A genetic scale of reading frame coding.

PubMed

Michel, Christian J

2014-08-21

The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. A first objective is the definition of a new and simple statistical parameter PrRFC for analysing the probability (efficiency) of reading frame coding (RFC) of any trinucleotide code. A second objective is to reveal different classes and subclasses of trinucleotide codes involved in reading frame coding: the circular codes of 20 trinucleotides and the bijective genetic codes of 20 trinucleotides coding the 20 amino acids. This approach allows us to propose a genetic scale of reading frame coding which ranges from 1/3 with the random codes (RFC probability identical in the three frames) to 1 with the comma-free circular codes (RFC probability maximal in the reading frame and null in the two shifted frames). This genetic scale shows, in particular, the reading frame coding probabilities of the 12,964,440 circular codes (PrRFC=83.2% in average), the 216 C(3) self-complementary circular codes (PrRFC=84.1% in average) including the code X identified in eukaryotic and prokaryotic genes (PrRFC=81.3%) and the 339,738,624 bijective genetic codes (PrRFC=61.5% in average) including the 52 codes without permuted trinucleotides (PrRFC=66.0% in average). Otherwise, the reading frame coding probabilities of each trinucleotide code coding an amino acid with the universal genetic code are also determined. The four amino acids Gly, Lys, Phe and Pro are coded by codes (not circular) with RFC probabilities equal to 2/3, 1/2, 1/2 and 2/3, respectively. The amino acid Leu is coded by a circular code (not comma-free) with a RFC probability equal to 18/19. The 15 other amino acids are coded by comma-free circular codes, i.e. with RFC probabilities equal to 1. The identification of coding properties in some classes of trinucleotide codes studied here may bring new insights in the origin and evolution of the genetic code. Copyright © 2014 Elsevier Ltd. All rights reserved.

A new compound arithmetic crossover-based genetic algorithm for constrained optimisation in enterprise systems

NASA Astrophysics Data System (ADS)

Jin, Chenxia; Li, Fachao; Tsang, Eric C. C.; Bulysheva, Larissa; Kataev, Mikhail Yu

2017-01-01

In many real industrial applications, the integration of raw data with a methodology can support economically sound decision-making. Furthermore, most of these tasks involve complex optimisation problems. Seeking better solutions is critical. As an intelligent search optimisation algorithm, genetic algorithm (GA) is an important technique for complex system optimisation, but it has internal drawbacks such as low computation efficiency and prematurity. Improving the performance of GA is a vital topic in academic and applications research. In this paper, a new real-coded crossover operator, called compound arithmetic crossover operator (CAC), is proposed. CAC is used in conjunction with a uniform mutation operator to define a new genetic algorithm CAC10-GA. This GA is compared with an existing genetic algorithm (AC10-GA) that comprises an arithmetic crossover operator and a uniform mutation operator. To judge the performance of CAC10-GA, two kinds of analysis are performed. First the analysis of the convergence of CAC10-GA is performed by the Markov chain theory; second, a pair-wise comparison is carried out between CAC10-GA and AC10-GA through two test problems available in the global optimisation literature. The overall comparative study shows that the CAC performs quite well and the CAC10-GA defined outperforms the AC10-GA.

Genetic code, hamming distance and stochastic matrices.

PubMed

He, Matthew X; Petoukhov, Sergei V; Ricci, Paolo E

2004-09-01

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are doubly stochastic and symmetric. We determine the frequency distributions of the Hamming distances, building blocks of the matrices, decomposition and iterations of matrices. We present an explicit decomposition formula for the genetic code-based matrix in terms of permutation matrices, which provides a hypercube representation of the genetic code. It is also observed that there is a Hamiltonian cycle in a genetic code-based hypercube.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

Capabilities needed for the next generation of thermo-hydraulic codes for use in real time applications

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

Arndt, S.A.

1997-07-01

The real-time reactor simulation field is currently at a crossroads in terms of the capability to perform real-time analysis using the most sophisticated computer codes. Current generation safety analysis codes are being modified to replace simplified codes that were specifically designed to meet the competing requirement for real-time applications. The next generation of thermo-hydraulic codes will need to have included in their specifications the specific requirement for use in a real-time environment. Use of the codes in real-time applications imposes much stricter requirements on robustness, reliability and repeatability than do design and analysis applications. In addition, the need for codemore » use by a variety of users is a critical issue for real-time users, trainers and emergency planners who currently use real-time simulation, and PRA practitioners who will increasingly use real-time simulation for evaluating PRA success criteria in near real-time to validate PRA results for specific configurations and plant system unavailabilities.« less

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code. Copyright © 2017 Elsevier Ltd. All rights reserved.

Critical roles for a genetic code alteration in the evolution of the genus Candida.

