization of the dihydroorotase domain of human CAD. Contradicting all assumptions, the structure reveals an active site enclosed by a flexible loop with two Zn²⁺ ions bridged by a carboxylated lysine and a third Zn coordinating a rare histidinate ion. Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis. Comparison with homologous bacterial enzymes supports a reclassification of the DHOase family and provides strong evidence against current models of the architecture of CAD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Time-domain seismic modeling in viscoelastic media for full waveform inversion on heterogeneous computing platforms with OpenCL

NASA Astrophysics Data System (ADS)

Fabien-Ouellet, Gabriel; Gloaguen, Erwan; Giroux, Bernard

2017-03-01

Full Waveform Inversion (FWI) aims at recovering the elastic parameters of the Earth by matching recordings of the ground motion with the direct solution of the wave equation. Modeling the wave propagation for realistic scenarios is computationally intensive, which limits the applicability of FWI. The current hardware evolution brings increasing parallel computing power that can speed up the computations in FWI. However, to take advantage of the diversity of parallel architectures presently available, new programming approaches are required. In this work, we explore the use of OpenCL to develop a portable code that can take advantage of the many parallel processor architectures now available. We present a program called SeisCL for 2D and 3D viscoelastic FWI in the time domain. The code computes the forward and adjoint wavefields using finite-difference and outputs the gradient of the misfit function given by the adjoint state method. To demonstrate the code portability on different architectures, the performance of SeisCL is tested on three different devices: Intel CPUs, NVidia GPUs and Intel Xeon PHI. Results show that the use of GPUs with OpenCL can speed up the computations by nearly two orders of magnitudes over a single threaded application on the CPU. Although OpenCL allows code portability, we show that some device-specific optimization is still required to get the best performance out of a specific architecture. Using OpenCL in conjunction with MPI allows the domain decomposition of large models on several devices located on different nodes of a cluster. For large enough models, the speedup of the domain decomposition varies quasi-linearly with the number of devices. Finally, we investigate two different approaches to compute the gradient by the adjoint state method and show the significant advantages of using OpenCL for FWI.

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

PubMed

Wolf, Y I; Aravind, L; Grishin, N V; Koonin, E V

1999-08-01

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the beta-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies-shared derived characters, such as extra domains or inserts-for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary "standard model" whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.

The chordate proteome history database.

PubMed

Levasseur, Anthony; Paganini, Julien; Dainat, Jacques; Thompson, Julie D; Poch, Olivier; Pontarotti, Pierre; Gouret, Philippe

2012-01-01

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

PubMed

Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

2016-01-07

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition

PubMed Central

Voogdt, Carlos G. P.; Bouwman, Lieneke I.; Kik, Marja J. L.; Wagenaar, Jaap A.; van Putten, Jos P. M.

2016-01-01

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions. PMID:26738735

Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.

PubMed

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-11-24

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.

Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

PubMed Central

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-01-01

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci. PMID:26596461

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE PAGES

Chandra, Vikas; Wu, Dalei; Li, Sheng; ...

2017-10-11

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

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

Chandra, Vikas; Wu, Dalei; Li, Sheng

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

The Role of Intelligent Agents in Advanced Information Systems

NASA Technical Reports Server (NTRS)

Kerschberg, Larry

1999-01-01

In this presentation we review the current ongoing research within George Mason University's (GMU) Center for Information Systems Integration and Evolution (CISE). We define characteristics of advanced information systems, discuss a family of agents for such systems, and show how GMU's Domain modeling tools and techniques can be used to define a product line Architecture for configuring NASA missions. These concepts can be used to define Advanced Engineering Environments such as those envisioned for NASA's new initiative for intelligent design and synthesis environments.

Massive expansion of the calpain gene family in unicellular eukaryotes.

PubMed

Zhao, Sen; Liang, Zhe; Demko, Viktor; Wilson, Robert; Johansen, Wenche; Olsen, Odd-Arne; Shalchian-Tabrizi, Kamran

2012-09-29

Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.

Massive expansion of the calpain gene family in unicellular eukaryotes

PubMed Central

2012-01-01

Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes. PMID:23020305

Technology Review of Multi-Agent Systems and Tools

DTIC Science & Technology

2005-06-01

over a network, including the Internet. A web services architecture is the logical evolution of object-oriented analysis and design coupled with...the logical evolution of components geared towards the architecture, design, implementation, and deployment of e-business solutions. As in object...querying. The Web Services architecture describes the principles behind the next generation of e- business architectures, presenting a logical evolution

Extensive Evolution of Cereal Ribosome-Inactivating Proteins Translates into Unique Structural Features, Activation Mechanisms, and Physiological Roles

PubMed Central

De Zaeytijd, Jeroen; Van Damme, Els J. M.

2017-01-01

Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can depurinate rRNAs thereby inhibiting protein translation. Although these proteins have also been detected in bacteria, fungi, and even some insects, they are especially prevalent in the plant kingdom. This review focuses on the RIPs from cereals. Studies on the taxonomical distribution and evolution of plant RIPs suggest that cereal RIPs have evolved at an enhanced rate giving rise to a large and heterogeneous RIP gene family. Furthermore, several cereal RIP genes are characterized by a unique domain architecture and the lack of a signal peptide. This advanced evolution of cereal RIPs translates into distinct structures, activation mechanisms, and physiological roles. Several cereal RIPs are characterized by activation mechanisms that include the proteolytic removal of internal peptides from the N-glycosidase domain, a feature not documented for non-cereal RIPs. Besides their role in defense against pathogenic fungi or herbivorous insects, cereal RIPs are also involved in endogenous functions such as adaptation to abiotic stress, storage, induction of senescence, and reprogramming of the translational machinery. The unique properties of cereal RIPs are discussed in this review paper. PMID:28353660

Optical, analog and digital domain architectural considerations for visual communications

NASA Astrophysics Data System (ADS)

Metz, W. A.

2008-01-01

The end of the performance entitlement historically achieved by classic scaling of CMOS devices is within sight, driven ultimately by fundamental limits. Performance entitlements predicted by classic CMOS scaling have progressively failed to be realized in recent process generations due to excessive leakage, increasing interconnect delays and scaling of gate dielectrics. Prior to reaching fundamental limits, trends in technology, architecture and economics will pressure the industry to adopt new paradigms. A likely response is to repartition system functions away from digital implementations and into new architectures. Future architectures for visual communications will require extending the implementation into the optical and analog processing domains. The fundamental properties of these domains will in turn give rise to new architectural concepts. The limits of CMOS scaling and impact on architectures will be briefly reviewed. Alternative approaches in the optical, electronic and analog domains will then be examined for advantages, architectural impact and drawbacks.

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.

2017-01-01

ABSTRACT The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota, Nanoarchaeota, and Korarchaeota. The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an overall similarity of archaeal and bacterial sensory modules but substantial differences in the signal output modules. The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. The complete list of histidine kinases and response regulators encoded in the analyzed archaeal genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSarchaea.html. PMID:29263101

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

PubMed

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2018-04-01

The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota , Nanoarchaeota , and Korarchaeota The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an overall similarity of archaeal and bacterial sensory modules but substantial differences in the signal output modules. The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. The complete list of histidine kinases and response regulators encoded in the analyzed archaeal genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSarchaea.html. Copyright © 2018 Galperin et al.

Crystal Structures of Apparent Saccharide Sensors from Histidine Kinase Receptors Prevalent in a Human Gut Symbiont

PubMed Central

Zhang, Zhen; Liu, Qun; Hendrickson, Wayne A.

2014-01-01

The adult human gut presents a complicated ecosystem where host-bacterium symbiosis plays an important role. Bacteroides thetaiotaomicron is a predominant member of the gut microflora, providing the human digestive tract with a large number of glycolytic enzymes. Expression of many of these enzymes appears to be controlled by histidine kinase receptors that are fused into unusual hybrid two-component systems that share homologous periplasmic sensor domains. These sensor domains belong to the third most populated (HK3) family based on a previous bioinformatics analysis of predicted histidine kinase sensors. Here, we present crystal structures of two sensor domains representative of the HK3 family. Each sensor is folded into three domains: two seven-bladed β-propeller domains and one β-sandwich domain. Both sensors form dimers in crystals and one sensor appears to be physiologically relevant. The folding characteristics in the individual domains, the domain organization, and the oligomeric architecture are all unique to the HK3 sensors. The sequence analysis of the HK3 sensors indicates that these sensors are shared among other signaling molecules, implying a combinatorial molecular evolution. PMID:24995510

Organically Grown Architectures: Creating Decentralized, Autonomous Systems by Embryomorphic Engineering

NASA Astrophysics Data System (ADS)

Doursat, René

Exploding growth growth in computational systems forces us to gradually replace rigid design and control with decentralization and autonomy. Information technologies will progress, instead, by"meta-designing" mechanisms of system self-assembly, self-regulation and evolution. Nature offers a great variety of efficient complex systems, in which numerous small elements form large-scale, adaptive patterns. The new engineering challenge is to recreate this self-organization and let it freely generate innovative designs under guidance. This article presents an original model of artificial system growth inspired by embryogenesis. A virtual organism is a lattice of cells that proliferate, migrate and self-pattern into differentiated domains. Each cell's fate is controlled by an internal gene regulatory network network. Embryomorphic engineering emphasizes hyperdistributed architectures, and their development as a prerequisite of evolutionary design.

Updating Our View of Organelle Genome Nucleotide Landscape

PubMed Central

Smith, David Roy

2012-01-01

Organelle genomes show remarkable variation in architecture and coding content, yet their nucleotide composition is relatively unvarying across the eukaryotic domain, with most having a high adenine and thymine (AT) content. Recent studies, however, have uncovered guanine and cytosine (GC)-rich mitochondrial and plastid genomes. These sequences come from a small but eclectic list of species, including certain green plants and animals. Here, I review GC-rich organelle DNAs and the insights they have provided into the evolution of nucleotide landscape. I emphasize that GC-biased mitochondrial and plastid DNAs are more widespread than once thought, sometimes occurring together in the same species, and suggest that the forces biasing their nucleotide content can differ both among and within lineages, and may be associated with specific genome architectural features and life history traits. PMID:22973299

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

PubMed Central

Urbach, Jonathan M.; Ausubel, Frederick M.

2017-01-01

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site–leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer. PMID:28096345

Uncovering the Legionella genus effector repertoire - strength in diversity and numbers

PubMed Central

Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

2016-01-01

Infection by the human pathogen Legionella pneumophila relies on the translocation of ~300 virulence proteins, termed effectors, which manipulate host-cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species, and predicted their effector repertoire using a previously validated machine-learning approach. This analysis revealed a treasure trove of 5,885 predicted effectors. The effector repertoire of different Legionella species was found to be largely non-overlapping, and only seven core-effectors were shared among all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from their natural protozoan hosts. Furthermore, we detected numerous novel conserved effector domains, and discovered new domain combinations, which allowed inferring yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution. PMID:26752266

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.

PubMed

Zhao, Chen; Pyle, Anna Marie

2016-06-01

Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron-encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2-Å and 2.1-Å resolution, respectively. These domains are more similar in architecture to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron-maturase complexes.

Life and evolution as physics

PubMed Central

Bejan, Adrian

2016-01-01

ABSTRACT What is evolution and why does it exist in the biological, geophysical and technological realms — in short, everywhere? Why is there a time direction — a time arrow — in the changes we know are happening every moment and everywhere? Why is the present different than the past? These are questions of physics, about everything, not just biology. The answer is that nothing lives, flows and moves unless it is driven by power. Physics sheds light on the natural engines that produce the power destroyed by the flows, and on the free morphing that leads to flow architectures naturally and universally. There is a unifying tendency across all domains to evolve into flow configurations that provide greater access for movement. This tendency is expressed as the constructal law of evolutionary flow organization everywhere. Here I illustrate how this law of physics accounts for and unites the life and evolution phenomena throughout nature, animate and inanimate. PMID:27489579

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

PubMed

Marchler-Bauer, Aron; Bo, Yu; Han, Lianyi; He, Jane; Lanczycki, Christopher J; Lu, Shennan; Chitsaz, Farideh; Derbyshire, Myra K; Geer, Renata C; Gonzales, Noreen R; Gwadz, Marc; Hurwitz, David I; Lu, Fu; Marchler, Gabriele H; Song, James S; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A; Zhang, Dachuan; Zheng, Chanjuan; Geer, Lewis Y; Bryant, Stephen H

2017-01-04

NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.

PubMed

Miller, William B; Torday, John S

2018-04-13

Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Domain architectures of the Scm3p protein provide insights into centromere function and evolution.

PubMed

Aravind, L; Iyer, Lakshminarayan M; Wu, Carl

2007-10-15

Recently, Scm3p has been shown to be a nonhistone component of centromeric chromatin that binds stoichiometrically to CenH3-H4 histones, and to be required for the assembly of kinetochores in Saccharomyces cerevisiae. Scm3p is conserved across fungi, and displays a remarkable variation in protein size, ranging from approximately 200 amino acids in S. cerevisiae to approximately 1300 amino acids in Neurospora crassa. This is primarily due a variable C-terminal segment that is linked to a conserved N-terminal, CenH3-interacting domain. We have discovered that the extended C-terminal region of Scm3p is strikingly characterized by lineage-specific fusions of single or multiple predicted DNA-binding domains different versions of the MYB and C2H2 zinc finger domains, AT-hooks, and a novel cysteine-rich metal-chelating cluster that are absent from the small versions of Scm3. Instead, S. cerevisiae point centromeres are recognized by components of the CBF3 DNA binding complex, which are conserved amongst close relatives of budding yeast, but are correspondingly absent from more distant fungi that possess regional centromeres. Hence, the C-terminal DNA binding motifs found in large Scm3p proteins may, along with CenH3, serve as a key epigenetic signal by recognizing and accommodating the lineage-specific diversity of centromere DNA in course of evolution.

A role for chromatin topology in imprinted domain regulation.

PubMed

MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

2016-02-01

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

d-Omix: a mixer of generic protein domain analysis tools.

PubMed

Wichadakul, Duangdao; Numnark, Somrak; Ingsriswang, Supawadee

2009-07-01

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g. hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well. The d-Omix web server is freely available at http://www.biotec.or.th/isl/Domix.

Discussion on final rifting evolution and breakup : insights from the Mid Norwegian - North East Greenland rifted system

NASA Astrophysics Data System (ADS)

Peron-Pinvidic, Gwenn; Terje Osmundsen, Per

2016-04-01

In terms of rifted margin studies, the characteristics of the distal and outer domains are among the today's most debated questions. The architecture and composition of deep margins are rarely well constrained and hence little understood. Except from in a handful number of cases (eg. Iberia-Newfoundland, Southern Australia, Red Sea), basement samples are not available to decipher between the various interpretations allowed by geophysical models. No consensus has been reached on the basement composition, tectonic structures, sedimentary geometries or magmatic content. The result is that non-unique end-member interpretations and models are still proposed in the literature. So, although these domains mark the connection between continents and oceans, and thus correspond to unique stages in the Earth's lithospheric life cycle, their spatial and temporal evolution are still unresolved. The Norwegian-Greenland Sea rift system represents an exceptional laboratory to work on questions related to rifting, rifted margin formation and sedimentary basin evolution. It has been extensively studied for decades by both the academic and the industry communities. The proven and expected oil and gas potentials led to the methodical acquisition of world-class geophysical datasets, which permit the detailed research and thorough testing of concepts at local and regional scales. This contribution is issued from a three years project funded by ExxonMobil aiming at better understanding the crustal-scale nature and evolution of the Norwegian-Greenland Sea. The idea was to take advantage of the data availability on this specific rift system to investigate further the full crustal conjugate scale history of rifting, confronting the various available datasets. In this contribution, we will review the possible structural and sedimentary geometries of the distal margin, and their connection to the oceanic domain. We will discuss the definition of 'breakup' and introduce a first order conceptual model that proposes a combined influence of tectonic and magmatic processes on the outbuilding of the distal, outer and oceanic domains.

A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters.

PubMed

Sun, Chia-Tsen; Chiang, Austin W T; Hwang, Ming-Jing

2017-10-27

Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

PubMed Central

Van Holle, Sofie; De Schutter, Kristof; Eggermont, Lore; Tsaneva, Mariya; Dang, Liuyi; Van Damme, Els J. M.

2017-01-01

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins. PMID:28587095

Dynamic configuration management of a multi-standard and multi-mode reconfigurable multi-ASIP architecture for turbo decoding

NASA Astrophysics Data System (ADS)

Lapotre, Vianney; Gogniat, Guy; Baghdadi, Amer; Diguet, Jean-Philippe

2017-12-01

The multiplication of connected devices goes along with a large variety of applications and traffic types needing diverse requirements. Accompanying this connectivity evolution, the last years have seen considerable evolutions of wireless communication standards in the domain of mobile telephone networks, local/wide wireless area networks, and Digital Video Broadcasting (DVB). In this context, intensive research has been conducted to provide flexible turbo decoder targeting high throughput, multi-mode, multi-standard, and power consumption efficiency. However, flexible turbo decoder implementations have not often considered dynamic reconfiguration issues in this context that requires high speed configuration switching. Starting from this assessment, this paper proposes the first solution that allows frame-by-frame run-time configuration management of a multi-processor turbo decoder without compromising the decoding performances.

High Performance GPU-Based Fourier Volume Rendering.

PubMed

Abdellah, Marwan; Eldeib, Ayman; Sharawi, Amr

2015-01-01

Fourier volume rendering (FVR) is a significant visualization technique that has been used widely in digital radiography. As a result of its (N (2)log⁡N) time complexity, it provides a faster alternative to spatial domain volume rendering algorithms that are (N (3)) computationally complex. Relying on the Fourier projection-slice theorem, this technique operates on the spectral representation of a 3D volume instead of processing its spatial representation to generate attenuation-only projections that look like X-ray radiographs. Due to the rapid evolution of its underlying architecture, the graphics processing unit (GPU) became an attractive competent platform that can deliver giant computational raw power compared to the central processing unit (CPU) on a per-dollar-basis. The introduction of the compute unified device architecture (CUDA) technology enables embarrassingly-parallel algorithms to run efficiently on CUDA-capable GPU architectures. In this work, a high performance GPU-accelerated implementation of the FVR pipeline on CUDA-enabled GPUs is presented. This proposed implementation can achieve a speed-up of 117x compared to a single-threaded hybrid implementation that uses the CPU and GPU together by taking advantage of executing the rendering pipeline entirely on recent GPU architectures.

Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

PubMed

Remington, David L

2015-12-01

Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Hadl: HUMS Architectural Description Language

NASA Technical Reports Server (NTRS)

Mukkamala, R.; Adavi, V.; Agarwal, N.; Gullapalli, S.; Kumar, P.; Sundaram, P.

2004-01-01

Specification of architectures is an important prerequisite for evaluation of architectures. With the increase m the growth of health usage and monitoring systems (HUMS) in commercial and military domains, the need far the design and evaluation of HUMS architectures has also been on the increase. In this paper, we describe HADL, HUMS Architectural Description Language, that we have designed for this purpose. In particular, we describe the features of the language, illustrate them with examples, and show how we use it in designing domain-specific HUMS architectures. A companion paper contains details on our design methodology of HUMS architectures.

Software Architecture Evolution

ERIC Educational Resources Information Center

Barnes, Jeffrey M.

2013-01-01

Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today's software architects, however,…

Nature of the protein universe

PubMed Central

Levitt, Michael

2009-01-01

The protein universe is the set of all proteins of all organisms. Here, all currently known sequences are analyzed in terms of families that have single-domain or multidomain architectures and whether they have a known three-dimensional structure. Growth of new single-domain families is very slow: Almost all growth comes from new multidomain architectures that are combinations of domains characterized by ≈15,000 sequence profiles. Single-domain families are mostly shared by the major groups of organisms, whereas multidomain architectures are specific and account for species diversity. There are known structures for a quarter of the single-domain families, and >70% of all sequences can be partially modeled thanks to their membership in these families. PMID:19541617

Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

PubMed Central

Culbertson, Jennifer; Kirby, Simon

2016-01-01

The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

PubMed

Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

2018-03-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks

PubMed Central

Grierson, Claire S.

2018-01-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli. Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution. PMID:29670941

A modern ionotropic glutamate receptor with a K(+) selectivity signature sequence.

PubMed

Janovjak, H; Sandoz, G; Isacoff, E Y

2011-01-01

Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K(+) channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.

NASA's Advanced Multimission Operations System: A Case Study in Formalizing Software Architecture Evolution

NASA Technical Reports Server (NTRS)

Barnes, Jeffrey M.

2011-01-01

All software systems of significant size and longevity eventually undergo changes to their basic architectural structure. Such changes may be prompted by evolving requirements, changing technology, or other reasons. Whatever the cause, software architecture evolution is commonplace in real world software projects. Recently, software architecture researchers have begun to study this phenomenon in depth. However, this work has suffered from problems of validation; research in this area has tended to make heavy use of toy examples and hypothetical scenarios and has not been well supported by real world examples. To help address this problem, I describe an ongoing effort at the Jet Propulsion Laboratory to re-architect the Advanced Multimission Operations System (AMMOS), which is used to operate NASA's deep-space and astrophysics missions. Based on examination of project documents and interviews with project personnel, I describe the goals and approach of this evolution effort and then present models that capture some of the key architectural changes. Finally, I demonstrate how approaches and formal methods from my previous research in architecture evolution may be applied to this evolution, while using languages and tools already in place at the Jet Propulsion Laboratory.

Software Technology for Adaptable, Reliable Systems (STARS). Software Architecture Seminar Report: Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-01-29

other processes, but that he arrived at his results in a different manner. Batory didn’t start with idioms; he performed a domain analysis and...abstracted idioms. Through domain analysis and domain modeling, new idioms can be found and the form of architecture can be the same. It was also questioned...Programming 5. Consensus Definition of Architecture 6. Inductive Analysis of Current Exemplars 7. VHDL (Bailor) 8. Ontological Structuring 3.3.3

Calcium-independent metal-ion catalytic mechanism of anthrax edema factor

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

Shen, Yuequan; Zhukovskaya, Natalia L.; Guo, Qing

2009-11-18

Edema factor (EF), a key anthrax exotoxin, has an anthrax protective antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase domain. Here, we report the crystal structures of CaM-bound EF, revealing the architecture of EF PABD. CaM has N- and C-terminal domains and each domain can bind two calcium ions. Calcium binding induces the conformational change of CaM from closed to open. Structures of the EF-CaM complex show how EF locks the N-terminal domain of CaM into a closed conformation regardless of its calcium-loading state. This represents a mechanism of how CaM effector alters the calcium affinity of CaM andmore » uncouples the conformational change of CaM from calcium loading. Furthermore, structures of EF-CaM complexed with nucleotides show that EF uses two-metal-ion catalysis, a prevalent mechanism in DNA and RNA polymerases. A histidine (H351) further facilitates the catalysis of EF by activating a water to deprotonate 3'OH of ATP. Mammalian adenylyl cyclases share no structural similarity with EF and they also use two-metal-ion catalysis, suggesting the catalytic mechanism-driven convergent evolution of two structurally diverse adenylyl cyclases.« less

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

PubMed Central

Barrera, Alejandro; Alastruey-Izquierdo, Ana; Martín, María J.; Cuesta, Isabel; Vizcaíno, Juan Antonio

2014-01-01

Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets. PMID:25033262

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.

PubMed

Barrera, Alejandro; Alastruey-Izquierdo, Ana; Martín, María J; Cuesta, Isabel; Vizcaíno, Juan Antonio

2014-07-01

Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets.

SIENA Customer Problem Statement and Requirements

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

L. Sauer; R. Clay; C. Adams

2000-08-01

This document describes the problem domain and functional requirements of the SIENA framework. The software requirements and system architecture of SIENA are specified in separate documents (called SIENA Software Requirement Specification and SIENA Software Architecture, respectively). While currently this version of the document describes the problems and captures the requirements within the Analysis domain (concentrating on finite element models), it is our intention to subsequent y expand this document to describe problems and capture requirements from the Design and Manufacturing domains. In addition, SIENA is designed to be extendible to support and integrate elements from the other domains (see SIENAmore » Software Architecture document).« less

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation.

PubMed

Yamazaki, Tomohiro; Souquere, Sylvie; Chujo, Takeshi; Kobelke, Simon; Chong, Yee Seng; Fox, Archa H; Bond, Charles S; Nakagawa, Shinichi; Pierron, Gerard; Hirose, Tetsuro

2018-06-21

A class of long noncoding RNAs (lncRNAs) has architectural functions in nuclear body construction; however, specific RNA domains dictating their architectural functions remain uninvestigated. Here, we identified the domains of the architectural NEAT1 lncRNA that construct paraspeckles. Systematic deletion of NEAT1 portions using CRISPR/Cas9 in haploid cells revealed modular domains of NEAT1 important for RNA stability, isoform switching, and paraspeckle assembly. The middle domain, containing functionally redundant subdomains, was responsible for paraspeckle assembly. Artificial tethering of the NONO protein to a NEAT1_2 mutant lacking the functional subdomains rescued paraspeckle assembly, and this required the NOPS dimerization domain of NONO. Paraspeckles exhibit phase-separated properties including susceptibility to 1,6-hexanediol treatment. RNA fragments of the NEAT1_2 subdomains preferentially bound NONO/SFPQ, leading to phase-separated aggregates in vitro. Thus, we demonstrate that the enrichment of NONO dimers on the redundant NEAT1_2 subdomains initiates construction of phase-separated paraspeckles, providing mechanistic insights into lncRNA-based nuclear body formation. Copyright © 2018 Elsevier Inc. All rights reserved.

Challenges in the Development and Evolution of Secure Open Architecture Command and Control Systems (Briefing Charts)

DTIC Science & Technology

2013-06-01

widgets for an OA system Design-time architecture: Browser, email, widget, DB, OS Go ogle Instance architecture: Chrome, Gmail, Google...provides functionally similar components or applications compatible with an OA system design Firefox Browser, WP, calendar Opera Instance...architecture: Firefox , AbiWord, Evolution, Fedora GPL Ab1Word Google Docs Instance ardlitecture: Fire fox, OR Google cal., Google Docs, Fedora

Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments.

PubMed

Aguilar-Hernández, Victor; Aguilar-Henonin, Laura; Guzmán, Plinio

2011-01-01

Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague. To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20-28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.

Isolated pores dissected from human two-pore channel 2 are functional

PubMed Central

Penny, Christopher J.; Rahman, Taufiq; Sula, Altin; Miles, Andrew J.; Wallace, B. A.; Patel, Sandip

2016-01-01

Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels. PMID:27941820

Isolated pores dissected from human two-pore channel 2 are functional.

PubMed

Penny, Christopher J; Rahman, Taufiq; Sula, Altin; Miles, Andrew J; Wallace, B A; Patel, Sandip

2016-12-12

Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca 2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca 2+ and Na + uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical 'pore-only' proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels.

A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution

PubMed Central

Rübben, Albert; Nordhoff, Ole

2013-01-01

Summary Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages. Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients. PMID:23336076

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

PubMed Central

Wang, Minglei; Yafremava, Liudmila S.; Caetano-Anollés, Derek; Mittenthal, Jay E.; Caetano-Anollés, Gustavo

2007-01-01

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya. PMID:17908824

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

PubMed Central

Rakshambikai, Ramaswamy; Gnanavel, Mutharasu; Srinivasan, Narayanaswamy

2014-01-01

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes–S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens–and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions. PMID:25255313

Surveillance alternatives : cost estimates and technical considerations for the en route domain

DOT National Transportation Integrated Search

1998-09-01

The report present cost estimates and technical performance projections for ten aircraft surveillance architectures. The architectures are intended for use in the en route flight domain, and are comprised of various combinations of Automatic Dependen...

Domain decomposition: A bridge between nature and parallel computers

NASA Technical Reports Server (NTRS)

Keyes, David E.

1992-01-01

Domain decomposition is an intuitive organizing principle for a partial differential equation (PDE) computation, both physically and architecturally. However, its significance extends beyond the readily apparent issues of geometry and discretization, on one hand, and of modular software and distributed hardware, on the other. Engineering and computer science aspects are bridged by an old but recently enriched mathematical theory that offers the subject not only unity, but also tools for analysis and generalization. Domain decomposition induces function-space and operator decompositions with valuable properties. Function-space bases and operator splittings that are not derived from domain decompositions generally lack one or more of these properties. The evolution of domain decomposition methods for elliptically dominated problems has linked two major algorithmic developments of the last 15 years: multilevel and Krylov methods. Domain decomposition methods may be considered descendants of both classes with an inheritance from each: they are nearly optimal and at the same time efficiently parallelizable. Many computationally driven application areas are ripe for these developments. A progression is made from a mathematically informal motivation for domain decomposition methods to a specific focus on fluid dynamics applications. To be introductory rather than comprehensive, simple examples are provided while convergence proofs and algorithmic details are left to the original references; however, an attempt is made to convey their most salient features, especially where this leads to algorithmic insight.

An ambiguity principle for assigning protein structural domains.

PubMed

Postic, Guillaume; Ghouzam, Yassine; Chebrek, Romain; Gelly, Jean-Christophe

2017-01-01

Ambiguity is the quality of being open to several interpretations. For an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. We postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. Because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equally valid domain annotations. However, knowledge and experience generally displace our ability to accept more than one way to decompose the structure of an object-in this case, a protein. This human bias in structure analysis is particularly harmful because it leads to ignoring potential avenues of research. We present an automated method capable of producing multiple alternative decompositions of protein structure (web server and source code available at www.dsimb.inserm.fr/sword/). Our innovative algorithm assigns structural domains through the hierarchical merging of protein units, which are evolutionarily preserved substructures that describe protein architecture at an intermediate level, between domain and secondary structure. To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. The relevance of our "multipartitioning" approach is shown through numerous examples of applications covering protein function, evolution, folding, and structure prediction. Finally, we introduce a measure for the structural ambiguity of protein molecules.

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.

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization.

PubMed

Kocot, Kevin M; Aguilera, Felipe; McDougall, Carmel; Jackson, Daniel J; Degnan, Bernard M

2016-01-01

An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.

Nanoscale nuclear architecture for cancer diagnosis by spatial-domain low-coherence quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Wang, Pin; Bista, Rajan K.; Khalbuss, Walid E.; Qiu, Wei; Staton, Kevin D.; Zhang, Lin; Brentnall, Teresa A.; Brand, Randall E.; Liu, Yang

2011-03-01

Alterations in nuclear architecture are the hallmark diagnostic characteristic of cancer cells. In this work, we show that the nuclear architectural characteristics quantified by spatial-domain low-coherence quantitative phase microscopy (SL-QPM), is more sensitive for the identification of cancer cells than conventional cytopathology. We demonstrated the importance of nuclear architectural characteristics in both an animal model of intestinal carcinogenesis - APC/Min mouse model and human cytology specimens with colorectal cancer by identifying cancer from cytologically noncancerous appearing cells. The determination of nanoscale nuclear architecture using this simple and practical optical instrument is a significant advance towards cancer diagnosis.

An Architecture for Continuous Data Quality Monitoring in Medical Centers.

PubMed

Endler, Gregor; Schwab, Peter K; Wahl, Andreas M; Tenschert, Johannes; Lenz, Richard

2015-01-01

In the medical domain, data quality is very important. Since requirements and data change frequently, continuous and sustainable monitoring and improvement of data quality is necessary. Working together with managers of medical centers, we developed an architecture for a data quality monitoring system. The architecture enables domain experts to adapt the system during runtime to match their specifications using a built-in rule system. It also allows arbitrarily complex analyses to be integrated into the monitoring cycle. We evaluate our architecture by matching its components to the well-known data quality methodology TDQM.

Health care professional workstation: software system construction using DSSA scenario-based engineering process.

PubMed

Hufnagel, S; Harbison, K; Silva, J; Mettala, E

1994-01-01

This paper describes a new method for the evolutionary determination of user requirements and system specifications called scenario-based engineering process (SEP). Health care professional workstations are critical components of large scale health care system architectures. We suggest that domain-specific software architectures (DSSAs) be used to specify standard interfaces and protocols for reusable software components throughout those architectures, including workstations. We encourage the use of engineering principles and abstraction mechanisms. Engineering principles are flexible guidelines, adaptable to particular situations. Abstraction mechanisms are simplifications for management of complexity. We recommend object-oriented design principles, graphical structural specifications, and formal components' behavioral specifications. We give an ambulatory care scenario and associated models to demonstrate SEP. The scenario uses health care terminology and gives patients' and health care providers' system views. Our goal is to have a threefold benefit. (i) Scenario view abstractions provide consistent interdisciplinary communications. (ii) Hierarchical object-oriented structures provide useful abstractions for reuse, understandability, and long term evolution. (iii) SEP and health care DSSA integration into computer aided software engineering (CASE) environments. These environments should support rapid construction and certification of individualized systems, from reuse libraries.

Environment and Architecture - a Paradigm Shift

NASA Astrophysics Data System (ADS)

di Battista, Valerio

The interaction of human cultures and the built environment allows a wide range of interpretations and has been studied inside the domain of many disciplines. This paper discusses three interpretations descending from a systemic approach to the question: - architecture as an "emergence" of the settlement system; - place (and space) as an "accumulator" of time and a "flux" of systems; - landscape as one representation/description of the human settlement. Architecture emerges as a new physical conformation or layout, or as a change in a specific site, arising from actions and representations of political, religious, economical or social powers, being shaped at all times by the material culture belonging to a specific time and place in the course of human evolution. Any inhabited space becomes over time a place as well as a landscape, i.e. a representation of the settlement and a relationship between setting and people. Therefore, any place owns a landscape which, in turn, is a system of physical systems; it could be defined as a system of sites that builds up its own structure stemming from the orographical features and the geometry of land surfaces that set out the basic characters of its space.

Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants.

PubMed

Mukherjee, Krishanu; Campos, Henry; Kolaczkowski, Bryan

2013-03-01

RNA interference (RNAi) is a eukaryotic molecular system that serves two primary functions: 1) gene regulation and 2) protection against selfish elements such as viruses and transposable DNA. Although the biochemistry of RNAi has been detailed in model organisms, very little is known about the broad-scale patterns and forces that have shaped RNAi evolution. Here, we provide a comprehensive evolutionary analysis of the Dicer protein family, which carries out the initial RNA recognition and processing steps in the RNAi pathway. We show that Dicer genes duplicated and diversified independently in early animal and plant evolution, coincident with the origins of multicellularity. We identify a strong signature of long-term protein-coding adaptation that has continually reshaped the RNA-binding pocket of the plant Dicer responsible for antiviral immunity, suggesting an evolutionary arms race with viral factors. We also identify key changes in Dicer domain architecture and sequence leading to specialization in either gene-regulatory or protective functions in animal and plant paralogs. As a whole, these results reveal a dynamic picture in which the evolution of Dicer function has driven elaboration of parallel RNAi functional pathways in animals and plants.

Executable Architecture Research at Old Dominion University

NASA Technical Reports Server (NTRS)

Tolk, Andreas; Shuman, Edwin A.; Garcia, Johnny J.

2011-01-01

Executable Architectures allow the evaluation of system architectures not only regarding their static, but also their dynamic behavior. However, the systems engineering community do not agree on a common formal specification of executable architectures. To close this gap and identify necessary elements of an executable architecture, a modeling language, and a modeling formalism is topic of ongoing PhD research. In addition, systems are generally defined and applied in an operational context to provide capabilities and enable missions. To maximize the benefits of executable architectures, a second PhD effort introduces the idea of creating an executable context in addition to the executable architecture. The results move the validation of architectures from the current information domain into the knowledge domain and improve the reliability of such validation efforts. The paper presents research and results of both doctoral research efforts and puts them into a common context of state-of-the-art of systems engineering methods supporting more agility.

Some aspects of the role of rift inheritance on Alpine-type orogens

NASA Astrophysics Data System (ADS)

Tugend, Julie; Manatschal, Gianreto; Mohn, Geoffroy; Chevrot, Sébastien

2017-04-01

Processes commonly recognized as fundamental for the formation of collisional orogens include oceanic subduction, arc-continent and continent-continent collision. As collisional belts result from the closure of oceanic basins and subsequent inversion of former rifted margins, their formation and evolution may also in theory be closely interlinked with the initial architecture of the former rifted margins. This assumption is indeed more likely to be applicable in the case of Alpine-type orogens, mainly controlled by mechanical processes and mostly devoid of arc-related magmatism. More and more studies from present-day magma-poor rifted margins illustrate the complex evolution of hyperextended domains (i.e. severely thinned continental crust (<10 km) and/or exhumed serpentinized mantle with relatively minor magmatic additions) between unequivocal continental and oceanic domains. In this contribution, we compare the deep structure of the Pyrenean and Alpine belts to discuss some aspects of the relative role of rift-inherited hyperextension and collisional processes in building Alpine-type orogens. The Pyrenees and Western to Central Alps respectively result from the inversion of a Late Jurassic to Mid Cretaceous and an Early to Middle Jurassic rift system eventually floored by hyperextended crust, exhumed mantle and/or proto-oceanic crust. In spite of uncertainties on the initial width of the hyperextended and proto-oceanic domains, the rift-related pre-collisional architecture of the Alps shows many similarities with that proposed for the Pyrenees. Remnants of these domains occur in the internal parts of both orogens, but they are largely affected by orogeny-related deformation and show a HP-LT to HT-MP metamorphic overprint in the Alps as a result of a polyphase deformation history. Yet, recent high-resolution tomographic images across the Pyrenees (PYROPE) and the Alps (CIFALPS) reveal a surprisingly comparable present-day overall crustal and lithospheric structure. Based on the comparison between the two orogens we discuss: (1) the nature and depth of decoupling levels inherited from hyperextension; (2) the implications for restorations and interpretations of orogenic roots (former hyperextended domains vs. lower crust only); and (3) the nature and major role of buttresses in controlling the final stage of collisional processes. Eventually, we discuss the variability of the role of rift-inheritance in building Alpine-type orogens. The Pyrenees seem to represent one extreme, where rift-inheritance is important at different stages of collisional processes. In contrast, in the Alps the role of rift-inheritance is subtler, likely because of its more complex and polyphase compressional deformation history.

Architecture Synthesis and Reduced-Cost Architectures for Human Exploration Missions

NASA Technical Reports Server (NTRS)

Woodcock, Gordon

2004-01-01

Development of architectures for human exploration missions has been pursued in the international aerospace community for a long time. This paper attempts a different approach and way of looking at architectures. Most of the emphasis is on lunar architectures with a brief look at Mars. The first step is to set forth overarching gods in order to understand origins of requirements. Then, principles and guidelines are developed for architecture formulation. It is argued that safety and cost are the primary factors. Alternative mission profiles are examined for adherence to the principles, and specific architectures formulated according to the guidelines. The guidelines themselves indicate preferred evolution paths from lunar to Mars architectures. Results of example calculations are given to illustrate the process, and an evolution path is recommended. Safety and cost criteria tend to conflict, but it is shown that cost-efficient architectures can be enhanced for good safety ratings at modest cost.

Analyses of Old “Prokaryotic” Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa

PubMed Central

Singh, Anupama; Jethva, Minesh; Singla-Pareek, Sneh L.; Pareek, Ashwani; Kushwaha, Hemant R.

2016-01-01

During evolution, various processes such as duplication, divergence, recombination, and many other events leads to the evolution of new genes with novel functions. These evolutionary events, thus significantly impact the evolution of cellular, physiological, morphological, and other phenotypic trait of organisms. While evolving, eukaryotes have acquired large number of genes from the earlier prokaryotes. This work is focused upon identification of old “prokaryotic” proteins in Arabidopsis and Oryza sativa genome, further highlighting their possible role(s) in the two genomes. Our results suggest that with respect to their genome size, the fraction of old “prokaryotic” proteins is higher in Arabidopsis than in Oryza sativa. The large fractions of such proteins encoding genes were found to be localized in various endo-symbiotic organelles. The domain architecture of the old “prokaryotic” proteins revealed similar distribution in both Arabidopsis and Oryza sativa genomes showing their conserved evolution. In Oryza sativa, the old “prokaryotic” proteins were more involved in developmental processes, might be due to constant man-made selection pressure for better agronomic traits/productivity. While in Arabidopsis, these proteins were involved in metabolic functions. Overall, the analysis indicates the distinct pattern of evolution of old “prokaryotic” proteins in Arabidopsis and Oryza sativa. PMID:27014324

Specification, Design, and Analysis of Advanced HUMS Architectures

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

2004-01-01

During the two-year project period, we have worked on several aspects of domain-specific architectures for HUMS. In particular, we looked at using scenario-based approach for the design and designed a language for describing such architectures. The language is now being used in all aspects of our HUMS design. In particular, we have made contributions in the following areas. 1) We have employed scenarios in the development of HUMS in three main areas. They are: (a) To improve reusability by using scenarios as a library indexing tool and as a domain analysis tool; (b) To improve maintainability by recording design rationales from two perspectives - problem domain and solution domain; (c) To evaluate the software architecture. 2) We have defined a new architectural language called HADL or HUMS Architectural Definition Language. It is a customized version of xArch/xADL. It is based on XML and, hence, is easily portable from domain to domain, application to application, and machine to machine. Specifications written in HADL can be easily read and parsed using the currently available XML parsers. Thus, there is no need to develop a plethora of software to support HADL. 3) We have developed an automated design process that involves two main techniques: (a) Selection of solutions from a large space of designs; (b) Synthesis of designs. However, the automation process is not an absolute Artificial Intelligence (AI) approach though it uses a knowledge-based system that epitomizes a specific HUMS domain. The process uses a database of solutions as an aid to solve the problems rather than creating a new design in the literal sense. Since searching is adopted as the main technique, the challenges involved are: (a) To minimize the effort in searching the database where a very large number of possibilities exist; (b) To develop representations that could conveniently allow us to depict design knowledge evolved over many years; (c) To capture the required information that aid the automation process.

Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution

PubMed Central

Zeng, Qinghong; Langereis, Martijn A.; van Vliet, Arno L. W.; Huizinga, Eric G.; de Groot, Raoul J.

2008-01-01

The hemagglutinin-esterases (HEs) are a family of viral envelope glycoproteins that mediate reversible attachment to O-acetylated sialic acids by acting both as lectins and as receptor-destroying enzymes (RDEs). Related HEs occur in influenza C, toro-, and coronaviruses, apparently as a result of relatively recent lateral gene transfer events. Here, we report the crystal structure of a coronavirus (CoV) HE in complex with its receptor. We show that CoV HE arose from an influenza C-like HE fusion protein (HEF). In the process, HE was transformed from a trimer into a dimer, whereas remnants of the fusion domain were adapted to establish novel monomer–monomer contacts. Whereas the structural design of the RDE-acetylesterase domain remained unaltered, the HE receptor-binding domain underwent remodeling to such extent that the ligand is now bound in opposite orientation. This is surprising, because the architecture of the HEF site was preserved in influenza A HA over a much larger evolutionary distance, a switch in receptor specificity and extensive antigenic variation notwithstanding. Apparently, HA and HEF are under more stringent selective constraints than HE, limiting their exploration of alternative binding-site topologies. We attribute the plasticity of the CoV HE receptor-binding site to evolutionary flexibility conferred by functional redundancy between HE and its companion spike protein S. Our findings offer unique insights into the structural and functional consequences of independent protein evolution after interviral gene exchange and open potential avenues to broad-spectrum antiviral drug design. PMID:18550812

Direct 4D printing via active composite materials.

PubMed

Ding, Zhen; Yuan, Chao; Peng, Xirui; Wang, Tiejun; Qi, H Jerry; Dunn, Martin L

2017-04-01

We describe an approach to print composite polymers in high-resolution three-dimensional (3D) architectures that can be rapidly transformed to a new permanent configuration directly by heating. The permanent shape of a component results from the programmed time evolution of the printed shape upon heating via the design of the architecture and process parameters of a composite consisting of a glassy shape memory polymer and an elastomer that is programmed with a built-in compressive strain during photopolymerization. Upon heating, the shape memory polymer softens, releases the constraint on the strained elastomer, and allows the object to transform into a new permanent shape, which can then be reprogrammed into multiple subsequent shapes. Our key advance, the markedly simplified creation of high-resolution complex 3D reprogrammable structures, promises to enable myriad applications across domains, including medical technology, aerospace, and consumer products, and even suggests a new paradigm in product design, where components are simultaneously designed to inhabit multiple configurations during service.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

PubMed

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Direct 4D printing via active composite materials

PubMed Central

Ding, Zhen; Yuan, Chao; Peng, Xirui; Wang, Tiejun; Qi, H. Jerry; Dunn, Martin L.

2017-01-01

We describe an approach to print composite polymers in high-resolution three-dimensional (3D) architectures that can be rapidly transformed to a new permanent configuration directly by heating. The permanent shape of a component results from the programmed time evolution of the printed shape upon heating via the design of the architecture and process parameters of a composite consisting of a glassy shape memory polymer and an elastomer that is programmed with a built-in compressive strain during photopolymerization. Upon heating, the shape memory polymer softens, releases the constraint on the strained elastomer, and allows the object to transform into a new permanent shape, which can then be reprogrammed into multiple subsequent shapes. Our key advance, the markedly simplified creation of high-resolution complex 3D reprogrammable structures, promises to enable myriad applications across domains, including medical technology, aerospace, and consumer products, and even suggests a new paradigm in product design, where components are simultaneously designed to inhabit multiple configurations during service. PMID:28439560

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with Alpha-Alpha Domain Architecture that Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence

PubMed Central

Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K.W.; Cane, David E.; Christianson, David W.

2015-01-01

Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with 3 Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed based on ~36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. PMID:26598179

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

PubMed Central

Leliaert, Frederik; Marcelino, Vanessa R

2018-01-01

Abstract Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss. PMID:29635329

Structural Framework and Architecture of the Paleoproterozoic Bryah and Padbury Basins from Integrated Potential Field and Geological Datasets: Towards an Understanding of the Basin Evolution

NASA Astrophysics Data System (ADS)

Nigro R A Ramos, L.; Aitken, A.; Occhipinti, S.; Lindsay, M.