PubMed

Silva, Raquel M; Paredes, João A; Moura, Gabriela R; Manadas, Bruno; Lima-Costa, Tatiana; Rocha, Rita; Miranda, Isabel; Gomes, Ana C; Koerkamp, Marian J G; Perrot, Michel; Holstege, Frank C P; Boucherie, Hélian; Santos, Manuel A S

2007-10-31

During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.

Arbitrariness is not enough: towards a functional approach to the genetic code.

PubMed

Lacková, Ľudmila; Matlach, Vladimír; Faltýnek, Dan

2017-12-01

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about "code" in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign's object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

Life is physics and chemistry and communication.

PubMed

Witzany, Guenther

2015-04-01

Manfred Eigen extended Erwin Schroedinger's concept of "life is physics and chemistry" through the introduction of information theory and cybernetic systems theory into "life is physics and chemistry and information." Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. © 2014 New York Academy of Sciences.

Semiconductor Whole Exome Sequencing for the Identification of Genetic Variants in Colombian Patients Clinically Diagnosed with Long QT Syndrome.

PubMed

Burgos, Mariana; Arenas, Alvaro; Cabrera, Rodrigo

2016-08-01

Inherited long QT syndrome (LQTS) is a cardiac channelopathy characterized by a prolongation of QT interval and the risk of syncope, cardiac arrest, and sudden cardiac death. Genetic diagnosis of LQTS is critical in medical practice as results can guide adequate management of patients and distinguish phenocopies such as catecholaminergic polymorphic ventricular tachycardia (CPVT). However, extensive screening of large genomic regions is required in order to reliably identify genetic causes. Semiconductor whole exome sequencing (WES) is a promising approach for the identification of variants in the coding regions of most human genes. DNA samples from 21 Colombian patients clinically diagnosed with LQTS were enriched for coding regions using multiplex polymerase chain reaction (PCR) and subjected to WES using a semiconductor sequencer. Semiconductor WES showed mean coverage of 93.6 % for all coding regions relevant to LQTS at >10× depth with high intra- and inter-assay depth heterogeneity. Fifteen variants were detected in 12 patients in genes associated with LQTS. Three variants were identified in three patients in genes associated with CPVT. Co-segregation analysis was performed when possible. All variants were analyzed with two pathogenicity prediction algorithms. The overall prevalence of LQTS and CPVT variants in our cohort was 71.4 %. All LQTS variants previously identified through commercial genetic testing were identified. Standardized WES assays can be easily implemented, often at a lower cost than sequencing panels. Our results show that WES can identify LQTS-causing mutations and permits differential diagnosis of related conditions in a real-world clinical setting. However, high heterogeneity in sequencing depth and low coverage in the most relevant genes is expected to be associated with reduced analytical sensitivity.

Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

PubMed

Seligmann, Hervé

2018-05-01

Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections. Copyright © 2018 Elsevier B.V. All rights reserved.

Essentials of Conservation Biotechnology: A mini review

NASA Astrophysics Data System (ADS)

Merlyn Keziah, S.; Subathra Devi, C.

2017-11-01

Equilibrium of biodiversity is essential for the maintenance of the ecosystem as they are interdependent on each other. The decline in biodiversity is a global problem and an inevitable threat to the mankind. Major threats include unsustainable exploitation, habitat destruction, fragmentation, transformation, genetic pollution, invasive exotic species and degradation. This review covers the management strategies of biotechnology which include sin situ, ex situ conservation, computerized taxonomic analysis through construction of phylogenetic trees, calculating genetic distance, prioritizing the group for conservation, digital preservation of biodiversities within the coding and decoding keys, molecular approaches to asses biodiversity like polymerase chain reaction, real time, randomly amplified polymorphic DNA, restriction fragment length polymorphism, amplified fragment length polymorphism, single sequence repeats, DNA finger printing, single nucleotide polymorphism, cryopreservation and vitrification.

[UNESCO's bioethical norms to avoid eugenic practices].

PubMed

Cruz-Coke, R

2000-06-01

The author, member of the UNESCO Bioethics Committee, participated in the preparation of the Universal Declaration about Human Genome and Human Rights, in 1997. The aim of this work is to analyze the initial articles of such Declaration, defining the bioethical principles that defend human dignity, freedom and rights, against the madness of the present biotechnological revolution. The development of genetics for the benefit of mankind will be guaranteed if these principles are honored. Genetic discrimination, reductionism and determinism, are identified by the author as perversions that, if used by biotechnologists, can lead to the rebirth of eugenism and racism, that were condemned by the Code of Nuremberg, in 1947. Investigators must assume their responsibility, respecting the principles of human dignity, the real freedom of research and solidarity among people. This attitude will avoid the use of genetics for purposes other than the welfare of mankind.