2017-12-01

The Bryah and Padbury Basins were developed along the northern margin of the Yilgarn Craton, in the southern portion of the Capricorn Orogen, which represents a Proterozoic tectonic zone that bounds the Yilgarn and Pilbara Cratons in Western Australia. These basins have been previously interpreted as developing in a rift, back-arc, and retro-arc foreland basins. Recent studies suggest that the Bryah Basin was deposited in a rift setting, while the overlying Padbury Basin evolved in a pro-foreland basin during the collision of the Yilgarn Craton and the Pilboyne block (formed by the Pilbara Craton and the Glenburgh Terrane), occurring in the Glenburgh Orogeny (2005-1960 Ma). This study focuses on characterizing the architecture and structural framework of the Bryah and Padbury Basins through analysis of geophysical and geological datasets, in order to better understand the different stages of the basins evolution. Gravity and magnetic data were used to define the main tectonic units and lithological boundaries, and to delineate major discontinuities in the upper and lower crust, as well as anomalies through a combination of map view interpretation and forward modelling. Geological mapping and drill core observations were linked with the geophysical interpretations. Fourteen magnetic domains are distinguished within the basins, while four main domains based on the Bouguer Anomaly are recognized. The highest gravity amplitude is related with an anomaly trending EW/NE-SW, which is coincident with the voluminous mafic rocks of the Bryah Basin, and may indicate the presence of an approximately 5km thick package of higher density mafic rocks. Magnetic depth estimations also indicate deep magnetic sources up to approximately 4,45km. These results can help to elucidate processes that occurred during the precursor rift of the early stages of the Bryah Basin, add information in relation to the basement control on sedimentation, allow the characterization of the varying thickness of the units from the Bryah and Padbury basins, and permit a synthesis describing basin evolution.

Space station needs, attributes and architectural options. Volume 4, attachment 1: Task 2 and 3 mission implementation and cost

NASA Technical Reports Server (NTRS)

1983-01-01

Mission scenario analysis and architectural concepts, alternative systems concepts, mission operations and architectural development, architectural analysis trades, evolution, configuration, and technology development are assessed.

An ambiguity principle for assigning protein structural domains

PubMed Central

Postic, Guillaume; Ghouzam, Yassine; Chebrek, Romain; Gelly, Jean-Christophe

2017-01-01

Ambiguity is the quality of being open to several interpretations. For an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. We postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. Because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equally valid domain annotations. However, knowledge and experience generally displace our ability to accept more than one way to decompose the structure of an object—in this case, a protein. This human bias in structure analysis is particularly harmful because it leads to ignoring potential avenues of research. We present an automated method capable of producing multiple alternative decompositions of protein structure (web server and source code available at www.dsimb.inserm.fr/sword/). Our innovative algorithm assigns structural domains through the hierarchical merging of protein units, which are evolutionarily preserved substructures that describe protein architecture at an intermediate level, between domain and secondary structure. To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. The relevance of our “multipartitioning” approach is shown through numerous examples of applications covering protein function, evolution, folding, and structure prediction. Finally, we introduce a measure for the structural ambiguity of protein molecules. PMID:28097215

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

PubMed

Cubeñas-Potts, Caelin; Corces, Victor G

2015-01-01

Metazoan genomes are organized into regions of topologically associating domains (TADs). TADs are demarcated by border elements, which are enriched for active genes and high occupancy architectural protein binding sites. We recently demonstrated that 3D chromatin architecture is dynamic in response to heat shock, a physiological stress that downregulates transcription and causes a global redistribution of architectural proteins. We utilized a quantitative measure of border strength after heat shock, transcriptional inhibition, and architectural protein knockdown to demonstrate that changes in both transcription and architectural protein occupancy contribute to heat shock-induced TAD dynamics. Notably, architectural proteins appear to play a more important role in altering 3D chromatin architecture. Here, we discuss the implications of our findings on previous studies evaluating the dynamics of TAD structure during cellular differentiation. We propose that the subset of variable TADs observed after differentiation are representative of cell-type specific gene expression and are biologically significant.

Time domain passivity controller for 4-channel time-delay bilateral teleoperation.

PubMed

Rebelo, Joao; Schiele, Andre

2015-01-01

This paper presents an extension of the time-domain passivity control approach to a four-channel bilateral controller under the effects of time delays. Time-domain passivity control has been used successfully to stabilize teleoperation systems with position-force and position-position controllers; however, the performance with such control architectures is sub-optimal both with and without time delays. This work extends the network representation of the time-domain passivity controller to the four-channel architecture, which provides perfect transparency to the user without time delay. The proposed architecture is based on modelling the controllers as dependent voltage sources and using only series passivity controllers. The obtained results are shown on a one degree-of-freedom setup and illustrate the stabilization behaviour of the proposed controller when time delay is present in the communication channel.

Architecture and morphology of coral reef sequences. Modeling and observations from uplifting islands of SE Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Pastier, Anne-Morwenn; Husson, Laurent; Bezos, Antoine; Pedoja, Kevin; Elliot, Mary; Hafidz, Abdul; Imran, Muhammad; Lacroix, Pascal; Robert, Xavier

2016-04-01

During the Late Neogene, sea level oscillations have profoundly shaped the morphology of the coastlines of intertropical zones, wherein relative sea level simultaneously controlled reef expansion and erosion of earlier reef bodies. In uplifted domains like SE Sulawesi, the sequences of fossil reefs display a variety of fossil morphologies. Similarly, the morphologies of the modern reefs are highly variable, including cliff notches, narrow fringing reefs, wide flat terraces, and barriers reefs. In this region, where uplift rates vary rapidly laterally, the entire set of morphologies is displayed within short distances. We developed a numerical model that predicts the architecture of fossil reefs sequences and apply it to observations from SE Sulawesi, accounting -amongst other parameters- for reef growth, coastal erosion, and uplift rates. The observations that we use to calibrate our models are mostly the morphology of both the onshore (dGPS and high-resolution Pleiades DEM) and offshore (sonar) coast, as well as U-Th radiometrically dated coral samples. Our method allows unravelling the spatial and temporal evolution of large domains on map view. Our analysis indicates that the architecture and morphology of uplifting coastlines is almost systematically polyphased (as attested by samples of different ages within a unique terrace), which assigns a primordial role to erosion, comparable to reef growth. Our models also reproduce the variety of modern morphologies, which are chiefly dictated by the uplift rates of the pre-existing morphology of the substratum, itself responding to the joint effects of reef building and subsequent erosion. In turn, we find that fossil and modern morphologies can be returned to uplift rates rather precisely, as the parametric window of each specific morphology is often narrow.

The Language of the Protein Universe

PubMed Central

Scaiewicz, Andrea; Levitt, Michael

2015-01-01

Proteins, the main cell machinery which play a major roll in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the “Rosetta Stone” of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. PMID:26451980

Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.

PubMed

Fox, Charles W; Wagner, James D; Cline, Sara; Thomas, Frances Ann; Messina, Frank J

2009-05-01

Independent populations subjected to similar environments often exhibit convergent evolution. An unresolved question is the frequency with which such convergence reflects parallel genetic mechanisms. We examined the convergent evolution of egg-laying behavior in the seed-feeding beetle Callosobruchus maculatus. Females avoid ovipositing on seeds bearing conspecific eggs, but the degree of host discrimination varies among geographic populations. In a previous experiment, replicate lines switched from a small host to a large one evolved reduced discrimination after 40 generations. We used line crosses to determine the genetic architecture underlying this rapid response. The most parsimonious genetic models included dominance and/or epistasis for all crosses. The genetic architecture underlying reduced discrimination in two lines was not significantly different from the architecture underlying differences between geographic populations, but the architecture underlying the divergence of a third line differed from all others. We conclude that convergence of this complex trait may in some cases involve parallel genetic mechanisms.

An Auto-Configuration System for the GMSEC Architecture and API

NASA Technical Reports Server (NTRS)

Moholt, Joseph; Mayorga, Arturo

2007-01-01

A viewgraph presentation on an automated configuration concept for The Goddard Mission Services Evolution Center (GMSEC) architecture and Application Program Interface (API) is shown. The topics include: 1) The Goddard Mission Services Evolution Center (GMSEC); 2) Automated Configuration Concept; 3) Implementation Approach; and 4) Key Components and Benefits.

Novel receptor-like kinases in cacao contain PR-1 extracellular domains.

PubMed

Teixeira, Paulo José Pereira Lima; Costa, Gustavo Gilson Lacerda; Fiorin, Gabriel Lorencini; Pereira, Gonçalo Amarante Guimarães; Mondego, Jorge Maurício Costa

2013-08-01

Members of the pathogenesis-related protein 1 (PR-1) family are well-known markers of plant defence responses, forming part of the arsenal of the secreted proteins produced on pathogen recognition. Here, we report the identification of two cacao (Theobroma cacao L.) PR-1s that are fused to transmembrane regions and serine/threonine kinase domains, in a manner characteristic of receptor-like kinases (RLKs). These proteins (TcPR-1f and TcPR-1g) were named PR-1 receptor kinases (PR-1RKs). Phylogenetic analysis of RLKs and PR-1 proteins from cacao indicated that PR-1RKs originated from a fusion between sequences encoding PR-1 and the kinase domain of a LecRLK (Lectin Receptor-Like Kinase). Retrotransposition marks surround TcPR-1f, suggesting that retrotransposition was involved in the origin of PR-1RKs. Genes with a similar domain architecture to cacao PR-1RKs were found in rice (Oryza sativa), barrel medic (Medicago truncatula) and a nonphototrophic bacterium (Herpetosiphon aurantiacus). However, their kinase domains differed from those found in LecRLKs, indicating the occurrence of convergent evolution. TcPR-1g expression was up-regulated in the biotrophic stage of witches' broom disease, suggesting a role for PR-1RKs during cacao defence responses. We hypothesize that PR-1RKs transduce a defence signal by interacting with a PR-1 ligand. © 2013 BSPP AND JOHN WILEY & SONS LTD.

VENI, video, VICI: The merging of computer and video technologies

NASA Technical Reports Server (NTRS)

Horowitz, Jay G.

1993-01-01

The topics covered include the following: High Definition Television (HDTV) milestones; visual information bandwidth; television frequency allocation and bandwidth; horizontal scanning; workstation RGB color domain; NTSC color domain; American HDTV time-table; HDTV image size; digital HDTV hierarchy; task force on digital image architecture; open architecture model; future displays; and the ULTIMATE imaging system.

An Agent-Based Dynamic Model for Analysis of Distributed Space Exploration Architectures

NASA Astrophysics Data System (ADS)

Sindiy, Oleg V.; DeLaurentis, Daniel A.; Stein, William B.

2009-07-01

A range of complex challenges, but also potentially unique rewards, underlie the development of exploration architectures that use a distributed, dynamic network of resources across the solar system. From a methodological perspective, the prime challenge is to systematically model the evolution (and quantify comparative performance) of such architectures, under uncertainty, to effectively direct further study of specialized trajectories, spacecraft technologies, concept of operations, and resource allocation. A process model for System-of-Systems Engineering is used to define time-varying performance measures for comparative architecture analysis and identification of distinguishing patterns among interoperating systems. Agent-based modeling serves as the means to create a discrete-time simulation that generates dynamics for the study of architecture evolution. A Solar System Mobility Network proof-of-concept problem is introduced representing a set of longer-term, distributed exploration architectures. Options within this set revolve around deployment of human and robotic exploration and infrastructure assets, their organization, interoperability, and evolution, i.e., a system-of-systems. Agent-based simulations quantify relative payoffs for a fully distributed architecture (which can be significant over the long term), the latency period before they are manifest, and the up-front investment (which can be substantial compared to alternatives). Verification and sensitivity results provide further insight on development paths and indicate that the framework and simulation modeling approach may be useful in architectural design of other space exploration mass, energy, and information exchange settings.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

An outer ramp to basin plain transect: Interacting pelagic and calciturbidite deposition in the Eocene-Oligocene of the Tuscan Domain, Adria Microplate (Italy)

NASA Astrophysics Data System (ADS)

Ielpi, Alessandro; Cornamusini, Gianluca

2013-08-01

The interaction of ramps, basin plains and turbidite systems on the scale of tens of km has been rarely observed in fossil examples. Deep marine Eocene-Oligocene beds are exposed in the axial zone of the Chianti Mountains, Italy, and compose a regionally continue stratigraphic succession known as the Scaglia Toscana Formation. The formation was deposited in the Tuscan Domain of the Adria Microplate. This research aims at depicting its depositional architecture and evolution in the type area. Stratigraphic and sedimentologic analyses were performed on a ca. 25 km-long transect that includes depositional systems sectioned both in the down- and along-dip directions. Shaly-carbonate deposits compose a complex of interacting ramps, basin plains and turbidite floor fan systems. Ramp deposits accumulated above the lysocline and in oxic conditions. Basin plain beds were deposited below the lysocline and were subject to episodes of oxygen depletion. Turbidity flows fed elongate fan lobes characterized by poor channelisation. The basin palaeogeography hampered the development of slope apron turbidite systems. The Eocene-Oligocene geodynamic setting of the Tuscan Domain was characterized by the evolution of a peripheral bulge and by the early structuring of a foredeep basin. Syn-sedimentary tectonism acted a primary role in the basin-scale arrangement. However other mechanisms also contributed to the local facies distribution, including the disposition of sediment-source areas and intrabasinal confinement morphologies, as well as relative oscillations of the depositional surface with respect to the lysocline and oxycline.

Inhibitory interneurons of the human prefrontal cortex display conserved evolution of the phenotype and related genes.

PubMed

Sherwood, Chet C; Raghanti, Mary Ann; Stimpson, Cheryl D; Spocter, Muhammad A; Uddin, Monica; Boddy, Amy M; Wildman, Derek E; Bonar, Christopher J; Lewandowski, Albert H; Phillips, Kimberley A; Erwin, Joseph M; Hof, Patrick R

2010-04-07

Inhibitory interneurons participate in local processing circuits, playing a central role in executive cognitive functions of the prefrontal cortex. Although humans differ from other primates in a number of cognitive domains, it is not currently known whether the interneuron system has changed in the course of primate evolution leading to our species. In this study, we examined the distribution of different interneuron subtypes in the prefrontal cortex of anthropoid primates as revealed by immunohistochemistry against the calcium-binding proteins calbindin, calretinin and parvalbumin. In addition, we tested whether genes involved in the specification, differentiation and migration of interneurons show evidence of positive selection in the evolution of humans. Our findings demonstrate that cellular distributions of interneuron subtypes in human prefrontal cortex are similar to other anthropoid primates and can be explained by general scaling rules. Furthermore, genes underlying interneuron development are highly conserved at the amino acid level in primate evolution. Taken together, these results suggest that the prefrontal cortex in humans retains a similar inhibitory circuitry to that in closely related primates, even though it performs functional operations that are unique to our species. Thus, it is likely that other significant modifications to the connectivity and molecular biology of the prefrontal cortex were overlaid on this conserved interneuron architecture in the course of human evolution.

Evolutionary genomics of LysM genes in land plants.

PubMed

Zhang, Xue-Cheng; Cannon, Steven B; Stacey, Gary

2009-08-03

The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive. We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant LysM phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of LYK genes. We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of LysM genes in plant kingdom. One of the two groups of tandemly arrayed plant LYK genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed LYK genes remains obscure. Given the fact that no animal LysM motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant LysM genes and is also informative with regard to evolutionary and functional studies of animal LysM genes.

Structural model of the dimeric Parkinson’s protein LRRK2 reveals a compact architecture involving distant interdomain contacts

PubMed Central

Guaitoli, Giambattista; Raimondi, Francesco; Gilsbach, Bernd K.; Gómez-Llorente, Yacob; Deyaert, Egon; Renzi, Fabiana; Li, Xianting; Schaffner, Adam; Jagtap, Pravin Kumar Ankush; Boldt, Karsten; von Zweydorf, Felix; Gotthardt, Katja; Lorimer, Donald D.; Yue, Zhenyu; Burgin, Alex; Janjic, Nebojsa; Sattler, Michael; Versées, Wim; Ueffing, Marius; Ubarretxena-Belandia, Iban; Kortholt, Arjan; Gloeckner, Christian Johannes

2016-01-01

Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson’s disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity—together with the LRR domain—to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD. PMID:27357661

Rift-drift transition in the Dangerous Grounds, South China Sea

NASA Astrophysics Data System (ADS)

Peng, Xi; Shen, Chuanbo; Mei, Lianfu; Zhao, Zhigang; Xie, Xiaojun

2018-04-01

The South China Sea (SCS) has a long record of rifting before and after subsequent seafloor spreading, affecting the wide continent of the Dangerous Grounds, and its scissor-shape opening manner results in the rifting structures that vary along this margin. Some 2000 km of regional multichannel seismic data combined with borehole and dredge data are interpreted to analyze the multistage rifting process, structural architecture and dynamic evolution across the entire Dangerous Grounds. Key sequence boundaries above the Cenozoic basement are identified and classified into the breakup unconformity and the rift end unconformity, which consist of the rift-related unconformities. Reflector T70 in the east of the Dangerous Grounds represents the breakup unconformity, which is likely corresponding to the spreading of the East Subbasin. T60 formed on the top of carbonate platform is time equivalent to the spreading of the Southwest Subbasin, marking the breakup unconformity of the central Dangerous Grounds. The termination of the spreading of the SCS is manifested by the rift end unconformity of T50 in the southwest and the final rift occurring in the northwest of the Dangerous Grounds is postponed to the rift end unconformity of T40. On the basis of the stratigraphic and structural analysis, distinct segments in the structural architecture of the syn-rift units and the ages of rift-drift transition show obvious change from the proximal zone to the distal zone. Three domains, which are the Reed Bank-Palawan Rift domain, the Dangerous Grounds Central Detachment domain and Nam Con Son Exhumation domain, reflect the propagation of the margin rifting developed initially by grabens formed by high angle faults, then large half-grabens controlled by listric faults and detachments and finally rotated fault blocks in the hyper-extended upper crust associated with missing lower crust or exhumed mantle revealing a migration and stepwise rifting process in the south margin of the SCS.

Insights into the innate immunome of actiniarians using a comparative genomic approach.

PubMed

van der Burg, Chloé A; Prentis, Peter J; Surm, Joachim M; Pavasovic, Ana

2016-11-02

Innate immune genes tend to be highly conserved in metazoans, even in early divergent lineages such as Cnidaria (jellyfish, corals, hydroids and sea anemones) and Porifera (sponges). However, constant and diverse selection pressures on the immune system have driven the expansion and diversification of different immune gene families in a lineage-specific manner. To investigate how the innate immune system has evolved in a subset of sea anemone species (Order: Actiniaria), we performed a comprehensive and comparative study using 10 newly sequenced transcriptomes, as well as three publically available transcriptomes, to identify the origins, expansions and contractions of candidate and novel immune gene families. We characterised five conserved genes and gene families, as well as multiple novel innate immune genes, including the newly recognised putative pattern recognition receptor CniFL. Single copies of TLR, MyD88 and NF-κB were found in most species, and several copies of IL-1R-like, NLR and CniFL were found in almost all species. Multiple novel immune genes were identified with domain architectures including the Toll/interleukin-1 receptor (TIR) homology domain, which is well documented as functioning in protein-protein interactions and signal transduction in immune pathways. We hypothesise that these genes may interact as novel proteins in immune pathways of cnidarian species. Novelty in the actiniarian immunome is not restricted to only TIR-domain-containing proteins, as we identify a subset of NLRs which have undergone neofunctionalisation and contain 3-5 N-terminal transmembrane domains, which have so far only been identified in two anthozoan species. This research has significance in understanding the evolution and origin of the core eumetazoan gene set, including how novel innate immune genes evolve. For example, the evolution of transmembrane domain containing NLRs indicates that these NLRs may be membrane-bound, while all other metazoan and plant NLRs are exclusively cytosolic receptors. This is one example of how species without an adaptive immune system may evolve innovative solutions to detect pathogens or interact with native microbiota. Overall, these results provide an insight into the evolution of the innate immune system, and show that early divergent lineages, such as actiniarians, have a diverse repertoire of conserved and novel innate immune genes.

Algorithm Classes for Architecture Research (ACAR)

DTIC Science & Technology

2010-03-01

Project Engineer BRADLEY J. PAUL , Chief Advanced Sensor Components Branch Advanced Sensor Components Branch Aerospace Components Division...establish the need for and the value of innovative research on domain-specific architectures, applications, and tools based on the challenges posed by...California / Information Sciences Institute (USC/ISI) conducted exploratory studies to establish the need for and the value of innovative research on domain

Evolution of genetic architecture under directional selection.

PubMed

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.

Space station needs, attributes and architectural options. Volume 1, attachment 1: Executive summary NASA

NASA Technical Reports Server (NTRS)

1983-01-01

User alignment plan, physical and life sciences and applications, commercial requirements national security, space operations, user needs, foreign contacts, mission scenario analysis and architectural concepts, alternative systems concepts, mission operations architectural development, architectural analysis trades, evolution, configuration, and technology development are discussed.

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.

PubMed

Mourad, Raphaël; Cuvier, Olivier

2016-05-01

Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1.

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

PubMed Central

Mourad, Raphaël; Cuvier, Olivier

2016-01-01

Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

PubMed Central

Foti, Rossana; Gnan, Stefano; Cornacchia, Daniela; Dileep, Vishnu; Bulut-Karslioglu, Aydan; Diehl, Sarah; Buness, Andreas; Klein, Felix A.; Huber, Wolfgang; Johnstone, Ewan; Loos, Remco; Bertone, Paul; Gilbert, David M.; Manke, Thomas; Jenuwein, Thomas; Buonomo, Sara C.B.

2016-01-01

Summary DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing of non-Lamin B1-bound late domains. We further demonstrate that Rif1 defines and restricts the interactions between replication-timing domains during the G1 phase, thereby revealing a function of Rif1 as organizer of nuclear architecture. Rif1 loss affects both number and replication-timing specificity of the interactions between replication-timing domains. In addition, during the S phase, Rif1 ensures that replication of interacting domains is temporally coordinated. In summary, our study identifies Rif1 as the molecular link between nuclear architecture and replication-timing establishment in mammals. PMID:26725008

Architecting the Human Space Flight Program with Systems Modeling Language (SysML)

NASA Technical Reports Server (NTRS)

Jackson, Maddalena M.; Fernandez, Michela Munoz; McVittie, Thomas I.; Sindiy, Oleg V.

2012-01-01

The next generation of missions in NASA's Human Space Flight program focuses on the development and deployment of highly complex systems (e.g., Orion Multi-Purpose Crew Vehicle, Space Launch System, 21st Century Ground System) that will enable astronauts to venture beyond low Earth orbit and explore the moon, near-Earth asteroids, and beyond. Architecting these highly complex system-of-systems requires formal systems engineering techniques for managing the evolution of the technical features in the information exchange domain (e.g., data exchanges, communication networks, ground software) and also, formal correlation of the technical architecture to stakeholders' programmatic concerns (e.g., budget, schedule, risk) and design development (e.g., assumptions, constraints, trades, tracking of unknowns). This paper will describe how the authors have applied System Modeling Language (SysML) to implement model-based systems engineering for managing the description of the End-to-End Information System (EEIS) architecture and associated development activities and ultimately enables stakeholders to understand, reason, and answer questions about the EEIS under design for proposed lunar Exploration Missions 1 and 2 (EM-1 and EM-2).

Enhanced service zone architecture for multiservices over IP

NASA Astrophysics Data System (ADS)

Michaely, Boaz; Mohan, Seshadri

2001-07-01

Recently, the field of IP Telephony has been experienced considerable evolution through the specification of new protocols and introduction of products implementing these protocols. We visualize IP Telephony evolving to soon offer multiservices encompassing not only voice, but also data, video and multimedia. While the progress has focused on refining protocols and architectures, very little attention has been given to business models for offering these services. This paper introduces the concept of a Service Zone, which from a service provider/network operator perspective fits within the operator's administrative domain, but is viewed as an independent zone with its own management and services, requiring minimal integration with the core network services. Besides its own management, the Enhanced Services Zone may also provide provisioning and maintenance features needed to provide the customer services and availability that subscribers expect from a telephony service providers. The platform must provide reliable service over time, be scalable to meet increased capacity demands, and be upgradeable to incorporate advanced services and features as they become available. Signaling flows are illustrated using SIP and H.323.

The language of the protein universe.

PubMed

Scaiewicz, Andrea; Levitt, Michael

2015-12-01

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Partial protein domains: evolutionary insights and bioinformatics challenges.

PubMed

Kelley, Lawrence A; Sternberg, Michael J E

2015-05-19

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

PubMed Central

Flower, Rosalyn; Choo, Siew Woh

2017-01-01

It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome. PMID:28282436

Automated monitoring of medical protocols: a secure and distributed architecture.

PubMed

Alsinet, T; Ansótegui, C; Béjar, R; Fernández, C; Manyà, F

2003-03-01

The control of the right application of medical protocols is a key issue in hospital environments. For the automated monitoring of medical protocols, we need a domain-independent language for their representation and a fully, or semi, autonomous system that understands the protocols and supervises their application. In this paper we describe a specification language and a multi-agent system architecture for monitoring medical protocols. We model medical services in hospital environments as specialized domain agents and interpret a medical protocol as a negotiation process between agents. A medical service can be involved in multiple medical protocols, and so specialized domain agents are independent of negotiation processes and autonomous system agents perform monitoring tasks. We present the detailed architecture of the system agents and of an important domain agent, the database broker agent, that is responsible of obtaining relevant information about the clinical history of patients. We also describe how we tackle the problems of privacy, integrity and authentication during the process of exchanging information between agents.

Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.

PubMed

Faure, Guilhem; Callebaut, Isabelle

2013-07-15

Describing domain architecture is a critical step in the functional characterization of proteins. However, some orphan domains do not match any profile stored in dedicated domain databases and are thereby difficult to analyze. We present here an original novel approach, called TREMOLO-HCA, for the analysis of orphan domain sequences and inspired from our experience in the use of Hydrophobic Cluster Analysis (HCA). Hidden relationships between protein sequences can be more easily identified from the PSI-BLAST results, using information on domain architecture, HCA plots and the conservation degree of amino acids that may participate in the protein core. This can lead to reveal remote relationships with known families of domains, as illustrated here with the identification of a hidden Tudor tandem in the human BAHCC1 protein and a hidden ET domain in the Saccharomyces cerevisiae Taf14p and human AF9 proteins. The results obtained in such a way are consistent with those provided by HHPRED, based on pairwise comparisons of HHMs. Our approach can, however, be applied even in absence of domain profiles or known 3D structures for the identification of novel families of domains. It can also be used in a reverse way for refining domain profiles, by starting from known protein domain families and identifying highly divergent members, hitherto considered as orphan. We provide a possible integration of this approach in an open TREMOLO-HCA package, which is fully implemented in python v2.7 and is available on request. Instructions are available at http://www.impmc.upmc.fr/∼callebau/tremolohca.html. isabelle.callebaut@impmc.upmc.fr Supplementary Data are available at Bioinformatics online.

Application of Multiprotocol Medical Imaging Communications and an Extended DICOM WADO Service in a Teleradiology Architecture

PubMed Central

Koutelakis, George V.; Anastassopoulos, George K.; Lymberopoulos, Dimitrios K.

2012-01-01

Multiprotocol medical imaging communication through the Internet is more flexible than the tight DICOM transfers. This paper introduces a modular multiprotocol teleradiology architecture that integrates DICOM and common Internet services (based on web, FTP, and E-mail) into a unique operational domain. The extended WADO service (a web extension of DICOM) and the other proposed services allow access to all levels of the DICOM information hierarchy as opposed to solely Object level. A lightweight client site is considered adequate, because the server site of the architecture provides clients with service interfaces through the web as well as invulnerable space for temporary storage, called as User Domains, so that users fulfill their applications' tasks. The proposed teleradiology architecture is pilot implemented using mainly Java-based technologies and is evaluated by engineers in collaboration with doctors. The new architecture ensures flexibility in access, user mobility, and enhanced data security. PMID:22489237

Bleogens: Cactus-Derived Anti-Candida Cysteine-Rich Peptides with Three Different Precursor Arrangements

PubMed Central

Loo, Shining; Kam, Antony; Xiao, Tianshu; Tam, James P.

2017-01-01

Cysteine-rich peptides (CRPs) play important host-defense roles in plants. However, information concerning CRPs in the Cactaceae (cactus) family is limited, with only a single cactus-derived CRP described to date. Here, we report the identification of 15 novel CRPs with three different precursor architectures, bleogens pB1-15 from Pereskia bleo of the Cactaceae family. By combining proteomic and transcriptomic methods, we showed that the prototype, bleogen pB1, contained 36 amino acid residues, a six-cysteine motif typical of the six-cysteine-hevein-like peptide (6C-HLP) family, and a type I two-domain precursor consisting of an endoplasmic reticulum (ER) and a mature domain. In contrast, the precursors of the other 14 bleogens contained a type II three-domain architecture with a propeptide domain inserted between the ER and the mature bleogen domain. Four of these 14 bleogens display a third type of architecture with a tandemly repeating bleogen domain. A search of the Onekp database revealed that <1% plant species possess three different precursor architectures for the biosynthesis of 6C-HLPs, including Lophophora williamsii, Pereskia aculeate, Portulaca cryptopetala, Portulaca oleracea, Portulaca suffruticosa, and Talinum sp. NMR analysis confirmed that bleogen pB1 has cystine-knot disulfide connectivity as well as a two-beta-sheet and a four-loop structural fold that is similar to other 6C-HLPs. Sequence analysis, structural studies, and in silico modeling revealed that bleogen pB1 has a cation-polar-cation motif, a signature heparin-binding motif that was confirmed by heparin affinity chromatography. Cell-based assays showed that bleogen pB1 is non-toxic to mammalian cells but functions as an anti-Candida peptide. Taken together, our findings provide insight into the occurrence, functions and precursor architectures of CRPs in the cactus family. PMID:29312404

75 FR 76647 - Special Conditions: Boeing Model 747-8 Airplanes, Systems and Data Networks Security-Isolation or...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-09

...: Digital systems architecture composed of several connected networks. The proposed network architecture..., communication, and navigation systems (Aircraft Control Domain), 2. Airline business and administrative support... system architectures. Furthermore, 14 CFR regulations and current system safety assessment policy and...

Formal Foundations for the Specification of Software Architecture.

DTIC Science & Technology

1995-03-01

Architectures For- mally: A Case-Study Using KWIC." Kestrel Institute, Palo Alto, CA 94304, April 1994. 58. Kang, Kyo C. Feature-Oriented Domain Analysis ( FODA ...6.3.5 Constraint-Based Architectures ................. 6-60 6.4 Summary ......... ............................. 6-63 VII. Analysis of Process-Based...between these architec- ture theories were investigated. A feasibility analysis on an image processing application demonstrated that architecture theories

Phase-field model of domain structures in ferroelectric thin films

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

Li, Y. L.; Hu, S. Y.; Liu, Z. K.

A phase-field model for predicting the coherent microstructure evolution in constrained thin films is developed. It employs an analytical elastic solution derived for a constrained film with arbitrary eigenstrain distributions. The domain structure evolution during a cubic{r_arrow}tetragonal proper ferroelectric phase transition is studied. It is shown that the model is able to simultaneously predict the effects of substrate constraint and temperature on the volume fractions of domain variants, domain-wall orientations, domain shapes, and their temporal evolution. {copyright} 2001 American Institute of Physics.

Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases.

PubMed

Pemberton, Travis A; Chen, Mengbin; Harris, Golda G; Chou, Wayne K W; Duan, Lian; Köksal, Mustafa; Genshaft, Alex S; Cane, David E; Christianson, David W

2017-04-11

Terpenoid synthases catalyze isoprenoid cyclization reactions underlying the generation of more than 80,000 natural products. Such dramatic chemodiversity belies the fact that these enzymes generally consist of only three domain folds designated as α, β, and γ. Catalysis by class I terpenoid synthases occurs exclusively in the α domain, which is found with α, αα, αβ, and αβγ domain architectures. Here, we explore the influence of domain architecture on catalysis by taxadiene synthase from Taxus brevifolia (TbTS, αβγ), fusicoccadiene synthase from Phomopsis amygdali (PaFS, (αα) 6 ), and ophiobolin F synthase from Aspergillus clavatus (AcOS, αα). We show that the cyclization fidelity and catalytic efficiency of the α domain of TbTS are severely compromised by deletion of the βγ domains; however, retention of the β domain preserves significant cyclization fidelity. In PaFS, we previously demonstrated that one α domain similarly influences catalysis by the other α domain [ Chen , M. , Chou , W. K. W. , Toyomasu , T. , Cane , D. E. , and Christianson , D. W. ( 2016 ) ACS Chem. Biol. 11 , 889 - 899 ]. Here, we show that the hexameric quaternary structure of PaFS enables cluster channeling. We also show that the α domains of PaFS and AcOS can be swapped so as to make functional chimeric αα synthases. Notably, both cyclization fidelity and catalytic efficiency are altered in all chimeric synthases. Twelve newly formed and uncharacterized C 20 diterpene products and three C 25 sesterterpene products are generated by these chimeras. Thus, engineered αβγ and αα terpenoid cyclases promise to generate chemodiversity in the greater family of terpenoid natural products.

A functional role of the extracellular domain of Crumbs in cell architecture and apicobasal polarity.

PubMed

Letizia, Annalisa; Ricardo, Sara; Moussian, Bernard; Martín, Nicolás; Llimargas, Marta

2013-05-15

Regulated cell shape changes in epithelial cells, which contribute to most organs and tissues, are at the basis of morphogenesis. Crumbs (Crb) is an essential apical determinant controlling epithelial apicobasal polarity. Here we provide evidence for a novel role of Crb apical localisation and stabilisation in controlling cell shape through apical domain organisation and adherens junction positioning. We find that Crb apical stabilisation requires the extracellular domain. In vivo results from Drosophila suggest that the extracellular domain assists Crb apical stabilisation by mediating Crb-Crb interactions at opposing cell membranes. We further confirm Crb-Crb extracellular interactions by showing that the extracellular domain of Crb is sufficient to promote cell aggregation in vitro. Furthermore, we report that Crb apical stabilisation mediated by the extracellular domain is also required for maintenance of Crb apicobasal polarity. Our results provide new insights into the mechanisms of apicobasal polarity and the cellular mechanisms of tissue architecture.

Framework for Architecture Trade Study Using MBSE and Performance Simulation

NASA Technical Reports Server (NTRS)

Ryan, Jessica; Sarkani, Shahram; Mazzuchim, Thomas

2012-01-01

Increasing complexity in modern systems as well as cost and schedule constraints require a new paradigm of system engineering to fulfill stakeholder needs. Challenges facing efficient trade studies include poor tool interoperability, lack of simulation coordination (design parameters) and requirements flowdown. A recent trend toward Model Based System Engineering (MBSE) includes flexible architecture definition, program documentation, requirements traceability and system engineering reuse. As a new domain MBSE still lacks governing standards and commonly accepted frameworks. This paper proposes a framework for efficient architecture definition using MBSE in conjunction with Domain Specific simulation to evaluate trade studies. A general framework is provided followed with a specific example including a method for designing a trade study, defining candidate architectures, planning simulations to fulfill requirements and finally a weighted decision analysis to optimize system objectives.

Constellation's Command, Control, Communications and Information (C3I) Architecture

NASA Technical Reports Server (NTRS)

Breidenthal, Julian C.

2007-01-01

Operations concepts are highly effective for: 1) Developing consensus; 2) Discovering stakeholder needs, goals, objectives; 3) Defining behavior of system components (especially emergent behaviors). An interoperability standard can provide an excellent lever to define the capabilities needed for system evolution. Two categories of architectures are needed in a program of this size are: 1) Generic - Needed for planning, design and construction standards; 2) Specific - Needed for detailed requirement allocations, interface specs. A wide variety of architectural views are needed to address stakeholder concerns, including: 1) Physical; 2) Information (structure, flow, evolution); 3) Processes (design, manufacturing, operations); 4) Performance; 5) Risk.

Interior Design in Architectural Education

ERIC Educational Resources Information Center

Gurel, Meltem O.; Potthoff, Joy K.

2006-01-01

The domain of interiors constitutes a point of tension between practicing architects and interior designers. Design of interior spaces is a significant part of architectural profession. Yet, to what extent does architectural education keep pace with changing demands in rendering topics that are identified as pertinent to the design of interiors?…

Semantic Web-Driven LMS Architecture towards a Holistic Learning Process Model Focused on Personalization

ERIC Educational Resources Information Center

Kerkiri, Tania

2010-01-01

A comprehensive presentation is here made on the modular architecture of an e-learning platform with a distinctive emphasis on content personalization, combining advantages from semantic web technology, collaborative filtering and recommendation systems. Modules of this architecture handle information about both the domain-specific didactic…

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity.

PubMed

Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia

2017-11-01

Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins

PubMed Central

2013-01-01

Background The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. Results By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. Conclusions We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications. PMID:24053117

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins.

PubMed

Mühlhausen, Stefanie; Kollmar, Martin

2013-09-22

The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications.

When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture

PubMed Central

Barik, Sailen

2008-01-01

The significance of the intron-exon structure of genes is a mystery. As eukaryotic proteins are made up of modular functional domains, each exon was suspected to encode some form of module; however, the definition of a module remained vague. Comparison of pre-mRNA splice junctions with the three-dimensional architecture of its protein product from different eukaryotes revealed that the junctions were far less likely to occur inside the α-helices and β-strands of proteins than within the more flexible linker regions (‘turns’ and ‘loops’) connecting them. The splice junctions were equally distributed in the different types of linkers and throughout the linker sequence, although a slight preference for the central region of the linker was observed. The avoidance of the α-helix and the β-strand by splice junctions suggests the existence of a selection pressure against their disruption, perhaps underscoring the investment made by nature in building these intricate secondary structures. A corollary is that the helix and the strand are the smallest integral architectural units of a protein and represent the minimal modules in the evolution of protein structure. These results should find use in comparative genomics, designing of cloning strategies, and in the mutual verification of genome sequences with protein structures. PMID:15381847

When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture.

PubMed

Barik, Sailen

2004-09-01

The significance of the intron-exon structure of genes is a mystery. As eukaryotic proteins are made up of modular functional domains, each exon was suspected to encode some form of module; however, the definition of a module remained vague. Comparison of pre-mRNA splice junctions with the three-dimensional architecture of its protein product from different eukaryotes revealed that the junctions were far less likely to occur inside the alpha-helices and beta-strands of proteins than within the more flexible linker regions ('turns' and 'loops') connecting them. The splice junctions were equally distributed in the different types of linkers and throughout the linker sequence, although a slight preference for the central region of the linker was observed. The avoidance of the alpha-helix and the beta-strand by splice junctions suggests the existence of a selection pressure against their disruption, perhaps underscoring the investment made by nature in building these intricate secondary structures. A corollary is that the helix and the strand are the smallest integral architectural units of a protein and represent the minimal modules in the evolution of protein structure. These results should find use in comparative genomics, designing of cloning strategies, and in the mutual verification of genome sequences with protein structures.

The Domain-Specific Software Architecture Program

DTIC Science & Technology

1992-06-01

Kang, K.C; Cohen, S.C: Jess, J.A; Novak, W.E; Peterson, A.S. Feature- Oriented Domain Analysis ( FODA ) Feasibility Study. (CMU/SEI-90-TR-21, ADA235785...perspective of a con- trols engineer solving a problem using an iterative process of simulation and analysis . The CMU/SEI-92-SR-9 1 I ~math AnalysislP...for schedulability analysis and Markov processes for the determination of reliability. Software architectures are derived from these formal models. ORA

The prefrontal landscape: implications of functional architecture for understanding human mentation and the central executive.

PubMed

Goldman-Rakic, P S

1996-10-29

The functional architecture of prefrontal cortex is central to our understanding of human mentation and cognitive prowess. This region of the brain is often treated as an undifferentiated structure, on the one hand, or as a mosaic of psychological faculties, on the other. This paper focuses on the working memory processor as a specialization of prefrontal cortex and argues that the different areas within prefrontal cortex represent iterations of this function for different information domains, including spatial cognition, object cognition and additionally, in humans, semantic processing. According to this parallel processing architecture, the 'central executive' could be considered an emergent property of multiple domain-specific processors operating interactively. These processors are specializations of different prefrontal cortical areas, each interconnected both with the domain-relevant long-term storage sites in posterior regions of the cortex and with appropriate output pathways.

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

PubMed

Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

2014-07-01

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains

PubMed Central

2012-01-01

Background Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species. Results In studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications. Conclusion Metazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution. PMID:22862991

The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism.

PubMed

Goldman, Aaron David; Beatty, Joshua T; Landweber, Laura F

2016-01-01

The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive architecture that is present in approximately 10% of all enzymes. It is generally assumed that this ubiquity in modern proteomes reflects an essential historical role in early protein-mediated metabolism. Here, we provide quantitative and comparative analyses to support several hypotheses about the early importance of the TIM barrel architecture. An information theoretical analysis of protein structures supports the hypothesis that the TIM barrel architecture could arise more easily by duplication and recombination compared to other mixed α/β structures. We show that TIM barrel enzymes corresponding to the most taxonomically broad superfamilies also have the broadest range of functions, often aided by metal and nucleotide-derived cofactors that are thought to reflect an earlier stage of metabolic evolution. By comparison to other putatively ancient protein architectures, we find that the functional diversity of TIM barrel proteins cannot be explained simply by their antiquity. Instead, the breadth of TIM barrel functions can be explained, in part, by the incorporation of a broad range of cofactors, a trend that does not appear to be shared by proteins in general. These results support the hypothesis that the simple and functionally general TIM barrel architecture may have arisen early in the evolution of protein biosynthesis and provided an ideal scaffold to facilitate the metabolic transition from ribozymes, peptides, and geochemical catalysts to modern protein enzymes.

Software-Based Safety Systems in Space - Learning from other Domains

NASA Astrophysics Data System (ADS)

Klicker, M.; Putzer, H.

2012-01-01

Increasing complexity and new emerging capabilities for manned and unmanned missions have been the hallmark of the past decades of space exploration. One of the drivers in this process was the ever increasing use of software and software-intensive systems to implement system functions necessary to the capabilities needed. The course of technological evolution suggests that this development will continue well into the future with a number of challenges for the safety community some of which shall be discussed in this paper. The current state of the art reveals a number of problems with developing and assessing safety critical software which explains the reluctance of the space community to rely on software-based safety measures to mitigate hazards. Among others, usually lack of trustworthy evidence of software integrity in all foreseeable situations and the difficulties to integrate software in the traditional safety analysis framework are cited. Experience from other domains and recent developments in modern software development methodologies and verification techniques are analysed for the suitability for space systems and an avionics architectural framework (see STANAG 4626) for the implementation of safety critical software is proposed. This is shown to create among other features the possibility of numerous degradation modes enhancing overall system safety and interoperability of computerized space systems. It also potentially simplifies international cooperation on a technical level by introducing a higher degree of compatibility. As software safety cannot be tested or argued into a system in hindsight, the development process and especially the architecture chosen are essential to establish safety properties for the software used to implement safety functions. The core of the safety argument revolves around the separation of different functions and software modules from each other by minimal coupling of functions and credible separation mechanisms in the architecture combined with rigorous development methodologies for the software itself.

Structural evolution of the P22-like phages: Comparison of Sf6 and P22 procapsid and virion architectures

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

Parent, Kristin N.; Gilcrease, Eddie B.; Casjens, Sherwood R., E-mail: sherwood.casjens@path.utah.edu

Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions ({approx} 7 A resolution), and the structuremore » of the entire, asymmetric Sf6 virion (16-A resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.« less

Origin and evolution of group XI secretory phospholipase A2 from flax (Linum usitatissimum) based on phylogenetic analysis of conserved domains.

PubMed

Gupta, Payal; Saini, Raman; Dash, Prasanta K

2017-07-01

Phospholipase A 2 (PLA 2 ) belongs to class of lipolytic enzymes (EC 3.1.1.4). Lysophosphatidic acid (LPA) and free fatty acids (FFAs) are the products of PLA 2 catalyzed hydrolysis of phosphoglycerides at sn-2 position. LPA and FFA that act as second mediators involved in the development and maturation of plants and animals. Mining of flax genome identified two phospholipase A 2 encoding genes, viz., LusPLA 2 I and LusPLA 2 II (Linum usitatissimum secretory phospholipase A 2 ). Molecular simulation of LusPLA 2 s with already characterized plant sPLA 2 s revealed the presence of conserved motifs and signature domains necessary to classify them as secretory phospholipase A 2 . Phylogenetic analysis of flax sPLA 2 with representative sPLA 2 s from other organisms revealed that they evolved rapidly via gene duplication/deletion events and shares a common ancestor. Our study is the first report of detailed phylogenetic analysis for secretory phospholipase A 2 in flax. Comparative genomic analysis of two LusPLA 2 s with earlier reported plant sPLA 2 s, based on their gene architectures, sequence similarities, and domain structures are presented elucidating the uniqueness of flax sPLA 2 .

ASAC Executive Assistant Architecture Description Summary

NASA Technical Reports Server (NTRS)

Roberts, Eileen; Villani, James A.

1997-01-01

In this technical document, we describe the system architecture developed for the Aviation System Analysis Capability (ASAC) Executive Assistant (EA). We describe the genesis and role of the ASAC system, discuss the objectives of the ASAC system and provide an overview of components and models within the ASAC system, discuss our choice for an architecture methodology, the Domain Specific Software Architecture (DSSA), and the DSSA approach to developing a system architecture, and describe the development process and the results of the ASAC EA system architecture. The document has six appendices.

On the Inevitable Intertwining of Requirements and Architecture

NASA Astrophysics Data System (ADS)

Sutcliffe, Alistair

The chapter investigates the relationship between architecture and requirements, arguing that architectural issues need to be addressed early in the RE process. Three trends are driving architectural implications for RE: the growth of intelligent, context-aware and adaptable systems. First the relationship between architecture and requirements is considered from a theoretical viewpoint of problem frames and abstract conceptual models. The relationships between architectural decisions and non-functional requirements is reviewed, and then the impact of architecture on the RE process is assessed using a case study of developing configurable, semi-intelligent software to support medical researchers in e-science domains.

Incorporation of Tenascin-C into the Extracellular Matrix by Periostin Underlies an Extracellular Meshwork Architecture*

PubMed Central

Kii, Isao; Nishiyama, Takashi; Li, Minqi; Matsumoto, Ken-ichi; Saito, Mitsuru; Amizuka, Norio; Kudo, Akira

2010-01-01

Extracellular matrix (ECM) underlies a complicated multicellular architecture that is subjected to significant forces from mechanical environment. Although various components of the ECM have been enumerated, mechanisms that evolve the sophisticated ECM architecture remain to be addressed. Here we show that periostin, a matricellular protein, promotes incorporation of tenascin-C into the ECM and organizes a meshwork architecture of the ECM. We found that both periostin null mice and tenascin-C null mice exhibited a similar phenotype, confined tibial periostitis, which possibly corresponds to medial tibial stress syndrome in human sports injuries. Periostin possessed adjacent domains that bind to tenascin-C and the other ECM protein: fibronectin and type I collagen, respectively. These adjacent domains functioned as a bridge between tenascin-C and the ECM, which increased deposition of tenascin-C on the ECM. The deposition of hexabrachions of tenascin-C may stabilize bifurcations of the ECM fibrils, which is integrated into the extracellular meshwork architecture. This study suggests a role for periostin in adaptation of the ECM architecture in the mechanical environment. PMID:19887451

Incorporation of tenascin-C into the extracellular matrix by periostin underlies an extracellular meshwork architecture.

PubMed

Kii, Isao; Nishiyama, Takashi; Li, Minqi; Matsumoto, Ken-Ichi; Saito, Mitsuru; Amizuka, Norio; Kudo, Akira

2010-01-15

Extracellular matrix (ECM) underlies a complicated multicellular architecture that is subjected to significant forces from mechanical environment. Although various components of the ECM have been enumerated, mechanisms that evolve the sophisticated ECM architecture remain to be addressed. Here we show that periostin, a matricellular protein, promotes incorporation of tenascin-C into the ECM and organizes a meshwork architecture of the ECM. We found that both periostin null mice and tenascin-C null mice exhibited a similar phenotype, confined tibial periostitis, which possibly corresponds to medial tibial stress syndrome in human sports injuries. Periostin possessed adjacent domains that bind to tenascin-C and the other ECM protein: fibronectin and type I collagen, respectively. These adjacent domains functioned as a bridge between tenascin-C and the ECM, which increased deposition of tenascin-C on the ECM. The deposition of hexabrachions of tenascin-C may stabilize bifurcations of the ECM fibrils, which is integrated into the extracellular meshwork architecture. This study suggests a role for periostin in adaptation of the ECM architecture in the mechanical environment.

Hardware architecture design of image restoration based on time-frequency domain computation

NASA Astrophysics Data System (ADS)

Wen, Bo; Zhang, Jing; Jiao, Zipeng

2013-10-01

The image restoration algorithms based on time-frequency domain computation is high maturity and applied widely in engineering. To solve the high-speed implementation of these algorithms, the TFDC hardware architecture is proposed. Firstly, the main module is designed, by analyzing the common processing and numerical calculation. Then, to improve the commonality, the iteration control module is planed for iterative algorithms. In addition, to reduce the computational cost and memory requirements, the necessary optimizations are suggested for the time-consuming module, which include two-dimensional FFT/IFFT and the plural calculation. Eventually, the TFDC hardware architecture is adopted for hardware design of real-time image restoration system. The result proves that, the TFDC hardware architecture and its optimizations can be applied to image restoration algorithms based on TFDC, with good algorithm commonality, hardware realizability and high efficiency.

Domain specific software architectures: Command and control

NASA Technical Reports Server (NTRS)

Braun, Christine; Hatch, William; Ruegsegger, Theodore; Balzer, Bob; Feather, Martin; Goldman, Neil; Wile, Dave

1992-01-01

GTE is the Command and Control contractor for the Domain Specific Software Architectures program. The objective of this program is to develop and demonstrate an architecture-driven, component-based capability for the automated generation of command and control (C2) applications. Such a capability will significantly reduce the cost of C2 applications development and will lead to improved system quality and reliability through the use of proven architectures and components. A major focus of GTE's approach is the automated generation of application components in particular subdomains. Our initial work in this area has concentrated in the message handling subdomain; we have defined and prototyped an approach that can automate one of the most software-intensive parts of C2 systems development. This paper provides an overview of the GTE team's DSSA approach and then presents our work on automated support for message processing.

Structuring and evolution of Neogene transcurrent basins in the Tellian foreland domain, north-eastern Tunisia

NASA Astrophysics Data System (ADS)

Melki, Fetheddine; Zouaghi, Taher; Harrab, Salah; Sainz, Antonio Casas; Bédir, Mourad; Zargouni, Fouad

2011-07-01

The Neogene sedimentary basins (Serravallian to Quaternary) of the Tellian tectonic foreland in north-eastern Tunisia formed within the overall NE-SW sinistral strike-slip tectonic framework of the Ras El Korane-Thibar and El Alia-Teboursouk fault systems. From stratigraphic logs, structural cross sections and interpretation of 2D seismic lines and boreholes, the pre-Neogene basement can be interpreted to be structured according to Eocene (NW-SE) compressional and Oligocene extensional phases. This basement comprises structural highs (anticlines and horsts) and subsiding areas (synclines, half-grabens and grabens) formed during the Neogene. The subsiding areas are delineated by faults striking N030E, N-S and N140E, defining (i) narrow, strongly subsiding synclines, (ii) lozenge-shaped basins and (iii) trapezoidal basins. The architecture of their fill results from the sedimentary balance between tectonics and eustatism. Halokinesis and clay diapirism (driven by Triassic and Neogene evaporites and clays) also played an important role in basin evolution, contributing to the formation of domes and diapirs along active faults.

Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry.

PubMed

Clark, Edward B; Hickinbotham, Simon J; Stepney, Susan

2017-05-01

We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description. We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring. © 2017 The Author(s).

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

2017-11-01

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

PubMed Central

Bryson, David M.; Ofria, Charles

2013-01-01

We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a broad range of challenges. PMID:24376669

The Golden Age of Software Architecture: A Comprehensive Survey

DTIC Science & Technology

2006-02-01

UML [14], under the leadership of (at the time) Rational, has integrated a number of design notations and developed a method for applying them...yes 97 survey, model Garlan. Research directions in SA [28] 54 yes 93 specific domains Cremer et al. The SA for scenario control in the Iowa...Environment of the Domain-Specific Software Architecture Project, ADAGE-IBM-92-11, Version 2.0, November, 1993 [23] J. Cremer , J. Kearney, Y. Papelis, and

Architecture of the Yeast RNA Polymerase II Open Complex and Regulation of Activity by TFIIF

PubMed Central

Fishburn, James

2012-01-01

To investigate the function and architecture of the open complex state of RNA polymerase II (Pol II), Saccharomyces cerevisiae minimal open complexes were assembled by using a series of heteroduplex HIS4 promoters, TATA binding protein (TBP), TFIIB, and Pol II. The yeast system demonstrates great flexibility in the position of active open complexes, spanning 30 to 80 bp downstream from TATA, consistent with the transcription start site scanning behavior of yeast Pol II. TFIIF unexpectedly modulates the activity of the open complexes, either repressing or stimulating initiation. The response to TFIIF was dependent on the sequence of the template strand within the single-stranded bubble. Mutations in the TFIIB reader and linker region, which were inactive on duplex DNA, were suppressed by the heteroduplex templates, showing that a major function of the TFIIB reader and linker is in the initiation or stabilization of single-stranded DNA. Probing of the architecture of the minimal open complexes with TFIIB-FeBABE [TFIIB–p-bromoacetamidobenzyl–EDTA-iron(III)] derivatives showed that the TFIIB core domain is surprisingly positioned away from Pol II, and the addition of TFIIF repositions the TFIIB core domain to the Pol II wall domain. Together, our results show an unexpected architecture of minimal open complexes and the regulation of activity by TFIIF and the TFIIB core domain. PMID:22025674

Alternative dimerization interfaces in the glucocorticoid receptor-α ligand binding domain.

PubMed

Bianchetti, Laurent; Wassmer, Bianca; Defosset, Audrey; Smertina, Anna; Tiberti, Marion L; Stote, Roland H; Dejaegere, Annick

2018-04-30

Nuclear hormone receptors (NRs) constitute a large family of multi-domain ligand-activated transcription factors. Dimerization is essential for their regulation, and both DNA binding domain (DBD) and ligand binding domain (LBD) are implicated in dimerization. Intriguingly, the glucocorticoid receptor-α (GRα) presents a DBD dimeric architecture similar to that of the homologous estrogen receptor-α (ERα), but an atypical dimeric architecture for the LBD. The physiological relevance of the proposed GRα LBD dimer is a subject of debate. We analyzed all GRα LBD homodimers observed in crystals using an energetic analysis based on the PISA and on the MM/PBSA methods and a sequence conservation analysis, using the ERα LBD dimer as a reference point. Several dimeric assemblies were observed for GRα LBD. The assembly generally taken to be physiologically relevant showed weak binding free energy and no significant residue conservation at the contact interface, while an alternative homodimer mediated by both helix 9 and C-terminal residues showed significant binding free energy and residue conservation. However, none of the GRα LBD assemblies found in crystals are as stable or conserved as the canonical ERα LBD dimer. GRα C-terminal sequence (F-domain) forms a steric obstacle to the canonical dimer assembly in all available structures. Our analysis calls for a re-examination of the currently accepted GRα homodimer structure and experimental investigations of the alternative architectures. This work questions the validity of the currently accepted architecture. This has implications for interpreting physiological data and for therapeutic design pertaining to glucocorticoid research. Copyright © 2018. Published by Elsevier B.V.

The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle

PubMed Central

Srinivasan, Jagan; Dillman, Adler R.; Macchietto, Marissa G.; Heikkinen, Liisa; Lakso, Merja; Fracchia, Kelley M.; Antoshechkin, Igor; Mortazavi, Ali; Wong, Garry; Sternberg, Paul W.

2013-01-01

Nematodes compose an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the “microworm”) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA-seq data, we predict 24,249 genes and 32,676 transcripts. Small RNA analysis revealed 248 microRNA (miRNA) hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. The RNA interference, dauer development, and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain-containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi-subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies. PMID:23410827

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

PubMed Central

Aguilera, Felipe; McDougall, Carmel

2017-01-01

Abstract Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium. PMID:28053006

Open System Architecture design for planet surface systems

NASA Technical Reports Server (NTRS)

Petri, D. A.; Pieniazek, L. A.; Toups, L. D.

1992-01-01

The Open System Architecture is an approach to meeting the needs for flexibility and evolution of the U.S. Space Exploration Initiative program of the manned exploration of the solar system and its permanent settlement. This paper investigates the issues that future activities of the planet exploration program must confront, defines the basic concepts that provide the basis for establishing an Open System Architecture, identifies the appropriate features of such an architecture, and discusses examples of Open System Architectures.

In situ visualization of domain structure evolution during field cooling in 0.67PMN-0.33PT single crystal

NASA Astrophysics Data System (ADS)

Ushakov, A. D.; Esin, A. A.; Chezganov, D. S.; Turygin, A. P.; Akhmatkhanov, A. R.; Hu, Q.; Sun, L.; Wei, X.; Shur, V. Ya

2017-10-01

The evolution of the domain structure during in-field cooling was in situ studied in [001]-cut single crystals of relaxor ferroelectric (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 (PMN-PT) with x = 0.33 with maximum of dielectric permittivity at 150°C. The main stages of domain evolution have been separated. The visualization of the static as-grown and polarized domain structures with high spatial resolution by piezoresponse force microscopy and scanning electron microscopy allowed measuring the characteristic features of maze and needle-like domain structures.

Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification.

PubMed

Ishengoma, Edson; Agaba, Morris

2017-02-16

Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Sequence analysis shows that giraffe has 94-99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.

Evolution and classification of the CRISPR-Cas systems

PubMed Central

S. Makarova, Kira; H. Haft, Daniel; Barrangou, Rodolphe; J. J. Brouns, Stan; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; J. M. Mojica, Francisco; I. Wolf, Yuri; Yakunin, Alexander F.; van der Oost, John; V. Koonin, Eugene

2012-01-01

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a `polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci. PMID:21552286

Bisphenol A (BPA) binding on full-length architectures of estrogen receptor.

PubMed

Liu, Yaquan; Qu, Kaili; Hai, Ying; Zhao, Chunyan

2018-08-01

Previous research has shown that the major toxicity mechanism for many environment chemicals is binding with estrogen receptor (ER) and blocking endogenous estrogen access, including bisphenol A (BPA). However, the molecular level understanding the global consequence of BPA binding on the full-length architectures of ER is largely unknown, which is a necessary stage to evaluate estrogen-like toxicity of BPA. In the present work, the consequence of BPA on full-length architectures of ER was firstly modeled based on molecular dynamics, focusing on the cross communication between multi-domains including ligand binding domain (LBD) and DNA binding domain (DBD). The study proved consequence of BPA upon full-length ER structure was dependent on long-range communications between multiple protein domains. The allosteric effects occurring in LBD units could alter dimerization formation through a crucial change in residue-residue connections, which resulted in relaxation of DBD. It indicated BPA could present consequence on the full-size receptor, not only on the separate domains, but also on the cross communication among LBD, DBD, and DNA molecules. It might provide detailed insight into the knowledge about the structural characteristics of ER and its role in gene regulation, which eventually helped us evaluate the estrogen-like toxicity upon BPA binding with full-length ER. © 2018 Wiley Periodicals, Inc.

Predicting chromatin architecture from models of polymer physics.

PubMed

Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario

2017-03-01

We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches. To identify the nature of architectural domains and their molecular determinants within a principled approach, we discuss models based on polymer physics. We show that basic concepts of interacting polymer physics explain chromatin spatial organization across chromosomal scales and cell types. The 3D structure of genomic loci can be derived with high accuracy and its molecular determinants identified by crossing information with epigenomic databases. In particular, we illustrate the case of the Sox9 locus, linked to human congenital disorders. The model in-silico predictions on the effects of genomic rearrangements are confirmed by available 5C data. That can help establishing new diagnostic tools for diseases linked to chromatin mis-folding, such as congenital disorders and cancer.

SAFARI optical system architecture and design concept

NASA Astrophysics Data System (ADS)

Pastor, Carmen; Jellema, Willem; Zuluaga-Ramírez, Pablo; Arrazola, David; Fernández-Rodriguez, M.; Belenguer, Tomás.; González Fernández, Luis M.; Audley, Michael D.; Evers, Jaap; Eggens, Martin; Torres Redondo, Josefina; Najarro, Francisco; Roelfsema, Peter

2016-07-01

SpicA FAR infrared Instrument, SAFARI, is one of the instruments planned for the SPICA mission. The SPICA mission is the next great leap forward in space-based far-infrared astronomy and will study the evolution of galaxies, stars and planetary systems. SPICA will utilize a deeply cooled 2.5m-class telescope, provided by European industry, to realize zodiacal background limited performance, and high spatial resolution. The instrument SAFARI is a cryogenic grating-based point source spectrometer working in the wavelength domain 34 to 230 μm, providing spectral resolving power from 300 to at least 2000. The instrument shall provide low and high resolution spectroscopy in four spectral bands. Low Resolution mode is the native instrument mode, while the high Resolution mode is achieved by means of a Martin-Pupplet interferometer. The optical system is all-reflective and consists of three main modules; an input optics module, followed by the Band and Mode Distributing Optics and the grating Modules. The instrument utilizes Nyquist sampled filled linear arrays of very sensitive TES detectors. The work presented in this paper describes the optical design architecture and design concept compatible with the current instrument performance and volume design drivers.

The spatial architecture of protein function and adaptation

PubMed Central

McLaughlin, Richard N.; Poelwijk, Frank J.; Raman, Arjun; Gosal, Walraj S.; Ranganathan, Rama

2014-01-01

Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function1, 2, 3, 4, 5. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself—the ability to tolerate mutation and to be adaptive to changing selection pressures6, 7, 8, 9, 10. To understand the relationship of the sector architecture to these properties, we developed a high-throughput quantitative method for a comprehensive single-mutation study in which every position is substituted individually to every other amino acid. Using a PDZ domain (PSD95pdz3) model system, we show that sector positions are functionally sensitive to mutation, whereas non-sector positions are more tolerant to substitution. In addition, we find that adaptation to a new binding specificity initiates exclusively through variation within sector residues. A combination of just two sector mutations located near and away from the ligand-binding site suffices to switch the binding specificity of PSD95pdz3 quantitatively towards a class-switching ligand. The localization of functional constraint and adaptive variation within the sector has important implications for understanding and engineering proteins. PMID:23041932

Time-varying spatial data integration and visualization: 4 Dimensions Environmental Observations Platform (4-DEOS)

NASA Astrophysics Data System (ADS)

Paciello, Rossana; Coviello, Irina; Filizzola, Carolina; Genzano, Nicola; Lisi, Mariano; Mazzeo, Giuseppe; Pergola, Nicola; Sileo, Giancanio; Tramutoli, Valerio

2014-05-01

In environmental studies the integration of heterogeneous and time-varying data, is a very common requirement for investigating and possibly visualize correlations among physical parameters underlying the dynamics of complex phenomena. Datasets used in such kind of applications has often different spatial and temporal resolutions. In some case superimposition of asynchronous layers is required. Traditionally the platforms used to perform spatio-temporal visual data analyses allow to overlay spatial data, managing the time using 'snapshot' data model, each stack of layers being labeled with different time. But this kind of architecture does not incorporate the temporal indexing neither the third spatial dimension which is usually given as an independent additional layer. Conversely, the full representation of a generic environmental parameter P(x,y,z,t) in the 4D space-time domain could allow to handle asynchronous datasets as well as less traditional data-products (e.g. vertical sections, punctual time-series, etc.) . In this paper we present the 4 Dimensions Environmental Observation Platform (4-DEOS), a system based on a web services architecture Client-Broker-Server. This platform is a new open source solution for both a timely access and an easy integration and visualization of heterogeneous (maps, vertical profiles or sections, punctual time series, etc.) asynchronous, geospatial products. The innovative aspect of the 4-DEOS system is that users can analyze data/products individually moving through time, having also the possibility to stop the display of some data/products and focus on other parameters for better studying their temporal evolution. This platform gives the opportunity to choose between two distinct display modes for time interval or for single instant. Users can choose to visualize data/products in two ways: i) showing each parameter in a dedicated window or ii) visualize all parameters overlapped in a single window. A sliding time bar, allows to follow the temporal evolution of the selected data/product. With this software, users have the possibility to identify events partially correlated each other not only in the spatial dimension but also in the time domain even at different time lags.

Nuclear Architecture of Mouse Spermatocytes: Chromosome Topology, Heterochromatin, and Nucleolus.

PubMed

Berrios, Soledad

2017-01-01

The nuclear organization of spermatocytes in meiotic prophase I is primarily determined by the synaptic organization of the bivalents that are bound by their telomeres to the nuclear envelope and described as arc-shaped trajectories through the 3D nuclear space. However, over this basic meiotic organization, a spermatocyte nuclear architecture arises that is based on higher-ordered patterns of spatial associations among chromosomal domains from different bivalents that are conditioned by the individual characteristics of chromosomes and the opportunity for interactions between their domains. Consequently, the nuclear architecture is species-specific and prone to modification by chromosomal rearrangements. This model is valid for the localization of any chromosomal domain in the meiotic prophase nucleus. However, constitutive heterochromatin plays a leading role in shaping nuclear territories. Thus, the nuclear localization of nucleoli depends on the position of NORs in nucleolar bivalents, but the association among nucleolar chromosomes mainly depends on the presence of constitutive heterochromatin that does not affect the expression of the ribosomal genes. Constitutive heterochromatin and nucleoli form complex nuclear territories whose distribution in the nuclear space is nonrandom, supporting the hypothesis regarding the existence of a species-specific nuclear architecture in first meiotic prophase spermatocytes. © 2017 S. Karger AG, Basel.

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

PubMed Central

Wolf, Maxim Y; Wolf, Yuri I; Koonin, Eugene V

2008-01-01

Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude. Conclusion Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution. Reviewers This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter), and Allan Drummond (nominated by Joel Bader). For the full reviews, please go to the Reviewers' Reports section. PMID:18840284

Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants.

PubMed

Peng, Fred Y; Weselake, Randall J

2013-05-01

The plant-specific B3 superfamily of transcription factors has diverse functions in plant growth and development. Using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 B3 transcription factor genes in the sequenced genome of Arabidopsis, Brassica rapa, castor bean (Ricinus communis), cocoa (Theobroma cacao), soybean (Glycine max), maize (Zea mays), and rice (Oryza sativa), respectively. The B3 superfamily has substantially expanded during the evolution in eudicots particularly in Brassicaceae, as compared to monocots in the analysis. We observed domain duplication in some of these B3 proteins, forming more complex domain architectures than currently understood. We found that the length of B3 domains exhibits a large variation, which may affect their exact number of α-helices and β-sheets in the core structure of B3 domains, and possibly have functional implications. Analysis of the public microarray data indicated that most of the B3 gene pairs encoding Arabidopsis-rice orthologs are preferentially expressed in different tissues, suggesting their different roles in these two species. Using ESTs in crops, we identified many B3 genes preferentially expressed in reproductive tissues. In a sequence-based quantitative trait loci analysis in rice and maize, we have found many B3 genes associated with traits such as grain yield, seed weight and number, and protein content. Our results provide a framework for future studies into the function of B3 genes in different phases of plant development, especially the ones related to traits in major crops.

Phylogeny of the TRAF/MATH domain.

PubMed

Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

2007-01-01

The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

A General Architecture for Intelligent Tutoring of Diagnostic Classification Problem Solving

PubMed Central

Crowley, Rebecca S.; Medvedeva, Olga

2003-01-01

We report on a general architecture for creating knowledge-based medical training systems to teach diagnostic classification problem solving. The approach is informed by our previous work describing the development of expertise in classification problem solving in Pathology. The architecture envelops the traditional Intelligent Tutoring System design within the Unified Problem-solving Method description Language (UPML) architecture, supporting component modularity and reuse. Based on the domain ontology, domain task ontology and case data, the abstract problem-solving methods of the expert model create a dynamic solution graph. Student interaction with the solution graph is filtered through an instructional layer, which is created by a second set of abstract problem-solving methods and pedagogic ontologies, in response to the current state of the student model. We outline the advantages and limitations of this general approach, and describe it’s implementation in SlideTutor–a developing Intelligent Tutoring System in Dermatopathology. PMID:14728159

Computer-implemented security evaluation methods, security evaluation systems, and articles of manufacture

DOEpatents

Muller, George; Perkins, Casey J.; Lancaster, Mary J.; MacDonald, Douglas G.; Clements, Samuel L.; Hutton, William J.; Patrick, Scott W.; Key, Bradley Robert

2015-07-28

Computer-implemented security evaluation methods, security evaluation systems, and articles of manufacture are described. According to one aspect, a computer-implemented security evaluation method includes accessing information regarding a physical architecture and a cyber architecture of a facility, building a model of the facility comprising a plurality of physical areas of the physical architecture, a plurality of cyber areas of the cyber architecture, and a plurality of pathways between the physical areas and the cyber areas, identifying a target within the facility, executing the model a plurality of times to simulate a plurality of attacks against the target by an adversary traversing at least one of the areas in the physical domain and at least one of the areas in the cyber domain, and using results of the executing, providing information regarding a security risk of the facility with respect to the target.

Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.

Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA

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

Sunita,S.; Zhenxing, H.; Swaathi, J.

2006-01-01

Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine ({psi}) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E. coli RluF at 2.6 Angstroms resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. Themore » structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of {psi}-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.« less

The domain architecture of the PtkA, the first tyrosine kinase from Mycobacterium tuberculosis differs from the conventional kinase architecture.

PubMed

Niesteruk, Anna; Jonker, Hendrik R A; Richter, Christian; Linhard, Verena; Sreeramulu, Sridhar; Schwalbe, Harald

2018-06-08

The discovery that MptpA (low-molecular-weight protein tyrosine phosphatase A) from Mycobacterium tuberculosis ( Mtb ) has an essential role for Mtb virulence has motivated research of tyrosine-specific phosphorylation in Mtb and other pathogenic bacteria. The phosphatase activity of MptpA is regulated via phosphorylation on Tyr-128 and Tyr-129. Thus far, only a single tyrosine-specific kinase, protein tyrosine kinase A (PtkA), encoded by the Rv2232 gene has been identified within the Mtb genome. MptpA undergoes phosphorylation by PtkA. PtkA is an atypical bacterial tyrosine kinase, as its sequence differs from the sequence consensus within this family. The lack of structural information on PtkA hampers the detailed characterization of the MptpA-PtkA interaction. Here, using NMR spectroscopy, we provide a detailed structural characterization of the PtkA architecture and describe its intra- and intermolecular interactions with MptpA. We found that PtkA's domain architecture differs from the conventional kinase architecture and is composed of two domains, the N-terminal highly flexible IDD PtkA and the C-terminal rigid KCD PtkA The interaction studies between the two domains together with the structural model of the IDD-KCD complex proposed in this study reveals that the IDD is unstructured and highly dynamic, allowing for a "fly-casting" like mechanism of transient interactions with the rigid KCD. This interaction modulates the accessibility of the KCD active site. In general, the structural and functional knowledge of PtkA gained in this study, is crucial for understanding the MptpA-PtkA interactions, catalytic mechanism and the role of kinase-phosphatase regulatory system in Mtb virulence. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Analyzing and designing object-oriented missile simulations with concurrency

NASA Astrophysics Data System (ADS)

Randorf, Jeffrey Allen

2000-11-01

A software object model for the six degree-of-freedom missile modeling domain is presented. As a precursor, a domain analysis of the missile modeling domain was started, based on the Feature-Oriented Domain Analysis (FODA) technique described by the Software Engineering Institute (SEI). It was subsequently determined the FODA methodology is functionally equivalent to the Object Modeling Technique. The analysis used legacy software documentation and code from the ENDOSIM, KDEC, and TFrames 6-DOF modeling tools, including other technical literature. The SEI Object Connection Architecture (OCA) was the template for designing the object model. Three variants of the OCA were considered---a reference structure, a recursive structure, and a reference structure with augmentation for flight vehicle modeling. The reference OCA design option was chosen for maintaining simplicity while not compromising the expressive power of the OMT model. The missile architecture was then analyzed for potential areas of concurrent computing. It was shown how protected objects could be used for data passing between OCA object managers, allowing concurrent access without changing the OCA reference design intent or structure. The implementation language was the 1995 release of Ada. OCA software components were shown how to be expressed as Ada child packages. While acceleration of several low level and other high operations level are possible on proper hardware, there was a 33% degradation of 4th order Runge-Kutta integrator performance of two simultaneous ordinary differential equations using Ada tasking on a single processor machine. The Defense Department's High Level Architecture was introduced and explained in context with the OCA. It was shown the HLA and OCA were not mutually exclusive architectures, but complimentary. HLA was shown as an interoperability solution, with the OCA as an architectural vehicle for software reuse. Further directions for implementing a 6-DOF missile modeling environment are discussed.

Creating and Manipulating Formalized Software Architectures to Support a Domain-Oriented Application Composition System

DTIC Science & Technology

1992-12-01

OOD) Paradigm ...... .... 2-7 2.4.3 Feature-Oriented Domain Analysis ( FODA ) ..... 2-7 2.4.4 Hierarchical Software Systems .................. 2-7...domain analysis ( FODA ) is one approach to domain analysis whose primary goal is to make domain products reusable (20:47). A domain model describes 2-5...7), among others. 2.4.3 Feature-Oriented Domain Analysis ( FODA ) Kang and others used the com- plete FODA methodology to successfully develop a window

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

PubMed Central

Bernardes, Juliana; Zaverucha, Gerson; Vaquero, Catherine; Carbone, Alessandra

2016-01-01

Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain duplications, the reconstruction of the history of protein architectures, and the estimation of protein domain age. Website and software: http://www.lcqb.upmc.fr/CLADE. PMID:27472895

The ADEPT Framework for Intelligent Autonomy

NASA Technical Reports Server (NTRS)

Ricard, Michael; Kolitz, Stephan

2003-01-01

This paper describes the design and implementation of Draper Laboratory's All-Domain Execution and Planning Technology (ADEPT) architecture for intelligent autonomy. Intelligent autonomy is the ability to plan and execute complex activities in a manner that provides rapid, effective response to stochastic and dynamic mission events. Thus, intelligent autonomy enables the high-level reasoning and adaptive behavior for an unmanned vehicle that is provided by an operator in man-in-the-loop systems. Draper s intelligent autonomy has architecture evolved over a decade and a half beginning in the mid 1980's culminating in an operational experiment funded under DARPA's Autonomous Minehunting and Mapping Technologies (AMMT) unmanned undersea vehicle program. ADEPT continues to be refined through its application to current programs that involve air vehicles, satellites and higher-level planning used to direct multiple vehicles. The objective of ADEPT is to solidify a proven, dependable software approach that can be quickly applied to new vehicles and domains. The architecture can be viewed as a hierarchical extension of the sense-think-act paradigm of intelligence and has strong parallels with the military's Observe-Orient-Decide-Act (OODA) loop. The key elements of the architecture are planning and decision-making nodes comprising modules for situation assessment, plan generation, plan implementation and coordination. A reusable, object-oriented software framework has been developed that implements these functions. As the architecture is applied to new areas, only the application specific software needs to be developed. This paper describes the core architecture in detail and discusses how this has been applied in the undersea, air, ground and space domains.

Exploring the transcription activator-like effectors scaffold versatility to expand the toolbox of designer nucleases

PubMed Central

2014-01-01

Background The past decade has seen the emergence of several molecular tools that render possible modification of cellular functions through accurate and easy addition, removal, or exchange of genomic DNA sequences. Among these technologies, transcription activator-like effectors (TALE) has turned out to be one of the most versatile and incredibly robust platform for generating targeted molecular tools as demonstrated by fusion to various domains such as transcription activator, repressor and nucleases. Results In this study, we generated a novel nuclease architecture based on the transcription activator-like effector scaffold. In contrast to the existing Tail to Tail (TtT) and head to Head (HtH) nuclease architectures based on the symmetrical association of two TALE DNA binding domains fused to the C-terminal (TtT) or N-terminal (HtH) end of FokI, this novel architecture consists of the asymmetrical association of two different engineered TALE DNA binding domains fused to the N- and C-terminal ends of FokI (TALE::FokI and FokI::TALE scaffolds respectively). The characterization of this novel Tail to Head (TtH) architecture in yeast enabled us to demonstrate its nuclease activity and define its optimal target configuration. We further showed that this architecture was able to promote substantial level of targeted mutagenesis at three endogenous loci present in two different mammalian cell lines. Conclusion Our results demonstrated that this novel functional TtH architecture which requires binding to only one DNA strand of a given endogenous locus has the potential to extend the targeting possibility of FokI-based TALE nucleases. PMID:24997498

Reference Architecture Model Enabling Standards Interoperability.

PubMed

Blobel, Bernd

2017-01-01

Advanced health and social services paradigms are supported by a comprehensive set of domains managed by different scientific disciplines. Interoperability has to evolve beyond information and communication technology (ICT) concerns, including the real world business domains and their processes, but also the individual context of all actors involved. So, the system must properly reflect the environment in front and around the computer as essential and even defining part of the health system. This paper introduces an ICT-independent system-theoretical, ontology-driven reference architecture model allowing the representation and harmonization of all domains involved including the transformation into an appropriate ICT design and implementation. The entire process is completely formalized and can therefore be fully automated.

A highly efficient 3D level-set grain growth algorithm tailored for ccNUMA architecture

NASA Astrophysics Data System (ADS)

Mießen, C.; Velinov, N.; Gottstein, G.; Barrales-Mora, L. A.

2017-12-01

A highly efficient simulation model for 2D and 3D grain growth was developed based on the level-set method. The model introduces modern computational concepts to achieve excellent performance on parallel computer architectures. Strong scalability was measured on cache-coherent non-uniform memory access (ccNUMA) architectures. To achieve this, the proposed approach considers the application of local level-set functions at the grain level. Ideal and non-ideal grain growth was simulated in 3D with the objective to study the evolution of statistical representative volume elements in polycrystals. In addition, microstructure evolution in an anisotropic magnetic material affected by an external magnetic field was simulated.

A single-chain TALEN architecture for genome engineering.

PubMed

Sun, Ning; Zhao, Huimin

2014-03-04

Transcription-activator like effector nucleases (TALENs) are tailor-made DNA endonucleases and serve as a powerful tool for genome engineering. Site-specific DNA cleavage can be made by the dimerization of FokI nuclease domains at custom-targeted genomic loci, where a pair of TALENs must be positioned in close proximity with an appropriate orientation. However, the simultaneous delivery and coordinated expression of two bulky TALEN monomers (>100 kDa) in cells may be problematic to implement for certain applications. Here, we report the development of a single-chain TALEN (scTALEN) architecture, in which two FokI nuclease domains are fused on a single polypeptide. The scTALEN was created by connecting two FokI nuclease domains with a 95 amino acid polypeptide linker, which was isolated from a linker library by high-throughput screening. We demonstrated that scTALENs were catalytically active as monomers in yeast and human cells. The use of this novel scTALEN architecture should reduce protein payload, simplify design and decrease production cost.

Extracellular chloride signals collagen IV network assembly during basement membrane formation

PubMed Central

Cummings, Christopher F.; Pedchenko, Vadim; Brown, Kyle L.; Colon, Selene; Rafi, Mohamed; Jones-Paris, Celestial; Pokydeshava, Elena; Liu, Min; Pastor-Pareja, Jose C.; Stothers, Cody; Ero-Tolliver, Isi A.; McCall, A. Scott; Vanacore, Roberto; Bhave, Gautam; Santoro, Samuel; Blackwell, Timothy S.; Zent, Roy; Pozzi, Ambra

2016-01-01

Basement membranes are defining features of the cellular microenvironment; however, little is known regarding their assembly outside cells. We report that extracellular Cl− ions signal the assembly of collagen IV networks outside cells by triggering a conformational switch within collagen IV noncollagenous 1 (NC1) domains. Depletion of Cl− in cell culture perturbed collagen IV networks, disrupted matrix architecture, and repositioned basement membrane proteins. Phylogenetic evidence indicates this conformational switch is a fundamental mechanism of collagen IV network assembly throughout Metazoa. Using recombinant triple helical protomers, we prove that NC1 domains direct both protomer and network assembly and show in Drosophila that NC1 architecture is critical for incorporation into basement membranes. These discoveries provide an atomic-level understanding of the dynamic interactions between extracellular Cl− and collagen IV assembly outside cells, a critical step in the assembly and organization of basement membranes that enable tissue architecture and function. Moreover, this provides a mechanistic framework for understanding the molecular pathobiology of NC1 domains. PMID:27216258

Performance evaluation of canny edge detection on a tiled multicore architecture

NASA Astrophysics Data System (ADS)

Brethorst, Andrew Z.; Desai, Nehal; Enright, Douglas P.; Scrofano, Ronald

2011-01-01

In the last few years, a variety of multicore architectures have been used to parallelize image processing applications. In this paper, we focus on assessing the parallel speed-ups of different Canny edge detection parallelization strategies on the Tile64, a tiled multicore architecture developed by the Tilera Corporation. Included in these strategies are different ways Canny edge detection can be parallelized, as well as differences in data management. The two parallelization strategies examined were loop-level parallelism and domain decomposition. Loop-level parallelism is achieved through the use of OpenMP,1 and it is capable of parallelization across the range of values over which a loop iterates. Domain decomposition is the process of breaking down an image into subimages, where each subimage is processed independently, in parallel. The results of the two strategies show that for the same number of threads, programmer implemented, domain decomposition exhibits higher speed-ups than the compiler managed, loop-level parallelism implemented with OpenMP.

Application of a Multimedia Service and Resource Management Architecture for Fault Diagnosis

PubMed Central

Castro, Alfonso; Sedano, Andrés A.; García, Fco. Javier; Villoslada, Eduardo

2017-01-01

Nowadays, the complexity of global video products has substantially increased. They are composed of several associated services whose functionalities need to adapt across heterogeneous networks with different technologies and administrative domains. Each of these domains has different operational procedures; therefore, the comprehensive management of multi-domain services presents serious challenges. This paper discusses an approach to service management linking fault diagnosis system and Business Processes for Telefónica’s global video service. The main contribution of this paper is the proposal of an extended service management architecture based on Multi Agent Systems able to integrate the fault diagnosis with other different service management functionalities. This architecture includes a distributed set of agents able to coordinate their actions under the umbrella of a Shared Knowledge Plane, inferring and sharing their knowledge with semantic techniques and three types of automatic reasoning: heterogeneous, ontology-based and Bayesian reasoning. This proposal has been deployed and validated in a real scenario in the video service offered by Telefónica Latam. PMID:29283398

Application of a Multimedia Service and Resource Management Architecture for Fault Diagnosis.

PubMed

Castro, Alfonso; Sedano, Andrés A; García, Fco Javier; Villoslada, Eduardo; Villagrá, Víctor A

2017-12-28

Nowadays, the complexity of global video products has substantially increased. They are composed of several associated services whose functionalities need to adapt across heterogeneous networks with different technologies and administrative domains. Each of these domains has different operational procedures; therefore, the comprehensive management of multi-domain services presents serious challenges. This paper discusses an approach to service management linking fault diagnosis system and Business Processes for Telefónica's global video service. The main contribution of this paper is the proposal of an extended service management architecture based on Multi Agent Systems able to integrate the fault diagnosis with other different service management functionalities. This architecture includes a distributed set of agents able to coordinate their actions under the umbrella of a Shared Knowledge Plane, inferring and sharing their knowledge with semantic techniques and three types of automatic reasoning: heterogeneous, ontology-based and Bayesian reasoning. This proposal has been deployed and validated in a real scenario in the video service offered by Telefónica Latam.

Two-dimensional optical architectures for the receive mode of phased-array antennas.

PubMed

Pastur, L; Tonda-Goldstein, S; Dolfi, D; Huignard, J P; Merlet, T; Maas, O; Chazelas, J

1999-05-10

We propose and experimentally demonstrate two optical architectures that process the receive mode of a p x p element phased-array antenna. The architectures are based on free-space propagation and switching of the channelized optical carriers of microwave signals. With the first architecture a direct transposition of the received signals in the optical domain is assumed. The second architecture is based on the optical generation and distribution of a microwave local oscillator matched in frequency and direction. Preliminary experimental results at microwave frequencies of approximately 3 GHz are presented.

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains

USDA-ARS?s Scientific Manuscript database

Understanding proteome evolution is important for deciphering processes that drive species diversity and adaptation. Herein, the dynamics of change in protein families and protein domains over the course of metazoan evolution was explored. Change, as defined by birth/death and duplication/deletion ...

An architecture for intelligent task interruption

NASA Technical Reports Server (NTRS)

Sharma, D. D.; Narayan, Srini

1990-01-01

In the design of real time systems the capability for task interruption is often considered essential. The problem of task interruption in knowledge-based domains is examined. It is proposed that task interruption can be often avoided by using appropriate functional architectures and knowledge engineering principles. Situations for which task interruption is indispensable, a preliminary architecture based on priority hierarchies is described.

The Emergence of Agent-Based Technology as an Architectural Component of Serious Games

NASA Technical Reports Server (NTRS)

Phillips, Mark; Scolaro, Jackie; Scolaro, Daniel

2010-01-01

The evolution of games as an alternative to traditional simulations in the military context has been gathering momentum over the past five years, even though the exploration of their use in the serious sense has been ongoing since the mid-nineties. Much of the focus has been on the aesthetics of the visuals provided by the core game engine as well as the artistry provided by talented development teams to produce not only breathtaking artwork, but highly immersive game play. Consideration of game technology is now so much a part of the modeling and simulation landscape that it is becoming difficult to distinguish traditional simulation solutions from game-based approaches. But games have yet to provide the much needed interactive free play that has been the domain of semi-autonomous forces (SAF). The component-based middleware architecture that game engines provide promises a great deal in terms of options for the integration of agent solutions to support the development of non-player characters that engage the human player without the deterministic nature of scripted behaviors. However, there are a number of hard-learned lessons on the modeling and simulation side of the equation that game developers have yet to learn, such as: correlation of heterogeneous systems, scalability of both terrain and numbers of non-player entities, and the bi-directional nature of simulation to game interaction provided by Distributed Interactive Simulation (DIS) and High Level Architecture (HLA).

Botulinum neurotoxin homologs in non-Clostridium species.

PubMed

Mansfield, Michael J; Adams, Jeremy B; Doxey, Andrew C

2015-01-30

Clostridial neurotoxins (CNTs) are the deadliest toxins known and the causative agents of botulism and tetanus. Despite their structural and functional complexity, no CNT homologs are currently known outside Clostridium. Here, we report the first homologs of Clostridium CNTs within the genome of the rice fermentation organism Weissella oryzae SG25. One gene in W. oryzae S25 encodes a protein with a four-domain architecture and HExxH protease motif common to botulinum neurotoxins (BoNTs). An adjacent gene with partial similarity to CNTs is also present, and both genes seem to have been laterally transferred into the W. oryzae genome from an unknown source. Identification of mobile, CNT-related genes outside of Clostridium has implications for our understanding of the evolution of this important toxin family. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains

PubMed Central

Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L

2006-01-01

Background Ubiquitin (Ub)-mediated signaling is one of the hallmarks of all eukaryotes. Prokaryotic homologs of Ub (ThiS and MoaD) and E1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. However, there is no evidence for entire protein modification systems with Ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. Hence, the evolutionary assembly of the eukaryotic Ub-signaling apparatus remains unclear. Results We systematically analyzed prokaryotic Ub-related β-grasp fold proteins using sensitive sequence profile searches and structural analysis. Consequently, we identified novel Ub-related proteins beyond the characterized ThiS, MoaD, TGS, and YukD domains. To understand their functional associations, we sought and recovered several conserved gene neighborhoods and domain architectures. These included novel associations involving diverse sulfur metabolism proteins, siderophore biosynthesis and the gene encoding the transfer mRNA binding protein SmpB, as well as domain fusions between Ub-like domains and PIN-domain related RNAses. Most strikingly, we found conserved gene neighborhoods in phylogenetically diverse bacteria combining genes for JAB domains (the primary de-ubiquitinating isopeptidases of the proteasomal complex), along with E1-like adenylating enzymes and different Ub-related proteins. Further sequence analysis of other conserved genes in these neighborhoods revealed several Ub-conjugating enzyme/E2-ligase related proteins. Genes for an Ub-like protein and a JAB domain peptidase were also found in the tail assembly gene cluster of certain caudate bacteriophages. Conclusion These observations imply that members of the Ub family had already formed strong functional associations with E1-like proteins, UBC/E2-related proteins, and JAB peptidases in the bacteria. Several of these Ub-like proteins and the associated protein families are likely to function together in signaling systems just as in eukaryotes. PMID:16859499

Architecture for the Interdisciplinary Earth Data Alliance

NASA Astrophysics Data System (ADS)

Richard, S. M.

2016-12-01

The Interdisciplinary Earth Data Alliance (IEDA) is leading an EarthCube (EC) Integrative Activity to develop a governance structure and technology framework that enables partner data systems to share technology, infrastructure, and practice for documenting, curating, and accessing heterogeneous geoscience data. The IEDA data facility provides capabilities in an extensible framework that enables domain-specific requirements for each partner system in the Alliance to be integrated into standardized cross-domain workflows. The shared technology infrastructure includes a data submission hub, a domain-agnostic file-based repository, an integrated Alliance catalog and a Data Browser for data discovery across all partner holdings, as well as services for registering identifiers for datasets (DOI) and samples (IGSN). The submission hub will be a platform that facilitates acquisition of cross-domain resource documentation and channels users into domain and resource-specific workflows tailored for each partner community. We are exploring an event-based message bus architecture with a standardized plug-in interface for adding capabilities. This architecture builds on the EC CINERGI metadata pipeline as well as the message-based architecture of the SEAD project. Plug-in components for file introspection to match entities to a data type registry (extending EC Digital Crust and Research Data Alliance work), extract standardized keywords (using CINERGI components), location, cruise, personnel and other metadata linkage information (building on GeoLink and existing IEDA partner components). The submission hub will feed submissions to appropriate partner repositories and service endpoints targeted by domain and resource type for distribution. The Alliance governance will adopt patterns (vocabularies, operations, resource types) for self-describing data services using standard HTTP protocol for simplified data access (building on EC GeoWS and other `RESTful' approaches). Exposure of resource descriptions (datasets and service distributions) for harvesting by commercial search engines as well as geoscience-data focused crawlers (like EC B-Cube crawler) will increase discoverability of IEDA resources with minimal effort by curators.

Semantic Interoperability Almost Without Using The Same Vocabulary: Is It Possible?

NASA Astrophysics Data System (ADS)

Krisnadhi, A. A.