Pragmatic turn in biology: From biological molecules to genetic content operators.

PubMed

Witzany, Guenther

2014-08-26

Erwin Schrödinger's question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

Can mathematics explain the evolution of human language?

PubMed

Witzany, Guenther

2011-09-01

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer science-based formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language.

Estimation of the Reactive Flow Model Parameters for an Ammonium Nitrate-Based Emulsion Explosive Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Ribeiro, J. B.; Silva, C.; Mendes, R.

2010-10-01

A real coded genetic algorithm methodology that has been developed for the estimation of the parameters of the reaction rate equation of the Lee-Tarver reactive flow model is described in detail. This methodology allows, in a single optimization procedure, using only one experimental result and, without the need of any starting solution, to seek the 15 parameters of the reaction rate equation that fit the numerical to the experimental results. Mass averaging and the plate-gap model have been used for the determination of the shock data used in the unreacted explosive JWL equation of state (EOS) assessment and the thermochemical code THOR retrieved the data used in the detonation products' JWL EOS assessments. The developed methodology was applied for the estimation of the referred parameters for an ammonium nitrate-based emulsion explosive using poly(methyl methacrylate) (PMMA)-embedded manganin gauge pressure-time data. The obtained parameters allow a reasonably good description of the experimental data and show some peculiarities arising from the intrinsic nature of this kind of composite explosive.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Genetic testing in cardiovascular diseases.

PubMed

Arndt, Anne-Karin; MacRae, Calum A

2014-05-01

The review is designed to outline the major developments in genetic testing in the cardiovascular arena in the past year or so. This is an exciting time in genetic testing as whole exome and whole genome approaches finally reach the clinic. These new approaches offer insight into disease causation in families in which this might previously have been inaccessible, and also bring a wide range of interpretative challenges. Among the most significant recent findings has been the extent of physiologic rare coding variation in the human genome. New disease genes have been identified through whole exome studies in neonatal arrhythmia, congenital heart disease and coronary artery disease that were simply inaccessible with other techniques. This has not only shed light on the challenges of genetic testing at this scale, but has also sharply defined the limits of prior gene-panel focused testing. As novel therapies targeting specific genetic subsets of disease become available, genetic testing will become a part of routine clinical care. The pace of change in sequencing technologies has begun to transform clinical medicine, and cardiovascular disease is no exception. The complexity of such studies emphasizes the importance of real-time communication between the genetics laboratory and genetically informed clinicians. New efforts in data and knowledge management will be central to the continued advancement of genetic testing.

Mathematical fundamentals for the noise immunity of the genetic code.

PubMed

Fimmel, Elena; Strüngmann, Lutz

2018-02-01

Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept. The genetic code can be seen as a key to biological self-organisation. All living organisms have the same molecular bases - an alphabet consisting of four letters (nitrogenous bases): adenine, cytosine, guanine, and thymine. Linearly ordered sequences of these bases contain the genetic information for synthesis of proteins in all forms of life. Thus, one of the most fascinating riddles of nature is to explain why the genetic code is as it is. Genetic coding possesses noise immunity which is the fundamental feature that allows to pass on the genetic information from parents to their descendants. Hence, since the time of the discovery of the genetic code, scientists have tried to explain the noise immunity of the genetic information. In this chapter we will discuss recent results in mathematical modelling of the genetic code with respect to noise immunity, in particular error-detection and error-correction. We will focus on two central properties: Degeneracy and frameshift correction. Different amino acids are encoded by different quantities of codons and a connection between this degeneracy and the noise immunity of genetic information is a long standing hypothesis. Biological implications of the degeneracy have been intensively studied and whether the natural code is a frozen accident or a highly optimised product of evolution is still controversially discussed. Symmetries in the structure of degeneracy of the genetic code are essential and give evidence of substantial advantages of the natural code over other possible ones. In the present chapter we will present a recent approach to explain the degeneracy of the genetic code by algorithmic methods from bioinformatics, and discuss its biological consequences. The biologists recognised this problem immediately after the detection of the non-overlapping structure of the genetic code, i.e., coding sequences are to be read in a unique way determined by their reading frame. But how does the reading head of the ribosome recognises an error in the grouping of codons, caused by e.g. insertion or deletion of a base, that can be fatal during the translation process and may result in nonfunctional proteins? In this chapter we will discuss possible solutions to the frameshift problem with a focus on the theory of so-called circular codes that were discovered in large gene populations of prokaryotes and eukaryotes in the early 90s. Circular codes allow to detect a frameshift of one or two positions and recently a beautiful theory of such codes has been developed using statistics, group theory and graph theory. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a duplex real-time RT-qPCR assay to monitor genome replication, gene expression and gene insert stability during in vivo replication of a prototype live attenuated canine distemper virus vector encoding SIV gag.