2016-12-01

Semantic interoperability, which is a key requirement in realizing cross-repository data integration, is often understood as using the same ontology or vocabulary. Consequently, within a particular domain, one can easily assume that there has to be one unifying domain ontology covering as many vocabulary terms in the domain as possible in order to realize any form of data integration across multiple data sources. Furthermore, the desire to provide very precise definition of those many terms led to the development of huge, foundational and domain ontologies that are comprehensive, but too complicated, restrictive, monolithic, and difficult to use and reuse, which cause common data providers to avoid using them. This problem is especially true in a domain as diverse as geosciences as it is virtually impossible to reach an agreement to the semantics of many terms (e.g., there are hundreds of definitions of forest used throughout the world). To overcome this challenge, modular ontology architecture has emerged in recent years, fueled among others, by advances in the ontology design pattern research. Each ontology pattern models only one key notion. It can act as a small module of a larger ontology. Such a module is developed in such a way that it is largely independent of how other notions in the same domain are modeled. This leads to an increased reusability. Furthermore, an ontology formed out of such modules would have an improved understandability over large, monolithic ontologies. Semantic interoperability in the aforementioned architecture is not achieved by enforcing the use of the same vocabulary, but rather, promoting alignment to the same ontology patterns. In this work, we elaborate how this architecture realizes the above idea. In particular, we describe how multiple data sources with differing perspectives and vocabularies can interoperate through this architecture. Building the solution upon semantic technologies such as Linked Data and the Web Ontology Language (OWL), we demonstrate how a data integration solution based on this idea can be realized over different data repositories.

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

Small Hydropower Plants in Pomerania: The Example of Evolution of Modern Industrial Brick Architecture

NASA Astrophysics Data System (ADS)

Macikowski, Bartosz

2017-10-01

Modernism is usually recognized and associated with the aesthetics of the International Style, represented by white-plastered, horizontally articulated architecture with skimpy decoration, where function was the main imperative of the architects’ ambitions. In Northern Europe though, Modernism also revealed its brick face, representing different manners, styles, and appearances. The brick face of Modernism reflected, in fact, the complexity of the modern change, breaking ties with the historic styles of the 19th century and being still present in the beginning of the 20th century. Regardless of the cosmopolitan character of the International Style and its unified aesthetics, architects tried to find and keep shades of individuality. This was especially visible in the references to either regional or even local traditions. This diversity of modernistic architecture is intensified by its different functions. The language of industrial architecture derives its forms directly from its nature of pure functional idiom, devoted to economic and functional optimization. The industrial form usually seems subordinate to the technical nature of objects. But regardless of that, in the 19th century and the first half of the 20th century we can observe an interesting evolution of styles and tendencies in industrial architecture, even in such a narrow and specific field like the architecture of small hydropower plants. The purpose of the research was to recognize the evolution of the architectural form of hydropower plants as a developing branch of industry in the first half of the 20th century. In Pomerania, during this period, a dynamic growth of investments took place, which concerned the use of the Pomeranian rivers’ potential to produce electric energy. At the end of the 19th century, electricity had a strong meaning as a symbol of a radical civilizational change, which influenced also the aesthetic aspects of architecture. This could suggest that the architecture of hydropower plants should be one of the carriers of the new progressive architecture. In fact, in the case of the Pomeranian hydropower plants, their technical solutions were among the most advanced and progressive solutions of those times, sometimes even experimental, adjusted to the diversity of local geographical conditions. Regardless of that, the architecture of the Pomeranian power plants was rather reflecting the diversity and dynamism of the aesthetic discourse of the time (sometimes even representing and adopting traditional or historical forms). The cascade of the power plants Podgaje (1928), Jastrowie (1930), and Ptusza (1930), all part of the same investment on the river Gwda, can be the example of the absorption and development of new aesthetic trends within the same stream of clinker architecture. The paper describes selected examples of Pomeranian power plants as a comparative study which could illustrate the evolution of the brick architecture of the beginning of the 20th century.

Traffic Simulations on Parallel Computers Using Domain Decomposition Techniques

DOT National Transportation Integrated Search

1995-01-01

Large scale simulations of Intelligent Transportation Systems (ITS) can only be acheived by using the computing resources offered by parallel computing architectures. Domain decomposition techniques are proposed which allow the performance of traffic...

Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice1[W

PubMed Central

Wu, Xinru; Tang, Ding; Li, Ming; Wang, Kejian; Cheng, Zhukuan

2013-01-01

Tiller angle and leaf angle are two important components of rice (Oryza sativa) plant architecture that play a crucial role in determining grain yield. Here, we report the cloning and characterization of the Loose Plant Architecture1 (LPA1) gene in rice, the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana). LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. LPA1 was also found to affect shoot gravitropism. Expression pattern analysis suggested that LPA1 influences plant architecture by affecting the gravitropism of leaf sheath pulvinus and lamina joint. However, LPA1 only influences gravity perception or signal transduction in coleoptile gravitropism by regulating the sedimentation rate of amyloplasts, distinct from the actions of LAZY1. LPA1 encodes a plant-specific INDETERMINATE DOMAIN protein and defines a novel subfamily of 28 INDETERMINATE DOMAIN proteins with several unique conserved features. LPA1 is localized in the nucleus and functions as an active transcriptional repressor, an activity mainly conferred by a conserved ethylene response factor-associated amphiphilic repression-like motif. Further analysis suggests that LPA1 participates in a complicated transcriptional and protein interaction network and has evolved novel functions distinct from SGR5. This study not only facilitates the understanding of gravitropism mechanisms but also generates a useful genetic material for rice breeding. PMID:23124325

Loose Plant Architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice.

PubMed

Wu, Xinru; Tang, Ding; Li, Ming; Wang, Kejian; Cheng, Zhukuan

2013-01-01

Tiller angle and leaf angle are two important components of rice (Oryza sativa) plant architecture that play a crucial role in determining grain yield. Here, we report the cloning and characterization of the Loose Plant Architecture1 (LPA1) gene in rice, the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana). LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. LPA1 was also found to affect shoot gravitropism. Expression pattern analysis suggested that LPA1 influences plant architecture by affecting the gravitropism of leaf sheath pulvinus and lamina joint. However, LPA1 only influences gravity perception or signal transduction in coleoptile gravitropism by regulating the sedimentation rate of amyloplasts, distinct from the actions of LAZY1. LPA1 encodes a plant-specific INDETERMINATE DOMAIN protein and defines a novel subfamily of 28 INDETERMINATE DOMAIN proteins with several unique conserved features. LPA1 is localized in the nucleus and functions as an active transcriptional repressor, an activity mainly conferred by a conserved ethylene response factor-associated amphiphilic repression-like motif. Further analysis suggests that LPA1 participates in a complicated transcriptional and protein interaction network and has evolved novel functions distinct from SGR5. This study not only facilitates the understanding of gravitropism mechanisms but also generates a useful genetic material for rice breeding.

The box C/D sRNP dimeric architecture is conserved across domain Archaea

PubMed Central

Bower-Phipps, Kathleen R.; Taylor, David W.; Wang, Hong-Wei; Baserga, Susan J.

2012-01-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2′-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species—Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus—indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain. PMID:22753779

The box C/D sRNP dimeric architecture is conserved across domain Archaea.

PubMed

Bower-Phipps, Kathleen R; Taylor, David W; Wang, Hong-Wei; Baserga, Susan J

2012-08-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein

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

Yuan Ping; Leser, George P.; Demeler, Borries

2008-09-01

The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high {alpha}-helical content. Together, the data indicate that the globular NA domains formmore » weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.« less

Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication.

PubMed

Zhou, Yong; Zhu, Jinyan; Li, Zhengyi; Yi, Chuandeng; Liu, Jun; Zhang, Honggen; Tang, Shuzhu; Gu, Minghong; Liang, Guohua

2009-09-01

Rice plant architecture is an important agronomic trait and a major determinant in high productivity. Panicle erectness is the preferred plant architecture in japonica rice, but the molecular mechanism underlying domestication of the erect panicle remains elusive. Here we report the map-based cloning of a major quantitative trait locus, qPE9-1, which plays an integral role in regulation of rice plant architecture including panicle erectness. The R6547 qPE9-1 gene encodes a 426-amino-acid protein, homologous to the keratin-associated protein 5-4 family. The gene is composed of three Von Willebrand factor type C domains, one transmembrane domain, and one 4-disulfide-core domain. Phenotypic comparisons of a set of near-isogenic lines and transgenic lines reveal that the functional allele (qPE9-1) results in drooping panicles, and the loss-of-function mutation (qpe9-1) leads to more erect panicles. In addition, the qPE9-1 locus regulates panicle and grain length, grain weight, and consequently grain yield. We propose that the panicle erectness trait resulted from a natural random loss-of-function mutation for the qPE9-1 gene and has subsequently been the target of artificial selection during japonica rice breeding.

Exploring the evolution of protein function in Archaea.

PubMed

Goncearenco, Alexander; Berezovsky, Igor N

2012-05-30

Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.

Ectopic Expression of GsSRK in Medicago sativa Reveals Its Involvement in Plant Architecture and Salt Stress Responses.

PubMed

Sun, Mingzhe; Qian, Xue; Chen, Chao; Cheng, Shufei; Jia, Bowei; Zhu, Yanming; Sun, Xiaoli

2018-01-01

Receptor-like kinases (RLK) play fundamental roles in plant growth and stress responses. Compared with other RLKs, little information is provided concerning the S-locus LecRLK subfamily, which is characterized by an extracellular G-type lectin domain and an S-locus-glycop domain. Until now, the function of the G-type lectin domain is still unknown. In a previous research, we identified a Glycine soja S-locus LecRLK gene GsSRK , which conferred increased salt stress tolerance in transgenic Arabidopsis . In this study, to investigate the role of the G-type lectin domain and to breed transgenic alfalfa with superior salt stress tolerance, we transformed the full-length GsSRK ( GsSRK-f ) and a truncated version of GsSRK ( GsSRK-t ) deleting the G-type lectin domain into alfalfa. Our results showed that overexpression of GsSRK-t , but not GsSRK-f , resulted in changes of plant architecture, as evidenced by more branches but shorter shoots of GsSRK-t transgenic alfalfa, indicating a potential role of the extracellular G-type lectin domain in regulating plant architecture. Furthermore, we also found that transgenic alfalfa overexpressing either GsSRK-f or GsSRK-t showed increased salt stress tolerance, and GsSRK-t transgenic alfalfa displayed better growth (more branches and higher fresh weight) than GsSRK-f lines under salt stress. In addition, our results suggested that both GsSRK-f and GsSRK-t were involved in ion homeostasis, ROS scavenging, and osmotic regulation. Under salt stress, the Na + content in the transgenic lines was significantly lower, while the K + content was slightly higher than that in WT. Moreover, the transgenic lines displayed reduced ion leakage and MDA content, but increased SOD activity and proline content than WT. Notably, no obvious difference in these physiological indices was observed between GsSRK-f and GsSRK-t transgenic lines, implying that deletion of the GsSRK G-type lectin domain does not affect its physiological function in salt stress responses. In conclusion, results in this research reveal the dual role of GsSRK in regulating both plant architecture and salt stress responses.

Technology for Space Station Evolution: the Data Management System

NASA Technical Reports Server (NTRS)

Abbott, L.

1990-01-01

Viewgraphs on the data management system (DMS) for the space station evolution are presented. Topics covered include DMS architecture and implementation approach; and an overview of the runtime object database.

A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

PubMed

Nokwe, Cardine N; Zacharias, Martin; Yagi, Hisashi; Hora, Manuel; Reif, Bernd; Goto, Yuji; Buchner, Johannes

2014-09-26

Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the VL domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol(-1), which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in VL domains of the κ family and not in VLλ or in VH domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Understanding cellular architecture in cancer cells

NASA Astrophysics Data System (ADS)

Bianco, Simone; Tang, Chao

2011-03-01

Understanding the development of cancer is an important goal for today's science. The morphology of cellular organelles, such as the nucleus, the nucleoli and the mitochondria, which is referred to as cellular architecture or cytoarchitecture, is an important indicator of the state of the cell. In particular, there are striking difference between the cellular architecture of a healthy cell versus a cancer cell. In this work we present a dynamical model for the evolution of organelles morphology in cancer cells. Using a dynamical systems approach, we describe the evolution of a cell on its way to cancer as a trajectory in a multidimensional morphology state. The results provided by this work may increase our insight on the mechanism of tumorigenesis and help build new therapeutic strategies.

De novo identification of highly diverged protein repeats by probabilistic consistency.

PubMed

Biegert, A; Söding, J

2008-03-15

An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments. We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance. Server: http://toolkit.tuebingen.mpg.de/hhrepid; Executables: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHrepID

Experimental demonstration of bandwidth on demand (BoD) provisioning based on time scheduling in software-defined multi-domain optical networks

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Li, Yajie; Wang, Xinbo; Chen, Bowen; Zhang, Jie

2016-09-01

A hierarchical software-defined networking (SDN) control architecture is designed for multi-domain optical networks with the Open Daylight (ODL) controller. The OpenFlow-based Control Virtual Network Interface (CVNI) protocol is deployed between the network orchestrator and the domain controllers. Then, a dynamic bandwidth on demand (BoD) provisioning solution is proposed based on time scheduling in software-defined multi-domain optical networks (SD-MDON). Shared Risk Link Groups (SRLG)-disjoint routing schemes are adopted to separate each tenant for reliability. The SD-MDON testbed is built based on the proposed hierarchical control architecture. Then the proposed time scheduling-based BoD (Ts-BoD) solution is experimentally demonstrated on the testbed. The performance of the Ts-BoD solution is evaluated with respect to blocking probability, resource utilization, and lightpath setup latency.

Eigensolution of finite element problems in a completely connected parallel architecture

NASA Technical Reports Server (NTRS)

Akl, F.; Morel, M.

1989-01-01

A parallel algorithm is presented for the solution of the generalized eigenproblem in linear elastic finite element analysis. The algorithm is based on a completely connected parallel architecture in which each processor is allowed to communicate with all other processors. The algorithm is successfully implemented on a tightly coupled MIMD parallel processor. A finite element model is divided into m domains each of which is assumed to process n elements. Each domain is then assigned to a processor or to a logical processor (task) if the number of domains exceeds the number of physical processors. The effect of the number of domains, the number of degrees-of-freedom located along the global fronts, and the dimension of the subspace on the performance of the algorithm is investigated. For a 64-element rectangular plate, speed-ups of 1.86, 3.13, 3.18, and 3.61 are achieved on two, four, six, and eight processors, respectively.

Ion Conduction in Microphase-Separated Block Copolymer Electrolytes

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

Kambe, Yu; Arges, Christopher G.; Patel, Shrayesh

2017-01-01

Microphase separation of block copolymers provides a promising route towards engineering a mechanically robust ion conducting film for electrochemical devices. The separation into two different nano-domains enables the film to simultaneously exhibit both high ion conductivity and mechanical robustness, material properties inversely related in most homopolymer and random copolymer electrolytes. To exhibit the maximum conductivity and mechanical robustness, both domains would span across macroscopic length scales enabling uninterrupted ion conduction. One way to achieve this architecture is through external alignment fields that are applied during the microphase separation process. In this review, we present the progress and challenges for aligningmore » the ionic domains in block copolymer electrolytes. A survey of alignment and characterization is followed by a discussion of how the nanoscale architecture affects the bulk conductivity and how alignment may be improved to maximize the number of participating conduction domains.« less

Methods and apparatus for constructing and implementing a universal extension module for processing objects in a database

NASA Technical Reports Server (NTRS)

Li, Chung-Sheng (Inventor); Smith, John R. (Inventor); Chang, Yuan-Chi (Inventor); Jhingran, Anant D. (Inventor); Padmanabhan, Sriram K. (Inventor); Hsiao, Hui-I (Inventor); Choy, David Mun-Hien (Inventor); Lin, Jy-Jine James (Inventor); Fuh, Gene Y. C. (Inventor); Williams, Robin (Inventor)

2004-01-01

Methods and apparatus for providing a multi-tier object-relational database architecture are disclosed. In one illustrative embodiment of the present invention, a multi-tier database architecture comprises an object-relational database engine as a top tier, one or more domain-specific extension modules as a bottom tier, and one or more universal extension modules as a middle tier. The individual extension modules of the bottom tier operationally connect with the one or more universal extension modules which, themselves, operationally connect with the database engine. The domain-specific extension modules preferably provide such functions as search, index, and retrieval services of images, video, audio, time series, web pages, text, XML, spatial data, etc. The domain-specific extension modules may include one or more IBM DB2 extenders, Oracle data cartridges and/or Informix datablades, although other domain-specific extension modules may be used.

Model-Unified Planning and Execution for Distributed Autonomous System Control

NASA Technical Reports Server (NTRS)

Aschwanden, Pascal; Baskaran, Vijay; Bernardini, Sara; Fry, Chuck; Moreno, Maria; Muscettola, Nicola; Plaunt, Chris; Rijsman, David; Tompkins, Paul

2006-01-01

The Intelligent Distributed Execution Architecture (IDEA) is a real-time architecture that exploits artificial intelligence planning as the core reasoning engine for interacting autonomous agents. Rather than enforcing separate deliberation and execution layers, IDEA unifies them under a single planning technology. Deliberative and reactive planners reason about and act according to a single representation of the past, present and future domain state. The domain state behaves the rules dictated by a declarative model of the subsystem to be controlled, internal processes of the IDEA controller, and interactions with other agents. We present IDEA concepts - modeling, the IDEA core architecture, the unification of deliberation and reaction under planning - and illustrate its use in a simple example. Finally, we present several real-world applications of IDEA, and compare IDEA to other high-level control approaches.

On-Board Software Reference Architecture for Payloads

NASA Astrophysics Data System (ADS)

Bos, Victor; Rugina, Ana; Trcka, Adam

2016-08-01

The goal of the On-board Software Reference Architecture for Payloads (OSRA-P) is to identify an architecture for payload software to harmonize the payload domain, to enable more reuse of common/generic payload software across different payloads and missions and to ease the integration of the payloads with the platform.To investigate the payload domain, recent and current payload instruments of European space missions have been analyzed. This led to a Payload Catalogue describing 12 payload instruments as well as a Capability Matrix listing specific characteristics of each payload. In addition, a functional decomposition of payload software was prepared which contains functionalities typically found in payload systems. The definition of OSRA-P was evaluated by case studies and a dedicated OSRA-P workshop to gather feedback from the payload community.

Observation on the transformation domains of super-elastic NiTi shape memory alloy and their evolutions during cyclic loading

NASA Astrophysics Data System (ADS)

Xie, Xi; Kan, Qianhua; Kang, Guozheng; Li, Jian; Qiu, Bo; Yu, Chao

2016-04-01

The strain field of a super-elastic NiTi shape memory alloy (SMA) and its variation during uniaxial cyclic tension-unloading were observed by a non-contact digital image correlation method, and then the transformation domains and their evolutions were indirectly investigated and discussed. It is seen that the super-elastic NiTi (SMA) exhibits a remarkable localized deformation and the transformation domains evolve periodically with the repeated cyclic tension-unloading within the first several cycles. However, the evolutions of transformation domains at the stage of stable cyclic transformation depend on applied peak stress: when the peak stress is low, no obvious transformation band is observed and the strain field is nearly uniform; when the peak stress is large enough, obvious transformation bands occur due to the residual martensite caused by the prevention of enriched dislocations to the reverse transformation from induced martensite to austenite. Temperature variations measured by an infrared thermal imaging method further verifies the formation and evolution of transformation domains.

Evolution and genome architecture in fungal plant pathogens.

PubMed

Möller, Mareike; Stukenbrock, Eva H

2017-12-01

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.

PubMed

Perez-Rueda, Ernesto; Hernandez-Guerrero, Rafael; Martinez-Nuñez, Mario Alberto; Armenta-Medina, Dagoberto; Sanchez, Israel; Ibarra, J Antonio

2018-01-01

Gene regulation at the transcriptional level is a central process in all organisms, and DNA-binding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: the DNA-binding domain (DBD) and an extra domain, which in this work we have named "companion domain" (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: i) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as "promiscuous" families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity

PubMed Central

Jackson, Daniel J.; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M.; Fleck, Claudia

2017-01-01

Abstract Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent “GS” domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. PMID:28961798

Caenorhabditis elegans Evolves a New Architecture for the Multi-aminoacyl-tRNA Synthetase Complex*

PubMed Central

Havrylenko, Svitlana; Legouis, Renaud; Negrutskii, Boris; Mirande, Marc

2011-01-01

MARS is an evolutionary conserved supramolecular assembly of aminoacyl-tRNA synthetases found in eukaryotes. This complex was thought to be ubiquitous in the deuterostome and protostome clades of bilaterians because similar complexes were isolated from arthropods and vertebrates. However, several features of the component enzymes suggested that in the nematode Caenorhabditis elegans, a species grouped with arthropods in modern phylogeny, this complex might not exist, or should display a significantly different structural organization. C. elegans was also taken as a model system to study in a multicellular organism amenable to experimental approaches, the reason for existence of these supramolecular entities. Here, using a proteomic approach, we have characterized the components of MARS in C. elegans. We show that this organism evolved a specific structural organization of this complex, which contains several bona fide components of the MARS complexes known so far, but also displays significant variations. These data highlight molecular evolution events that took place after radiation of bilaterians. Remarkably, it shows that expansion of MARS assembly in metazoans is not linear, but is the result of additions but also of subtractions along evolution. We then undertook an experimental approach, using inactivation of the endogenous copy of methionyl-tRNA synthetase by RNAi and expression of transgenic variants, to understand the role in complex assembly and the in vivo functionality, of the eukaryotic-specific domains appended to aminoacyl-tRNA synthetases. We show that rescue of the worms and assembly of transgenic variants into MARS rest on the presence of these appended domains. PMID:21685384

Caenorhabditis elegans evolves a new architecture for the multi-aminoacyl-tRNA synthetase complex.

PubMed

Havrylenko, Svitlana; Legouis, Renaud; Negrutskii, Boris; Mirande, Marc

2011-08-12

MARS is an evolutionary conserved supramolecular assembly of aminoacyl-tRNA synthetases found in eukaryotes. This complex was thought to be ubiquitous in the deuterostome and protostome clades of bilaterians because similar complexes were isolated from arthropods and vertebrates. However, several features of the component enzymes suggested that in the nematode Caenorhabditis elegans, a species grouped with arthropods in modern phylogeny, this complex might not exist, or should display a significantly different structural organization. C. elegans was also taken as a model system to study in a multicellular organism amenable to experimental approaches, the reason for existence of these supramolecular entities. Here, using a proteomic approach, we have characterized the components of MARS in C. elegans. We show that this organism evolved a specific structural organization of this complex, which contains several bona fide components of the MARS complexes known so far, but also displays significant variations. These data highlight molecular evolution events that took place after radiation of bilaterians. Remarkably, it shows that expansion of MARS assembly in metazoans is not linear, but is the result of additions but also of subtractions along evolution. We then undertook an experimental approach, using inactivation of the endogenous copy of methionyl-tRNA synthetase by RNAi and expression of transgenic variants, to understand the role in complex assembly and the in vivo functionality, of the eukaryotic-specific domains appended to aminoacyl-tRNA synthetases. We show that rescue of the worms and assembly of transgenic variants into MARS rest on the presence of these appended domains.

Birth of an oceanic spreading center at a magma-poor rift system.

PubMed

Gillard, Morgane; Sauter, Daniel; Tugend, Julie; Tomasi, Simon; Epin, Marie-Eva; Manatschal, Gianreto

2017-11-08

Oceanic crust is continuously created at mid-oceanic ridges and seafloor spreading represents one of the main processes of plate tectonics. However, if oceanic crust architecture, composition and formation at present-day oceanic ridges are largely described, the processes governing the birth of a spreading center remain enigmatic. Understanding the transition between inherited continental and new oceanic domains is a prerequisite to constrain one of the last major unsolved problems of plate tectonics, namely the formation of a stable divergent plate boundary. In this paper, we present newly released high-resolution seismic reflection profiles that image the complete transition from unambiguous continental to oceanic crusts in the Gulf of Guinea. Based on these high-resolution seismic sections we show that onset of oceanic seafloor spreading is associated with the formation of a hybrid crust in which thinned continental crust and/or exhumed mantle is sandwiched between magmatic intrusive and extrusive bodies. This crust results from a polyphase evolution showing a gradual transition from tectonic-driven to magmatic-driven processes. The results presented in this paper provide a characterization of the domain in which lithospheric breakup occurs and enable to define the processes controlling formation of a new plate boundary.

Architecture and Assembly of HIV Integrase Multimers in the Absence of DNA Substrates*

PubMed Central

Bojja, Ravi Shankar; Andrake, Mark D.; Merkel, George; Weigand, Steven; Dunbrack, Roland L.; Skalka, Anna Marie

2013-01-01

We have applied small angle x-ray scattering and protein cross-linking coupled with mass spectrometry to determine the architectures of full-length HIV integrase (IN) dimers in solution. By blocking interactions that stabilize either a core-core domain interface or N-terminal domain intermolecular contacts, we show that full-length HIV IN can form two dimer types. One is an expected dimer, characterized by interactions between two catalytic core domains. The other dimer is stabilized by interactions of the N-terminal domain of one monomer with the C-terminal domain and catalytic core domain of the second monomer as well as direct interactions between the two C-terminal domains. This organization is similar to the “reaching dimer” previously described for wild type ASV apoIN and resembles the inner, substrate binding dimer in the crystal structure of the PFV intasome. Results from our small angle x-ray scattering and modeling studies indicate that in the absence of its DNA substrate, the HIV IN tetramer assembles as two stacked reaching dimers that are stabilized by core-core interactions. These models of full-length HIV IN provide new insight into multimer assembly and suggest additional approaches for enzyme inhibition. PMID:23322775

Integrated Modular Avionics for Spacecraft: Earth Observation Use Case Demonstrator

NASA Astrophysics Data System (ADS)

Deredempt, Marie-Helene; Rossignol, Alain; Hyounet, Philippe

2013-08-01

Integrated Modular Avionics (IMA) for Space, as European Space Agency initiative, aimed to make applicable to space domain the time and space partitioning concepts and particularly the ARINC 653 standard [1][2]. Expected benefits of such an approach are development flexibility, capability to provide differential V&V for different criticality level functionalities and to integrate late or In-Orbit delivery. This development flexibility could improve software subcontracting, industrial organization and software reuse. Time and space partitioning technique facilitates integration of software functions as black boxes and integration of decentralized function such as star tracker in On Board Computer to save mass and power by limiting electronics resources. In aeronautical domain, Integrated Modular Avionics architecture is based on a network of LRU (Line Replaceable Unit) interconnected by AFDX (Avionic Full DupleX). Time and Space partitioning concept is applicable to LRU and provides independent partitions which inter communicate using ARINC 653 communication ports. Using End System (LRU component) intercommunication between LRU is managed in the same way than intercommunication between partitions in LRU. In such architecture an application developed using only communication port can be integrated in an LRU or another one without impacting the global architecture. In space domain, a redundant On Board Computer controls (ground monitoring TM) and manages the platform (ground command TC) in terms of power, solar array deployment, attitude, orbit, thermal, maintenance, failure detection and recovery isolation. In addition, Payload units and platform units such as RIU, PCDU, AOCS units (Star tracker, Reaction wheels) are considered in this architecture. Interfaces are mainly realized through MIL-STD-1553B busses and SpaceWire and this could be considered as the main constraint for IMA implementation in space domain. During the first phase of IMA SP project, ARINC653 impact was analyzed. Requirements and architecture for space domain were defined [3][4] and System Executive platforms (based on Xtratum, Pike OS, and AIR) were developed with RTEMS as Guest OS. This paper focuses on the demonstrator developed by Astrium as part of IMA SP project. This demonstrator has the objective to confirm operational software partitioning feasibility above Xtratum System Executive Platform with acceptable CPU overhead.

Learning Outcomes in Affective Domain within Contemporary Architectural Curricula

ERIC Educational Resources Information Center

Savic, Marko; Kashef, Mohamad

2013-01-01

Contemporary architectural education has shifted from the traditional focus on providing students with specific knowledge and skill sets or "inputs" to outcome based, student-centred educational approach. Within the outcome based model, students' performance is assessed against measureable objectives that relate acquired knowledge…

Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

PubMed Central

Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I.; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan; Dekker, Job; Taylor, James; Corces, Victor G.

2013-01-01

Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. PMID:23706625

SEL Ada reuse analysis and representations

NASA Technical Reports Server (NTRS)

Kester, Rush

1990-01-01

Overall, it was revealed that the pattern of Ada reuse has evolved from initial reuse of utility components into reuse of generalized application architectures. Utility components were both domain-independent utilities, such as queues and stacks, and domain-specific utilities, such as those that implement spacecraft orbit and attitude mathematical functions and physics or astronomical models. The level of reuse was significantly increased with the development of a generalized telemetry simulator architecture. The use of Ada generics significantly increased the level of verbatum reuse, which is due to the ability, using Ada generics, to parameterize the aspects of design that are configurable during reuse. A key factor in implementing generalized architectures was the ability to use generic subprogram parameters to tailor parts of the algorithm embedded within the architecture. The use of object oriented design (in which objects model real world entities) significantly improved the modularity for reuse. Encapsulating into packages the data and operations associated with common real world entities creates natural building blocks for reuse.

Harmonizing routinely collected health information for strengthening quality management in health systems: requirements and practice.

PubMed

Prodinger, Birgit; Tennant, Alan; Stucki, Gerold; Cieza, Alarcos; Üstün, Tevfik Bedirhan

2016-10-01

Our aim was to specify the requirements of an architecture to serve as the foundation for standardized reporting of health information and to provide an exemplary application of this architecture. The World Health Organization's International Classification of Functioning, Disability and Health (ICF) served as the conceptual framework. Methods to establish content comparability were the ICF Linking Rules. The Rasch measurement model, as a special case of additive conjoint measurement, which satisfies the required criteria for fundamental measurement, allowed for the development of a common metric foundation for measurement unit conversion. Secondary analysis of data from the North Yorkshire Survey was used to illustrate these methods. Patients completed three instruments and the items were linked to the ICF. The Rasch measurement model was applied, first to each scale, and then to items across scales which were linked to a common domain. Based on the linking of items to the ICF, the majority of items were grouped into two domains, Mobility and Self-care. Analysis of the individual scales and of items linked to a common domain across scales satisfied the requirements of the Rasch measurement model. The measurement unit conversion between items from the three instruments linked to the Mobility and Self-care domains, respectively, was demonstrated. The realization of an ICF-based architecture for information on patients' functioning enables harmonization of health information while allowing clinicians and researchers to continue using their existing instruments. This architecture will facilitate access to comprehensive and consistently reported health information to serve as the foundation for informed decision-making. © The Author(s) 2016.

Crystal structure, biochemical and genetic characterization of yeast and E. cuniculi TAF(II)5 N-terminal domain: implications for TFIID assembly.

PubMed

Romier, Christophe; James, Nicole; Birck, Catherine; Cavarelli, Jean; Vivarès, Christian; Collart, Martine A; Moras, Dino

2007-05-18

General transcription factor TFIID plays an essential role in transcription initiation by RNA polymerase II at numerous promoters. However, understanding of the assembly and a full structural characterization of this large 15 subunit complex is lacking. TFIID subunit TAF(II)5 has been shown to be present twice in this complex and to be critical for the function and assembly of TFIID. Especially, the TAF(II)5 N-terminal domain is required for its incorporation within TFIID and immuno-labelling experiments carried out by electron microscopy at low resolution have suggested that this domain might homodimerize, possibly explaining the three-lobed architecture of TFIID. However, the resolution at which the electron microscopy (EM) analyses were conducted is not sufficient to determine whether homodimerization occurs or whether a more intricate assembly implying other subunits is required. Here we report the X-ray structures of the fully evolutionary conserved C-terminal sub-domain of the TAF(II)5 N terminus, from yeast and the mammalian parasite Encephalitozoon cuniculi. This sub-domain displays a novel fold with specific surfaces having conserved physico-chemical properties that can form protein-protein interactions. Although a crystallographic dimer implying one of these surfaces is present in one of the crystal forms, several biochemical analyses show that this sub-domain is monomeric in solution, even at various salt conditions and in presence of different divalent cations. Consequently, the N-terminal sub-domain of the TAF(II)5 N terminus, which is homologous to a dimerization motif but has not been fully conserved during evolution, was studied by analytical ultracentrifugation and yeast genetics. Our results show that this sub-domain dimerizes at very high concentration but is neither required for yeast viability, nor for incorporation of two TAF(II)5 molecules within TFIID and for the assembly of this complex. Altogether, although our results do not argue in favour of a homodimerization of the TAF(II)5 N-terminal domain, our structural analyses suggest a role for this domain in assembly of TFIID and its related complexes SAGA, STAGA, TFTC and PCAF.

Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains.

PubMed

Pazos, F; Heredia, P; Valencia, A; de las Rivas, J

2001-12-01

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO. Copyright 2001 Wiley-Liss, Inc.

Data Strategies to Support Automated Multi-Sensor Data Fusion in a Service Oriented Architecture

DTIC Science & Technology

2008-06-01

and employ vast quantities of content. This dissertation provides two software architectural patterns and an auto-fusion process that guide the...UDDI), Simple Order Access Protocol (SOAP), Java, Maritime Domain Awareness (MDA), Business Process Execution Language for Web Service (BPEL4WS) 16...content. This dissertation provides two software architectural patterns and an auto-fusion process that guide the development of a distributed

The Combat Cloud: Enabling Multi-Domain Command and Control Across the Range of Military Operations

DTIC Science & Technology

2017-03-01

and joint by their very nature.3 The Combat Cloud architecture will enable MDC2 by increasing the interoperability of existing networks...order to provide operating platforms with a robust architecture that communicates with relevant players, operates at reduced levels of connectivity...responsibility or aircraft platform, and a Combat Cloud architecture helps focus thought toward achieving efficient MDC2 and effects rather than

Tectonic evolution of the Salton Sea inferred from seismic reflection data

USGS Publications Warehouse

Brothers, D.S.; Driscoll, N.W.; Kent, G.M.; Harding, A.J.; Babcock, J.M.; Baskin, R.L.

2009-01-01

Oblique extension across strike-slip faults causes subsidence and leads to the formation of pull-apart basins such as the Salton Sea in southern California. The formation of these basins has generally been studied using laboratory experiments or numerical models. Here we combine seismic reflection data and geological observations from the Salton Sea to understand the evolution of this nascent pull-apart basin. Our data reveal the presence of a northeast-trending hinge zone that separates the sea into northern and southern sub-basins. Differential subsidence (10 mm yr 1) in the southern sub-basin suggests the existence of northwest-dipping basin-bounding faults near the southern shoreline, which may control the spatial distribution of young volcanism. Rotated and truncated strata north of the hinge zone suggest that the onset of extension associated with this pull-apart basin began after 0.5 million years ago. We suggest that slip is partitioned spatially and temporally into vertical and horizontal domains in the Salton Sea. In contrast to previous models based on historical seismicity patterns, the rapid subsidence and fault architecture that we document in the southern part of the sea are consistent with experimental models for pull-apart basins. ?? 2009 Macmillan Publishers Limited.

Identification of a gene encoding a membrane-anchored toll-like receptor 5 (TLR5M) in Oplegnathus fasciatus that responds to flagellin challenge and activates NF-κB.

PubMed

Umasuthan, Navaneethaiyer; Bathige, S D N K; Thulasitha, William Shanthakumar; Jayasooriya, R G P T; Shin, Younhee; Lee, Jehee

2017-03-01

Toll-like receptor 5 (TLR5) recognizes bacterial flagellin and induces the downstream signaling through the myeloid differentiation primary response gene 88 (MyD88) protein to produce proinflammatory cytokines. In this study, we describe a TLR5 membrane form (OfTLR5M) and its adaptor protein MyD88 (OfMyD88) in rock bream, Oplegnathus fasciatus. Both Oftlr5m (6.7 kb) and Ofmyd88 (3.7 kb) genes displayed a quinquepartite structure with five exons and four introns. Protein structure of OfTLR5M revealed the conventional architecture of TLRs featured by an extracellular domain with 22 leucine rich repeats (LRR), a transmembrane domain and an endodomain with TIR motif. Primary OfTLR5M sequence shared a higher homology with teleost TLR5M. The evolutional analysis confirmed that TLR5 identified in the current study is a membrane receptor and the data further suggested the co-evolution of the membrane-anchored and soluble forms of TLR5 in teleosts. Inter-lineage comparison of gene structures in vertebrates indicated that the tlr5m gene has evolved with extensive rearrangement; whereas, the myd88 gene has maintained a stable structure throughout the evolution. Inspection of 5' flanking region of these genes disclosed the presence of several transcription factor binding sites including NF-κB. Quantitative real-time PCR (qPCR) detected Oftlr5m mRNA in eleven tissues with the highest abundance in liver. In vivo flagellin administration strongly induced the transcripts of both Oftlr5m and Ofmyd88 in gills and head kidney tissues suggesting their ligand-mediated upregulation. In a luciferase assay, HEK293T cells transiently transfected with Oftlr5m and Ofmyd88 demonstrated a higher NF-κB activity than the mock control, and the luciferase activity was intensified when cells were stimulated with flagellin. Collectively, our study represents the genomic, evolutional, expressional and functional insights into a receptor and adaptor molecules of teleost origin that are involved in flagellin sensing. Copyright © 2017 Elsevier Ltd. All rights reserved.

PANDA: Protein function prediction using domain architecture and affinity propagation.

PubMed

Wang, Zheng; Zhao, Chenguang; Wang, Yiheng; Sun, Zheng; Wang, Nan

2018-02-22

We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .

Semi-automated ontology generation and evolution

NASA Astrophysics Data System (ADS)

Stirtzinger, Anthony P.; Anken, Craig S.

2009-05-01

Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural components referenced above and identify a potential technology transition path to Scott AFB's Tanker Airlift Control Center (TACC) which serves as the Air Operations Center (AOC) for the Air Mobility Command (AMC).

Working Notes from the 1992 AAAI Workshop on Automating Software Design. Theme: Domain Specific Software Design

NASA Technical Reports Server (NTRS)

Keller, Richard M. (Editor); Barstow, David; Lowry, Michael R.; Tong, Christopher H.

1992-01-01

The goal of this workshop is to identify different architectural approaches to building domain-specific software design systems and to explore issues unique to domain-specific (vs. general-purpose) software design. Some general issues that cut across the particular software design domain include: (1) knowledge representation, acquisition, and maintenance; (2) specialized software design techniques; and (3) user interaction and user interface.

Information Architecture: Notes toward a New Curriculum.

ERIC Educational Resources Information Center

Latham, Don

2002-01-01

Considers the evolution of information architectures as a field of professional education. Topics include the need for an interdisciplinary approach; balancing practical skills with theoretical concepts; and key content areas, including information organization, graphic design, computer science, user and usability studies, and communication.…

Hypertext Interchange Using ICA.

ERIC Educational Resources Information Center

Rada, Roy; And Others

1995-01-01

Discusses extended ICA (Integrated Chameleon Architecture), a public domain toolset for generating text-to-hypertext translators. A system called SGML-MUCH has been developed using E-ICA (Extended Integrated Chameleon Architecture) and is presented as a case study with converters for the hypertext systems MUCH, Guide, Hyperties, and Toolbook.…

76 FR 36861 - Special Conditions: Gulfstream Model GVI Airplane; Electronic Systems Security Isolation or...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-23

... incorporate the following novel or unusual design features: Digital systems architecture composed of several connected networks. The proposed architecture and network configuration may be used for, or interfaced with... navigation systems (aircraft control domain), 2. Airline business and administrative support (airline...

A Modular, Data Driven System: Architecture for GSFC Ground Systems: GSFC's Mission Services Evolution Center (GMSEC)

NASA Technical Reports Server (NTRS)

Cary, Everett; Smith, Danford

2004-01-01

The GSFC Mission Services Evolution Center (GMSEC) was established in 2001 to coordinate ground and flight data systems development and services at NASA's Goddard Space Flight Center (GSFC). GMSEC system architecture represents a new way to build the next generation systems to be used for a variety of missions for years to come. The old approach was to find or build the best products available and integrate them into a reusable system to meet everyone's needs. The new approach assumes that needs, products, and technology will change.

[Hotels and sanatoria: the influence of tuberculosis on mass tourism architecture].

PubMed

Morales, Eduardo Jiménez; Díaz, Ingrid Carolina Vargas

2017-01-01

The aim of this article is to verify the influence of tuberculosis on mass tourism architecture. To achieve this, the paper analyses the typological evolution of the hotel since the middle of the nineteenth century, when the first sanatoria appeared in the alpine resorts. A study that creates links between the progress in architecture and the medical therapy advances. The goal is to highlight the hybridisation process between both architectural typologies. Although this overlapping is developed until the Second World War, the influence of its mixture is still present in contemporary mass tourism architecture.

An efficient, scalable, and adaptable framework for solving generic systems of level-set PDEs

PubMed Central

Mosaliganti, Kishore R.; Gelas, Arnaud; Megason, Sean G.

2013-01-01

In the last decade, level-set methods have been actively developed for applications in image registration, segmentation, tracking, and reconstruction. However, the development of a wide variety of level-set PDEs and their numerical discretization schemes, coupled with hybrid combinations of PDE terms, stopping criteria, and reinitialization strategies, has created a software logistics problem. In the absence of an integrative design, current toolkits support only specific types of level-set implementations which restrict future algorithm development since extensions require significant code duplication and effort. In the new NIH/NLM Insight Toolkit (ITK) v4 architecture, we implemented a level-set software design that is flexible to different numerical (continuous, discrete, and sparse) and grid representations (point, mesh, and image-based). Given that a generic PDE is a summation of different terms, we used a set of linked containers to which level-set terms can be added or deleted at any point in the evolution process. This container-based approach allows the user to explore and customize terms in the level-set equation at compile-time in a flexible manner. The framework is optimized so that repeated computations of common intensity functions (e.g., gradient and Hessians) across multiple terms is eliminated. The framework further enables the evolution of multiple level-sets for multi-object segmentation and processing of large datasets. For doing so, we restrict level-set domains to subsets of the image domain and use multithreading strategies to process groups of subdomains or level-set functions. Users can also select from a variety of reinitialization policies and stopping criteria. Finally, we developed a visualization framework that shows the evolution of a level-set in real-time to help guide algorithm development and parameter optimization. We demonstrate the power of our new framework using confocal microscopy images of cells in a developing zebrafish embryo. PMID:24501592

An efficient, scalable, and adaptable framework for solving generic systems of level-set PDEs.

PubMed

Mosaliganti, Kishore R; Gelas, Arnaud; Megason, Sean G

2013-01-01

In the last decade, level-set methods have been actively developed for applications in image registration, segmentation, tracking, and reconstruction. However, the development of a wide variety of level-set PDEs and their numerical discretization schemes, coupled with hybrid combinations of PDE terms, stopping criteria, and reinitialization strategies, has created a software logistics problem. In the absence of an integrative design, current toolkits support only specific types of level-set implementations which restrict future algorithm development since extensions require significant code duplication and effort. In the new NIH/NLM Insight Toolkit (ITK) v4 architecture, we implemented a level-set software design that is flexible to different numerical (continuous, discrete, and sparse) and grid representations (point, mesh, and image-based). Given that a generic PDE is a summation of different terms, we used a set of linked containers to which level-set terms can be added or deleted at any point in the evolution process. This container-based approach allows the user to explore and customize terms in the level-set equation at compile-time in a flexible manner. The framework is optimized so that repeated computations of common intensity functions (e.g., gradient and Hessians) across multiple terms is eliminated. The framework further enables the evolution of multiple level-sets for multi-object segmentation and processing of large datasets. For doing so, we restrict level-set domains to subsets of the image domain and use multithreading strategies to process groups of subdomains or level-set functions. Users can also select from a variety of reinitialization policies and stopping criteria. Finally, we developed a visualization framework that shows the evolution of a level-set in real-time to help guide algorithm development and parameter optimization. We demonstrate the power of our new framework using confocal microscopy images of cells in a developing zebrafish embryo.

Engineering intelligent tutoring systems

NASA Technical Reports Server (NTRS)

Warren, Kimberly C.; Goodman, Bradley A.

1993-01-01

We have defined an object-oriented software architecture for Intelligent Tutoring Systems (ITS's) to facilitate the rapid development, testing, and fielding of ITS's. This software architecture partitions the functionality of the ITS into a collection of software components with well-defined interfaces and execution concept. The architecture was designed to isolate advanced technology components, partition domain dependencies, take advantage of the increased availability of commercial software packages, and reduce the risks involved in acquiring ITS's. A key component of the architecture, the Executive, is a publish and subscribe message handling component that coordinates all communication between ITS components.

Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies.

PubMed

Huber, B; Whibley, A; Poul, Y L; Navarro, N; Martin, A; Baxter, S; Shah, A; Gilles, B; Wirth, T; McMillan, W O; Joron, M

2015-05-01

Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.

Enabling the On-line Intrinsic Evolution of Analog Controllers

NASA Technical Reports Server (NTRS)

Gwaltney, David A.; Ferguson, Michael I.

2005-01-01

The intrinsic evolution of analog controllers to provide closed-loop control of the speed of a DC motor has been previously demonstrated at NASA Marshall Space Flight Center. A side effect of the evolutionary process is that during evolution there are necessarily poor configurations to be evaluated that could cause damage to the plant, This paper concerns the development and implementation of a safe Evolvable Analog Controller (EAC) architecture able to evolve controllers on-line even in the presence of these poor configurations, The EAC concept is discussed and experimental results are presented that show the feasibility of the approach This EAC architecture represents the first in a series of steps required to make deployment of an evolvable controller a reality.

Enabling the On-Line Intrinsic Evolution of Analog Controllers

NASA Technical Reports Server (NTRS)

Gwaltney, David A.; Ferguson, Michael I.

2005-01-01

The intrinsic evolution of analog controllers to provide closed-loop control of the speed of a DC motor has been previously demonstrated at NASA Marshall Space Flight Center. A side fleet of the evolutionary process is that during evolution there are necessarily poor configurations to be evaluated that could cause damage to the plant. This paper concern the development and implementation of a safe Evolvable Analog Controller (EAC) architecture able to evolve controllers on-line even in the presence of these poor configurations. The EAC concept is discussed and experimental results are presented that show the feasibility of the approach This EAC architecture represents the first in a series of steps required to make deployment of an evolvable controller a reality.