PubMed

Coleman, John W; Wright, Kevin J; Wallace, Olivia L; Sharma, Palka; Arendt, Heather; Martinez, Jennifer; DeStefano, Joanne; Zamb, Timothy P; Zhang, Xinsheng; Parks, Christopher L

2015-03-01

Advancement of new vaccines based on live viral vectors requires sensitive assays to analyze in vivo replication, gene expression and genetic stability. In this study, attenuated canine distemper virus (CDV) was used as a vaccine delivery vector and duplex 2-step quantitative real-time RT-PCR (RT-qPCR) assays specific for genomic RNA (gRNA) or mRNA have been developed that concurrently quantify coding sequences for the CDV nucleocapsid protein (N) and a foreign vaccine antigen (SIV Gag). These amplicons, which had detection limits of about 10 copies per PCR reaction, were used to show that abdominal cavity lymphoid tissues were a primary site of CDV vector replication in infected ferrets, and importantly, CDV gRNA or mRNA was undetectable in brain tissue. In addition, the gRNA duplex assay was adapted for monitoring foreign gene insert genetic stability during in vivo replication by analyzing the ratio of CDV N and SIV gag genomic RNA copies over the course of vector infection. This measurement was found to be a sensitive probe for assessing the in vivo genetic stability of the foreign gene insert. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of a Novel De Novo Heterozygous Deletion in the SOX10 Gene in Waardenburg Syndrome Type II Using Next-Generation Sequencing.

PubMed

Li, Haonan; Jin, Peng; Hao, Qian; Zhu, Wei; Chen, Xia; Wang, Ping

2017-11-01

Waardenburg syndrome (WS) is a rare autosomal dominant disorder associated with pigmentation abnormalities and sensorineural hearing loss. In this study, we investigated the genetic cause of WSII in a patient and evaluated the reliability of the targeted next-generation exome sequencing method for the genetic diagnosis of WS. Clinical evaluations were conducted on the patient and targeted next-generation sequencing (NGS) was used to identify the candidate genes responsible for WSII. Multiplex ligation-dependent probe amplification (MLPA) and real-time quantitative polymerase chain reaction (qPCR) were performed to confirm the targeted NGS results. Targeted NGS detected the entire deletion of the coding sequence (CDS) of the SOX10 gene in the WSII patient. MLPA results indicated that all exons of the SOX10 heterozygous deletion were detected; no aberrant copy number in the PAX3 and microphthalmia-associated transcription factor (MITF) genes was found. Real-time qPCR results identified the mutation as a de novo heterozygous deletion. This is the first report of using a targeted NGS method for WS candidate gene sequencing; its accuracy was verified by using the MLPA and qPCR methods. Our research provides a valuable method for the genetic diagnosis of WS.

Novel numerical and graphical representation of DNA sequences and proteins.

PubMed

Randić, M; Novic, M; Vikić-Topić, D; Plavsić, D

2006-12-01

We have introduced novel numerical and graphical representations of DNA, which offer a simple and unique characterization of DNA sequences. The numerical representation of a DNA sequence is given as a sequence of real numbers derived from a unique graphical representation of the standard genetic code. There is no loss of information on the primary structure of a DNA sequence associated with this numerical representation. The novel representations are illustrated with the coding sequences of the first exon of beta-globin gene of half a dozen species in addition to human. The method can be extended to proteins as is exemplified by humanin, a 24-aa peptide that has recently been identified as a specific inhibitor of neuronal cell death induced by familial Alzheimer's disease mutant genes.

The neutral emergence of error minimized genetic codes superior to the standard genetic code.

PubMed

Massey, Steven E

2016-11-07

The standard genetic code (SGC) assigns amino acids to codons in such a way that the impact of point mutations is reduced, this is termed 'error minimization' (EM). The occurrence of EM has been attributed to the direct action of selection, however it is difficult to explain how the searching of alternative codes for an error minimized code can occur via codon reassignments, given that these are likely to be disruptive to the proteome. An alternative scenario is that EM has arisen via the process of genetic code expansion, facilitated by the duplication of genes encoding charging enzymes and adaptor molecules. This is likely to have led to similar amino acids being assigned to similar codons. Strikingly, we show that if during code expansion the most similar amino acid to the parent amino acid, out of the set of unassigned amino acids, is assigned to codons related to those of the parent amino acid, then genetic codes with EM superior to the SGC easily arise. This scheme mimics code expansion via the gene duplication of charging enzymes and adaptors. The result is obtained for a variety of different schemes of genetic code expansion and provides a mechanistically realistic manner in which EM has arisen in the SGC. These observations might be taken as evidence for self-organization in the earliest stages of life. Copyright © 2016 Elsevier Ltd. All rights reserved.

Charge scheduling of an energy storage system under time-of-use pricing and a demand charge.

PubMed

Yoon, Yourim; Kim, Yong-Hyuk

2014-01-01

A real-coded genetic algorithm is used to schedule the charging of an energy storage system (ESS), operated in tandem with renewable power by an electricity consumer who is subject to time-of-use pricing and a demand charge. Simulations based on load and generation profiles of typical residential customers show that an ESS scheduled by our algorithm can reduce electricity costs by approximately 17%, compared to a system without an ESS and by 8% compared to a scheduling algorithm based on net power.

Charge Scheduling of an Energy Storage System under Time-of-Use Pricing and a Demand Charge

PubMed Central

Yoon, Yourim

2014-01-01

A real-coded genetic algorithm is used to schedule the charging of an energy storage system (ESS), operated in tandem with renewable power by an electricity consumer who is subject to time-of-use pricing and a demand charge. Simulations based on load and generation profiles of typical residential customers show that an ESS scheduled by our algorithm can reduce electricity costs by approximately 17%, compared to a system without an ESS and by 8% compared to a scheduling algorithm based on net power. PMID:25197720

Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

USGS Publications Warehouse

Chen, C.; Xia, J.; Liu, J.; Feng, G.

2006-01-01

Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant result is that final solution is determined by the average model derived from multiple trials instead of one computation due to the randomness in a genetic algorithm procedure. These advantages were demonstrated by synthetic and real-world examples of inversion of potential-field data. ?? 2005 Elsevier Ltd. All rights reserved.

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

PubMed Central

Wong, J. Tze-Fei; Ng, Siu-Kin; Mat, Wai-Kin; Hu, Taobo; Xue, Hong

2016-01-01

The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets. PMID:26999216

Crucial steps to life: From chemical reactions to code using agents.

PubMed

Witzany, Guenther

2016-02-01

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the "central dogma," "one gene one protein" and "non-coding DNA is junk" were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning non-random genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not fit with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.

New knowledge-based genetic algorithm for excavator boom structural optimization

NASA Astrophysics Data System (ADS)

Hua, Haiyan; Lin, Shuwen

2014-03-01

Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the configurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, are taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem.

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

PubMed

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

A Bayesian network coding scheme for annotating biomedical information presented to genetic counseling clients.

PubMed

Green, Nancy

2005-04-01

We developed a Bayesian network coding scheme for annotating biomedical content in layperson-oriented clinical genetics documents. The coding scheme supports the representation of probabilistic and causal relationships among concepts in this domain, at a high enough level of abstraction to capture commonalities among genetic processes and their relationship to health. We are using the coding scheme to annotate a corpus of genetic counseling patient letters as part of the requirements analysis and knowledge acquisition phase of a natural language generation project. This paper describes the coding scheme and presents an evaluation of intercoder reliability for its tag set. In addition to giving examples of use of the coding scheme for analysis of discourse and linguistic features in this genre, we suggest other uses for it in analysis of layperson-oriented text and dialogue in medical communication.

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma.

PubMed

Alkalaeva, Elena; Mikhailova, Tatiana

2017-03-01

The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here. © 2017 WILEY Periodicals, Inc.

Genetic hotels for the standard genetic code: evolutionary analysis based upon novel three-dimensional algebraic models.

PubMed

José, Marco V; Morgado, Eberto R; Govezensky, Tzipe

2011-07-01

Herein, we rigorously develop novel 3-dimensional algebraic models called Genetic Hotels of the Standard Genetic Code (SGC). We start by considering the primeval RNA genetic code which consists of the 16 codons of type RNY (purine-any base-pyrimidine). Using simple algebraic operations, we show how the RNA code could have evolved toward the current SGC via two different intermediate evolutionary stages called Extended RNA code type I and II. By rotations or translations of the subset RNY, we arrive at the SGC via the former (type I) or via the latter (type II), respectively. Biologically, the Extended RNA code type I, consists of all codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The Extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. Since the dimensions of remarkable subsets of the Genetic Hotels are not necessarily integer numbers, we also introduce the concept of algebraic fractal dimension. A general decoding function which maps each codon to its corresponding amino acid or the stop signals is also derived. The Phenotypic Hotel of amino acids is also illustrated. The proposed evolutionary paths are discussed in terms of the existing theories of the evolution of the SGC. The adoption of 3-dimensional models of the Genetic and Phenotypic Hotels will facilitate the understanding of the biological properties of the SGC.

Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility

PubMed Central

Caetano-Anollés, Gustavo; Wang, Minglei; Caetano-Anollés, Derek

2013-01-01

The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the ‘operational’ RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure. PMID:23991065

Reducing the genetic code induces massive rearrangement of the proteome

PubMed Central

O’Donoghue, Patrick; Prat, Laure; Kucklick, Martin; Schäfer, Johannes G.; Riedel, Katharina; Rinehart, Jesse; Söll, Dieter; Heinemann, Ilka U.