A Numerical Study of Scalable Cardiac Electro-Mechanical Solvers on HPC Architectures

PubMed Central

Colli Franzone, Piero; Pavarino, Luca F.; Scacchi, Simone

2018-01-01

We introduce and study some scalable domain decomposition preconditioners for cardiac electro-mechanical 3D simulations on parallel HPC (High Performance Computing) architectures. The electro-mechanical model of the cardiac tissue is composed of four coupled sub-models: (1) the static finite elasticity equations for the transversely isotropic deformation of the cardiac tissue; (2) the active tension model describing the dynamics of the intracellular calcium, cross-bridge binding and myofilament tension; (3) the anisotropic Bidomain model describing the evolution of the intra- and extra-cellular potentials in the deforming cardiac tissue; and (4) the ionic membrane model describing the dynamics of ionic currents, gating variables, ionic concentrations and stretch-activated channels. This strongly coupled electro-mechanical model is discretized in time with a splitting semi-implicit technique and in space with isoparametric finite elements. The resulting scalable parallel solver is based on Multilevel Additive Schwarz preconditioners for the solution of the Bidomain system and on BDDC preconditioned Newton-Krylov solvers for the non-linear finite elasticity system. The results of several 3D parallel simulations show the scalability of both linear and non-linear solvers and their application to the study of both physiological excitation-contraction cardiac dynamics and re-entrant waves in the presence of different mechano-electrical feedbacks. PMID:29674971

RAFT Nano-constructs: surfing to biological applications.

PubMed

Boturyn, Didier; Defrancq, Eric; Dolphin, Gunnar T; Garcia, Julian; Labbe, Pierre; Renaudet, Olivier; Dumy, Pascal

2008-02-01

Biologically programmed molecular recognition provides the basis of all natural systems and supplies evolution-optimized functional materials from self-assembly of a limited number of molecular building blocks. Biomolecules such as peptides, nucleic acids and carbohydrates represent a diverse supply of structural building blocks for the chemist to design and fabricate new functional nanostructured architectures. In this context, we review here the chemistry we have developed to conjugate peptides with nucleic acids, carbohydrates, and organic molecules, as well as combinations thereof using a template-assembled approach. With this methodology, we have prepared new integrated functional systems exhibiting designed properties in the field of nanovectors, biosensors as well as controlled peptide self-assembly. Thus this molecular engineering approach allows for the rational design of systems with integrated tailor-made properties and paves the way to more elaborate applications by bottom-up design in the domain of nanobiosciences.

Mirror neurons and the social nature of language: the neural exploitation hypothesis.

PubMed

Gallese, Vittorio

2008-01-01

This paper discusses the relevance of the discovery of mirror neurons in monkeys and of the mirror neuron system in humans to a neuroscientific account of primates' social cognition and its evolution. It is proposed that mirror neurons and the functional mechanism they underpin, embodied simulation, can ground within a unitary neurophysiological explanatory framework important aspects of human social cognition. In particular, the main focus is on language, here conceived according to a neurophenomenological perspective, grounding meaning on the social experience of action. A neurophysiological hypothesis--the "neural exploitation hypothesis"--is introduced to explain how key aspects of human social cognition are underpinned by brain mechanisms originally evolved for sensorimotor integration. It is proposed that these mechanisms were later on adapted as new neurofunctional architecture for thought and language, while retaining their original functions as well. By neural exploitation, social cognition and language can be linked to the experiential domain of action.

Evolving neural networks for strategic decision-making problems.

PubMed

Kohl, Nate; Miikkulainen, Risto

2009-04-01

Evolution of neural networks, or neuroevolution, has been a successful approach to many low-level control problems such as pole balancing, vehicle control, and collision warning. However, certain types of problems-such as those involving strategic decision-making-have remained difficult for neuroevolution to solve. This paper evaluates the hypothesis that such problems are difficult because they are fractured: The correct action varies discontinuously as the agent moves from state to state. A method for measuring fracture using the concept of function variation is proposed and, based on this concept, two methods for dealing with fracture are examined: neurons with local receptive fields, and refinement based on a cascaded network architecture. Experiments in several benchmark domains are performed to evaluate how different levels of fracture affect the performance of neuroevolution methods, demonstrating that these two modifications improve performance significantly. These results form a promising starting point for expanding neuroevolution to strategic tasks.

Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

NASA Astrophysics Data System (ADS)

McKinney, B. A.; Crowe, J. E., Jr.; Voss, H. U.; Crooke, P. S.; Barney, N.; Moore, J. H.

2006-02-01

We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual’s response to the smallpox vaccine.

A comparison of VLSI architectures for time and transform domain decoding of Reed-Solomon codes

NASA Technical Reports Server (NTRS)

Hsu, I. S.; Truong, T. K.; Deutsch, L. J.; Satorius, E. H.; Reed, I. S.

1988-01-01

It is well known that the Euclidean algorithm or its equivalent, continued fractions, can be used to find the error locator polynomial needed to decode a Reed-Solomon (RS) code. It is shown that this algorithm can be used for both time and transform domain decoding by replacing its initial conditions with the Forney syndromes and the erasure locator polynomial. By this means both the errata locator polynomial and the errate evaluator polynomial can be obtained with the Euclidean algorithm. With these ideas, both time and transform domain Reed-Solomon decoders for correcting errors and erasures are simplified and compared. As a consequence, the architectures of Reed-Solomon decoders for correcting both errors and erasures can be made more modular, regular, simple, and naturally suitable for VLSI implementation.

Complexity of parallel implementation of domain decomposition techniques for elliptic partial differential equations

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

Gropp, W.D.; Keyes, D.E.

1988-03-01

The authors discuss the parallel implementation of preconditioned conjugate gradient (PCG)-based domain decomposition techniques for self-adjoint elliptic partial differential equations in two dimensions on several architectures. The complexity of these methods is described on a variety of message-passing parallel computers as a function of the size of the problem, number of processors and relative communication speeds of the processors. They show that communication startups are very important, and that even the small amount of global communication in these methods can significantly reduce the performance of many message-passing architectures.

Magnetic bubbles and domain evolution in Fe/Gd multilayer nanodots

NASA Astrophysics Data System (ADS)

Wang, T. T.; Liu, W.; Dai, Z. M.; Zhao, X. T.; Zhao, X. G.; Zhang, Z. D.

2018-04-01

The formation of magnetic bubbles and the domain-evolution processes, induced by a perpendicular magnetic field in Fe/Gd multilayer films and nanodots, have been investigated. At room temperature, the stripe domains in a continuous film transform into magnetic bubbles in an external field, while bubbles form spontaneously in nanodots due to the existence of shape anisotropy. When the temperature decreases to 20 K, the enhancement of the perpendicular magnetic anisotropy of the samples results in an increase of the domain size in the continuous film and the magnetization-reversal behavior of each nanodot becomes independent, and most reversed dots do not depend on each other, indicating the magnetic characteristics of a single domain. The present research provides further understanding of the evolution of magnetic bubbles in the Fe/Gd system and suggests their promising applications in patterned recording materials.

Software synthesis using generic architectures

NASA Technical Reports Server (NTRS)

Bhansali, Sanjay

1993-01-01

A framework for synthesizing software systems based on abstracting software system designs and the design process is described. The result of such an abstraction process is a generic architecture and the process knowledge for customizing the architecture. The customization process knowledge is used to assist a designer in customizing the architecture as opposed to completely automating the design of systems. Our approach using an implemented example of a generic tracking architecture which was customized in two different domains is illustrated. How the designs produced using KASE compare to the original designs of the two systems, and current work and plans for extending KASE to other application areas are described.

The Evolution of Mission Architectures for Human Lunar Exploration

NASA Technical Reports Server (NTRS)

Everett, S. F.

1995-01-01

Defining transportation architectures for the human exploration of the Moon is a complex task due to the multitude of mission scenarios available. The mission transportation architecture recently proposed for the First Lunar Outpost (FLO) was not designed from carefully predetermined mission requirements and goals, but evolved from an initial set of requirements, which were continually modified as studies revealed that some early assumptions were not optimal. This paper focuses on the mission architectures proposed for FLO and investigates how these transportation architectures evolved. A comparison of the strengths and weaknesses of the three distinct mission architectures are discussed, namely (1) Lunar Orbit Rendezvous, (2) staging from the Cislunar Libration Point, and (3) direct to the lunar surface. In addition, several new and revolutionary architectures are discussed.

The Evolution of Academic Library Architecture: A Summary.

ERIC Educational Resources Information Center

Toombs, Kenneth E.

1992-01-01

Reviews the history of architectural developments in academic libraries. Highlights include natural lighting and the invention of the incandescent bulb; compact shelving; open versus closed stacks; modular construction methods; central air conditioning and controlled environments; interior arrangements; access to handicapped users and staff; and…

Standby Power Management Architecture for Deep-Submicron Systems

DTIC Science & Technology

2006-05-19

Driver 61 5.1 Quark PicoNode System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 5.2 Power Domain Architecture... Quark system protocol stack. . . . . . . . . . . . . . . . . . . . . . . . . . . 62 5.2 Quark system block diagram...the implementation of the chip using an industry-standard place and route design flow. Lastly some measurements from the chip are presented. 5.1 Quark

10th Annual CMMI Technology Conference and User Group Tutorial Session

DTIC Science & Technology

2010-11-15

Reuse That Pays Off: Software Product Lines BUSINESS GOALS/ APPLICATION DOMAIN ARCHITECTURE COMPONENTS and SERVICES pertain to share an are built... services PRODUCT LINES = STRATEGIC REUSE CMMI V1.3 and Architecture Oct 2010 © 2010 Carnegie Mellon University 46 91 CMMI V1.3 and Architecture © 2010... product component, the performance mustquality attribute can sometimes be partitioned for unique allocation to each product component as a derived

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.

PubMed

Leipe, Detlef D; Koonin, Eugene V; Aravind, L

2004-10-08

Using sequence profile analysis and sequence-based structure predictions, we define a previously unrecognized, widespread class of P-loop NTPases. The signal transduction ATPases with numerous domains (STAND) class includes the AP-ATPases (animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators) and NACHT NTPases (e.g. NAIP, TLP1, Het-E-1) that have been studied extensively in the context of apoptosis, pathogen response in animals and plants, and transcriptional regulation in bacteria. We show that, in addition to these well-characterized protein families, the STAND class includes several other groups of (predicted) NTPase domains from diverse signaling and transcription regulatory proteins from bacteria and eukaryotes, and three Archaea-specific families. We identified the STAND domain in several biologically well-characterized proteins that have not been suspected to have NTPase activity, including soluble adenylyl cyclases, nephrocystin 3 (implicated in polycystic kidney disease), and Rolling pebble (a regulator of muscle development); these findings are expected to facilitate elucidation of the functions of these proteins. The STAND class belongs to the additional strand, catalytic E division of P-loop NTPases together with the AAA+ ATPases, RecA/helicase-related ATPases, ABC-ATPases, and VirD4/PilT-like ATPases. The STAND proteins are distinguished from other P-loop NTPases by the presence of unique sequence motifs associated with the N-terminal helix and the core strand-4, as well as a C-terminal helical bundle that is fused to the NTPase domain. This helical module contains a signature GxP motif in the loop between the two distal helices. With the exception of the archaeal families, almost all STAND NTPases are multidomain proteins containing three or more domains. In addition to the NTPase domain, these proteins typically contain DNA-binding or protein-binding domains, superstructure-forming repeats, such as WD40 and TPR, and enzymatic domains involved in signal transduction, including adenylate cyclases and kinases. By analogy to the AAA+ ATPases, it can be predicted that STAND NTPases use the C-terminal helical bundle as a "lever" to transmit the conformational changes brought about by NTP hydrolysis to effector domains. STAND NTPases represent a novel paradigm in signal transduction, whereby adaptor, regulatory switch, scaffolding, and, in some cases, signal-generating moieties are combined into a single polypeptide. The STAND class consists of 14 distinct families, and the evolutionary history of most of these families is riddled with dramatic instances of lineage-specific expansion and apparent horizontal gene transfer. The STAND NTPases are most abundant in developmentally and organizationally complex prokaryotes and eukaryotes. Transfer of genes for STAND NTPases from bacteria to eukaryotes on several occasions might have played a significant role in the evolution of eukaryotic signaling systems.

A Research Agenda for Service-Oriented Architecture (SOA): Maintenance and Evolution of Service-Oriented Systems

DTIC Science & Technology

2010-03-01

service consumers, and infrastructure. Techniques from any iterative and incremental software development methodology followed by the organiza- tion... Service -Oriented Architecture Environment (CMU/SEI-2008-TN-008). Software Engineering Institute, Carnegie Mellon University, 2008. http://www.sei.cmu.edu...Integrating Legacy Software into a Service Oriented Architecture.” Proceedings of the 10th European Conference on Software Maintenance (CSMR 2006). Bari

Stratal stacking patterns and tectono-sedimentary evolution of hyperextended magma-poor rifted margins

NASA Astrophysics Data System (ADS)

Ribes, C.; Gillard, M.; Epin, M. E.; Ghienne, J. F.; Manatschal, G.; Karner, G. D.; Johnson, C. A.

2016-12-01

Research on the formation and evolution of deep-water rifted margins has undergone a major paradigm shift in recent years. An increasing number of studies of present-day and fossil rifted margins allow us to identify and characterize the structural architecture of the most distal parts of rifted margins, the so-called hyperextended, magma-poor rifted margins. However, at present, little is known about the depositional environments, sedimentary facies, stacking patterns, subsidence and thermal history within these domains. In this context, characterizing the stratal stacking patterns and understanding their spatial and temporal evolution is a new challenge. The major difficulty comes from the fact that the observed stratigraphic geometries and facies relationships are a result of the complex interplay between sediment supply and available accommodation, which is controlled by not only the regional generation of accommodation, but also by local tectono-magmatic processes. These parameters are poorly constrained or even sufficiently known in these tectonic settings. Indeed, the complex structural evolution of hyperextended magma-poor rifted margins, including the development of poly-phase in-sequence and out of sequence extensional detachment faults and associated mantle exhumation and magmatic activity, can generate complex accommodation patterns over a highly structured top basement. The presentation summarizes early results concerning the controlling parameters on ultra-deep water stratigraphic stacking patterns and to provide a conceptual framework. This observation-driven approach combines fieldwork from fossil Alpine Tethys margins exposed in the Alps and the analysis of seismic reflection data from present-day deep water rifted margins such as the Australian-Antarctic, East India and Iberia-Newfoundland margins.

A reference architecture for the component factory

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Caldiera, Gianluigi; Cantone, Giovanni

1992-01-01

Software reuse can be achieved through an organization that focuses on utilization of life cycle products from previous developments. The component factory is both an example of the more general concepts of experience and domain factory and an organizational unit worth being considered independently. The critical features of such an organization are flexibility and continuous improvement. In order to achieve these features we can represent the architecture of the factory at different levels of abstraction and define a reference architecture from which specific architectures can be derived by instantiation. A reference architecture is an implementation and organization independent representation of the component factory and its environment. The paper outlines this reference architecture, discusses the instantiation process, and presents some examples of specific architectures by comparing them in the framework of the reference model.

Evolution of System Architectures: Where Do We Need to Fail Next?

NASA Astrophysics Data System (ADS)

Bermudez, Luis; Alameh, Nadine; Percivall, George

2013-04-01

Innovation requires testing and failing. Thomas Edison was right when he said "I have not failed. I've just found 10,000 ways that won't work". For innovation and improvement of standards to happen, service Architectures have to be tested and tested. Within the Open Geospatial Consortium (OGC), testing of service architectures has occurred for the last 15 years. This talk will present an evolution of these service architectures and a possible future path. OGC is a global forum for the collaboration of developers and users of spatial data products and services, and for the advancement and development of international standards for geospatial interoperability. The OGC Interoperability Program is a series of hands-on, fast paced, engineering initiatives to accelerate the development and acceptance of OGC standards. Each initiative is organized in threads that provide focus under a particular theme. The first testbed, OGC Web Services phase 1, completed in 2003 had four threads: Common Architecture, Web Mapping, Sensor Web and Web Imagery Enablement. The Common Architecture was a cross-thread theme, to ensure that the Web Mapping and Sensor Web experiments built on a base common architecture. The architecture was based on the three main SOA components: Broker, Requestor and Provider. It proposed a general service model defining service interactions and dependencies; categorization of service types; registries to allow discovery and access of services; data models and encodings; and common services (WMS, WFS, WCS). For the latter, there was a clear distinction on the different services: Data Services (e.g. WMS), Application services (e.g. Coordinate transformation) and server-side client applications (e.g. image exploitation). The latest testbed, OGC Web Service phase 9, completed in 2012 had 5 threads: Aviation, Cross-Community Interoperability (CCI), Security and Services Interoperability (SSI), OWS Innovations and Compliance & Interoperability Testing & Evaluation (CITE). Compared to the first testbed, OWS-9 did not have a separate common architecture thread. Instead the emphasis was on brokering information models, securing them and making data available efficiently on mobile devices. The outcome is an architecture based on usability and non-intrusiveness while leveraging mediation of information models from different communities. This talk will use lessons learned from the evolution from OGC Testbed phase 1 to phase 9 to better understand how global and complex infrastructures evolve to support many communities including the Earth System Science Community.

Training Plan. Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-01-29

Modeling Software Reuse Technology: Feature Oriented Domain Analysis ( FODA ). SEI, Carnegie Mellon University, May 1992. 8. Component Provider’s...events to the services of the domain. 4. Feature Oriented Domain Analysis ( FODA ) [COHEN92] The FODA method produces feature models. Feature models provide...Architecture FODA Feature-Oriented Domain Analysis GOTS Government-Off-The-Shelf Pap A-49 STARS-VC-B003/001/00 29 imaty 1994 MS Master of Science NEC

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

PubMed Central

Supple, Megan A.; Hines, Heather M.; Dasmahapatra, Kanchon K.; Lewis, James J.; Nielsen, Dahlia M.; Lavoie, Christine; Ray, David A.; Salazar, Camilo; McMillan, W. Owen; Counterman, Brian A.

2013-01-01

Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations. PMID:23674305

Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex

PubMed Central

Coppola, David; White, Leonard E.; Wolf, Fred

2015-01-01

The architecture of iso-orientation domains in the primary visual cortex (V1) of placental carnivores and primates apparently follows species invariant quantitative laws. Dynamical optimization models assuming that neurons coordinate their stimulus preferences throughout cortical circuits linking millions of cells specifically predict these invariants. This might indicate that V1’s intrinsic connectome and its functional architecture adhere to a single optimization principle with high precision and robustness. To validate this hypothesis, it is critical to closely examine the quantitative predictions of alternative candidate theories. Random feedforward wiring within the retino-cortical pathway represents a conceptually appealing alternative to dynamical circuit optimization because random dimension-expanding projections are believed to generically exhibit computationally favorable properties for stimulus representations. Here, we ask whether the quantitative invariants of V1 architecture can be explained as a generic emergent property of random wiring. We generalize and examine the stochastic wiring model proposed by Ringach and coworkers, in which iso-orientation domains in the visual cortex arise through random feedforward connections between semi-regular mosaics of retinal ganglion cells (RGCs) and visual cortical neurons. We derive closed-form expressions for cortical receptive fields and domain layouts predicted by the model for perfectly hexagonal RGC mosaics. Including spatial disorder in the RGC positions considerably changes the domain layout properties as a function of disorder parameters such as position scatter and its correlations across the retina. However, independent of parameter choice, we find that the model predictions substantially deviate from the layout laws of iso-orientation domains observed experimentally. Considering random wiring with the currently most realistic model of RGC mosaic layouts, a pairwise interacting point process, the predicted layouts remain distinct from experimental observations and resemble Gaussian random fields. We conclude that V1 layout invariants are specific quantitative signatures of visual cortical optimization, which cannot be explained by generic random feedforward-wiring models. PMID:26575467

Structural style and tectonic evolution of the easternmost Gulf of Aden conjugate margins (Socotra - Southern Oman)

NASA Astrophysics Data System (ADS)

Nonn, Chloe; Leroy, Sylvie; Castilla, Raymi; de Clarens, Philippe; Lescanne, Marc

2016-04-01

Observations from distal rifted margins in present day magma-poor rifted margins led to the discovery of hyperextended crust and exhumed sub-continental mantle. This finding allowed to better figure out how thinning process are accommodate by tectonic structures, forming various crustal domains, as the deformation localized towards the future area of breakup. However, some of the current challenges are about clarifying how factors as oblique kinematic, pre-existing structures and volcanism can control the 3D geometry and crustal architecture of the passive margins? A key to better understand the rifting evolution in its entirety is to study conjugate margins. The gulf of Aden is a young oceanic basin (with a global trend about N75°E) oblique to the divergence (about 30°N), separating Arabia from Somalia of less than 800 km. Thanks to its immerged margins and its thin post-rift sediment cover, the gulf of Aden basin is a natural laboratory to investigate conjugate margins and strain localisation throughout the rift history. In this contribution, we focus our interest on offshore Socotra Island (Yemen) and its conjugate in Southeastern Oman. This area extends from Socotra-Hadbeen (SHFZ) and the eastern Gulf of Aden fault zones (EGAFZ). In the easternmost part of the gulf of Aden, we provide new insights into crustal deformation and emplacement of the new oceanic crust thanks to bathymetric, magnetic, gravimetric data and single-, multi-channel, high speed seismic reflection data collected during Encens-Sheba (2000), Encens (2006) and the more recent Marges-Aden (2012) cruises respectively. The results obtained after compilation of these data, previous geological (field works) and geophysical (receiver functions, Pn-tomography, magnetic anomalies, heat flow) studies on the focused area, allowed us to provide new structural mapping and stratigraphic correlation between onshore and offshore parts of Socotra and Oman margins. We precisely defined and map crustal domains, syn-tectonic structures and oblique accommodation zones to highlighted asymmetrical margins, characterized by strong lateral variability of crustal domains along and across strike. From external to internal domains of the margins and in between SHFZ and EGAFZ (first-order segment), this study details sharp necking domain and complex transition from hyperextended to oceanic crust characterized by: (i) hyperextended crust affected by volcanic extrusions; (ii) detachment faulting in the distal part of the margins allowing exhumation; (iii) volcanic constructions in the exhumation domain; (iv) a complex proto-oceanic crust. We highlight a significant second-order segmentation characterized by six N20°E trending transfer zones, limiting seven 25 - 60 km length segments and affecting necking domain as well as the ocean-continent transition. Based on interpretative cross-sections and detailed stratigraphic analysis, we discuss the complex temporal and spatial evolution of conjugate margins: (i) the margins segmentation and the relationship with structural inheritance (ii) the set-up of a long-offset detachment fault and the nature of the exhumed basement (iv) the origin and timing of magmatic events and the onset of proto-oceanic crust.

An AFDX Network for Spacecraft Data Handling

NASA Astrophysics Data System (ADS)

Deredempt, Marie-Helene; Kollias, Vangelis; Sun, Zhili; Canamares, Ernest; Ricco, Philippe

2014-08-01

In aeronautical domain, ARINC-664 Part 7 specification (AFDX) [4] provides the enabling technology for interfacing equipment in Integrated Modular Avionics (IMA) architectures. The complementary part of AFDX for a complete interoperability - Time and Space Partitioning (ARINC 653) concepts [1]- was already studied as part of space domain ESA roadmap (i.e. IMA4Space project)Standardized IMA based architecture is already considered in aeronautical domain as more flexible, reliable and secure. Integration and validation become simple, using a common set of tools and data base and could be done by part on different means with the same definition (hardware and software test benches, flight control or alarm test benches, simulator and flight test installation).In some area, requirements in terms of data processing are quite similar in space domain and the concept could be applicable to take benefit of the technology itself and of the panel of hardware and software solutions and tools available on the market. The Mission project (Methodology and assessment for the applicability of ARINC-664 (AFDX) in Satellite/Spacecraft on-board communicatION networks), as an FP7 initiative for bringing terrestrial SME research into the space domain started to evaluate the applicability of the standard in space domain.

Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system

DOE PAGES

Wagner, Jonathan M.; Chan, Sum; Evans, Timothy J.; ...

2016-02-27

The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB 1 and EccD 1. The periplasmic domain of EccB 1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. Themore » repeat domains of EccB 1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD 1 has a ubiquitin-like fold and forms a dimer with a negatively charged groove. In conclusion, these structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.« less

Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system

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

Wagner, Jonathan M.; Chan, Sum; Evans, Timothy J.

The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB 1 and EccD 1. The periplasmic domain of EccB 1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. Themore » repeat domains of EccB 1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD 1 has a ubiquitin-like fold and forms a dimer with a negatively charged groove. In conclusion, these structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.« less

Architecture for an advanced biomedical collaboration domain for the European paediatric cancer research community (ABCD-4-E).

PubMed

Nitzlnader, Michael; Falgenhauer, Markus; Gossy, Christian; Schreier, Günter

2015-01-01

Today, progress in biomedical research often depends on large, interdisciplinary research projects and tailored information and communication technology (ICT) support. In the context of the European Network for Cancer Research in Children and Adolescents (ENCCA) project the exchange of data between data source (Source Domain) and data consumer (Consumer Domain) systems in a distributed computing environment needs to be facilitated. This work presents the requirements and the corresponding solution architecture of the Advanced Biomedical Collaboration Domain for Europe (ABCD-4-E). The proposed concept utilises public as well as private cloud systems, the Integrating the Healthcare Enterprise (IHE) framework and web-based applications to provide the core capabilities in accordance with privacy and security needs. The utility of crucial parts of the concept was evaluated by prototypic implementation. A discussion of the design indicates that the requirements of ENCCA are fully met. A whole system demonstration is currently being prepared to verify that ABCD-4-E has the potential to evolve into a domain-bridging collaboration platform in the future.

Origin and Evolution of the Sponge Aggregation Factor Gene Family.

PubMed

Grice, Laura F; Gauthier, Marie E A; Roper, Kathrein E; Fernàndez-Busquets, Xavier; Degnan, Sandie M; Degnan, Bernard M

2017-05-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self-nonself recognition systems in the animal kingdom. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Assessment of the integration capability of system architectures from a complex and distributed software systems perspective

NASA Astrophysics Data System (ADS)

Leuchter, S.; Reinert, F.; Müller, W.

2014-06-01

Procurement and design of system architectures capable of network centric operations demand for an assessment scheme in order to compare different alternative realizations. In this contribution an assessment method for system architectures targeted at the C4ISR domain is presented. The method addresses the integration capability of software systems from a complex and distributed software system perspective focusing communication, interfaces and software. The aim is to evaluate the capability to integrate a system or its functions within a system-of-systems network. This method uses approaches from software architecture quality assessment and applies them on the system architecture level. It features a specific goal tree of several dimensions that are relevant for enterprise integration. These dimensions have to be weighed against each other and totalized using methods from the normative decision theory in order to reflect the intention of the particular enterprise integration effort. The indicators and measurements for many of the considered quality features rely on a model based view on systems, networks, and the enterprise. That means it is applicable to System-of-System specifications based on enterprise architectural frameworks relying on defined meta-models or domain ontologies for defining views and viewpoints. In the defense context we use the NATO Architecture Framework (NAF) to ground respective system models. The proposed assessment method allows evaluating and comparing competing system designs regarding their future integration potential. It is a contribution to the system-of-systems engineering methodology.

Switching from Computer to Microcomputer Architecture Education

ERIC Educational Resources Information Center

Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

2010-01-01

In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to…

Fuzzy-Neural Controller in Service Requests Distribution Broker for SOA-Based Systems

NASA Astrophysics Data System (ADS)

Fras, Mariusz; Zatwarnicka, Anna; Zatwarnicki, Krzysztof

The evolution of software architectures led to the rising importance of the Service Oriented Architecture (SOA) concept. This architecture paradigm support building flexible distributed service systems. In the paper the architecture of service request distribution broker designed for use in SOA-based systems is proposed. The broker is built with idea of fuzzy control. The functional and non-functional request requirements in conjunction with monitoring of execution and communication links are used to distribute requests. Decisions are made with use of fuzzy-neural network.

Domain organizations of modular extracellular matrix proteins and their evolution.

PubMed

Engel, J

1996-11-01

Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

Mission Systems Open Architecture Science and Technology (MOAST) program

NASA Astrophysics Data System (ADS)

Littlejohn, Kenneth; Rajabian-Schwart, Vahid; Kovach, Nicholas; Satterthwaite, Charles P.

2017-04-01

The Mission Systems Open Architecture Science and Technology (MOAST) program is an AFRL effort that is developing and demonstrating Open System Architecture (OSA) component prototypes, along with methods and tools, to strategically evolve current OSA standards and technical approaches, promote affordable capability evolution, reduce integration risk, and address emerging challenges [1]. Within the context of open architectures, the program is conducting advanced research and concept development in the following areas: (1) Evolution of standards; (2) Cyber-Resiliency; (3) Emerging Concepts and Technologies; (4) Risk Reduction Studies and Experimentation; and (5) Advanced Technology Demonstrations. Current research includes the development of methods, tools, and techniques to characterize the performance of OMS data interconnection methods for representative mission system applications. Of particular interest are the OMS Critical Abstraction Layer (CAL), the Avionics Service Bus (ASB), and the Bulk Data Transfer interconnects, as well as to develop and demonstrate cybersecurity countermeasures techniques to detect and mitigate cyberattacks against open architecture based mission systems and ensure continued mission operations. Focus is on cybersecurity techniques that augment traditional cybersecurity controls and those currently defined within the Open Mission System and UCI standards. AFRL is also developing code generation tools and simulation tools to support evaluation and experimentation of OSA-compliant implementations.

A Successful Component Architecture for Interoperable and Evolvable Ground Data Systems

NASA Technical Reports Server (NTRS)

Smith, Danford S.; Bristow, John O.; Wilmot, Jonathan

2006-01-01

The National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) has adopted an open architecture approach for satellite control centers and is now realizing benefits beyond those originally envisioned. The Goddard Mission Services Evolution Center (GMSEC) architecture utilizes standardized interfaces and a middleware software bus to allow functional components to be easily integrated. This paper presents the GMSEC architectural goals and concepts, the capabilities enabled and the benefits realized by adopting this framework approach. NASA experiences with applying the GMSEC architecture on multiple missions are discussed. The paper concludes with a summary of lessons learned, future directions for GMSEC and the possible applications beyond NASA GSFC.

C2 Product-Centric Approach to Transforming Current C4ISR Information Architectures

DTIC Science & Technology

2004-06-01

each type of environment . For “Cultural Feature” Entity Kind only the “Land” Domain is defined and for “ Environmental ” Entity Kind only the...take advantage of both worlds. In particular, the unifying concept of a Model-Driven Architecture (MDA) under development by the Object Management...Exchange Requirements (IER) to an XML environment . FCS [4] developers have embraced both UML and XML for their architectures and MIP [5] too is migrating

Distributed video coding for wireless video sensor networks: a review of the state-of-the-art architectures.

PubMed

Imran, Noreen; Seet, Boon-Chong; Fong, A C M

2015-01-01

Distributed video coding (DVC) is a relatively new video coding architecture originated from two fundamental theorems namely, Slepian-Wolf and Wyner-Ziv. Recent research developments have made DVC attractive for applications in the emerging domain of wireless video sensor networks (WVSNs). This paper reviews the state-of-the-art DVC architectures with a focus on understanding their opportunities and gaps in addressing the operational requirements and application needs of WVSNs.

Verified OS Interface Code Synthesis

DTIC Science & Technology

2016-12-01

in this case we are using the ARMv7 processor architecture ). The application accomplishes this task by issuing the swi (“software interrupt...manual version 4.0.0) on the ARM architecture . To alleviate this problem,we developed an XML-based domain specific language (DSL) in which each...Untyped Retype Table 2.1: seL4 Architecture Independent System Calls. of r2, r3, r4 and r5 into the message registers of the thread’s IPC buffer and

The Effects of Race Conditions When Implementing Single-Source Redundant Clock Trees in Triple Modular Redundant Synchronous Architectures

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; Kim, Hak S.; Phan, Anthony M.; Seidleck, Christina M.; Label, Kenneth A.; Pellish, Jonathan A.; Campola, Michael J.

2016-01-01

We present the challenges that arise when using redundant clock domains due to their time-skew. Radiation data show that a singular clock domain provides an improved triple modular redundant (TMR) scheme over redundant clocks.

The Prp19 WD40 Domain Contains a Conserved Protein Interaction Region Essential for its Function

PubMed Central

Vander Kooi, Craig W.; Ren, Liping; Xu, Ping; Ohi, Melanie D.; Gould, Kathleen L.; Chazin, Walter J.

2010-01-01

Summary Prp19 is a member of the WD40-repeat family of E3 ubiquitin ligases and a conserved eukaryotic RNA splicing factor essential for activation and stabilization of the spliceosome. To understand the role of the WD40 repeat domain of Prp19 we have determined its structure using X-ray crystallography. The domain has a distorted seven bladed WD40 architecture with significant asymmetry due to irregular packing of blades one and seven into the core of the WD40 domain. Structure-based mutagenesis identified a highly conserved surface centered around blade five that is required for the physical interaction between Prp19 and Cwc2, another essential splicing factor. This region is found to be required for Prp19 function and yeast viability. Experiments in vitro and in vivo demonstrate that two molecules of Cwc2 bind to the Prp19 tetramer. These coupled structural and functional studies provide a model for the functional architecture of Prp19. PMID:20462492

Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma.

PubMed

Peng, Xiao-Nu; Wang, Jing; Zhang, Wei

2017-08-01

Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.

Tectono-sedimentary evolution of the eastern Gulf of Aden conjugate passive margins: Narrowness and asymmetry in oblique rifting context

NASA Astrophysics Data System (ADS)

Nonn, Chloé; Leroy, Sylvie; Khanbari, Khaled; Ahmed, Abdulhakim

2017-11-01

Here, we focus on the yet unexplored eastern Gulf of Aden, on Socotra Island (Yemen), Southeastern Oman and offshore conjugate passive margins between the Socotra-Hadbeen (SHFZ) and the eastern Gulf of Aden fracture zones. Our interpretation leads to onshore-offshore stratigraphic correlation between the passive margins. We present a new map reflecting the boundaries between the crustal domains (proximal, necking, hyper-extended, exhumed mantle, proto-oceanic and oceanic domains) and structures using bathymetry, magnetic surveys and seismic reflection data. The most striking result is that the magma-poor conjugate margins exhibit asymmetrical architecture since the thinning phase (Upper Rupelian-Burdigalian). Their necking domains are sharp ( 40-10 km wide) and their hyper-extended domains are narrow and asymmetric ( 10-40 km wide on the Socotra margin and 50-80 km wide on the Omani margin). We suggest that this asymmetry is related to the migration of the rift center producing significant lower crustal flow and sequential faulting in the hyper-extended domain. Throughout the Oligo-Miocene rifting, far-field forces dominate and the deformation is accommodated along EW to N110°E northward-dipping low angle normal faults. Convection in the mantle near the SHFZ may be responsible of change in fault dip polarity in the Omani hyper-extended domain. We show the existence of a northward-dipping detachment fault formed at the beginning of the exhumation phase (Burdigalien). It separates the northern upper plate (Oman) from southern lower plate (Socotra Island) and may have generated rift-induced decompression melting and volcanism affecting the upper plate. We highlight multiple generations of detachment faults exhuming serpentinized subcontinental mantle in the ocean-continent transition. Associated to significant decompression melting, final detachment fault may have triggered the formation of a proto-oceanic crust at 17.6 Ma and induced late volcanism up to 10 Ma. Finally, the setting up of a steady-state oceanic spreading center occurs at 17 Ma.

Polynomial Calculus: Rethinking the Role of Calculus in High Schools

ERIC Educational Resources Information Center

Grant, Melva R.; Crombie, William; Enderson, Mary; Cobb, Nell

2016-01-01

Access to advanced study in mathematics, in general, and to calculus, in particular, depends in part on the conceptual architecture of these knowledge domains. In this paper, we outline an alternative conceptual architecture for elementary calculus. Our general strategy is to separate basic concepts from the particular advanced techniques used in…

The Architecture, Dynamics, and Development of Mental Processing: Greek, Chinese, or Universal?

ERIC Educational Resources Information Center

Demetriou, A.; Kui, Z.X.; Spanoudis, G.; Christou, C.; Kyriakides, L.; Platsidou, M.

2005-01-01

This study compared Greeks with Chinese, from 8 to 14 years of age, on measures of processing efficiency, working memory, and reasoning. All processes were addressed through three domains of relations: verbal/propositional, quantitative, and visuo/spatial. Structural equations modelling and rating scale analysis showed that the architecture and…

Using Real and Simulated TNOs to Constrain the Outer Solar System

NASA Astrophysics Data System (ADS)

Kaib, Nathan

2018-04-01

Over the past 2-3 decades our understanding of the outer solar system’s history and current state has evolved dramatically. An explosion in the number of detected trans-Neptunian objects (TNOs) coupled with simultaneous advances in numerical models of orbital dynamics has driven this rapid evolution. However, successfully constraining the orbital architecture and evolution of the outer solar system requires accurately comparing simulation results with observational datasets. This process is challenging because observed datasets are influenced by orbital discovery biases as well as TNO size and albedo distributions. Meanwhile, such influences are generally absent from numerical results. Here I will review recent work I and others have undertaken using numerical simulations in concert with catalogs of observed TNOs to constrain the outer solar system’s current orbital architecture and past evolution.

Application-specific coarse-grained reconfigurable array: architecture and design methodology

NASA Astrophysics Data System (ADS)

Zhou, Li; Liu, Dongpei; Zhang, Jianfeng; Liu, Hengzhu

2015-06-01

Coarse-grained reconfigurable arrays (CGRAs) have shown potential for application in embedded systems in recent years. Numerous reconfigurable processing elements (PEs) in CGRAs provide flexibility while maintaining high performance by exploring different levels of parallelism. However, a difference remains between the CGRA and the application-specific integrated circuit (ASIC). Some application domains, such as software-defined radios (SDRs), require flexibility with performance demand increases. More effective CGRA architectures are expected to be developed. Customisation of a CGRA according to its application can improve performance and efficiency. This study proposes an application-specific CGRA architecture template composed of generic PEs (GPEs) and special PEs (SPEs). The hardware of the SPE can be customised to accelerate specific computational patterns. An automatic design methodology that includes pattern identification and application-specific function unit generation is also presented. A mapping algorithm based on ant colony optimisation is provided. Experimental results on the SDR target domain show that compared with other ordinary and application-specific reconfigurable architectures, the CGRA generated by the proposed method performs more efficiently for given applications.

Simplified Parallel Domain Traversal

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

Erickson III, David J

2011-01-01

Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel programming approaches, we have designed DStep, a flexible system that greatly simplifies efficient parallelization of domain traversal techniques at scale. In order to deliver both simplicity to users as well as scalability on HPC platforms, we introduce a novel two-tiered communication architecture for managing and exploiting asynchronous communication loads. We also integrate our design with advanced parallel I/O techniques that operate directly on native simulation output. We demonstrate DStep bymore » performing teleconnection analysis across ensemble runs of terascale atmospheric CO{sub 2} and climate data, and we show scalability results on up to 65,536 IBM BlueGene/P cores.« less

The Generalized Support Software (GSS) Domain Engineering Process: An Object-Oriented Implementation and Reuse Success at Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Condon, Steven; Hendrick, Robert; Stark, Michael E.; Steger, Warren

1997-01-01

The Flight Dynamics Division (FDD) of NASA's Goddard Space Flight Center (GSFC) recently embarked on a far-reaching revision of its process for developing and maintaining satellite support software. The new process relies on an object-oriented software development method supported by a domain specific library of generalized components. This Generalized Support Software (GSS) Domain Engineering Process is currently in use at the NASA GSFC Software Engineering Laboratory (SEL). The key facets of the GSS process are (1) an architecture for rapid deployment of FDD applications, (2) a reuse asset library for FDD classes, and (3) a paradigm shift from developing software to configuring software for mission support. This paper describes the GSS architecture and process, results of fielding the first applications, lessons learned, and future directions

Architecture of a mixed-mode electrophysiological signal acquisition interface.

PubMed

Shen, Ding-Lan; Chen, Jyun-Min

2012-01-01

This paper proposes mixed-mode architecture for the acquisition interface of electrophysiological signals. The architecture advances the analog-to-digital converter (ADC) from the second chopper signal in the conventional approach and performs the second chopper operation in the digital domain. The demanded low-pass filter (LPF) is realized with a digital type. The analog LPF in feedback path is substituted with a digital one accompanying with a digital-to-analog converter (DAC). The analog variation is decreased due to the digitization of these operations. The entire architecture is simulated with the ECG input in a behavior model of Simulink.

A general architecture for intelligent training systems

NASA Technical Reports Server (NTRS)

Loftin, R. Bowen

1987-01-01

A preliminary design of a general architecture for autonomous intelligent training systems was developed. The architecture integrates expert system technology with teaching/training methodologies to permit the production of systems suitable for use by NASA, other government agencies, industry, and academia in the training of personnel for the performance of complex, mission-critical tasks. The proposed architecture consists of five elements: a user interface, a domain expert, a training session manager, a trainee model, and a training scenario generator. The design of this architecture was guided and its efficacy tested through the development of a system for use by Mission Control Center Flight Dynamics Officers in training to perform Payload-Assist Module Deploys from the orbiter.

Module Architecture for in Situ Space Laboratories

NASA Technical Reports Server (NTRS)

Sherwood, Brent

2010-01-01

The paper analyzes internal outfitting architectures for space exploration laboratory modules. ISS laboratory architecture is examined as a baseline for comparison; applicable insights are derived. Laboratory functional programs are defined for seven planet-surface knowledge domains. Necessary and value-added departures from the ISS architecture standard are defined, and three sectional interior architecture options are assessed for practicality and potential performance. Contemporary guidelines for terrestrial analytical laboratory design are found to be applicable to the in-space functional program. Densepacked racks of system equipment, and high module volume packing ratios, should not be assumed as the default solution for exploration laboratories whose primary activities include un-scriptable investigations and experimentation on the system equipment itself.

Implications of behavioral architecture for the evolution of self-organized division of labor.

PubMed

Duarte, A; Scholtens, E; Weissing, F J

2012-01-01

Division of labor has been studied separately from a proximate self-organization and an ultimate evolutionary perspective. We aim to bring together these two perspectives. So far this has been done by choosing a behavioral mechanism a priori and considering the evolution of the properties of this mechanism. Here we use artificial neural networks to allow for a more open architecture. We study whether emergent division of labor can evolve in two different network architectures; a simple feedforward network, and a more complex network that includes the possibility of self-feedback from previous experiences. We focus on two aspects of division of labor; worker specialization and the ratio of work performed for each task. Colony fitness is maximized by both reducing idleness and achieving a predefined optimal work ratio. Our results indicate that architectural constraints play an important role for the outcome of evolution. With the simplest network, only genetically determined specialization is possible. This imposes several limitations on worker specialization. Moreover, in order to minimize idleness, networks evolve a biased work ratio, even when an unbiased work ratio would be optimal. By adding self-feedback to the network we increase the network's flexibility and worker specialization evolves under a wider parameter range. Optimal work ratios are more easily achieved with the self-feedback network, but still provide a challenge when combined with worker specialization.

Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor

PubMed Central

Duarte, A.; Scholtens, E.; Weissing, F. J.

2012-01-01

Division of labor has been studied separately from a proximate self-organization and an ultimate evolutionary perspective. We aim to bring together these two perspectives. So far this has been done by choosing a behavioral mechanism a priori and considering the evolution of the properties of this mechanism. Here we use artificial neural networks to allow for a more open architecture. We study whether emergent division of labor can evolve in two different network architectures; a simple feedforward network, and a more complex network that includes the possibility of self-feedback from previous experiences. We focus on two aspects of division of labor; worker specialization and the ratio of work performed for each task. Colony fitness is maximized by both reducing idleness and achieving a predefined optimal work ratio. Our results indicate that architectural constraints play an important role for the outcome of evolution. With the simplest network, only genetically determined specialization is possible. This imposes several limitations on worker specialization. Moreover, in order to minimize idleness, networks evolve a biased work ratio, even when an unbiased work ratio would be optimal. By adding self-feedback to the network we increase the network's flexibility and worker specialization evolves under a wider parameter range. Optimal work ratios are more easily achieved with the self-feedback network, but still provide a challenge when combined with worker specialization. PMID:22457609

The Architecture of the Pollen Hoarding Syndrome in Honey Bees: Implications for Understanding Social Evolution, Behavioral Syndromes, and Selective Breeding

PubMed Central

Rueppell, Olav

2014-01-01

Social evolution has influenced every aspect of contemporary honey bee biology, but the details are difficult to reconstruct. The reproductive ground plan hypothesis of social evolution proposes that central regulators of the gonotropic cycle of solitary insects have been coopted to coordinate social complexity in honey bees, such as the division of labor among workers. The predicted trait associations between reproductive physiology and social behavior have been identified in the context of the pollen hoarding syndrome, a larger suite of interrelated traits. The genetic architecture of this syndrome is characterized by a partially overlapping genetic architecture with several consistent, pleiotropic QTL. Despite these central QTL and an integrated hormonal regulation, separate aspects of the pollen hoarding syndrome may evolve independently due to peripheral QTL and additionally segregating genetic variance. The characterization of the pollen hoarding syndrome has also demonstrated that this syndrome involves many non-behavioral traits, which may be the case for numerous “behavioral” syndromes. Furthermore, the genetic architecture of the pollen hoarding syndrome has implications for breeding programs for improving honey health and other desirable traits: If these traits are comparable to the pollen hoarding syndrome, consistent pleiotropic QTL will enable marker assisted selection, while sufficient additional genetic variation may permit the dissociation of trade-offs for efficient multiple trait selection. PMID:25506100

The Architecture of the Pollen Hoarding Syndrome in Honey Bees: Implications for Understanding Social Evolution, Behavioral Syndromes, and Selective Breeding.