2014-01-01

Expanding the genetic code is an important aim of synthetic biology, but some organisms developed naturally expanded genetic codes long ago over the course of evolution. Less than 1% of all sequenced genomes encode an operon that reassigns the stop codon UAG to pyrrolysine (Pyl), a genetic code variant that results from the biosynthesis of Pyl-tRNAPyl. To understand the selective advantage of genetically encoding more than 20 amino acids, we constructed a markerless tRNAPyl deletion strain of Methanosarcina acetivorans (ΔpylT) that cannot decode UAG as Pyl or grow on trimethylamine. Phenotypic defects in the ΔpylT strain were evident in minimal medium containing methanol. Proteomic analyses of wild type (WT) M. acetivorans and ΔpylT cells identified 841 proteins from >7,000 significant peptides detected by MS/MS. Protein production from UAG-containing mRNAs was verified for 19 proteins. Translation of UAG codons was verified by MS/MS for eight proteins, including identification of a Pyl residue in PylB, which catalyzes the first step of Pyl biosynthesis. Deletion of tRNAPyl globally altered the proteome, leading to >300 differentially abundant proteins. Reduction of the genetic code from 21 to 20 amino acids led to significant down-regulation in translation initiation factors, amino acid metabolism, and methanogenesis from methanol, which was offset by a compensatory (100-fold) up-regulation in dimethyl sulfide metabolic enzymes. The data show how a natural proteome adapts to genetic code reduction and indicate that the selective value of an expanded genetic code is related to carbon source range and metabolic efficiency. PMID:25404328

Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria.

PubMed

Bender, Aline; Hajieva, Parvana; Moosmann, Bernd

2008-10-28

Humans and most other animals use 2 different genetic codes to translate their hereditary information: the standard code for nuclear-encoded proteins and a modern variant of this code in mitochondria. Despite the pivotal role of the genetic code for cell biology, the functional significance of the deviant mitochondrial code has remained enigmatic since its first description in 1979. Here, we show that profound and functionally beneficial alterations on the encoded protein level were causative for the AUA codon reassignment from isoleucine to methionine observed in most mitochondrial lineages. We demonstrate that this codon reassignment leads to a massive accumulation of the easily oxidized amino acid methionine in the highly oxidative inner mitochondrial membrane. This apparently paradoxical outcome can yet be smoothly settled if the antioxidant surface chemistry of methionine is taken into account, and we present direct experimental evidence that intramembrane accumulation of methionine exhibits antioxidant and cytoprotective properties in living cells. Our results unveil that methionine is an evolutionarily selected antioxidant building block of respiratory chain complexes. Collective protein alterations can thus constitute the selective advantage behind codon reassignments, which authenticates the "ambiguous decoding" hypothesis of genetic code evolution. Oxidative stress has shaped the mitochondrial genetic code.

The accuracy of real-time procedure coding by theatre nurses: a comparison with the central national system.

PubMed

Maclean, Donald; Younes, Hakim Ben; Forrest, Margaret; Towers, Hazel K

2012-03-01

Accurate and timely clinical data are required for clinical and organisational purposes and is especially important for patient management, audit of surgical performance and the electronic health record. The recent introduction of computerised theatre management systems has enabled real-time (point-of-care) operative procedure coding by clinical staff. However the accuracy of these data is unknown. The aim of this Scottish study was to compare the accuracy of theatre nurses' real-time coding on the local theatre management system with the central Scottish Morbidity Record (SMR01). Paired procedural codes were recorded, qualitatively graded for precision and compared (n = 1038). In this study, real-time, point-of-care coding by theatre nurses resulted in significant coding errors compared with the central SMR01 database. Improved collaboration between full-time coders and clinical staff using computerised decision support systems is suggested.

A programmable metasurface with dynamic polarization, scattering and focusing control

NASA Astrophysics Data System (ADS)

Yang, Huanhuan; Cao, Xiangyu; Yang, Fan; Gao, Jun; Xu, Shenheng; Li, Maokun; Chen, Xibi; Zhao, Yi; Zheng, Yuejun; Li, Sijia

2016-10-01

Diverse electromagnetic (EM) responses of a programmable metasurface with a relatively large scale have been investigated, where multiple functionalities are obtained on the same surface. The unit cell in the metasurface is integrated with one PIN diode, and thus a binary coded phase is realized for a single polarization. Exploiting this anisotropic characteristic, reconfigurable polarization conversion is presented first. Then the dynamic scattering performance for two kinds of sources, i.e. a plane wave and a point source, is carefully elaborated. To tailor the scattering properties, genetic algorithm, normally based on binary coding, is coupled with the scattering pattern analysis to optimize the coding matrix. Besides, inverse fast Fourier transform (IFFT) technique is also introduced to expedite the optimization process of a large metasurface. Since the coding control of each unit cell allows a local and direct modulation of EM wave, various EM phenomena including anomalous reflection, diffusion, beam steering and beam forming are successfully demonstrated by both simulations and experiments. It is worthwhile to point out that a real-time switch among these functionalities is also achieved by using a field-programmable gate array (FPGA). All the results suggest that the proposed programmable metasurface has great potentials for future applications.

A programmable metasurface with dynamic polarization, scattering and focusing control

PubMed Central

Yang, Huanhuan; Cao, Xiangyu; Yang, Fan; Gao, Jun; Xu, Shenheng; Li, Maokun; Chen, Xibi; Zhao, Yi; Zheng, Yuejun; Li, Sijia

2016-01-01

Diverse electromagnetic (EM) responses of a programmable metasurface with a relatively large scale have been investigated, where multiple functionalities are obtained on the same surface. The unit cell in the metasurface is integrated with one PIN diode, and thus a binary coded phase is realized for a single polarization. Exploiting this anisotropic characteristic, reconfigurable polarization conversion is presented first. Then the dynamic scattering performance for two kinds of sources, i.e. a plane wave and a point source, is carefully elaborated. To tailor the scattering properties, genetic algorithm, normally based on binary coding, is coupled with the scattering pattern analysis to optimize the coding matrix. Besides, inverse fast Fourier transform (IFFT) technique is also introduced to expedite the optimization process of a large metasurface. Since the coding control of each unit cell allows a local and direct modulation of EM wave, various EM phenomena including anomalous reflection, diffusion, beam steering and beam forming are successfully demonstrated by both simulations and experiments. It is worthwhile to point out that a real-time switch among these functionalities is also achieved by using a field-programmable gate array (FPGA). All the results suggest that the proposed programmable metasurface has great potentials for future applications. PMID:27774997

A programmable metasurface with dynamic polarization, scattering and focusing control.

PubMed

Yang, Huanhuan; Cao, Xiangyu; Yang, Fan; Gao, Jun; Xu, Shenheng; Li, Maokun; Chen, Xibi; Zhao, Yi; Zheng, Yuejun; Li, Sijia

2016-10-24

Diverse electromagnetic (EM) responses of a programmable metasurface with a relatively large scale have been investigated, where multiple functionalities are obtained on the same surface. The unit cell in the metasurface is integrated with one PIN diode, and thus a binary coded phase is realized for a single polarization. Exploiting this anisotropic characteristic, reconfigurable polarization conversion is presented first. Then the dynamic scattering performance for two kinds of sources, i.e. a plane wave and a point source, is carefully elaborated. To tailor the scattering properties, genetic algorithm, normally based on binary coding, is coupled with the scattering pattern analysis to optimize the coding matrix. Besides, inverse fast Fourier transform (IFFT) technique is also introduced to expedite the optimization process of a large metasurface. Since the coding control of each unit cell allows a local and direct modulation of EM wave, various EM phenomena including anomalous reflection, diffusion, beam steering and beam forming are successfully demonstrated by both simulations and experiments. It is worthwhile to point out that a real-time switch among these functionalities is also achieved by using a field-programmable gate array (FPGA). All the results suggest that the proposed programmable metasurface has great potentials for future applications.

Stop Codon Reassignment in the Wild

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

Ivanova, Natalia; Schwientek, Patrick; Tripp, H. James

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hostsmore » must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences« less

The fourfold way of the genetic code.

PubMed

Jiménez-Montaño, Miguel Angel

2009-11-01

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.

Optical image encryption based on real-valued coding and subtracting with the help of QR code

NASA Astrophysics Data System (ADS)

Deng, Xiaopeng

2015-08-01

A novel optical image encryption based on real-valued coding and subtracting is proposed with the help of quick response (QR) code. In the encryption process, the original image to be encoded is firstly transformed into the corresponding QR code, and then the corresponding QR code is encoded into two phase-only masks (POMs) by using basic vector operations. Finally, the absolute values of the real or imaginary parts of the two POMs are chosen as the ciphertexts. In decryption process, the QR code can be approximately restored by recording the intensity of the subtraction between the ciphertexts, and hence the original image can be retrieved without any quality loss by scanning the restored QR code with a smartphone. Simulation results and actual smartphone collected results show that the method is feasible and has strong tolerance to noise, phase difference and ratio between intensities of the two decryption light beams.

CMCpy: Genetic Code-Message Coevolution Models in Python

PubMed Central

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

The evolution of the genetic code: Impasses and challenges.