PubMed

Rueppell, Olav

2014-05-01

Social evolution has influenced every aspect of contemporary honey bee biology, but the details are difficult to reconstruct. The reproductive ground plan hypothesis of social evolution proposes that central regulators of the gonotropic cycle of solitary insects have been coopted to coordinate social complexity in honey bees, such as the division of labor among workers. The predicted trait associations between reproductive physiology and social behavior have been identified in the context of the pollen hoarding syndrome, a larger suite of interrelated traits. The genetic architecture of this syndrome is characterized by a partially overlapping genetic architecture with several consistent, pleiotropic QTL. Despite these central QTL and an integrated hormonal regulation, separate aspects of the pollen hoarding syndrome may evolve independently due to peripheral QTL and additionally segregating genetic variance. The characterization of the pollen hoarding syndrome has also demonstrated that this syndrome involves many non-behavioral traits, which may be the case for numerous "behavioral" syndromes. Furthermore, the genetic architecture of the pollen hoarding syndrome has implications for breeding programs for improving honey health and other desirable traits: If these traits are comparable to the pollen hoarding syndrome, consistent pleiotropic QTL will enable marker assisted selection, while sufficient additional genetic variation may permit the dissociation of trade-offs for efficient multiple trait selection.

The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens.

PubMed

Oppenheim, Sara J; Gould, Fred; Hopper, Keith R

2018-03-01

Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group. Here we investigate the response of Chloridea virescens, a generalist that feeds on diverse plant species, to selection for performance on a novel host, Physalis angulata (Solanaceae). P. angulata is the preferred host of Chloridea subflexa, a narrow specialist on the genus Physalis. In previous experiments, we found that the performance of C. subflexa on P. angulata depends on many loci of small effect distributed throughout the genome, but whether the same architecture would be involved in the generalist's adoption of P. angulata was unknown. Here we report a rapid response to selection in C. virescens for performance on P. angulata, and establish that the genetic architecture of intraspecific variation is quite similar to that of the interspecific differences in terms of the number, distribution, and effect sizes of the QTL involved. We discuss the impact of genetic architecture on the ability of Heliothine moths to respond to varying ecological selection pressures.

Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol

PubMed Central

Lakshminarasimhan, Mahadevan; Curth, Ute; Moniot, Sebastien; Mosalaganti, Shyamal; Raunser, Stefan; Steegborn, Clemens

2013-01-01

Sirtuins are NAD+-dependent protein deacetylases regulating metabolism, stress responses and ageing processes. Among the seven mammalian Sirtuins, Sirt1 is the physiologically best-studied isoform. It regulates nuclear functions such as chromatin remodelling and gene transcription, and it appears to mediate beneficial effects of a low calorie diet which can partly be mimicked by the Sirt1 activating polyphenol resveratrol. The molecular details of Sirt1 domain architecture and regulation, however, are little understood. It has a unique N-terminal domain and CTD (C-terminal domain) flanking a conserved Sirtuin catalytic core and these extensions are assumed to mediate Sirt1-specific features such as homo-oligomerization and activation by resveratrol. To analyse the architecture of human Sirt1 and functions of its N- and C-terminal extensions, we recombinantly produced Sirt1 and Sirt1 deletion constructs as well as the AROS (active regulator of Sirt1) protein. We then studied Sirt1 features such as molecular size, secondary structure and stimulation by small molecules and AROS. We find that Sirt1 is monomeric and has extended conformations in its flanking domains, likely disordered especially in the N-terminus, resulting in an increased hydrodynamic radius. Nevertheless, both termini increase Sirt1 deacetylase activity, indicating a regulatory function. We also find an unusual but defined conformation for AROS protein, which fails, however, to stimulate Sirt1. Resveratrol, in contrast, activates the Sirt1 catalytic core independent of the terminal domains, indicating a binding site within the catalytic core and suggesting that small molecule activators for other isoforms might also exist. PMID:23548308

A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells.

PubMed

Schulein, Ralf; Guye, Patrick; Rhomberg, Thomas A; Schmid, Michael C; Schröder, Gunnar; Vergunst, Annette C; Carena, Ilaria; Dehio, Christoph

2005-01-18

Bacterial type IV secretion (T4S) systems mediate the transfer of macromolecular substrates into various target cells, e.g., the conjugative transfer of DNA into bacteria or the transfer of virulence proteins into eukaryotic host cells. The T4S apparatus VirB of the vascular tumor-inducing pathogen Bartonella henselae causes subversion of human endothelial cell (HEC) function. Here we report the identification of multiple protein substrates of VirB, which, upon translocation into HEC, mediate all known VirB-dependent cellular changes. These Bartonella-translocated effector proteins (Beps) A-G are encoded together with the VirB system and the T4S coupling protein VirD4 on a Bartonella-specific pathogenicity island. The Beps display a modular architecture, suggesting an evolution by extensive domain duplication and reshuffling. The C terminus of each Bep harbors at least one copy of the Bep-intracellular delivery domain and a short positively charged tail sequence. This biparte C terminus constitutes a transfer signal that is sufficient to mediate VirB/VirD4-dependent intracellular delivery of reporter protein fusions. The Bep-intracellular delivery domain is also present in conjugative relaxases of bacterial conjugation systems. We exemplarily show that the C terminus of such a conjugative relaxase mediates protein transfer through the Bartonella henselae VirB/VirD4 system into HEC. Conjugative relaxases may thus represent the evolutionary origin of the here defined T4S signal for protein transfer into human cells.

A scalable architecture for extracting, aligning, linking, and visualizing multi-Int data

NASA Astrophysics Data System (ADS)

Knoblock, Craig A.; Szekely, Pedro

2015-05-01

An analyst today has a tremendous amount of data available, but each of the various data sources typically exists in their own silos, so an analyst has limited ability to see an integrated view of the data and has little or no access to contextual information that could help in understanding the data. We have developed the Domain-Insight Graph (DIG) system, an innovative architecture for extracting, aligning, linking, and visualizing massive amounts of domain-specific content from unstructured sources. Under the DARPA Memex program we have already successfully applied this architecture to multiple application domains, including the enormous international problem of human trafficking, where we extracted, aligned and linked data from 50 million online Web pages. DIG builds on our Karma data integration toolkit, which makes it easy to rapidly integrate structured data from a variety of sources, including databases, spreadsheets, XML, JSON, and Web services. The ability to integrate Web services allows Karma to pull in live data from the various social media sites, such as Twitter, Instagram, and OpenStreetMaps. DIG then indexes the integrated data and provides an easy to use interface for query, visualization, and analysis.

Developing a modular architecture for creation of rule-based clinical diagnostic criteria.

PubMed

Hong, Na; Pathak, Jyotishman; Chute, Christopher G; Jiang, Guoqian

2016-01-01

With recent advances in computerized patient records system, there is an urgent need for producing computable and standards-based clinical diagnostic criteria. Notably, constructing rule-based clinical diagnosis criteria has become one of the goals in the International Classification of Diseases (ICD)-11 revision. However, few studies have been done in building a unified architecture to support the need for diagnostic criteria computerization. In this study, we present a modular architecture for enabling the creation of rule-based clinical diagnostic criteria leveraging Semantic Web technologies. The architecture consists of two modules: an authoring module that utilizes a standards-based information model and a translation module that leverages Semantic Web Rule Language (SWRL). In a prototype implementation, we created a diagnostic criteria upper ontology (DCUO) that integrates ICD-11 content model with the Quality Data Model (QDM). Using the DCUO, we developed a transformation tool that converts QDM-based diagnostic criteria into Semantic Web Rule Language (SWRL) representation. We evaluated the domain coverage of the upper ontology model using randomly selected diagnostic criteria from broad domains (n = 20). We also tested the transformation algorithms using 6 QDM templates for ontology population and 15 QDM-based criteria data for rule generation. As the results, the first draft of DCUO contains 14 root classes, 21 subclasses, 6 object properties and 1 data property. Investigation Findings, and Signs and Symptoms are the two most commonly used element types. All 6 HQMF templates are successfully parsed and populated into their corresponding domain specific ontologies and 14 rules (93.3 %) passed the rule validation. Our efforts in developing and prototyping a modular architecture provide useful insight into how to build a scalable solution to support diagnostic criteria representation and computerization.

Library Development Handbook. Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1993-10-29

features. This feature benefits the individual not versed in the terminology of the domain. When class requirements become part of the domain criteria, they... franchisee - Group to whom a franchise is granted. generic architecture - A collection of high-level paradigms and constraints that characterize the

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

PubMed Central

Nasir, Arshan; Naeem, Aisha; Khan, Muhammad Jawad; Lopez-Nicora, Horacio D.; Caetano-Anollés, Gustavo

2011-01-01

The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups. PMID:24710297

Evolving BioAssay Ontology (BAO): modularization, integration and applications

PubMed Central

2014-01-01

The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and datasets. PMID:25093074

Evolving BioAssay Ontology (BAO): modularization, integration and applications.

PubMed

Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

2014-01-01

The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and datasets.

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

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

Arampatzis, Giorgos, E-mail: garab@math.uoc.gr; Katsoulakis, Markos A., E-mail: markos@math.umass.edu; Plechac, Petr, E-mail: plechac@math.udel.edu

2012-10-01

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decompositionmore » corresponds to a decomposition of the Markov generator into a hierarchy of operators and can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). Based on this operator decomposition, we formulate parallel Fractional step kinetic Monte Carlo algorithms by employing the Trotter Theorem and its randomized variants; these schemes, (a) are partially asynchronous on each fractional step time-window, and (b) are characterized by their communication schedule between processors. The proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules. We carry out a detailed benchmarking of the parallel KMC schemes using available exact solutions, for example, in Ising-type systems and we demonstrate the capabilities of the method to simulate complex spatially distributed reactions at very large scales on GPUs. Finally, we discuss work load balancing between processors and propose a re-balancing scheme based on probabilistic mass transport methods.« less

Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins

PubMed Central

2008-01-01

Background Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. Results The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family. Conclusion We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms. PMID:18430232

Utilizing IHE-based Electronic Health Record systems for secondary use.

PubMed

Holzer, K; Gall, W

2011-01-01

Due to the increasing adoption of Electronic Health Records (EHRs) for primary use, the number of electronic documents stored in such systems will soar in the near future. In order to benefit from this development in secondary fields such as medical research, it is important to define requirements for the secondary use of EHR data. Furthermore, analyses of the extent to which an IHE (Integrating the Healthcare Enterprise)-based architecture would fulfill these requirements could provide further information on upcoming obstacles for the secondary use of EHRs. A catalog of eight core requirements for secondary use of EHR data was deduced from the published literature, the risk analysis of the IHE profile MPQ (Multi-Patient Queries) and the analysis of relevant questions. The IHE-based architecture for cross-domain, patient-centered document sharing was extended to a cross-patient architecture. We propose an IHE-based architecture for cross-patient and cross-domain secondary use of EHR data. Evaluation of this architecture concerning the eight core requirements revealed positive fulfillment of six and the partial fulfillment of two requirements. Although not regarded as a primary goal in modern electronic healthcare, the re-use of existing electronic medical documents in EHRs for research and other fields of secondary application holds enormous potential for the future. Further research in this respect is necessary.

PDS4 - Some Principles for Agile Data Curation

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Crichton, D. J.; Hardman, S. H.; Joyner, R.; Algermissen, S.; Padams, J.

2015-12-01

PDS4, a research data management and curation system for NASA's Planetary Science Archive, was developed using principles that promote the characteristics of agile development. The result is an efficient system that produces better research data products while using less resources (time, effort, and money) and maximizes their usefulness for current and future scientists. The key principle is architectural. The PDS4 information architecture is developed and maintained independent of the infrastructure's process, application and technology architectures. The information architecture is based on an ontology-based information model developed to leverage best practices from standard reference models for digital archives, digital object registries, and metadata registries and capture domain knowledge from a panel of planetary science domain experts. The information model provides a sharable, stable, and formal set of information requirements for the system and is the primary source for information to configure most system components, including the product registry, search engine, validation and display tools, and production pipelines. Multi-level governance is also allowed for the effective management of the informational elements at the common, discipline, and project level. This presentation will describe the development principles, components, and uses of the information model and how an information model-driven architecture exhibits characteristics of agile curation including early delivery, evolutionary development, adaptive planning, continuous improvement, and rapid and flexible response to change.

Analysis OpenMP performance of AMD and Intel architecture for breaking waves simulation using MPS

NASA Astrophysics Data System (ADS)

Alamsyah, M. N. A.; Utomo, A.; Gunawan, P. H.

2018-03-01

Simulation of breaking waves by using Navier-Stokes equation via moving particle semi-implicit method (MPS) over close domain is given. The results show the parallel computing on multicore architecture using OpenMP platform can reduce the computational time almost half of the serial time. Here, the comparison using two computer architectures (AMD and Intel) are performed. The results using Intel architecture is shown better than AMD architecture in CPU time. However, in efficiency, the computer with AMD architecture gives slightly higher than the Intel. For the simulation by 1512 number of particles, the CPU time using Intel and AMD are 12662.47 and 28282.30 respectively. Moreover, the efficiency using similar number of particles, AMD obtains 50.09 % and Intel up to 49.42 %.

A task control architecture for autonomous robots

NASA Technical Reports Server (NTRS)

Simmons, Reid; Mitchell, Tom

1990-01-01

An architecture is presented for controlling robots that have multiple tasks, operate in dynamic domains, and require a fair degree of autonomy. The architecture is built on several layers of functionality, including a distributed communication layer, a behavior layer for querying sensors, expanding goals, and executing commands, and a task level for managing the temporal aspects of planning and achieving goals, coordinating tasks, allocating resources, monitoring, and recovering from errors. Application to a legged planetary rover and an indoor mobile manipulator is described.

Hypercluster Parallel Processor

NASA Technical Reports Server (NTRS)

Blech, Richard A.; Cole, Gary L.; Milner, Edward J.; Quealy, Angela

1992-01-01

Hypercluster computer system includes multiple digital processors, operation of which coordinated through specialized software. Configurable according to various parallel-computing architectures of shared-memory or distributed-memory class, including scalar computer, vector computer, reduced-instruction-set computer, and complex-instruction-set computer. Designed as flexible, relatively inexpensive system that provides single programming and operating environment within which one can investigate effects of various parallel-computing architectures and combinations on performance in solution of complicated problems like those of three-dimensional flows in turbomachines. Hypercluster software and architectural concepts are in public domain.

In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP).

PubMed

Quinn, Jeffrey J; Chang, Howard Y

2015-01-01

Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a technique for dissecting the functional domains of a target RNA in situ. For an RNA of interest, dChIRP can identify domain-level intramolecular and intermolecular RNA-RNA, RNA-protein, and RNA-DNA interactions and maps the RNA's genomic binding sites with higher precision than domain-agnostic methods. We illustrate how this technique has been applied to the roX1 lncRNA to resolve its domain-level architecture, discover its protein- and chromatin-interacting domains, and map its occupancy on the X chromosome.

Adapting clinical paradigms to the challenges of cancer clonal evolution.

PubMed

Murugaesu, Nirupa; Chew, Su Kit; Swanton, Charles

2013-06-01

Emerging evidence suggests that cancer branched evolution may affect biomarker validation, clinical outcome, and emergence of drug resistance. The changing spatial and temporal nature of cancer subclonal architecture during the disease course suggests the need for longitudinal prospective studies of cancer evolution and robust and clinically implementable pathologic definitions of intratumor heterogeneity, genetic diversity, and chromosomal instability. Furthermore, subclonal heterogeneous events in tumors may evade detection through conventional biomarker strategies and influence clinical outcome. Minimally invasive methods for the study of cancer evolution and new approaches to clinical study design, incorporating understanding of the dynamics of tumor clonal architectures through treatment and during acquisition of drug resistance, have been suggested as important areas for development. Coordinated efforts will be required by the scientific and clinical trial communities to adapt to the challenges of detecting infrequently occurring somatic events that may influence clinical outcome and to understand the dynamics of cancer evolution and the waxing and waning of tumor subclones over time in advanced metastatic epithelial malignancies. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

PubMed Central

2013-01-01

Background Guanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuable information can be acquired from amino acid composition data. To address this concern, in-depth analyses of the amino acid composition of the complete proteomes from 63 archaea, 270 bacteria, and 128 eukaryotes were performed. Results Principal component analysis of the amino acid matrices showed that the main contributors to proteomic architecture were genomic GC variation, phylogeny, and environmental influences. GC pressure drove positive selection on Ala, Arg, Gly, Pro, Trp, and Val, and adverse selection on Asn, Lys, Ile, Phe, and Tyr. The physico-chemical framework of the complete proteomes withstood GC pressure by frequency complementation of GC-dependent amino acid pairs with similar physico-chemical properties. Gln, His, Ser, and Val were responsible for phylogeny and their constituted components could differentiate archaea, bacteria, and eukaryotes. Environmental niche was also a significant factor in determining proteomic architecture, especially for archaea for which the main amino acids were Cys, Leu, and Thr. In archaea, hyperthermophiles, acidophiles, mesophiles, psychrophiles, and halophiles gathered successively along the environment-based principal component. Concordance between proteomic architecture and the genetic code was also related closely to genomic GC content, phylogeny, and lifestyles. Conclusions Large-scale analyses of the complete proteomes of a wide range of organisms suggested that amino acid composition retained the trace of GC variation, phylogeny, and environmental influences during evolution. The findings from this study will help in the development of a global understanding of proteome evolution, and even biological evolution. PMID:24088322

Origin and Evolution of the Sponge Aggregation Factor Gene Family

PubMed Central

Grice, Laura F.; Gauthier, Marie E.A.; Roper, Kathrein E.; Fernàndez-Busquets, Xavier; Degnan, Sandie M.

2017-01-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self–nonself recognition systems in the animal kingdom. PMID:28104746

Information architecture for a planetary 'exploration web'

NASA Technical Reports Server (NTRS)

Lamarra, N.; McVittie, T.

2002-01-01

'Web services' is a common way of deploying distributed applications whose software components and data sources may be in different locations, formats, languages, etc. Although such collaboration is not utilized significantly in planetary exploration, we believe there is significant benefit in developing an architecture in which missions could leverage each others capabilities. We believe that an incremental deployment of such an architecture could significantly contribute to the evolution of increasingly capable, efficient, and even autonomous remote exploration.

Interpretive Analysis of the Joint Maritime Command Information System (JMCIS) Sensitive Compartmented Information (SCI) Local Area Network (LAN) security Requirements

DTIC Science & Technology

1994-09-01

as Copernicus brought about a revolutionary paradigm shift in astronomy , the Copernicus Architecture was so named because it represents a...34 ........................................ 7 3. The Navy’s Copernicus Architecture .......................................... 8 B . SY ST E M S...evolution of JMCIS are DoD’s Corporate Information Management (CIM), The Joint Staffs "C41 for the Warrior", and the Navy’s Copernicus architecture programs

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems. Volume 2 Understanding Open Architecture Software Systems: Licensing and Security Research and Recommendations

DTIC Science & Technology

2016-01-06

of- breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The... commercially priced closed source software components, to be used in the design, implementation, deployment, and evolution of open architecture (OA... breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The Department

Sex-dependent expression of behavioural genetic architectures and the evolution of sexual dimorphism.

PubMed

Han, Chang S; Dingemanse, Niels J

2017-10-11

Empirical studies imply that sex-specific genetic architectures can resolve evolutionary conflicts between males and females, and thereby facilitate the evolution of sexual dimorphism. Sex-specificity of behavioural genetic architectures has, however, rarely been considered. Moreover, as the expression of genetic (co)variances is often environment-dependent, general inferences on sex-specific genetic architectures require estimates of quantitative genetics parameters under multiple conditions. We measured exploration and aggression in pedigreed populations of southern field crickets ( Gryllus bimaculatus ) raised on either naturally balanced (free-choice) or imbalanced (protein-deprived) diets. For each dietary condition, we measured for each behavioural trait (i) level of sexual dimorphism, (ii) level of sex-specificity of survival selection gradients, (iii) level of sex-specificity of additive genetic variance, and (iv) strength of the cross-sex genetic correlation. We report here evidence for sexual dimorphism in behaviour as well as sex-specificity in the expression of genetic (co)variances as predicted by theory. The additive genetic variances of exploration and aggression were significantly greater in males compared with females. Cross-sex genetic correlations were highly positive for exploration but deviating (significantly) from one for aggression; findings were consistent across dietary treatments. This suggests that genetic architectures characterize the sexually dimorphic focal behaviours across various key environmental conditions in the wild. Our finding also highlights that sexual conflict can be resolved by evolving sexually independent genetic architectures. © 2017 The Author(s).

Frequency-Domain Streak Camera and Tomography for Ultrafast Imaging of Evolving and Channeled Plasma Accelerator Structures

NASA Astrophysics Data System (ADS)

Li, Zhengyan; Zgadzaj, Rafal; Wang, Xiaoming; Reed, Stephen; Dong, Peng; Downer, Michael C.

2010-11-01

We demonstrate a prototype Frequency Domain Streak Camera (FDSC) that can capture the picosecond time evolution of the plasma accelerator structure in a single shot. In our prototype Frequency-Domain Streak Camera, a probe pulse propagates obliquely to a sub-picosecond pump pulse that creates an evolving nonlinear index "bubble" in fused silica glass, supplementing a conventional Frequency Domain Holographic (FDH) probe-reference pair that co-propagates with the "bubble". Frequency Domain Tomography (FDT) generalizes Frequency-Domain Streak Camera by probing the "bubble" from multiple angles and reconstructing its morphology and evolution using algorithms similar to those used in medical CAT scans. Multiplexing methods (Temporal Multiplexing and Angular Multiplexing) improve data storage and processing capability, demonstrating a compact Frequency Domain Tomography system with a single spectrometer.

The Common Evolution of Geometry and Architecture from a Geodetic Point of View

NASA Astrophysics Data System (ADS)

Bellone, T.; Fiermonte, F.; Mussio, L.

2017-05-01

Throughout history the link between geometry and architecture has been strong and while architects have used mathematics to construct their buildings, geometry has always been the essential tool allowing them to choose spatial shapes which are aesthetically appropriate. Sometimes it is geometry which drives architectural choices, but at other times it is architectural innovation which facilitates the emergence of new ideas in geometry. Among the best known types of geometry (Euclidean, projective, analytical, Topology, descriptive, fractal,…) those most frequently employed in architectural design are: - Euclidean Geometry - Projective Geometry - The non-Euclidean geometries. Entire architectural periods are linked to specific types of geometry. Euclidean geometry, for example, was the basis for architectural styles from Antiquity through to the Romanesque period. Perspective and Projective geometry, for their part, were important from the Gothic period through the Renaissance and into the Baroque and Neo-classical eras, while non-Euclidean geometries characterize modern architecture.

The Effects of Race Conditions when Implementing Single-Source Redundant Clock Trees in Triple Modular Redundant Synchronous Architectures

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; Label, Kenneth A.; Pellish, Jonathan

2016-01-01

We present the challenges that arise when using redundant clock domains due to their clock-skew. Heavy-ion radiation data show that a singular clock domain (DTMR) provides an improved TMR methodology for SRAM-based FPGAs over redundant clocks.

Linking and Combining Distributed Operations Facilities using NASA's "GMSEC" Systems Architectures

NASA Technical Reports Server (NTRS)

Smith, Danford; Grubb, Thomas; Esper, Jaime

2008-01-01

NASA's Goddard Mission Services Evolution Center (GMSEC) ground system architecture has been in development since late 2001, has successfully supported eight orbiting satellites and is being applied to many of NASA's future missions. GMSEC can be considered an event-driven service-oriented architecture built around a publish/subscribe message bus middleware. This paper briefly discusses the GMSEC technical approaches which have led to significant cost savings and risk reduction for NASA missions operated at the Goddard Space Flight Center (GSFC). The paper then focuses on the development and operational impacts of extending the architecture across multiple mission operations facilities.

Enhancer-Derived lncRNAs Regulate Genome Architecture: Fact or Fiction?

PubMed

Fanucchi, Stephanie; Mhlanga, Musa M

2017-06-01

How does the non-coding portion of the genome contribute to the regulation of genome architecture? A recent paper by Tan et al. focuses on the relationship between cis-acting complex-trait-associated lincRNAs and the formation of chromosomal contacts in topologically associating domains (TADs). Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering tough, highly compressible, biodegradable hydrogels by tuning the network architecture.

PubMed

Gu, Dunyin; Tan, Shereen; Xu, Chenglong; O'Connor, Andrea J; Qiao, Greg G

2017-06-20

By precisely tuning the network architecture, tough, highly compressible hydrogels were engineered. The hydrogels were made by interconnecting high-functionality hydrophobic domains through linear tri-block chains, consisting of soft hydrophilic middle blocks, flanked with flexible hydrophobic blocks. In showing their applicability, the efficient encapsulation and prolonged release of hydrophobic drugs were achieved.

Usage of Thin-Client/Server Architecture in Computer Aided Education

ERIC Educational Resources Information Center

Cimen, Caghan; Kavurucu, Yusuf; Aydin, Halit

2014-01-01

With the advances of technology, thin-client/server architecture has become popular in multi-user/single network environments. Thin-client is a user terminal in which the user can login to a domain and run programs by connecting to a remote server. Recent developments in network and hardware technologies (cloud computing, virtualization, etc.)…

Architectures for Distributed and Complex M-Learning Systems: Applying Intelligent Technologies

ERIC Educational Resources Information Center

Caballe, Santi, Ed.; Xhafa, Fatos, Ed.; Daradoumis, Thanasis, Ed.; Juan, Angel A., Ed.

2009-01-01

Over the last decade, the needs of educational organizations have been changing in accordance with increasingly complex pedagogical models and with the technological evolution of e-learning environments with very dynamic teaching and learning requirements. This book explores state-of-the-art software architectures and platforms used to support…

Investigating the influence of DNAPL spill characteristics on source zone architecture and mass removal in pool-dominated source zones

NASA Astrophysics Data System (ADS)

Wallace, K. A.; Abriola, L.; Chen, M.; Ramsburg, A.; Pennell, K. D.; Christ, J.

2009-12-01

Multiphase, compositional simulators were employed to investigate the spill characteristics and subsurface properties that lead to pool-dominated, dense non-aqueous phase liquid (DNAPL) source zone architectures. DNAPL pools commonly form at textural interfaces where low permeability lenses restrict the vertical migration of DNAPL, allowing for DNAPL to accumulate, reaching high saturation. Significant pooling has been observed in bench-scale experiments and field settings. However, commonly employed numerical simulations rarely predict the pooling suspected in the field. Given the importance of pooling on the efficacy of mass recovery and the down-gradient contaminant signal, it is important to understand the predominant factors affecting the creation of pool-dominated source zones and their subsequent mass discharge. In this work, contaminant properties, spill characteristics and subsurface permeability were varied to investigate the factors contributing to the development of a pool-dominated source zone. DNAPL infiltration and entrapment simulations were conducted in two- and three-dimensional domains using the University of Texas Chemical Compositional (UTCHEM) simulator. A modified version of MT3DMS was then used to simulate DNAPL dissolution and mass discharge. Numerical mesh size was varied to investigate the importance of numerical model parameters on simulations results. The temporal evolution of commonly employed source zone architecture metrics, such as the maximum DNAPL saturation, first and second spatial moments, and fraction of DNAPL mass located in pools, was monitored to determine how the source zone architecture evolved with time. Mass discharge was monitored to identify the link between source zone architecture and down-gradient contaminant flux. Contaminant characteristics and the presence of extensive low permeability lenses appeared to have the most influence on the development of a pool-dominated source zone. The link between DNAPL mass recovery and contaminant mass discharge was significantly influenced by the fraction of mass residing in DNAPL pools. The greater the fraction of mass residing in DNAPL pools the greater the likelihood for significant reductions in contaminant mass discharge at modest levels of mass removal. These results will help guide numerical and experimental studies on the remediation of pool-dominated source zones and will likely guide future source zone characterization efforts.

An architecture for a continuous, user-driven, and data-driven application of clinical guidelines and its evaluation.

PubMed

Shalom, Erez; Shahar, Yuval; Lunenfeld, Eitan

2016-02-01

Design, implement, and evaluate a new architecture for realistic continuous guideline (GL)-based decision support, based on a series of requirements that we have identified, such as support for continuous care, for multiple task types, and for data-driven and user-driven modes. We designed and implemented a new continuous GL-based support architecture, PICARD, which accesses a temporal reasoning engine, and provides several different types of application interfaces. We present the new architecture in detail in the current paper. To evaluate the architecture, we first performed a technical evaluation of the PICARD architecture, using 19 simulated scenarios in the preeclampsia/toxemia domain. We then performed a functional evaluation with the help of two domain experts, by generating patient records that simulate 60 decision points from six clinical guideline-based scenarios, lasting from two days to four weeks. Finally, 36 clinicians made manual decisions in half of the scenarios, and had access to the automated GL-based support in the other half. The measures used in all three experiments were correctness and completeness of the decisions relative to the GL. Mean correctness and completeness in the technical evaluation were 1±0.0 and 0.96±0.03 respectively. The functional evaluation produced only several minor comments from the two experts, mostly regarding the output's style; otherwise the system's recommendations were validated. In the clinically oriented evaluation, the 36 clinicians applied manually approximately 41% of the GL's recommended actions. Completeness increased to approximately 93% when using PICARD. Manual correctness was approximately 94.5%, and remained similar when using PICARD; but while 68% of the manual decisions included correct but redundant actions, only 3% of the actions included in decisions made when using PICARD were redundant. The PICARD architecture is technically feasible and is functionally valid, and addresses the realistic continuous GL-based application requirements that we have defined; in particular, the requirement for care over significant time frames. The use of the PICARD architecture in the domain we examined resulted in enhanced completeness and in reduction of redundancies, and is potentially beneficial for general GL-based management of chronic patients. Copyright © 2015 Elsevier Inc. All rights reserved.

Proceedings of the First Workshop on Service-Oriented Architectures and Software Product Lines

DTIC Science & Technology

2008-05-01

Addison-Wesley, Har- low, 2000. [8] Kang, K., Cohen, S., Hess, J., Novak, W., & Peterson, S. Feature-Oriented Domain Analysis ( FODA ) Feasibility...Intensive Systems-Description, 2000. [17] K. Kang, S. Cohen, J. Hess, W. No- vak, and S. Peterson. Feature- Oriented Domain Analysis ( FODA ...product models. SPF modeling employs many approaches such as Feature- Oriented Domain Analysis and extensions to existing approaches such as UML

Executing CLIPS expert systems in a distributed environment

NASA Technical Reports Server (NTRS)

Taylor, James; Myers, Leonard

1990-01-01

This paper describes a framework for running cooperating agents in a distributed environment to support the Intelligent Computer Aided Design System (ICADS), a project in progress at the CAD Research Unit of the Design Institute at the California Polytechnic State University. Currently, the systems aids an architectural designer in creating a floor plan that satisfies some general architectural constraints and project specific requirements. At the core of ICADS is the Blackboard Control System. Connected to the blackboard are any number of domain experts called Intelligent Design Tools (IDT). The Blackboard Control System monitors the evolving design as it is being drawn and helps resolve conflicts from the domain experts. The user serves as a partner in this system by manipulating the floor plan in the CAD system and validating recommendations made by the domain experts. The primary components of the Blackboard Control System are two expert systems executed by a modified CLIPS shell. The first is the Message Handler. The second is the Conflict Resolver. The Conflict Resolver synthesizes the suggestions made by the domain experts, which can be either CLIPS expert systems, or compiled C programs. In DEMO1, the current ICADS prototype, the CLIPS domain expert systems are Acoustics, Lighting, Structural, and Thermal; the compiled C domain experts are the CAD system and the User Interface.

Identification of a missing link in the evolution of an enzyme into a transcriptional regulator.

PubMed

Durante-Rodríguez, Gonzalo; Mancheño, José Miguel; Rivas, Germán; Alfonso, Carlos; García, José Luis; Díaz, Eduardo; Carmona, Manuel

2013-01-01

The evolution of transcriptional regulators through the recruitment of DNA-binding domains by enzymes is a widely held notion. However, few experimental approaches have directly addressed this hypothesis. Here we report the reconstruction of a plausible pathway for the evolution of an enzyme into a transcriptional regulator. The BzdR protein is the prototype of a subfamily of prokaryotic transcriptional regulators that controls the expression of genes involved in the anaerobic degradation of benzoate. We have shown that BzdR consists of an N-terminal DNA-binding domain connected through a linker to a C-terminal effector-binding domain that shows significant identity to the shikimate kinase (SK). The construction of active synthetic BzdR-like regulators by fusing the DNA-binding domain of BzdR to the Escherichia coli SKI protein strongly supports the notion that an ancestral SK domain could have been involved in the evolutionary origin of BzdR. The loss of the enzymatic activity of the ancestral SK domain was essential for it to evolve as a regulatory domain in the current BzdR protein. This work also supports the view that enzymes precede the emergence of the regulatory systems that may control their expression.

NASA evolution of exploration architectures

NASA Technical Reports Server (NTRS)

Roberts, Barney B.

1991-01-01

A series of charts and diagrams is used to provide a detailed overview of the evolution of NASA space exploration architectures. The pre-Apollo programs including the Werner von Braun feasibility study are discussed and the evolution of the Apollo program itself is treated in detail. The post-Apollo era is reviewed and attention is given to the resurgence of strategic planning exemplified by both ad hoc and formal efforts at planning. Results of NASA's study of the main elements of the Space Exploration Initiative which examined technical scenarios, science opportunities, required technologies, international considerations, institutional strengths and needs, and resource estimates are presented. The 90-day study concludes that, among other things, major investments in challenging technologies are required, the scientific opportunities provided by the program are considerable, current launch capabilities are inadequate, and Space Station Freedom is essential.

A multitasking general executive for compound continuous tasks.

PubMed

Salvucci, Dario D

2005-05-06

As cognitive architectures move to account for increasingly complex real-world tasks, one of the most pressing challenges involves understanding and modeling human multitasking. Although a number of existing models now perform multitasking in real-world scenarios, these models typically employ customized executives that schedule tasks for the particular domain but do not generalize easily to other domains. This article outlines a general executive for the Adaptive Control of Thought-Rational (ACT-R) cognitive architecture that, given independent models of individual tasks, schedules and interleaves the models' behavior into integrated multitasking behavior. To demonstrate the power of the proposed approach, the article describes an application to the domain of driving, showing how the general executive can interleave component subtasks of the driving task (namely, control and monitoring) and interleave driving with in-vehicle secondary tasks (radio tuning and phone dialing). 2005 Lawrence Erlbaum Associates, Inc.

Supporting diagnosis and treatment in medical care based on Big Data processing.

PubMed

Lupşe, Oana-Sorina; Crişan-Vida, Mihaela; Stoicu-Tivadar, Lăcrămioara; Bernard, Elena

2014-01-01

With information and data in all domains growing every day, it is difficult to manage and extract useful knowledge for specific situations. This paper presents an integrated system architecture to support the activity in the Ob-Gin departments with further developments in using new technology to manage Big Data processing - using Google BigQuery - in the medical domain. The data collected and processed with Google BigQuery results from different sources: two Obstetrics & Gynaecology Departments, the TreatSuggest application - an application for suggesting treatments, and a home foetal surveillance system. Data is uploaded in Google BigQuery from Bega Hospital Timişoara, Romania. The analysed data is useful for the medical staff, researchers and statisticians from public health domain. The current work describes the technological architecture and its processing possibilities that in the future will be proved based on quality criteria to lead to a better decision process in diagnosis and public health.

Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy.

PubMed

Li, Hongbin; Fernandez, Julio M

2003-11-14

The elastic I-band part of muscle protein titin contains two tandem immunoglobulin (Ig) domain regions of distinct mechanical properties. Until recently, the only known structure was that of the I27 module of the distal region, whose mechanical properties have been reported in detail. Recently, the structure of the first proximal domain, I1, has been resolved at 2.1A. In addition to the characteristic beta-sandwich structure of all titin Ig domains, the crystal structure of I1 showed an internal disulfide bridge that was proposed to modulate its mechanical extensibility in vivo. Here, we use single molecule force spectroscopy and protein engineering to examine the mechanical architecture of this domain. In contrast to the predictions made from the X-ray crystal structure, we find that the formation of a disulfide bridge in I1 is a relatively rare event in solution, even under oxidative conditions. Furthermore, our studies of the mechanical stability of I1 modules engineered with point mutations reveal significant differences between the mechanical unfolding of the I1 and I27 modules. Our study illustrates the varying mechanical architectures of the titin Ig modules.

HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG.

PubMed Central

Churchill, M E; Jones, D N; Glaser, T; Hefner, H; Searles, M A; Travers, A A

1995-01-01

The high mobility group (HMG) protein HMG-D from Drosophila melanogaster is a highly abundant chromosomal protein that is closely related to the vertebrate HMG domain proteins HMG1 and HMG2. In general, chromosomal HMG domain proteins lack sequence specificity. However, using both NMR spectroscopy and standard biochemical techniques we show that binding of HMG-D to a single DNA site is sequence selective. The preferred duplex DNA binding site comprises at least 5 bp and contains the deformable dinucleotide TG embedded in A/T-rich sequences. The TG motif constitutes a common core element in the binding sites of the well-characterized sequence-specific HMG domain proteins. We show that a conserved aromatic residue in helix 1 of the HMG domain may be involved in recognition of this core sequence. In common with other HMG domain proteins HMG-D binds preferentially to DNA sites that are stably bent and underwound, therefore HMG-D can be considered an architecture-specific protein. Finally, we show that HMG-D bends DNA and may confer a superhelical DNA conformation at a natural DNA binding site in the Drosophila fushi tarazu scaffold-associated region. Images PMID:7720717

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

The formation and evolution of domain walls

NASA Technical Reports Server (NTRS)

Press, William H.; Ryden, Barbara S.; Spergel, David N.

1991-01-01

Domain walls are sheet-like defects produced when the low energy vacuum has isolated degenerate minima. The researchers' computer code follows the evolution of a scalar field, whose dynamics are determined by its Lagrangian density. The topology of the scalar field determines the evolution of the domain walls. This approach treats both wall dynamics and reconnection. The researchers investigated not only potentials that produce single domain walls, but also potentials that produce a network of walls and strings. These networks arise in axion models where the U(1) Peccei-Quinn symmetry is broken into Z sub N discrete symmetries. If N equals 1, the walls are bounded by strings and the network quickly disappears. For N greater than 1, the network of walls and strings behaved qualitatively just as the wall network shown in the figures given here. This both confirms the researchers' pessimistic view that domain walls cannot play an important role in the formation of large scale structure and implies that axion models with multiple minimum can be cosmologically disastrous.

Big cats as a model system for the study of the evolution of intelligence.

PubMed

Borrego, Natalia

2017-08-01

Currently, carnivores, and felids in particular, are vastly underrepresented in cognitive literature, despite being an ideal model system for tests of social and ecological intelligence hypotheses. Within Felidae, big cats (Panthera) are uniquely suited to studies investigating the evolutionary links between social, ecological, and cognitive complexity. Intelligence likely did not evolve in a unitary way but instead evolved as the result of mutually reinforcing feedback loops within the physical and social environments. The domain-specific social intelligence hypothesis proposes that social complexity drives only the evolution of cognitive abilities adapted only to social domains. The domain-general hypothesis proposes that the unique demands of social life serve as a bootstrap for the evolution of superior general cognition. Big cats are one of the few systems in which we can directly address conflicting predictions of the domain-general and domain-specific hypothesis by comparing cognition among closely related species that face roughly equivalent ecological complexity but vary considerably in social complexity. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of the Translocation and Assembly Module (TAM)

PubMed Central

Heinz, Eva; Selkrig, Joel; Belousoff, Matthew J.; Lithgow, Trevor

2015-01-01

Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function. The central component of this machinery is BamA, an Omp85 protein that is essential and found in all Gram-negative bacteria. An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB. We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages. A comprehensive phylogenetic and secondary structure analysis of the TamB protein family revealed that TamB was present very early in the evolution of bacteria. Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands. Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi. PMID:25994932

Solar hydrogen production using epitaxial SrTiO 3 on a GaAs photovoltaic

DOE PAGES

Kornblum, L.; Fenning, D. P.; Faucher, J.; ...

2016-12-22

We demonstrate an oxide-stabilized III–V photoelectrode architecture for solar fuel production from water in neutral pH. For this tunable architecture we demonstrate 100% Faradaic efficiency for hydrogen evolution, and incident photon-to-current efficiencies (IPCE) exceeding 50%. High IPCE for hydrogen evolution is a consequence of the low-loss interface achieved via epitaxial growth of a thin oxide on a GaAs solar cell. Developing optimal energetic alignment across the interfaces of the photoelectrode using well-established III–V technology is key to obtaining high performance. This advance constitutes a critical milestone towards efficient, unassisted fuel production from solar energy.

Distributed Information Search and Retrieval for Astronomical Resource Discovery and Data Mining

NASA Astrophysics Data System (ADS)

Murtagh, Fionn; Guillaume, Damien

Information search and retrieval has become by nature a distributed task. We look at tools and techniques which are of importance in this area. Current technological evolution can be summarized as the growing stability and cohesiveness of distributed architectures of searchable objects. The objects themselves are more often than not multimedia, including published articles or grey literature reports, yellow page services, image data, catalogs, presentation and online display materials, and ``operations'' information such as scheduling and publicly accessible proposal information. The evolution towards distributed architectures, protocols and formats, and the direction of our own work, are focussed on in this paper.

3D genomics imposes evolution of the domain model of eukaryotic genome organization.

PubMed

Razin, Sergey V; Vassetzky, Yegor S

2017-02-01

The hypothesis that the genome is composed of a patchwork of structural and functional domains (units) that may be either active or repressed was proposed almost 30 years ago. Here, we examine the evolution of the domain model of eukaryotic genome organization in view of the expansion of genome-scale techniques in the twenty-first century that have provided us with a wealth of information on genome organization, folding, and functioning.

Centromeric enrichment of LINE-1 retrotransposons and its significance for the chromosome evolution of Phyllostomid bats.

PubMed

de Sotero-Caio, Cibele Gomes; Cabral-de-Mello, Diogo Cavalcanti; Calixto, Merilane da Silva; Valente, Guilherme Targino; Martins, Cesar; Loreto, Vilma; de Souza, Maria José; Santos, Neide

2017-10-01

Despite their ubiquitous incidence, little is known about the chromosomal distribution of long interspersed elements (LINEs) in mammalian genomes. Phyllostomid bats, characterized by lineages with distinct trends of chromosomal evolution coupled with remarkable ecological and taxonomic diversity, represent good models to understand how these repetitive sequences contribute to the evolution of genome architecture and its link to lineage diversification. To test the hypothesis that LINE-1 sequences were important modifiers of bat genome architecture, we characterized the distribution of LINE-1-derived sequences on genomes of 13 phyllostomid species within a phylogenetic framework. We found massive accumulation of LINE-1 elements in the centromeres of most species: a rare phenomenon on mammalian genomes. We hypothesize that expansion of these elements has occurred early in the radiation of phyllostomids and recurred episodically. LINE-1 expansions on centromeric heterochromatin probably spurred chromosomal change before the radiation of phyllostomids into the extant 11 subfamilies and contributed to the high degree of karyotypic variation observed among different lineages. Understanding centromere architecture in a variety of taxa promises to explain how lineage-specific changes on centromere structure can contribute to karyotypic diversity while not disrupting functional constraints for proper cell division.

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

PubMed Central

Spang, Anja; Saw, Jimmy H.; Lind, Anders E.; Ettema, Thijs J. G.

2013-01-01

The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. PMID:24348093

Switching from computer to microcomputer architecture education

NASA Astrophysics Data System (ADS)

Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

2010-03-01

In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to microcomputer architecture. The authors present their strategies towards a successful crossing of boundaries between engineering disciplines. This communication aims at providing a different aspect on professional courses that are, nowadays, addressed at the expense of traditional courses.

Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution

DOE PAGES

Sunden, Fanny; AlSadhan, Ishraq; Lyubimov, Artem; ...

2017-10-25

Members of enzyme superfamilies specialize in different reactions but often exhibit catalytic promiscuity for one another's reactions, consistent with catalytic promiscuity as an important driver in the evolution of new enzymes. Wanting to understand how catalytic promiscuity and other factors may influence evolution across a superfamily, we turned to the well-studied alkaline phosphatase (AP) superfamily, comparing three of its members, two evolutionarily distinct phosphatases and a phosphodiesterase. Here, we mutated distinguishing active-site residues to generate enzymes that had a common Zn 2+ bimetallo core but little sequence similarity and different auxiliary domains. We then tested the catalytic capabilities of thesemore » pruned enzymes with a series of substrates. A substantial rate enhancement of ~1011-fold for both phosphate mono- and diester hydrolysis by each enzyme indicated that the Zn 2+ bimetallo core is an effective mono/di-esterase generalist and that the bimetallo cores were not evolutionarily tuned to prefer their cognate reactions. In contrast, our pruned enzymes were ineffective sulfatases, and this limited promiscuity may have provided a driving force for founding the distinct one-metal-ion branch that contains all known AP superfamily sulfatases. Finally, our pruned enzymes exhibited 10 7–10 8-fold phosphotriesterase rate enhancements, despite absence of such enzymes within the AP superfamily. We speculate that the superfamily active-site architecture involved in nucleophile positioning prevents accommodation of the additional triester substituent. Overall, we suggest that catalytic promiscuity, and the ease or difficulty of remodeling and building onto existing protein scaffolds, have greatly influenced the course of enzyme evolution. Uncovering principles and properties of enzyme function, promiscuity, and repurposing provides lessons for engineering new enzymes.« less

Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution

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

Sunden, Fanny; AlSadhan, Ishraq; Lyubimov, Artem

Members of enzyme superfamilies specialize in different reactions but often exhibit catalytic promiscuity for one another's reactions, consistent with catalytic promiscuity as an important driver in the evolution of new enzymes. Wanting to understand how catalytic promiscuity and other factors may influence evolution across a superfamily, we turned to the well-studied alkaline phosphatase (AP) superfamily, comparing three of its members, two evolutionarily distinct phosphatases and a phosphodiesterase. Here, we mutated distinguishing active-site residues to generate enzymes that had a common Zn 2+ bimetallo core but little sequence similarity and different auxiliary domains. We then tested the catalytic capabilities of thesemore » pruned enzymes with a series of substrates. A substantial rate enhancement of ~1011-fold for both phosphate mono- and diester hydrolysis by each enzyme indicated that the Zn 2+ bimetallo core is an effective mono/di-esterase generalist and that the bimetallo cores were not evolutionarily tuned to prefer their cognate reactions. In contrast, our pruned enzymes were ineffective sulfatases, and this limited promiscuity may have provided a driving force for founding the distinct one-metal-ion branch that contains all known AP superfamily sulfatases. Finally, our pruned enzymes exhibited 10 7–10 8-fold phosphotriesterase rate enhancements, despite absence of such enzymes within the AP superfamily. We speculate that the superfamily active-site architecture involved in nucleophile positioning prevents accommodation of the additional triester substituent. Overall, we suggest that catalytic promiscuity, and the ease or difficulty of remodeling and building onto existing protein scaffolds, have greatly influenced the course of enzyme evolution. Uncovering principles and properties of enzyme function, promiscuity, and repurposing provides lessons for engineering new enzymes.« less

Frequency-Domain Streak Camera and Tomography for Ultrafast Imaging of Evolving and Channeled Plasma Accelerator Structures

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

Li Zhengyan; Zgadzaj, Rafal; Wang Xiaoming

2010-11-04

We demonstrate a prototype Frequency Domain Streak Camera (FDSC) that can capture the picosecond time evolution of the plasma accelerator structure in a single shot. In our prototype Frequency-Domain Streak Camera, a probe pulse propagates obliquely to a sub-picosecond pump pulse that creates an evolving nonlinear index 'bubble' in fused silica glass, supplementing a conventional Frequency Domain Holographic (FDH) probe-reference pair that co-propagates with the 'bubble'. Frequency Domain Tomography (FDT) generalizes Frequency-Domain Streak Camera by probing the 'bubble' from multiple angles and reconstructing its morphology and evolution using algorithms similar to those used in medical CAT scans. Multiplexing methods (Temporalmore » Multiplexing and Angular Multiplexing) improve data storage and processing capability, demonstrating a compact Frequency Domain Tomography system with a single spectrometer.« less

AMPHION: Specification-based programming for scientific subroutine libraries

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Waldinger, Richard; Stickel, Mark

1994-01-01

AMPHION is a knowledge-based software engineering (KBSE) system that guides a user in developing a diagram representing a formal problem specification. It then automatically implements a solution to this specification as a program consisting of calls to subroutines from a library. The diagram provides an intuitive domain oriented notation for creating a specification that also facilitates reuse and modification. AMPHION'S architecture is domain independent. AMPHION is specialized to an application domain by developing a declarative domain theory. Creating a domain theory is an iterative process that currently requires the joint expertise of domain experts and experts in automated formal methods for software development.

Large-scale brain networks in affective and social neuroscience: Towards an integrative functional architecture of the brain

PubMed Central

Barrett, Lisa Feldman; Satpute, Ajay

2013-01-01

Understanding how a human brain creates a human mind ultimately depends on mapping psychological categories and concepts to physical measurements of neural response. Although it has long been assumed that emotional, social, and cognitive phenomena are realized in the operations of separate brain regions or brain networks, we demonstrate that it is possible to understand the body of neuroimaging evidence using a framework that relies on domain general, distributed structure-function mappings. We review current research in affective and social neuroscience and argue that the emerging science of large-scale intrinsic brain networks provides a coherent framework for a domain-general functional architecture of the human brain. PMID:23352202

Enhancing Autonomy of Aerial Systems Via Integration of Visual Sensors into Their Avionics Suite

DTIC Science & Technology

2016-09-01

aerial platform for subsequent visual sensor integration. 14. SUBJECT TERMS autonomous system, quadrotors, direct method, inverse ...CONTROLLER ARCHITECTURE .....................................................43 B. INVERSE DYNAMICS IN THE VIRTUAL DOMAIN ......................45 1...control station GPS Global-Positioning System IDVD inverse dynamics in the virtual domain ILP integer linear program INS inertial-navigation system

Static Extraction and Conformance Analysis of Hierarchical Runtime Architectural Structure

DTIC Science & Technology

2010-05-14

Example: CryptoDB 253 Architectural Component Java Class Note CustomerManager cryptodb.test.CustomerManager AKA “ crypto consumer” CustomerManager.Receipts...PROVIDERS PLAIN KEYID KEYMANAGEMENT KEYSTORAGE CRYPTO (+) (+) (+) (+) (+) (+) (+)(+) Figure 7.29: CryptoDB: Level-0 OOG with String objects...better understand this communication, we declared different domains for plain-text (PLAIN), encrypted ( CRYPTO ), alias identifier (ALIASID), and key

The genetic architecture of pediatric cognitive abilities in the Philadelphia Neurodevelopmental Cohort

PubMed Central

Robinson, Elise B.; Kirby, Andrew; Ruparel, Kosha; Yang, Jian; McGrath, Lauren; Anttila, Verneri; Neale, Benjamin M.; Merikangas, Kathleen; Lehner, Thomas; Sleiman, Patrick M.A.; Daly, Mark J.; Gur, Ruben; Gur, Raquel; Hakonarson, Hakon

2014-01-01

The objective of this analysis was to examine the genetic architecture of diverse cognitive abilities in children and adolescents, including the magnitude of common genetic effects and patterns of shared and unique genetic influences. Subjects included 3,689 members of the Philadelphia Neurodevelopmental Cohort, a general population sample of ages 8-21 years who completed an extensive battery of cognitive tests. We used genome-wide complex trait analysis (GCTA) to estimate the SNP-based heritability of each domain, as well as the genetic correlation between all domains that showed significant genetic influence. Several of the individual domains suggested strong influence of common genetic variants (e.g. reading ability, h2g=0.43, p=4e-06; emotion identification, h2g=0.36, p=1e-05; verbal memory, h2g=0.24, p=0.005). The genetic correlations highlighted trait domains that are candidates for joint interrogation in future genetic studies (e.g. language reasoning and spatial reasoning, r(g)=0.72, p=0.007). These results can be used to structure future genetic and neuropsychiatric investigations of diverse cognitive abilities. PMID:25023143

Chimeric TALE recombinases with programmable DNA sequence specificity.

PubMed

Mercer, Andrew C; Gaj, Thomas; Fuller, Roberta P; Barbas, Carlos F

2012-11-01

Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.

A study of space station needs, attributes and architectural options, volume 2, technical. Book 3: Economic benefits, costs and programmatics

NASA Technical Reports Server (NTRS)

1983-01-01

The economic benefits, cost analysis, and industrial uses of the manned space station are investigated. Mission payload costs are examined in relation to alternative architectures and projected technological evolution. Various approaches to industrial involvement for financing, development, and marketing of space station resources are described.

A Roadmap for caGrid, an Enterprise Grid Architecture for Biomedical Research

PubMed Central

Saltz, Joel; Hastings, Shannon; Langella, Stephen; Oster, Scott; Kurc, Tahsin; Payne, Philip; Ferreira, Renato; Plale, Beth; Goble, Carole; Ervin, David; Sharma, Ashish; Pan, Tony; Permar, Justin; Brezany, Peter; Siebenlist, Frank; Madduri, Ravi; Foster, Ian; Shanbhag, Krishnakant; Mead, Charlie; Hong, Neil Chue

2012-01-01

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG™) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities. PMID:18560123

A roadmap for caGrid, an enterprise Grid architecture for biomedical research.

PubMed

Saltz, Joel; Hastings, Shannon; Langella, Stephen; Oster, Scott; Kurc, Tahsin; Payne, Philip; Ferreira, Renato; Plale, Beth; Goble, Carole; Ervin, David; Sharma, Ashish; Pan, Tony; Permar, Justin; Brezany, Peter; Siebenlist, Frank; Madduri, Ravi; Foster, Ian; Shanbhag, Krishnakant; Mead, Charlie; Chue Hong, Neil

2008-01-01

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities.

The Robustness of a Signaling Complex to Domain Rearrangements Facilitates Network Evolution

PubMed Central

Sato, Paloma M.; Yoganathan, Kogulan; Jung, Jae H.; Peisajovich, Sergio G.

2014-01-01

The rearrangement of protein domains is known to have key roles in the evolution of signaling networks and, consequently, is a major tool used to synthetically rewire networks. However, natural mutational events leading to the creation of proteins with novel domain combinations, such as in frame fusions followed by domain loss, retrotranspositions, or translocations, to name a few, often simultaneously replace pre-existing genes. Thus, while proteins with new domain combinations may establish novel network connections, it is not clear how the concomitant deletions are tolerated. We investigated the mechanisms that enable signaling networks to tolerate domain rearrangement-mediated gene replacements. Using as a model system the yeast mitogen activated protein kinase (MAPK)-mediated mating pathway, we analyzed 92 domain-rearrangement events affecting 11 genes. Our results indicate that, while domain rearrangement events that result in the loss of catalytic activities within the signaling complex are not tolerated, domain rearrangements can drastically alter protein interactions without impairing function. This suggests that signaling complexes can maintain function even when some components are recruited to alternative sites within the complex. Furthermore, we also found that the ability of the complex to tolerate changes in interaction partners does not depend on long disordered linkers that often connect domains. Taken together, our results suggest that some signaling complexes are dynamic ensembles with loose spatial constraints that could be easily re-shaped by evolution and, therefore, are ideal targets for cellular engineering. PMID:25490747

Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

PubMed

Eu, Byung Chan

2008-09-07

In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel.

Contextual cloud-based service oriented architecture for clinical workflow.

PubMed

Moreno-Conde, Jesús; Moreno-Conde, Alberto; Núñez-Benjumea, Francisco J; Parra-Calderón, Carlos

2015-01-01

Given that acceptance of systems within the healthcare domain multiple papers highlighted the importance of integrating tools with the clinical workflow. This paper analyse how clinical context management could be deployed in order to promote the adoption of cloud advanced services and within the clinical workflow. This deployment will be able to be integrated with the eHealth European Interoperability Framework promoted specifications. Throughout this paper, it is proposed a cloud-based service-oriented architecture. This architecture will implement a context management system aligned with the HL7 standard known as CCOW.

Using dSTORM to probe the molecular architecture of filopodia

NASA Astrophysics Data System (ADS)

Ahmed, Sohail; Chou, Amy; Sem, K. P.; Thankiah, Sudaharan; Wright, Graham; Lim, John; Hariharan, Srivats

2014-03-01

IRSp53 is a Cdc42 effector and a member of the Inverse-Bin-Amphiphysins-Rvs (I-BAR) domain family which can induce negative membrane curvature. IRSp53 generates filopodia by coupling membrane protrusion (I-BAR domain) with actin dynamics through its SH3 domain binding partners. Dynamin 1 (Dyn1), a large GTPase associated with endocytosis, is a novel interacting partner of IRSp53 that localises to filopodia. Using rapid time-lapse TIRF microscopy we have shown that Dyn1 localized to a subcellular region just behind Mena at the leading edge, or in filopodial tip complexes when co-expressed with IRSp53. Dyn1-GFP was strongly localized in the filopodial shaft during the early phase of elongation, after which it moved rearward, suggestive of a role in early filopodia assembly. Mena and Eps8, accumulate at the tip complex in sequence and are involved in filopodial extension and retraction, respectively (Chou at al, 2014 submitted). Here we describe the use of dSTORM to investigate the molecular architecture of filopodia and in particular the size of the F-actin bundle in these structures. The data suggest that direct Stochastic Optical Reconstruction Microscopy (dSTORM) in combination with other techniques will allow the molecular architecture of

Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

PubMed

Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

2016-05-24

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.

The evolution of sex ratio differences and inflorescence architectures in Begonia (Begoniaceae).

PubMed

Twyford, Alex D; Ennos, Richard A; White, Chris D; Ali, Mobina Shaukat; Kidner, Catherine A

2014-02-01

A major benefit conferred by monoecy is the ability to alter floral sex ratio in response to selection. In monoecious species that produce flowers of a given sex at set positions on the inflorescence, floral sex ratio may be related to inflorescence architecture. We studied the loci underlying differences in inflorescence architecture between two monoecious Begonia species and related this to floral sex ratios. We performed trait comparisons and quantitative trait locus (QTL) mapping in a segregating backcross population between Central American Begonia plebeja and B. conchifolia. We focused on traits related to inflorescence architecture, sex ratios, and other reproductive traits. The inflorescence branching pattern of B. conchifolia was more asymmetric than B. plebeja, which in turn affects the floral sex ratio. Colocalizing QTLs of moderate effect influenced both the number of male flowers and the fate decisions of axillary meristems, demonstrating the close link between inflorescence architecture and sex ratio. Additional QTLs were found for stamen number (30% variance explained, VE) and pollen sterility (12.3% VE). One way in which Begonia species develop different floral sex ratios is through modifications of their inflorescence architecture. The potential pleiotropic action of QTL on inflorescence branching and floral sex ratios may have major implications for trait evolution and responses to selection. The presence of a single QTL of large effect on stamen number may allow rapid divergence for this key floral trait. We propose candidate loci for stamen number and inflorescence branching for future characterization.

Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication

PubMed Central

Korithoski, Bryan; Kolaczkowski, Oralia; Mukherjee, Krishanu; Kola, Reema; Earl, Chandra; Kolaczkowski, Bryan

2015-01-01

The RIG-like receptors (RLRs) are related proteins that identify viral RNA in the cytoplasm and activate cellular immune responses, primarily through direct protein-protein interactions with the signal transducer, IPS1. Although it has been well established that the RLRs, RIG-I and MDA5, activate IPS1 through binding between the twin caspase activation and recruitment domains (CARDs) on the RLR and a homologous CARD on IPS1, it is less clear which specific RLR CARD(s) are required for this interaction, and almost nothing is known about how the RLR-IPS1 interaction evolved. In contrast to what has been observed in the presence of immune-modulating K63-linked polyubiquitin, here we show that—in the absence of ubiquitin—it is the first CARD domain of human RIG-I and MDA5 (CARD1) that binds directly to IPS1 CARD, and not the second (CARD2). Although the RLRs originated in the earliest animals, both the IPS1 gene and the twin-CARD domain architecture of RIG-I and MDA5 arose much later in the deuterostome lineage, probably through a series of tandem partial-gene duplication events facilitated by tight clustering of RLRs and IPS1 in the ancestral deuterostome genome. Functional differentiation of RIG-I CARD1 and CARD2 appears to have occurred early during this proliferation of RLR and related CARDs, potentially driven by adaptive coevolution between RIG-I CARD domains and IPS1 CARD. However, functional differentiation of MDA5 CARD1 and CARD2 occurred later. These results fit a general model in which duplications of protein-protein interaction domains into novel gene contexts could facilitate the expansion of signaling networks and suggest a potentially important role for functionally-linked gene clusters in generating novel immune-signaling pathways. PMID:26356745

Reader Architectures for Wireless Surface Acoustic Wave Sensors.

PubMed

Lurz, Fabian; Ostertag, Thomas; Scheiner, Benedict; Weigel, Robert; Koelpin, Alexander

2018-05-28

Wireless surface acoustic wave (SAW) sensors have some unique features that make them promising for industrial metrology. Their decisive advantage lies in their purely passive operation and the wireless readout capability allowing the installation also at particularly inaccessible locations. Furthermore, they are small, low-cost and rugged components on highly stable substrate materials and thus particularly suited for harsh environments. Nevertheless, a sensor itself does not carry out any measurement but always requires a suitable excitation and interrogation circuit: a reader. A variety of different architectures have been presented and investigated up to now. This review paper gives a comprehensive survey of the present state of reader architectures such as time domain sampling (TDS), frequency domain sampling (FDS) and hybrid concepts for both SAW resonators and reflective SAW delay line sensors. Furthermore, critical performance parameters such as measurement accuracy, dynamic range, update rate, and hardware costs of the state of the art in science and industry are presented, compared and discussed.

Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.

PubMed

Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J

2017-01-01

Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

Independent Axes of Genetic Variation and Parallel Evolutionary Divergence Of Opercle Bone Shape in Threespine Stickleback

PubMed Central

Kimmel, Charles B.; Cresko, William A.; Phillips, Patrick C.; Ullmann, Bonnie; Currey, Mark; von Hippel, Frank; Kristjánsson, Bjarni K.; Gelmond, Ofer; McGuigan, Katrina

2014-01-01

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance– covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture. PMID:22276538

Image and Morphology in Modern Theory of Architecture

NASA Astrophysics Data System (ADS)

Yankovskaya, Y. S.; Merenkov, A. V.

2017-11-01

This paper is devoted to some important and fundamental problems of the modern Russian architectural theory. These problems are: methodological and technological retardation; substitution of the modern professional architectural theoretical knowledge by the humanitarian concepts; preference of the traditional historical or historical-theoretical research. One of the most probable ways is the formation of useful modern subject (and multi-subject)-oriented concepts in architecture. To get over the criticism and distrust of the architectural theory is possible through the recognition of an important role of the subject (architect, consumer, contractor, ruler, etc.) and direction of the practical tasks of the forming human environment in the today’s rapidly changing world and post-industrial society. In this article we consider the evolution of two basic concepts for the theory of architecture such as the image and morphology.

Masticatory muscle architecture in the Laotian rock rat Laonastes aenigmamus (Mammalia, Rodentia): new insights into the evolution of hystricognathy.

PubMed

Hautier, Lionel; Saksiri, Soonchan

2009-10-01

We present the first descriptive comparison of the skull, mandible and jaw muscles of the recently recovered Laotian rock rat Laonastes aenigmamus. The gross anatomy of five specimens captured in Laos and internal architecture of the jaw musculature were studied using dissections. The following muscles are described: temporal, masseter, pterygoids, digastric, mylohyoid, geniohyoid and transverse mandibular. The description of the masticatory apparatus of L. aenigmamus offers a rare opportunity to assess the order of establishment of the morphological characters during the evolution of Ctenohystrica. Striking convergences have occurred during the evolution of Diatomyidae and L. aenigmamus presents a unique combination of myological features that corresponds to a mixture of sciurognathous and hystricognathous characters. If L. aenigmamus is a sciurognathous rodent, we have to assume that it independently acquired a pars reflexa of the superficial masseter. We show for the first time that the development of this pars reflexa has occurred several times during the evolution of Ctenohystrica and can no longer be considered a synapomorphic feature of 'Hystricognathi'. These results bring new insights into the evolution of hystricognathy and have profound implications for the interpretation of the fossil record of early hystricognath rodents.

Domain walls in the extensions of the Standard Model

NASA Astrophysics Data System (ADS)

Krajewski, Tomasz; Lalak, Zygmunt; Lewicki, Marek; Olszewski, Paweł

2018-05-01

Our main interest is the evolution of domain walls of the Higgs field in the early Universe. The aim of this paper is to understand how dynamics of Higgs domain walls could be influenced by yet unknown interactions from beyond the Standard Model. We assume that the Standard Model is valid up to certain, high, energy scale Λ and use the framework of the effective field theory to describe physics below that scale. Performing numerical simulations with different values of the scale Λ we are able to extend our previous analysis [1]. Our recent numerical simulations show that evolution of Higgs domain walls is rather insensitive to interactions beyond the Standard Model as long as masses of new particles are grater than 1012 GeV. For lower values of Λ the RG improved effective potential is strongly modified at field strengths crucial to the evolution of domain walls. However, we find that even for low values of Λ, Higgs domain walls decayed shortly after their formation for generic initial conditions. On the other hand, in simulations with specifically chosen initial conditions Higgs domain walls can live longer and enter the scaling regime. We also determine the energy spectrum of gravitational waves produced by decaying domain walls of the Higgs field. For generic initial field configurations the amplitude of the signal is too small to be observed in planned detectors.

Rift systems in the southern North Atlantic: why did some fail and others not?

NASA Astrophysics Data System (ADS)

Nirrengarten, M.; Manatschal, G.; Tugend, J.; Kusznir, N. J.; Sauter, D.

2017-12-01

Orphan, Rockall, Porcupine, Parentis and Pyrenean Basins are failed rift systems surrounding the southern North Atlantic Ocean. The failure or succeessing of a rift system is intimately linked to the question of what controls lithospheric breakup and what keeps oceanic spreading alive. Extension rates and the thermal structure are usually the main parameters invoked. However, between the rifts that succeeded and those that failed, the relative control and relative importance of these parameters is not clear. Cessation of driving forces, strain hardening or competition between concurrent rifts are hypotheses often used to explain rift failure. In this work, we aim to analyze the influence of far field forces on the abandon of rift systems in the southern North Atlantic domain using plate kinematic modeling. A new reconstruction approach that integrates the spatio-temporal evolution of rifted basins has been developed. The plate modeling is based on the definition, mapping and restoration of rift domains using 3D gravity inversions methods that provide crustal thickness maps. The kinematic description of each rift system enables us to discuss the local rift evolution relative to the far field kinematic framework. The resulting model shows a strong segmentation of the different rift systems during extreme crustal thinning that are crosscut by V-shape propagators linked to the exhumation of mantle and emplacement of first oceanic crust. The northward propagating lithospheric breakup of the southern North Atlantic may be partly triggered and channeled by extreme lithospheric thinning. However, at Aptian-Albian time, the northward propagating lithospheric breakup diverts and is partitioned along a transtensional system resulting in the abandon of the Orphan and Rockall basins. The change in the propagation direction may be related to a local strain weakening along existing/inherited transfer zones and/or, alternatively, to a more global plate reorganization. The cessation of the Bay of Biscay-Pyrenean system is related to the northward motion of Africa at Campanian/Santonian time, resulting in a competition between incipient seafloor spreading and far field forces. A concordance between far field forces, lithospheric architecture and strain weakening seems necessary to create a sustainable oceanic domain.

Muscovite-Dehydration Melting: A Textural Study of a Key Reaction in Transforming Continental Margin Strata Into a Migmatitic Orogenic Core

NASA Astrophysics Data System (ADS)

Dyck, B. J.; St Onge, M. R.; Waters, D. J.; Searle, M. P.

2015-12-01

Metamorphosed continental margin sedimentary sequences, which comprise the dominant tectonostratigraphic assemblage exposed in orogenic hinterlands, are crucial to understanding the architecture and evolution of collisional mountain belts. This study explores the textural effect of anatexis in amphibolite-grade conditions and documents the mineral growth mechanisms that control nucleation and growth of K-feldspar, sillimanite and silicate melt. The constrained textural evolution follows four stages: 1) Nucleation - K-feldspar is documented to nucleate epitaxially on isomorphic plagioclase in quartzofeldspathic (psammitic) domains, whereas sillimanite nucleates in the Al-rich (pelitic) domain, initially on [001] mica planes. The first melt forms at the site of muscovite breakdown. 2) Chemically driven growth - In the quartzofeldspathic domain, K-feldspar progressively replaces plagioclase by a K+ - Na+ cation transfer reaction, driven by the freeing of muscovite-bound K+ during breakdown of the mica. Sillimanite forms intergrowths with the remaining hydrous melt components, contained initially in ovoid clots. 3) Merge and coarsening - With an increase in pressure, melt and sillimanite migrate away from clots along grain boundaries. A melt threshold is reached once the grain-boundary network is wetted by melt, increasing the length-scale of diffusion, resulting in grain boundary migration and grain-size coarsening. The melt threshold denotes the transition to an open-system on the lithology scale, where melt is a transient phase. 4) Residual melt crystallization - Residual melt crystallizes preferentially on existing peritectic grains as anatectic quartz, plagioclase, and K-feldspar. As the system cools and closes, grain growth forces melt into the intersections of grain-boundaries, recognized as irregular shaped melt films, or as intergrowths of the volatile-rich phases (i.e. Tur-Ms-Ap). In the Himalayan metamorphic core these processes result in the formation of: pelitic K-feldspar augen gneiss, stockwork leucogranites, and an effective strengthening of the hinterland, as evidenced by a switch in tectonic deformation style, from thin-skinned cover sequence thrust imbrication and folding to out-of-sequence basement-involved thick-skinned thrusting and folding.

Internet-enabled collaborative agent-based supply chains

NASA Astrophysics Data System (ADS)

Shen, Weiming; Kremer, Rob; Norrie, Douglas H.

2000-12-01

This paper presents some results of our recent research work related to the development of a new Collaborative Agent System Architecture (CASA) and an Infrastructure for Collaborative Agent Systems (ICAS). Initially being proposed as a general architecture for Internet based collaborative agent systems (particularly complex industrial collaborative agent systems), the proposed architecture is very suitable for managing the Internet enabled complex supply chain for a large manufacturing enterprise. The general collaborative agent system architecture with the basic communication and cooperation services, domain independent components, prototypes and mechanisms are described. Benefits of implementing Internet enabled supply chains with the proposed infrastructure are discussed. A case study on Internet enabled supply chain management is presented.

Big data processing in the cloud - Challenges and platforms

NASA Astrophysics Data System (ADS)

Zhelev, Svetoslav; Rozeva, Anna

2017-12-01

Choosing the appropriate architecture and technologies for a big data project is a difficult task, which requires extensive knowledge in both the problem domain and in the big data landscape. The paper analyzes the main big data architectures and the most widely implemented technologies used for processing and persisting big data. Clouds provide for dynamic resource scaling, which makes them a natural fit for big data applications. Basic cloud computing service models are presented. Two architectures for processing big data are discussed, Lambda and Kappa architectures. Technologies for big data persistence are presented and analyzed. Stream processing as the most important and difficult to manage is outlined. The paper highlights main advantages of cloud and potential problems.

Disentangling the control of tectonics, eustasy, trophic conditions and climate on shallow-marine carbonate production during the Aalenian-Oxfordian interval: From the western France platform to the western Tethyan domain

NASA Astrophysics Data System (ADS)

Andrieu, Simon; Brigaud, Benjamin; Barbarand, Jocelyn; Lasseur, Eric; Saucède, Thomas

2016-11-01

The objective of this work is to improve our understanding of the processes controlling changes in the architecture and facies of intracontinental carbonate platforms. We examined the facies and sequence stratigraphy of Aalenian to Oxfordian limestones of western France. Seventy-seven outcrop sections were studied and thirty-one sedimentary facies identified in five depositional environments ranging from lower offshore to backshore. Platform evolution was reconstructed along a 500 km cross-section. Twenty-two depositional sequences were identified on the entire western France platform and correlated with European third-order sequences at the biozone level, demonstrating that eustasy was the major factor controlling the cyclic trend of accommodation. The tectonic subsidence rate was computed from accommodation measurements from the Aalenian to the Oxfordian in key localities. Tectonism controlled the sedimentation rate and platform architecture at a longer time scale. Tectonic subsidence triggered the demise of carbonate production at the Bathonian/Callovian boundary while the uplift made possible the recovery of carbonate platform from Caen to Le Mans during the mid Oxfordian. Topography of the Paleozoic basement mainly controlled lateral variations of paleodepth within the western France platform until the mid Bathonian. A synthesis of carbonate production in the western Tethyan domain at that time was conducted. Stages of high carbonate production during the Bajocian/Bathonian and the middle to late Oxfordian are synchronous with low δ13C, high eccentricity intervals, and rather dry climate promoting (1) evaporation and carbonate supersaturation, and (2) oligotrophic conditions. Periods of low carbonate production during the Aalenian and from the middle Callovian to early Oxfordian correlate with high δ13C and low eccentricity intervals, characterized by wet climate and less oligotrophic conditions. Such conditions tend to diminish growth potential of carbonate platforms. This work highlights the importance of climate control on carbonate growth and demise at large scale in western Tethyan epicontinental seas.

Specializing architectures for the type 2 diabetes mellitus care use cases with a focus on process management.

PubMed

Uribe, Gustavo A; Blobel, Bernd; López, Diego M; Ruiz, Alonso A

2015-01-01

The development of software supporting inter-disciplinary systems like the type 2 diabetes mellitus care requires the deployment of methodologies designed for this type of interoperability. The GCM framework allows the architectural description of such systems and the development of software solutions based on it. A first step of the GCM methodology is the definition of a generic architecture, followed by its specialization for specific use cases. This paper describes the specialization of the generic architecture of a system, supporting Type 2 diabetes mellitus glycemic control, for a pharmacotherapy use case. It focuses on the behavioral aspect of the system, i.e. the policy domain and the definition of the rules governing the system. The design of this architecture reflects the inter-disciplinary feature of the methodology. Finally, the resulting architecture allows building adaptive, intelligent and complete systems.

High Order Semi-Lagrangian Advection Scheme

NASA Astrophysics Data System (ADS)

Malaga, Carlos; Mandujano, Francisco; Becerra, Julian

2014-11-01

In most fluid phenomena, advection plays an important roll. A numerical scheme capable of making quantitative predictions and simulations must compute correctly the advection terms appearing in the equations governing fluid flow. Here we present a high order forward semi-Lagrangian numerical scheme specifically tailored to compute material derivatives. The scheme relies on the geometrical interpretation of material derivatives to compute the time evolution of fields on grids that deform with the material fluid domain, an interpolating procedure of arbitrary order that preserves the moments of the interpolated distributions, and a nonlinear mapping strategy to perform interpolations between undeformed and deformed grids. Additionally, a discontinuity criterion was implemented to deal with discontinuous fields and shocks. Tests of pure advection, shock formation and nonlinear phenomena are presented to show performance and convergence of the scheme. The high computational cost is considerably reduced when implemented on massively parallel architectures found in graphic cards. The authors acknowledge funding from Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).

Multiwavelength optical source at 12.5-GHz optical spacing based on a coupled optoelectronic oscillator with a whispering gallery mode resonator

NASA Astrophysics Data System (ADS)

Kossakovski, Dmitri; Solomatine, Iouri V.; Morozov, Nikolai; Ilchenko, Vladimir S.

2004-06-01

The evolution of optical networks calls for denser channel grids and increased number of channels. Additionally, there is a system architecture benefit to eliminate the banks of DFB lasers that act as light sources for individual channels, and use instead a single multi-wavelength source. We have demonstrated a compact multi-wavelength optical source (MWS) for 12.5 GHz DWDM. At least 16 channels are observed within 3 dB optical power bandwidth with optical spectrum contrast ratio exceeding 28 dB. The source is based on a coupled opto-electronic oscillator (COEO) with an optical whispering gallery mode (WGM) microresonator. Free spectral range of the resonator determines the spacing of the optical channels in the MWS. The spacing can be scaled up or down depending on design requirements. The resonator is robustly packaged and fiber pigtailed. In the RF domain the MWS acts as oscillator with operational frequency of 12.5 GHz.

Distributed Cooperation Solution Method of Complex System Based on MAS

NASA Astrophysics Data System (ADS)

Weijin, Jiang; Yuhui, Xu

To adapt the model in reconfiguring fault diagnosing to dynamic environment and the needs of solving the tasks of complex system fully, the paper introduced multi-Agent and related technology to the complicated fault diagnosis, an integrated intelligent control system is studied in this paper. Based on the thought of the structure of diagnostic decision and hierarchy in modeling, based on multi-layer decomposition strategy of diagnosis task, a multi-agent synchronous diagnosis federation integrated different knowledge expression modes and inference mechanisms are presented, the functions of management agent, diagnosis agent and decision agent are analyzed, the organization and evolution of agents in the system are proposed, and the corresponding conflict resolution algorithm in given, Layered structure of abstract agent with public attributes is build. System architecture is realized based on MAS distributed layered blackboard. The real world application shows that the proposed control structure successfully solves the fault diagnose problem of the complex plant, and the special advantage in the distributed domain.

ROADMs for reconfigurable metro networks

NASA Astrophysics Data System (ADS)

Homa, Jonathan; Bala, Krishna

2009-01-01

Reconfigurable Optical Add-Drop Multiplexers (ROADMs) are the key nodal sub-systems that are used to implement modern DWDM networks. They provide network flexibility by switching wavelengths among fibers under software control without expensive conversion to the electronic domain. They speed up provisioning time, reduce operational costs and eliminate human errors. Two general types of ROADMs are used in Metro optical networks, two-degree and multi-degree, where the degree refers to the numbers of DWDM fibers entering and exiting the ROADM node. A twodegree ROADM is like a location on a highway with off and on ramps to drop off and accept local traffic while a multidegree ROADM is like an interchange where highways meet and is used for interconnecting DWDM rings or for mesh networking. The paper describes two-degree and multi-degree ROADM architectures and how these relate to the technology alternatives used to implement the ROADMs themselves. Focus is provided on the role and expected evolution of the wavelength selective switch (WSS) which is the primary engine used to power ROADMs.

Potomacapnos apeleutheron gen. et sp. nov., a new Early Cretaceous angiosperm from the Potomac Group and its implications for the evolution of eudicot leaf architecture.

PubMed

Jud, Nathan A; Hickey, Leo J

2013-12-01

Eudicots diverged early in the evolution of flowering plants and now comprise more than 70% of angiosperm species. In spite of the importance of eudicots, our understanding of the early evolution of this clade is limited by a poor fossil record and uncertainty about the order of early phylogenetic branching. The study of Lower Cretaceous fossils can reveal much about the evolution, morphology, and ecology of the eudicots. Fossils described here were collected from Aptian sediments of the Potomac Group exposed at the Dutch Gap locality in Virginia, USA. Specimens were prepared by degaging, then described and compared with leaves of relevant extant and fossil plants. We conducted a phylogenetic analysis of morphological characters using parsimony while constraining the tree search with the topology found through molecular phylogenetic analyses. The new species is closely related to ranunculalean eudicots and has leaf architecture remarkably similar to some living Fumarioideae (Papaveraceae). These are the oldest eudicot megafossils from North America, and they show complex leaf architecture reflecting developmental pathways unique to extant eudicots. The morphology and small size of the fossils suggest that they were herbaceous plants, as is seen in other putative early eudicots. The absence of co-occurring tricolpate pollen at Dutch Gap either (1) reflects low preservation probability for pollen of entomophilous herbs or (2) indicates that some leaf features of extant eudicots appeared before the origin of tricolpate pollen.

Characterization of Inclusions in Evolution of Sodium Sulfate Using Terahertz Time-domain Spectroscopy.

PubMed

Bao, Rima; Wu, Zhikui; Li, Hao; Wang, Fang; Miao, Xinyang; Feng, Chengjing

2017-01-01

The study of fluid inclusion is one of the important means to understanding the evolution of mineral crystals, and can therefore provide original information of mineral evolution. In the process of evolution, outside factors such as temperature and pressure, directly affect the number and size of inclusions, and thus are related to the properties of crystals. In this paper, terahertz time-domain spectroscopy (THz-TDS) was used to detect sodium sulfate crystals with different growth temperatures, and absorption coefficient spectra of the samples were obtained. It is suggested that the evolution of sodium sulfate could be divided into two stages, and 80°C was the turning point. X-ray diffraction (XRD) and polarizing microscopy were used to support this conclusion. The research showed that THz-TDS could characterize the evolution of mineral crystals, and it had a unique advantage in terms of crystal evolution.

Seed tissue and nutrient partitioning, a case for the nucellus.

PubMed

Lu, Jing; Magnani, Enrico

2018-06-05

Flowering plants display a large spectrum of seed architectures. The volume ratio of maternal versus zygotic seed tissues changes considerably among species and underlies different nutrient-storing strategies. Such diversity arose through the evolution of cell elimination programs that regulate the relative growth of one tissue over another to become the major storage compartment. The elimination of the nucellus maternal tissue is regulated by developmental programs that marked the origin of angiosperms and outlined the most ancient seed architectures. This review focuses on such a defining mechanism for seed evolution and discusses the role of nucellus development in seed tissues and nutrient partitioning at the light of novel discoveries on its molecular regulation.

Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T*

PubMed Central

Wang, Weijun; Yan, Ruoyu; Nocek, Boguslaw P.; Vuong, Thu V.; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Gatenholm, Paul; Toriz, Guillermo; Tenkanen, Maija; Savchenko, Alexei; Master, Emma R.

2016-01-01

Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups. Herein, a family GH115 enzymefrom the marine bacterium Saccharophagus degradans 2-40T, SdeAgu115A, demonstrated activity toward glucuronoxylan and oligomers thereof with preference toward MeGlcAp linked to internal xylopyranosyl residues. Unique biochemical characteristics of NaCl activation were also observed. The crystal structure of SdeAgu115A revealed a five-domain architecture, with an additional insertion C+ domain that had significant impact on the domain arrangement of SdeAgu115A monomer and its dimerization. The participation of domain C+ in substrate binding was supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp-335, the catalytic essentiality of Glu-216 was revealed by site-specific mutagenesis. A primary sequence analysis suggested that the SdeAgu115A architecture is shared by more than half of GH115 members, thus defining a distinct archetype for GH115 enzymes. PMID:27129264

From scenarios to domain models: processes and representations

NASA Astrophysics Data System (ADS)

Haddock, Gail; Harbison, Karan

1994-03-01

The domain specific software architectures (DSSA) community has defined a philosophy for the development of complex systems. This philosophy improves productivity and efficiency by increasing the user's role in the definition of requirements, increasing the systems engineer's role in the reuse of components, and decreasing the software engineer's role to the development of new components and component modifications only. The scenario-based engineering process (SEP), the first instantiation of the DSSA philosophy, has been adopted by the next generation controller project. It is also the chosen methodology of the trauma care information management system project, and the surrogate semi-autonomous vehicle project. SEP uses scenarios from the user to create domain models and define the system's requirements. Domain knowledge is obtained from a variety of sources including experts, documents, and videos. This knowledge is analyzed using three techniques: scenario analysis, task analysis, and object-oriented analysis. Scenario analysis results in formal representations of selected scenarios. Task analysis of the scenario representations results in descriptions of tasks necessary for object-oriented analysis and also subtasks necessary for functional system analysis. Object-oriented analysis of task descriptions produces domain models and system requirements. This paper examines the representations that support the DSSA philosophy, including reference requirements, reference architectures, and domain models. The processes used to create and use the representations are explained through use of the scenario-based engineering process. Selected examples are taken from the next generation controller project.

BH-ShaDe: A Software Tool That Assists Architecture Students in the III-Structured Task of Housing Design

ERIC Educational Resources Information Center

Millan, Eva; Belmonte, Maria-Victoria; Ruiz-Montiel, Manuela; Gavilanes, Juan; Perez-de-la-Cruz, Jose-Luis

2016-01-01

In this paper, we present BH-ShaDe, a new software tool to assist architecture students learning the ill-structured domain/task of housing design. The software tool provides students with automatic or interactively generated floor plan schemas for basic houses. The students can then use the generated schemas as initial seeds to develop complete…

A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells

PubMed Central

Schulein, Ralf; Guye, Patrick; Rhomberg, Thomas A.; Schmid, Michael C.; Schröder, Gunnar; Vergunst, Annette C.; Carena, Ilaria; Dehio, Christoph

2005-01-01

Bacterial type IV secretion (T4S) systems mediate the transfer of macromolecular substrates into various target cells, e.g., the conjugative transfer of DNA into bacteria or the transfer of virulence proteins into eukaryotic host cells. The T4S apparatus VirB of the vascular tumor-inducing pathogen Bartonella henselae causes subversion of human endothelial cell (HEC) function. Here we report the identification of multiple protein substrates of VirB, which, upon translocation into HEC, mediate all known VirB-dependent cellular changes. These Bartonella-translocated effector proteins (Beps) A-G are encoded together with the VirB system and the T4S coupling protein VirD4 on a Bartonella-specific pathogenicity island. The Beps display a modular architecture, suggesting an evolution by extensive domain duplication and reshuffling. The C terminus of each Bep harbors at least one copy of the Bep-intracellular delivery domain and a short positively charged tail sequence. This biparte C terminus constitutes a transfer signal that is sufficient to mediate VirB/VirD4-dependent intracellular delivery of reporter protein fusions. The Bep-intracellular delivery domain is also present in conjugative relaxases of bacterial conjugation systems. We exemplarily show that the C terminus of such a conjugative relaxase mediates protein transfer through the Bartonella henselae VirB/VirD4 system into HEC. Conjugative relaxases may thus represent the evolutionary origin of the here defined T4S signal for protein transfer into human cells. PMID:15642951

Evolution of the Standard Simulation Architecture

DTIC Science & Technology

2004-06-01

Interoperability Workshop, Paper 02S-SIW-016. 5. Deitel & Deitel , 2001. “C++ How to Program , Third Edition.” Prentice Hall, Inc., Upper Saddle...carefully followed for software to be successfully reused in other programs . The Standard Simulation Architecture (SSA) promotes these principles...capabilities described in this paper have been developed and successfully used on various government programs . This paper attempts to bring these

SAMS--a systems architecture for developing intelligent health information systems.

PubMed

Yılmaz, Özgün; Erdur, Rıza Cenk; Türksever, Mustafa

2013-12-01

In this paper, SAMS, a novel health information system architecture for developing intelligent health information systems is proposed and also some strategies for developing such systems are discussed. The systems fulfilling this architecture will be able to store electronic health records of the patients using OWL ontologies, share patient records among different hospitals and provide physicians expertise to assist them in making decisions. The system is intelligent because it is rule-based, makes use of rule-based reasoning and has the ability to learn and evolve itself. The learning capability is provided by extracting rules from previously given decisions by the physicians and then adding the extracted rules to the system. The proposed system is novel and original in all of these aspects. As a case study, a system is implemented conforming to SAMS architecture for use by dentists in the dental domain. The use of the developed system is described with a scenario. For evaluation, the developed dental information system will be used and tried by a group of dentists. The development of this system proves the applicability of SAMS architecture. By getting decision support from a system derived from this architecture, the cognitive gap between experienced and inexperienced physicians can be compensated. Thus, patient satisfaction can be achieved, inexperienced physicians are supported in decision making and the personnel can improve their knowledge. A physician can diagnose a case, which he/she has never diagnosed before, using this system. With the help of this system, it will be possible to store general domain knowledge in this system and the personnel's need to medical guideline documents will be reduced.

Fault architecture and deformation processes within poorly lithified rift sediments, Central Greece

NASA Astrophysics Data System (ADS)

Loveless, Sian; Bense, Victor; Turner, Jenni

2011-11-01

Deformation mechanisms and resultant fault architecture are primary controls on the permeability of faults in poorly lithified sediments. We characterise fault architecture using outcrop studies, hand samples, thin sections and grain-size data from a minor (1-10 m displacement) normal-fault array exposed within Gulf of Corinth rift sediments, Central Greece. These faults are dominated by mixed zones with poorly developed fault cores and damage zones. In poorly lithified sediment deformation is distributed across the mixed zone as beds are entrained and smeared. We find particulate flow aided by limited distributed cataclasis to be the primary deformation mechanism. Deformation may be localised in more competent sediments. Stratigraphic variations in sediment competency, and the subsequent alternating distributed and localised strain causes complexities within the mixed zone such as undeformed blocks or lenses of cohesive sediment, or asperities at the mixed zone/protolith boundary. Fault tip bifurcation and asperity removal are important processes in the evolution of these fault zones. Our results indicate that fault zone architecture and thus permeability is controlled by a range of factors including lithology, stratigraphy, cementation history and fault evolution, and that minor faults in poorly lithified sediment may significantly impact subsurface fluid flow.

Problems of Implementing SCORM in an Enterprise Distance Learning Architecture: SCORM Incompatibility across Multiple Web Domains.

ERIC Educational Resources Information Center

Engelbrecht, Jeffrey C.

2003-01-01

Delivering content to distant users located in dispersed networks, separated by firewalls and different web domains requires extensive customization and integration. This article outlines some of the problems of implementing the Sharable Content Object Reference Model (SCORM) in the Marine Corps' Distance Learning System (MarineNet) and extends…

Early tectonic evolution of the Thomson Orogen in Queensland inferred from constrained magnetic and gravity data

NASA Astrophysics Data System (ADS)

Spampinato, Giovanni P. T.; Betts, Peter G.; Ailleres, Laurent; Armit, Robin J.

2015-05-01

The crustal architecture as well as the kinematic evolution of the Thomson Orogen in Queensland is poorly resolved because the region is concealed under thick Phanerozoic sedimentary basins and the basement geology is known from limited drill holes. Combined potential field and seismic interpretation indicates that the Thomson Orogen is characterized by prominent regional NE- and NW-trending structural grain defined by long wavelength and low amplitude geophysical anomalies. The 'smooth' magnetic signature is interpreted to reflect deeply buried source bodies in the mid- to lower crust. Short wavelength positive magnetic features that correlate with negative gravity anomalies are interpreted to represent shallower granitic intrusions. They appear to be focused along major fault zones that might have controlled the locus for magmatism. The eastern Thomson Orogen is characterized by a prominent NE structural grain and orthogonal faults and fold interference patterns resulting in a series of troughs and highs. The western Thomson Orogen consists of a series of NW-trending structures interpreted to reflect reverse faults. Sedimentation and basin development are interpreted to have initiated in the Neoproterozoic to Early Cambrian during E-W- to ENE-WSW extension, possibly related to the Rodinia break-up. This extensional event was followed by Late Cambrian shortening recorded in the Maneroo Platform and the Diamantina River Domain which possibly correlates with the Delamerian Orogeny. Renewed deposition and volcanism occurred during the Ordovician and may have continued until Late Silurian, resulting in thinned Proterozoic basement crust and extensive basin systems that formed in a distal continental back-arc environment. Our interpretation places the Thomson Orogen to the west of the Neoproterozoic passive margin preserved in the Anakie Inlier. The region is likely to represent the internal extensional architecture during the Rodinia break-up that has been subsequently extensively modified by multiple extensional basin forming events and transient episodes of crustal shortening and basin inversion.

Thermal Control System Automation Project (TCSAP)

NASA Technical Reports Server (NTRS)

Boyer, Roger L.

1991-01-01

Information is given in viewgraph form on the Space Station Freedom (SSF) Thermal Control System Automation Project (TCSAP). Topics covered include the assembly of the External Thermal Control System (ETCS); the ETCS functional schematic; the baseline Fault Detection, Isolation, and Recovery (FDIR), including the development of a knowledge based system (KBS) for application of rule based reasoning to the SSF ETCS; TCSAP software architecture; the High Fidelity Simulator architecture; the TCSAP Runtime Object Database (RODB) data flow; KBS functional architecture and logic flow; TCSAP growth and evolution; and TCSAP relationships.

A U.S. perspective on the human exploration and expansion on the planet Mars

NASA Technical Reports Server (NTRS)

Roberts, Barney B.; Connolly, John F.

1992-01-01

A NASA perspective on the human exploration of Mars is presented which is based on the fundamental background available from the many previous studies. A hypothetical architecture of the Mars surface system is described which represents the complete spectrum of envisioned activities. Using the Strategic Implementation Architecture it is possible to construct a thoughtful roadmap which would enable a logical and flexible evolution of missions. Based on that architecture a suite of Martian surface elements is proposed to provide increasing levels of capability to the maturing infrastructure.

A multidisciplinary study on the crustal architecture and tectonic evolution of the Biligiri Rangan Block, southern India: Implications for Neoarchean plate tectonics

NASA Astrophysics Data System (ADS)

Raveendran Thankamoni, Ratheesh Kumar

2017-04-01

Southern India is comprised of a collage of crustal blocks ranging in age from Archean to Neoproterozoic. Previous studies considered the Archean high-grade granulite terrain to the north of the Southern Granuilte Terrain (SGT) of southern India as the part of the Dharwar Craton and hence subdivided this craton into western, central and eastern provinces. This contribution presents my detailed examinations on the least studied Central Dharwar Province, comprising the Biligiri Rangan (BR) - Male Mahadeshwara (MM) Hills domain composed predominantly of charnockites. One of my recent study (Ratheesh-Kumar et al., 2016) for the first time provided necessary evidence for Neoarchean subduction-accretion-collision tectonic evolution of this domain as a separate crustal block which has been named as Biligiri Rangan Block (BRB) by using a multidisciplinary approach involving field investigation, petrography, mineral chemistry, thermodynamic modeling of metamorphic P-T evolution, and LA-ICPMS U-Pb and Lu-Hf analyses of zircons on representative rocks together with regional-scale crustal thickness model derived using isostatic gravimetric geophysical method. The important findings of this study are: (1) The BRB preserves the vestiges of a Mesoarchean primitive continental crust as indicated by the age (ca. 3207) and positive ɛHf value (+2.7) of quartzofeldspathic gneiss occurred in the central part of the block (2) The charnockites and associated mafic granulites and granites provide ages between ca. 2650 Ma and ca. 2498 Ma with large negative ɛHf values are suggestive of Neoarchean charnockitization and crustal remelting (3) New geochemical data of charnockites and mafic granulites from BRB are consistent with arc magmatic rocks generated through oceanic plate subduction (4) Delineation of a suture zone along the Kollegal structural lineament bounding the BRB and the Western Dharwar Craton surmised from the occurrences of quartzite-iron formation intercalations and also mafic-ultramafic lenses along this lineament with their evolution through a clockwise prograde and retrograde metamorphism in a subduction zone setting at a high-pressure of 18-19 kbar and temperature of ˜840°C (5) Spatial variation of crustal thickness data reveal high crustal thickness in the Biligiri Rangan and the Nilgiri Blocks, and are attributed to a more competently thickened crust resulted by the subduction and collision processes. Based on these results, this study proposes a new tectonic model for the evolution of the BRB that envisages eastward subduction of the Western Dharwar oceanic crust beneath the BRB along the Kollegal suture zone resulted in the arc magmatism during the Neoarchean. The relevance of this study relies on the fact that the proposed evolutionary model revises the existing debates on the tectonic framework and evolution of the Archean terranes of southern India.

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

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

Saad, Tony; Sutherland, James C.

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

DOE PAGES

Saad, Tony; Sutherland, James C.

2016-05-04

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

Eigensolution of finite element problems in a completely connected parallel architecture

NASA Technical Reports Server (NTRS)

Akl, Fred A.; Morel, Michael R.

1989-01-01

A parallel algorithm for the solution of the generalized eigenproblem in linear elastic finite element analysis, (K)(phi)=(M)(phi)(omega), where (K) and (M) are of order N, and (omega) is of order q is presented. The parallel algorithm is based on a completely connected parallel architecture in which each processor is allowed to communicate with all other processors. The algorithm has been successfully implemented on a tightly coupled multiple-instruction-multiple-data (MIMD) parallel processing computer, Cray X-MP. A finite element model is divided into m domains each of which is assumed to process n elements. Each domain is then assigned to a processor, or to a logical processor (task) if the number of domains exceeds the number of physical processors. The macro-tasking library routines are used in mapping each domain to a user task. Computational speed-up and efficiency are used to determine the effectiveness of the algorithm. The effect of the number of domains, the number of degrees-of-freedom located along the global fronts and the dimension of the subspace on the performance of the algorithm are investigated. For a 64-element rectangular plate, speed-ups of 1.86, 3.13, 3.18 and 3.61 are achieved on two, four, six and eight processors, respectively.

Parallel eigenanalysis of finite element models in a completely connected architecture

NASA Technical Reports Server (NTRS)

Akl, F. A.; Morel, M. R.

1989-01-01

A parallel algorithm is presented for the solution of the generalized eigenproblem in linear elastic finite element analysis, (K)(phi) = (M)(phi)(omega), where (K) and (M) are of order N, and (omega) is order of q. The concurrent solution of the eigenproblem is based on the multifrontal/modified subspace method and is achieved in a completely connected parallel architecture in which each processor is allowed to communicate with all other processors. The algorithm was successfully implemented on a tightly coupled multiple-instruction multiple-data parallel processing machine, Cray X-MP. A finite element model is divided into m domains each of which is assumed to process n elements. Each domain is then assigned to a processor or to a logical processor (task) if the number of domains exceeds the number of physical processors. The macrotasking library routines are used in mapping each domain to a user task. Computational speed-up and efficiency are used to determine the effectiveness of the algorithm. The effect of the number of domains, the number of degrees-of-freedom located along the global fronts and the dimension of the subspace on the performance of the algorithm are investigated. A parallel finite element dynamic analysis program, p-feda, is documented and the performance of its subroutines in parallel environment is analyzed.

A New Model for Allosteric Regulation of Phenylalanine Hydroxylase: Implications for Disease and Therapeutics

PubMed Central

Stith, Linda; Lawrence, Sarah H.; Andrake, Mark; Dunbrack, Roland L.

2013-01-01

The structural basis for allosteric regulation of phenylalanine hydroxylase (PAH), whose dysfunction causes phenylketonuria (PKU), is poorly understood. A new morpheein model for PAH allostery is proposed to consist of a dissociative equilibrium between two architecturally different tetramers whose interconversion requires a ~90° rotation between the PAH catalytic and regulatory domains, the latter of which contains an ACT domain. This unprecedented model is supported by in vitro data on purified full length rat and human PAH. The conformational change is both predicted to and shown to render the tetramers chromatographically separable using ion exchange methods. One novel aspect of the activated tetramer model is an allosteric phenylalanine binding site at the inter-subunit interface of ACT domains. Amino acid ligand-stabilized ACT domain dimerization follows the multimerization and ligand binding behavior of ACT domains present in other proteins in the PDB. Spectroscopic, chromatographic, and electrophoretic methods demonstrate a PAH equilibrium consisting of two architecturally distinct tetramers as well as dimers. We postulate that PKU-associated mutations may shift the PAH quaternary structure equilibrium in favor of the low activity assemblies. Pharmacological chaperones that stabilize the ACT:ACT interface can potentially provide PKU patients with a novel small molecule therapeutic. PMID:23296088

Mission Services Evolution Center Message Bus

NASA Technical Reports Server (NTRS)

Mayorga, Arturo; Bristow, John O.; Butschky, Mike

2011-01-01

The Goddard Mission Services Evolution Center (GMSEC) Message Bus is a robust, lightweight, fault-tolerant middleware implementation that supports all messaging capabilities of the GMSEC API. This architecture is a distributed software system that routes messages based on message subject names and knowledge of the locations in the network of the interested software components.

φ-evo: A program to evolve phenotypic models of biological networks.

PubMed

Henry, Adrien; Hemery, Mathieu; François, Paul

2018-06-01

Molecular networks are at the core of most cellular decisions, but are often difficult to comprehend. Reverse engineering of network architecture from their functions has proved fruitful to classify and predict the structure and function of molecular networks, suggesting new experimental tests and biological predictions. We present φ-evo, an open-source program to evolve in silico phenotypic networks performing a given biological function. We include implementations for evolution of biochemical adaptation, adaptive sorting for immune recognition, metazoan development (somitogenesis, hox patterning), as well as Pareto evolution. We detail the program architecture based on C, Python 3, and a Jupyter interface for project configuration and network analysis. We illustrate the predictive power of φ-evo by first recovering the asymmetrical structure of the lac operon regulation from an objective function with symmetrical constraints. Second, we use the problem of hox-like embryonic patterning to show how a single effective fitness can emerge from multi-objective (Pareto) evolution. φ-evo provides an efficient approach and user-friendly interface for the phenotypic prediction of networks and the numerical study of evolution itself.

Evolution of Bow-Tie Architectures in Biology

PubMed Central

Friedlander, Tamar; Mayo, Avraham E.; Tlusty, Tsvi; Alon, Uri

2015-01-01

Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. PMID:25798588

Architecture of Allosteric Materials and Edge Modes

NASA Astrophysics Data System (ADS)

Yan, Le; Ravasio, Riccardo; Brito, Carolina; Wyart, Matthieu

Allostery, a long-range elasticity-mediated interaction, remains the biggest mystery decades after its discovery in proteins. We introduce a numerical scheme to evolve functional materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures and the correlations among them can be computed. As an example, we consider an ``allosteric'' task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites and that the amplitude of the elastic response varies non-monotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a new window to study the relationship between structure, function, and correlations emerging during evolution. L.Y. was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915. M.W. thanks the Swiss National Science Foundation for support under Grant No. 200021-165509 and the Simons Foundation Grant (#454953 Matthieu Wyart).

Formalism Challenges of the Cougaar Model Driven Architecture

NASA Technical Reports Server (NTRS)

Bohner, Shawn A.; George, Boby; Gracanin, Denis; Hinchey, Michael G.

2004-01-01

The Cognitive Agent Architecture (Cougaar) is one of the most sophisticated distributed agent architectures developed today. As part of its research and evolution, Cougaar is being studied for application to large, logistics-based applications for the Department of Defense (DoD). Anticipiting future complex applications of Cougaar, we are investigating the Model Driven Architecture (MDA) approach to understand how effective it would be for increasing productivity in Cougar-based development efforts. Recognizing the sophistication of the Cougaar development environment and the limitations of transformation technologies for agents, we have systematically developed an approach that combines component assembly in the large and transformation in the small. This paper describes some of the key elements that went into the Cougaar Model Driven Architecture approach and the characteristics that drove the approach.

Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution.

PubMed

Jenkins, Dafyd J; Stekel, Dov J

2010-02-01

Gene regulation is one important mechanism in producing observed phenotypes and heterogeneity. Consequently, the study of gene regulatory network (GRN) architecture, function and evolution now forms a major part of modern biology. However, it is impossible to experimentally observe the evolution of GRNs on the timescales on which living species evolve. In silico evolution provides an approach to studying the long-term evolution of GRNs, but many models have either considered network architecture from non-adaptive evolution, or evolution to non-biological objectives. Here, we address a number of important modelling and biological questions about the evolution of GRNs to the realistic goal of biomass production. Can different commonly used simulation paradigms, in particular deterministic and stochastic Boolean networks, with and without basal gene expression, be used to compare adaptive with non-adaptive evolution of GRNs? Are these paradigms together with this goal sufficient to generate a range of solutions? Will the interaction between a biological goal and evolutionary dynamics produce trade-offs between growth and mutational robustness? We show that stochastic basal gene expression forces shrinkage of genomes due to energetic constraints and is a prerequisite for some solutions. In systems that are able to evolve rates of basal expression, two optima, one with and one without basal expression, are observed. Simulation paradigms without basal expression generate bloated networks with non-functional elements. Further, a range of functional solutions was observed under identical conditions only in stochastic networks. Moreover, there are trade-offs between efficiency and yield, indicating an inherent intertwining of fitness and evolutionary dynamics.

Evolution of a protein folding nucleus.

PubMed

Xia, Xue; Longo, Liam M; Sutherland, Mason A; Blaber, Michael

2016-07-01

The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome. © 2015 The Protein Society.

The importance of structural softening for the evolution and architecture of passive margins

PubMed Central

Duretz, T.; Petri, B.; Mohn, G.; Schmalholz, S. M.; Schenker, F. L.; Müntener, O.

2016-01-01

Lithospheric extension can generate passive margins that bound oceans worldwide. Detailed geological and geophysical studies in present and fossil passive margins have highlighted the complexity of their architecture and their multi-stage deformation history. Previous modeling studies have shown the significant impact of coarse mechanical layering of the lithosphere (2 to 4 layer crust and mantle) on passive margin formation. We built upon these studies and design high-resolution (~100–300 m) thermo-mechanical numerical models that incorporate finer mechanical layering (kilometer scale) mimicking tectonically inherited heterogeneities. During lithospheric extension a variety of extensional structures arises naturally due to (1) structural softening caused by necking of mechanically strong layers and (2) the establishment of a network of weak layers across the deforming multi-layered lithosphere. We argue that structural softening in a multi-layered lithosphere is the main cause for the observed multi-stage evolution and architecture of magma-poor passive margins. PMID:27929057

Evolution of the Florida Launch Site Architecture: Embracing Multiple Customers, Enhancing Launch Opportunities

NASA Technical Reports Server (NTRS)

Colloredo, Scott; Gray, James A.

2011-01-01

The impending conclusion of the Space Shuttle Program and the Constellation Program cancellation unveiled in the FY2011 President's budget created a large void for human spaceflight capability and specifically launch activity from the Florida launch Site (FlS). This void created an opportunity to re-architect the launch site to be more accommodating to the future NASA heavy lift and commercial space industry. The goal is to evolve the heritage capabilities into a more affordable and flexible launch complex. This case study will discuss the FlS architecture evolution from the trade studies to select primary launch site locations for future customers, to improving infrastructure; promoting environmental remediation/compliance; improving offline processing, manufacturing, & recovery; developing range interface and control services with the US Air Force, and developing modernization efforts for the launch Pad, Vehicle Assembly Building, Mobile launcher, and supporting infrastructure. The architecture studies will steer how to best invest limited modernization funding from initiatives like the 21 st elSe and other potential funding.

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain: Periplasmic Ligand Binding Protein Dret_0059

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

Wu, R.; Wilton, R.; Cuff, M. E.

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes butmore » have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.« less

Identification of a Novel TGF-β-Binding Site in the Zona Pellucida C-terminal (ZP-C) Domain of TGF-β-Receptor-3 (TGFR-3)

PubMed Central

Diestel, Uschi; Resch, Marcus; Meinhardt, Kathrin; Weiler, Sigrid; Hellmann, Tina V.; Mueller, Thomas D.; Nickel, Joachim; Eichler, Jutta; Muller, Yves A.

2013-01-01

The zona pellucida (ZP) domain is present in extracellular proteins such as the zona pellucida proteins and tectorins and participates in the formation of polymeric protein networks. However, the ZP domain also occurs in the cytokine signaling co-receptor transforming growth factor β (TGF-β) receptor type 3 (TGFR-3, also known as betaglycan) where it contributes to cytokine ligand recognition. Currently it is unclear how the ZP domain architecture enables this dual functionality. Here, we identify a novel major TGF-β-binding site in the FG loop of the C-terminal subdomain of the murine TGFR-3 ZP domain (ZP-C) using protein crystallography, limited proteolysis experiments, surface plasmon resonance measurements and synthetic peptides. In the murine 2.7 Å crystal structure that we are presenting here, the FG-loop is disordered, however, well-ordered in a recently reported homologous rat ZP-C structure. Surprisingly, the adjacent external hydrophobic patch (EHP) segment is registered differently in the rat and murine structures suggesting that this segment only loosely associates with the remaining ZP-C fold. Such a flexible and temporarily-modulated association of the EHP segment with the ZP domain has been proposed to control the polymerization of ZP domain-containing proteins. Our findings suggest that this flexibility also extends to the ZP domain of TGFR-3 and might facilitate co-receptor ligand interaction and presentation via the adjacent FG-loop. This hints that a similar C-terminal region of the ZP domain architecture possibly regulates both the polymerization of extracellular matrix proteins and cytokine ligand recognition of TGFR-3. PMID:23826237

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.

PubMed

Wu, R; Wilton, R; Cuff, M E; Endres, M; Babnigg, G; Edirisinghe, J N; Henry, C S; Joachimiak, A; Schiffer, M; Pokkuluri, P R

2017-04-01

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from Lake Retba, in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously, and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport. © 2017 The Protein Society.

Evolution of the snake body form reveals homoplasy in amniote Hox gene function.

PubMed

Head, Jason J; Polly, P David

2015-04-02

Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior-posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.

The neural architecture of expert calendar calculation: a matter of strategy?

PubMed

Fehr, Thorsten; Wallace, Gregory L; Erhard, Peter; Herrmann, Manfred

2011-08-01

Savants and prodigies are individuals with exceptional skills in particular mental domains. In the present study we used functional magnetic resonance imaging to examine neural correlates of calendar calculation in two individuals, a savant with Asperger's disorder and a self-taught mathematical prodigy. If there is a modular neural organization of exceptional performance in a specific mental domain, calendar calculation should be reflected in a considerable overlap in the recruitment of brain circuits across expert individuals. However, considerable individual differences in activation patterns during calendar calculation were noted. The present results indicate that activation patterns produced by complex mental processing, such as calendar calculation, seem to be influenced strongly by learning history and idiosyncratic strategy usage rather than a modular neural organization. Thus, well-known individual differences in complex cognition play a major role even in experts with exceptional abilities in a particular mental domain and should in particular be considered when examining the neural architecture of complex mental processes and skills.

Structure of the Zinc-Bound Amino-Terminal Domain of the NMDA Receptor NR2B Subunit

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

Karakas, E.; Simorowski, N; Furukawa, H

2009-01-01

N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors (iGluRs) that mediate the majority of fast excitatory synaptic transmission in the mammalian brain. One of the hallmarks for the function of NMDA receptors is that their ion channel activity is allosterically regulated by binding of modulator compounds to the extracellular amino-terminal domain (ATD) distinct from the L-glutamate-binding domain. The molecular basis for the ATD-mediated allosteric regulation has been enigmatic because of a complete lack of structural information on NMDA receptor ATDs. Here, we report the crystal structures of ATD from the NR2B NMDA receptor subunit in the zinc-freemore » and zinc-bound states. The structures reveal the overall clamshell-like architecture distinct from the non-NMDA receptor ATDs and molecular determinants for the zinc-binding site, ion-binding sites, and the architecture of the putative phenylethanolamine-binding site.« less

Hypercube matrix computation task

NASA Technical Reports Server (NTRS)

Calalo, Ruel H.; Imbriale, William A.; Jacobi, Nathan; Liewer, Paulett C.; Lockhart, Thomas G.; Lyzenga, Gregory A.; Lyons, James R.; Manshadi, Farzin; Patterson, Jean E.

1988-01-01

A major objective of the Hypercube Matrix Computation effort at the Jet Propulsion Laboratory (JPL) is to investigate the applicability of a parallel computing architecture to the solution of large-scale electromagnetic scattering problems. Three scattering analysis codes are being implemented and assessed on a JPL/California Institute of Technology (Caltech) Mark 3 Hypercube. The codes, which utilize different underlying algorithms, give a means of evaluating the general applicability of this parallel architecture. The three analysis codes being implemented are a frequency domain method of moments code, a time domain finite difference code, and a frequency domain finite elements code. These analysis capabilities are being integrated into an electromagnetics interactive analysis workstation which can serve as a design tool for the construction of antennas and other radiating or scattering structures. The first two years of work on the Hypercube Matrix Computation effort is summarized. It includes both new developments and results as well as work previously reported in the Hypercube Matrix Computation Task: Final Report for 1986 to 1987 (JPL Publication 87-18).

Modular, Cost-Effective, Extensible Avionics Architecture for Secure, Mobile Communications

NASA Technical Reports Server (NTRS)

Ivancic, William D.

2006-01-01

Current onboard communication architectures are based upon an all-in-one communications management unit. This unit and associated radio systems has regularly been designed as a one-off, proprietary system. As such, it lacks flexibility and cannot adapt easily to new technology, new communication protocols, and new communication links. This paper describes the current avionics communication architecture and provides a historical perspective of the evolution of this system. A new onboard architecture is proposed that allows full use of commercial-off-the-shelf technologies to be integrated in a modular approach thereby enabling a flexible, cost-effective and fully deployable design that can take advantage of ongoing advances in the computer, cryptography, and telecommunications industries.

Modular, Cost-Effective, Extensible Avionics Architecture for Secure, Mobile Communications

NASA Technical Reports Server (NTRS)

Ivancic, William D.

2007-01-01

Current onboard communication architectures are based upon an all-in-one communications management unit. This unit and associated radio systems has regularly been designed as a one-off, proprietary system. As such, it lacks flexibility and cannot adapt easily to new technology, new communication protocols, and new communication links. This paper describes the current avionics communication architecture and provides a historical perspective of the evolution of this system. A new onboard architecture is proposed that allows full use of commercial-off-the-shelf technologies to be integrated in a modular approach thereby enabling a flexible, cost-effective and fully deployable design that can take advantage of ongoing advances in the computer, cryptography, and telecommunications industries.

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

PubMed Central

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-01

Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies. PMID:19154605

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.

PubMed

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-20

Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

Did Convergent Protein Evolution Enable Phytoplasmas to Generate 'Zombie Plants'?

PubMed

Rümpler, Florian; Gramzow, Lydia; Theißen, Günter; Melzer, Rainer

2015-12-01

Phytoplasmas are pathogenic bacteria that reprogram plant development such that leaf-like structures instead of floral organs develop. Infected plants are sterile and mainly serve to propagate phytoplasmas and thus have been termed 'zombie plants'. The developmental reprogramming relies on specific interactions of the phytoplasma protein SAP54 with a small subset of MADS-domain transcription factors. Here, we propose that SAP54 folds into a structure that is similar to that of the K-domain, a protein-protein interaction domain of MADS-domain proteins. We suggest that undergoing convergent structural and sequence evolution, SAP54 evolved to mimic the K-domain. Given the high specificity of resulting developmental alterations, phytoplasmas might be used to study flower development in genetically intractable plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Birth and death of protein domains: A simple model of evolution explains power law behavior

PubMed Central

Karev, Georgy P; Wolf, Yuri I; Rzhetsky, Andrey Y; Berezovskaya, Faina S; Koonin, Eugene V

2002-01-01

Background Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. Results A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i) domain birth (duplication with divergence), ii) death (inactivation and/or deletion), and iii) innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer). This formalism can be described as a birth, death and innovation model (BDIM). The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational models, are considered in details and the distributions of the equilibrium frequencies of domain families of different size are determined for each case. We apply the BDIM formalism to the analysis of the domain family size distributions in prokaryotic and eukaryotic proteomes and show an excellent fit between these empirical data and a particular form of the model, the second-order balanced linear BDIM. Calculation of the parameters of these models suggests surprisingly high innovation rates, comparable to the total domain birth (duplication) and elimination rates, particularly for prokaryotic genomes. Conclusions We show that a straightforward model of genome evolution, which does not explicitly include selection, is sufficient to explain the observed distributions of domain family sizes, in which power laws appear as asymptotic. However, for the model to be compatible with the data, there has to be a precise balance between domain birth, death and innovation rates, and this is likely to be maintained by selection. The developed approach is oriented at a mathematical description of evolution of domain composition of proteomes, but a simple reformulation could be applied to models of other evolving networks with preferential attachment. PMID:12379152

Birth and death of protein domains: a simple model of evolution explains power law behavior.

PubMed

Karev, Georgy P; Wolf, Yuri I; Rzhetsky, Andrey Y; Berezovskaya, Faina S; Koonin, Eugene V

2002-10-14

Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i) domain birth (duplication with divergence), ii) death (inactivation and/or deletion), and iii) innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer). This formalism can be described as a birth, death and innovation model (BDIM). The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational models, are considered in details and the distributions of the equilibrium frequencies of domain families of different size are determined for each case. We apply the BDIM formalism to the analysis of the domain family size distributions in prokaryotic and eukaryotic proteomes and show an excellent fit between these empirical data and a particular form of the model, the second-order balanced linear BDIM. Calculation of the parameters of these models suggests surprisingly high innovation rates, comparable to the total domain birth (duplication) and elimination rates, particularly for prokaryotic genomes. We show that a straightforward model of genome evolution, which does not explicitly include selection, is sufficient to explain the observed distributions of domain family sizes, in which power laws appear as asymptotic. However, for the model to be compatible with the data, there has to be a precise balance between domain birth, death and innovation rates, and this is likely to be maintained by selection. The developed approach is oriented at a mathematical description of evolution of domain composition of proteomes, but a simple reformulation could be applied to models of other evolving networks with preferential attachment.

Model-Drive Architecture for Agent-Based Systems

NASA Technical Reports Server (NTRS)

Gradanin, Denis; Singh, H. Lally; Bohner, Shawn A.; Hinchey, Michael G.

2004-01-01

The Model Driven Architecture (MDA) approach uses a platform-independent model to define system functionality, or requirements, using some specification language. The requirements are then translated to a platform-specific model for implementation. An agent architecture based on the human cognitive model of planning, the Cognitive Agent Architecture (Cougaar) is selected for the implementation platform. The resulting Cougaar MDA prescribes certain kinds of models to be used, how those models may be prepared and the relationships of the different kinds of models. Using the existing Cougaar architecture, the level of application composition is elevated from individual components to domain level model specifications in order to generate software artifacts. The software artifacts generation is based on a metamodel. Each component maps to a UML structured component which is then converted into multiple artifacts: Cougaar/Java code, documentation, and test cases.

A reconfigurable multicarrier demodulator architecture

NASA Technical Reports Server (NTRS)

Kwatra, S. C.; Jamali, M. M.

1991-01-01

An architecture based on parallel and pipline design approaches has been developed for the Frequency Division Multiple Access/Time Domain Multiplexed (FDMA/TDM) conversion system. The architecture has two main modules namely the transmultiplexer and the demodulator. The transmultiplexer has two pipelined modules. These are the shared multiplexed polyphase filter and the Fast Fourier Transform (FFT). The demodulator consists of carrier, clock, and data recovery modules which are interactive. Progress on the design of the MultiCarrier Demodulator (MCD) using commercially available chips and Application Specific Integrated Circuits (ASIC) and simulation studies using Viewlogic software will be presented at the conference.

A framework for semantic interoperability in healthcare: a service oriented architecture based on health informatics standards.

PubMed

Ryan, Amanda; Eklund, Peter

2008-01-01

Healthcare information is composed of many types of varying and heterogeneous data. Semantic interoperability in healthcare is especially important when all these different types of data need to interact. Presented in this paper is a solution to interoperability in healthcare based on a standards-based middleware software architecture used in enterprise solutions. This architecture has been translated into the healthcare domain using a messaging and modeling standard which upholds the ideals of the Semantic Web (HL7 V3) combined with a well-known standard terminology of clinical terms (SNOMED CT).

A fast, programmable hardware architecture for spaceborne SAR processing

NASA Technical Reports Server (NTRS)

Bennett, J. R.; Cumming, I. G.; Lim, J.; Wedding, R. M.

1983-01-01

The launch of spaceborne SARs during the 1980's is discussed. The satellite SARs require high quality and high throughput ground processors. Compression ratios in range and azimuth of greater than 500 and 150 respectively lead to frequency domain processing and data computation rates in excess of 2000 million real operations per second for C-band SARs under consideration. Various hardware architectures are examined and two promising candidates and proceeds to recommend a fast, programmable hardware architecture for spaceborne SAR processing are selected. Modularity and programmability are introduced as desirable attributes for the purpose of HTSP hardware selection.

Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression.

PubMed

van Steensel, Bas; Belmont, Andrew S

2017-05-18

In metazoan cell nuclei, hundreds of large chromatin domains are in close contact with the nuclear lamina. Such lamina-associated domains (LADs) are thought to help organize chromosomes inside the nucleus and have been associated with gene repression. Here, we discuss the properties of LADs, the molecular mechanisms that determine their association with the nuclear lamina, their dynamic links with other nuclear compartments, and their proposed roles in gene regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

Superfluid Boson-Fermion Mixture: Structure Formation and Collective Periodic Motion

NASA Astrophysics Data System (ADS)

Mitra, A.

2018-01-01

Multiple periodic domain formation due to a modulation instability in a boson-fermion mixture superfluid in the unitary regime has been studied. The periodicity of the structure evolves with time. At the early stage of evolution, bosonic domains show the periodic nature, whereas the periodicity in the fermionic (Cooper pair) domains appears at the late stage of evolution. The nature of interatomic interspecies interactions affects the domain formation. In a harmonic trap, the mixture executes an undamped oscillation. The frequency of the oscillation depends on the relative coupling strength between boson-fermion and fermion-fermion. The repulsive boson-fermion interaction reduces the oscillation frequency, whereas the attractive interaction enhances the frequency significantly.

Functional innovation from changes in protein domains and their combinations.

PubMed

Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

2016-06-01

Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Functional Properties at Domain Walls in BiFeO3: Electrical, Magnetic, and Structural investigations

NASA Astrophysics Data System (ADS)

He, Qing; Yang, C.-H.; Yu, P.; Gajek, M.; Seidel, J.; Ramesh, R.; Wang, F.; Chu, Y.-H.; Martin, L. W.; Spaldin, N.; Rother, A.

2009-03-01

BiFeO3 (BFO) is a widely studied robust ferroelectric, antiferromagnetic multiferroic. Conducting-atomic force microscopy studies reveal the presence of enhanced conductivity at certain types of domain walls in BFO. We have completed detailed TEM studies of the physical structure at these domain walls as well as in-depth DFT calculations of the evolution of electronic structure at these domain walls. These studies reveal two major contributions to the observed conduction: the formation of an electrostatic potential at the domain walls as well as a structurally-driven change in the electronic structure (i.e., a lower band gap locally) at the domain walls. We will discuss the use of optical characterization techniques as a way of probing this change in electronic structure at domain walls as well as detailed IV characterization both in atmospheric and UHV environments. Finally, the evolution of magnetism at these domain walls has been studied through the use of photoemission measurements. Initial findings point to a significant change in the magnetic order at these domain walls in BFO.

Adaptive Acquisition: An Evolving Framework for Tailoring Engineering and Procurement of Defense Systems

DTIC Science & Technology

2017-01-31

mapping critical business workflows and then optimizing them with appropriate evolutionary technology choices is often called “ Product Line Architecture... technologies , products , services, and processes, and the USG evaluates them against its 360o requirements objectives, and refines them as appropriate, clarity...in rapidly evolving technological domains (e.g. by applying best commercial practices for open standard product line architecture.) An MP might be

Derivation of Rigid Body Analysis Models from Vehicle Architecture Abstractions

DTIC Science & Technology

2011-06-17

models of every type have their basis in some type of physical representation of the design domain. Rather than describing three-dimensional continua of...arrangement, while capturing just enough physical detail to be used as the basis for a meaningful representation of the design , and eventually, analyses that...permit architecture assessment. The design information captured by the abstractions is available at the very earliest stages of the vehicle

Software Architecture Evolution

DTIC Science & Technology

2013-12-01

system’s major components occurring via a Java Message Service message bus [69]. This architecture was designed to promote loose coupling of soft- ware...play reconfiguration of the system. The components were Java -based and platform-independent; the interfaces by which they communicated were based on...The MPCS database, a MySQL database used for storing telemetry as well as some other information, such as logs and commanding data [68]. This

"Fly-by-Wireless" : A Revolution in Aerospace Architectures for Instrumentation and Control

NASA Technical Reports Server (NTRS)

Studor, George F.

2007-01-01

The conference presentation provides background information on Fly-by-Wireless technologies as well as reasons for implementation, CANEUS project goals, cost of change for instrumentation, reliability, focus areas, conceptual Hybrid SHMS architecture for future space habitats, real world problems that the technology can solve, evolution of Micro-WIS systems, and a WLEIDS system overview and end-to-end system design.

Drawing on Experience: How Domain Knowledge Is Reflected in Sketches of Scientific Structures and Processes

ERIC Educational Resources Information Center

Jee, Benjamin D.; Gentner, Dedre; Uttal, David H.; Sageman, Bradley; Forbus, Kenneth; Manduca, Cathryn A.; Ormand, Carol J.; Shipley, Thomas F.; Tikoff, Basil

2014-01-01

Capturing the nature of students' mental representations and how they change with learning is a primary goal in science education research. This can be challenging in spatially intense domains, such as geoscience, architecture, and engineering. In this research, we test whether sketching can be used to gauge level of expertise in geoscience,…

Multilevel semantic analysis and problem-solving in the flight-domain

NASA Technical Reports Server (NTRS)

Chien, R. T.

1982-01-01

The use of knowledge-base architecture and planning control; mechanisms to perform an intelligent monitoring task in the flight domain is addressed. The route level, the trajectory level, and parts of the aerodynamics level are demonstrated. Hierarchical planning and monitoring conceptual levels, functional-directed mechanism rationalization, and using deep-level mechanism models for diagnoses of dependent failures are discussed.

An Architecture and Methodology for Creating a Domain-Independent, Plan-Based Intelligent Tutoring System.

ERIC Educational Resources Information Center

Vassileva, Julita

1990-01-01

Discusses the structure of intelligent tutoring systems (ITSs) and describes the development of a new structure for ITSs that is not domain dependent and is more readily adaptable by individual teachers. Pedagogical rules that help decide how much student control versus how much teacher control is present in the system are discussed. (14…

Frequency Domain Beamforming for a Deep Space Network Downlink Array

NASA Technical Reports Server (NTRS)

Navarro, Robert

2012-01-01

This paper describes a frequency domain beamformer to array up to 8 antennas of NASA's Deep Space Network currently in development. The objective of this array is to replace and enhance the capability of the DSN 70m antennas with multiple 34m antennas for telemetry, navigation and radio science use. The array will coherently combine the entire 500 MHz of usable bandwidth available to DSN receivers. A frequency domain beamforming architecture was chosen over a time domain based architecture to handle the large signal bandwidth and efficiently perform delay and phase calibration. The antennas of the DSN are spaced far enough apart that random atmospheric and phase variations between antennas need to be calibrated out on an ongoing basis in real-time. The calibration is done using measurements obtained from a correlator. This DSN Downlink Array expands upon a proof of concept breadboard array built previously to develop the technology and will become an operational asset of the Deep Space Network. Design parameters for frequency channelization, array calibration and delay corrections will be presented as well a method to efficiently calibrate the array for both wide and narrow bandwidth telemetry.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

PubMed

Roux-Rouquie, M; Marilley, M

2000-09-15

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

PubMed Central

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-01

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix. PMID:25550503

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR.

PubMed

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-13

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.

Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and Its Interaction with Contactin 2 (CNTN2)*

PubMed Central

Lu, Zhuoyang; Reddy, M. V. V. V. Sekhar; Liu, Jianfang; Kalichava, Ana; Liu, Jiankang; Zhang, Lei; Chen, Fang; Wang, Yun; Holthauzen, Luis Marcelo F.; White, Mark A.; Seshadrinathan, Suchithra; Zhong, Xiaoying; Ren, Gang; Rudenko, Gabby

2016-01-01

Contactin-associated protein-like 2 (CNTNAP2) is a large multidomain neuronal adhesion molecule implicated in a number of neurological disorders, including epilepsy, schizophrenia, autism spectrum disorder, intellectual disability, and language delay. We reveal here by electron microscopy that the architecture of CNTNAP2 is composed of a large, medium, and small lobe that flex with respect to each other. Using epitope labeling and fragments, we assign the F58C, L1, and L2 domains to the large lobe, the FBG and L3 domains to the middle lobe, and the L4 domain to the small lobe of the CNTNAP2 molecular envelope. Our data reveal that CNTNAP2 has a very different architecture compared with neurexin 1α, a fellow member of the neurexin superfamily and a prototype, suggesting that CNTNAP2 uses a different strategy to integrate into the synaptic protein network. We show that the ectodomains of CNTNAP2 and contactin 2 (CNTN2) bind directly and specifically, with low nanomolar affinity. We show further that mutations in CNTNAP2 implicated in autism spectrum disorder are not segregated but are distributed over the whole ectodomain. The molecular shape and dimensions of CNTNAP2 place constraints on how CNTNAP2 integrates in the cleft of axo-glial and neuronal contact sites and how it functions as an organizing and adhesive molecule. PMID:27621318

A bioarchitectonic approach to the modular engineering of metabolism.

PubMed

Kerfeld, Cheryl A

2017-09-26

Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions. By virtue of their potential for 'plug and play' into new contexts, modules can be viewed as units of both evolution and engineering. Through consideration of lessons learned from recent efforts to install new metabolic modules into cells and the emerging understanding of the structure, function and assembly of protein-based organelles, bacterial microcompartments, a structural bioengineering approach is described: one that builds from an architectural vocabulary of protein domains. This bioarchitectonic approach to engineering cellular metabolism can be applied to microbial cell factories, used in the programming of members of synthetic microbial communities or used to attain additional levels of metabolic organization in eukaryotic cells for increasing primary productivity and as the foundation of a green economy.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Author(s).

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

PubMed

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

Punctuated evolution and robustness in morphogenesis

PubMed Central

Grigoriev, D.; Reinitz, J.; Vakulenko, S.; Weber, A.

2014-01-01

This paper presents an analytic approach to the pattern stability and evolution problem in morphogenesis. The approach used here is based on the ideas from the gene and neural network theory. We assume that gene networks contain a number of small groups of genes (called hubs) controlling morphogenesis process. Hub genes represent an important element of gene network architecture and their existence is empirically confirmed. We show that hubs can stabilize morphogenetic pattern and accelerate the morphogenesis. The hub activity exhibits an abrupt change depending on the mutation frequency. When the mutation frequency is small, these hubs suppress all mutations and gene product concentrations do not change, thus, the pattern is stable. When the environmental pressure increases and the population needs new genotypes, the genetic drift and other effects increase the mutation frequency. For the frequencies that are larger than a critical amount the hubs turn off; and as a result, many mutations can affect phenotype. This effect can serve as an engine for evolution. We show that this engine is very effective: the evolution acceleration is an exponential function of gene redundancy. Finally, we show that the Eldredge-Gould concept of punctuated evolution results from the network architecture, which provides fast evolution, control of evolvability, and pattern robustness. To describe analytically the effect of exponential acceleration, we use mathematical methods developed recently for hard combinatorial problems, in particular, for so-called k-SAT problem, and numerical simulations. PMID:24996115

Seedling architecture and life history evolution in pines

Treesearch

Steven H. Strauss; F. Thomas Ledig

1985-01-01

Much of the work on life history evolution in plants has dealt with allocation of reproductive effort (Abrahamson 1975; Abrahamson and Gadgil 1973; Gaines et al. 1974; McNaughton 1975; Oka 1976; Stearns 1976, 1977, 1980; Newell and Tramer 1978; Primack 1979). The juvenile period, however, occupies a major and critical portion of the life cycle of many species....

From Online to Ubiquitous Cities: The Technical Transformation of Virtual Communities

NASA Astrophysics Data System (ADS)

Anthopoulos, Leonidas; Fitsilis, Panos

Various digital city projects, from the online cases (e.g. the America on Line) to the ubiquitous cities of South Korea, have achieved in creating technically 'physical' areas for the virtual communities, which share knowledge of common interest. Moreover, digital cities can succeed in simplifying citizen access to public information and services. Early digital cities deliver 'smart' and social services to citizens even with no digital skills, closing digital divide and establishing digital areas of trust in local communities. This paper presents the evolution of the digital cities, from the web to the ubiquitous architecture. It uses the latest digital city architecture and the current conditions of the digital city of Trikala (Greece), in order to present the evolution procedure of a digital city.

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

PubMed Central

Varela, Ignacio; Fisher, Rosalie; McGranahan, Nicholas; Matthews, Nicholas; Santos, Claudio R; Martinez, Pierre; Phillimore, Benjamin; Begum, Sharmin; Rabinowitz, Adam; Spencer-Dene, Bradley; Gulati, Sakshi; Bates, Paul A; Stamp, Gordon; Pickering, Lisa; Gore, Martin; Nicol, David L; Hazell, Steven; Futreal, P Andrew; Stewart, Aengus; Swanton, Charles

2015-01-01

Clear cell renal carcinomas (ccRCCs) can display intratumor heterogeneity (ITH). We applied multiregion exome sequencing (M-seq) to resolve the genetic architecture and evolutionary histories of ten ccRCCs. Ultra-deep sequencing identified ITH in all cases. We found that 73–75% of identified ccRCC driver aberrations were subclonal, confounding estimates of driver mutation prevalence. ITH increased with the number of biopsies analyzed, without evidence of saturation in most tumors. Chromosome 3p loss and VHL aberrations were the only ubiquitous events. The proportion of C>T transitions at CpG sites increased during tumor progression. M-seq permits the temporal resolution of ccRCC evolution and refines mutational signatures occurring during tumor development. PMID:24487277

Dynamic imaging in electrical impedance tomography of the human chest with online transition matrix identification.

PubMed

Moura, Fernando Silva; Aya, Julio Cesar Ceballos; Fleury, Agenor Toledo; Amato, Marcelo Britto Passos; Lima, Raul Gonzalez

2010-02-01

One of the electrical impedance tomography objectives is to estimate the electrical resistivity distribution in a domain based only on electrical potential measurements at its boundary generated by an imposed electrical current distribution into the boundary. One of the methods used in dynamic estimation is the Kalman filter. In biomedical applications, the random walk model is frequently used as evolution model and, under this conditions, poor tracking ability of the extended Kalman filter (EKF) is achieved. An analytically developed evolution model is not feasible at this moment. The paper investigates the identification of the evolution model in parallel to the EKF and updating the evolution model with certain periodicity. The evolution model transition matrix is identified using the history of the estimated resistivity distribution obtained by a sensitivity matrix based algorithm and a Newton-Raphson algorithm. To numerically identify the linear evolution model, the Ibrahim time-domain method is used. The investigation is performed by numerical simulations of a domain with time-varying resistivity and by experimental data collected from the boundary of a human chest during normal breathing. The obtained dynamic resistivity values lie within the expected values for the tissues of a human chest. The EKF results suggest that the tracking ability is significantly improved with this approach.

A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa

PubMed Central

Rivero, Francisco; Muramoto, Tetsuya; Meyer, Ann-Kathrin; Urushihara, Hideko; Uyeda, Taro QP; Kitayama, Chikako

2005-01-01

Background Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. Formins act as profilin-modulated processive actin nucleators conserved throughout a wide range of eukaryotes. Results We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum. With the exception of ForI and ForC all other formins conform to the domain structure GBD/FH3-FH1-FH2-DAD, where DAD is the Diaphanous autoinhibition domain and GBD/FH3 is the Rho GTPase-binding domain/formin homology 3 domain that we propose to represent a single domain. ForC lacks a FH1 domain, ForI lacks recognizable GBD/FH3 and DAD domains and ForA, E and J have additional unique domains. To establish the relationship between formins of Dictyostelium and other organisms we constructed a phylogenetic tree based on the alignment of FH2 domains. Real-time PCR was used to study the expression pattern of formin genes. Expression of forC, D, I and J increased during transition to multi-cellular stages, while the rest of genes displayed less marked developmental variations. During sexual development, expression of forH and forI displayed a significant increase in fusion competent cells. Conclusion Our analysis allows some preliminary insight into the functionality of Dictyostelium formins: all isoforms might display actin nucleation activity and, with the exception of ForI, might also be susceptible to autoinhibition and to regulation by Rho GTPases. The architecture GBD/FH3-FH1-FH2-DAD appears common to almost all Dictyostelium, fungal and metazoan formins, for which we propose the denomination of conventional formins, and implies a common regulatory mechanism. PMID:15740615

A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa.

PubMed

Rivero, Francisco; Muramoto, Tetsuya; Meyer, Ann-Kathrin; Urushihara, Hideko; Uyeda, Taro Q P; Kitayama, Chikako

2005-03-01

Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. Formins act as profilin-modulated processive actin nucleators conserved throughout a wide range of eukaryotes. We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum. With the exception of ForI and ForC all other formins conform to the domain structure GBD/FH3-FH1-FH2-DAD, where DAD is the Diaphanous autoinhibition domain and GBD/FH3 is the Rho GTPase-binding domain/formin homology 3 domain that we propose to represent a single domain. ForC lacks a FH1 domain, ForI lacks recognizable GBD/FH3 and DAD domains and ForA, E and J have additional unique domains. To establish the relationship between formins of Dictyostelium and other organisms we constructed a phylogenetic tree based on the alignment of FH2 domains. Real-time PCR was used to study the expression pattern of formin genes. Expression of forC, D, I and J increased during transition to multi-cellular stages, while the rest of genes displayed less marked developmental variations. During sexual development, expression of forH and forI displayed a significant increase in fusion competent cells. Our analysis allows some preliminary insight into the functionality of Dictyostelium formins: all isoforms might display actin nucleation activity and, with the exception of ForI, might also be susceptible to autoinhibition and to regulation by Rho GTPases. The architecture GBD/FH3-FH1-FH2-DAD appears common to almost all Dictyostelium, fungal and metazoan formins, for which we propose the denomination of conventional formins, and implies a common regulatory mechanism.