PubMed

Kun, Ádám; Radványi, Ádám

2018-02-01

The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed. Thus we suggest a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes. Alternatively, amino acids without handles or with a handle consisting of a single adenine, like in contemporary coenzymes could have been employed. All three scenarios can be tested in in vitro compartmentalized systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic coding and gene expression - new Quadruplet genetic coding model

NASA Astrophysics Data System (ADS)

Shankar Singh, Rama

2012-07-01

Successful demonstration of human genome project has opened the door not only for developing personalized medicine and cure for genetic diseases, but it may also answer the complex and difficult question of the origin of life. It may lead to making 21st century, a century of Biological Sciences as well. Based on the central dogma of Biology, genetic codons in conjunction with tRNA play a key role in translating the RNA bases forming sequence of amino acids leading to a synthesized protein. This is the most critical step in synthesizing the right protein needed for personalized medicine and curing genetic diseases. So far, only triplet codons involving three bases of RNA, transcribed from DNA bases, have been used. Since this approach has several inconsistencies and limitations, even the promise of personalized medicine has not been realized. The new Quadruplet genetic coding model proposed and developed here involves all four RNA bases which in conjunction with tRNA will synthesize the right protein. The transcription and translation process used will be the same, but the Quadruplet codons will help overcome most of the inconsistencies and limitations of the triplet codes. Details of this new Quadruplet genetic coding model and its subsequent potential applications including relevance to the origin of life will be presented.

Investigating the optimal passive and active vibration controls of adjacent buildings based on performance indices using genetic algorithms

NASA Astrophysics Data System (ADS)

Hadi, Muhammad N. S.; Uz, Mehmet E.

2015-02-01

This study proposes the optimal passive and active damper parameters for achieving the best results in seismic response mitigation of coupled buildings connected to each other by dampers. The optimization to minimize the H2 and H∞ norms in the performance indices is carried out by genetic algorithms (GAs). The final passive and active damper parameters are checked for adjacent buildings connected to each other under El Centro NS 1940 and Kobe NS 1995 excitations. Using real coded GA in H∞ norm, the optimal controller gain is obtained by different combinations of the measurement as the feedback for designing the control force between the buildings. The proposed method is more effective than other metaheuristic methods and more feasible, although the control force increased. The results in the active control system show that the response of adjacent buildings is reduced in an efficient manner.

A COTS-Based Replacement Strategy for Aging Avionics Computers

DTIC Science & Technology

2001-12-01

Communication Control Unit. A COTS-Based Replacement Strategy for Aging Avionics Computers COTS Microprocessor Real Time Operating System New Native Code...Native Code Objec ts Native Code Thread Real - Time Operating System Legacy Function x Virtual Component Environment Context Switch Thunk Add-in Replace

User's Manual for PCSMS (Parallel Complex Sparse Matrix Solver). Version 1.

NASA Technical Reports Server (NTRS)

Reddy, C. J.

2000-01-01

PCSMS (Parallel Complex Sparse Matrix Solver) is a computer code written to make use of the existing real sparse direct solvers to solve complex, sparse matrix linear equations. PCSMS converts complex matrices into real matrices and use real, sparse direct matrix solvers to factor and solve the real matrices. The solution vector is reconverted to complex numbers. Though, this utility is written for Silicon Graphics (SGI) real sparse matrix solution routines, it is general in nature and can be easily modified to work with any real sparse matrix solver. The User's Manual is written to make the user acquainted with the installation and operation of the code. Driver routines are given to aid the users to integrate PCSMS routines in their own codes.

GA-optimized feedforward-PID tracking control for a rugged electrohydraulic system design.

PubMed

Sarkar, B K; Mandal, P; Saha, R; Mookherjee, S; Sanyal, D

2013-11-01

Rugged electrohydraulic systems are preferred for remote and harsh applications. Despite the low bandwidth, large deadband and flow nonlinearities in proportional valves valve and highly nonlinear friction in industry-grade cylinders that comprise rugged systems, their maintenance are much easier than very sophisticated and delicate servocontrol and servocylinder systems. With the target of making the easily maintainable system to perform comparably to a servosystem, a feedforward control has been designed here for compensating the nonlinearities. A PID feedback of the piston displacement has been employed in tandem for absorbing the unmodeled effects. All the controller parameters have been optimized by a real-coded genetic algorithm. The agreement between the achieved real-time responses for step and sinusoidal demands with those achieved by modern servosystems clearly establishes the acceptability of the controller design. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Comparison of two non-convex mixed-integer nonlinear programming algorithms applied to autoregressive moving average model structure and parameter estimation

NASA Astrophysics Data System (ADS)

Uilhoorn, F. E.

2016-10-01

In this article, the stochastic modelling approach proposed by Box and Jenkins is treated as a mixed-integer nonlinear programming (MINLP) problem solved with a mesh adaptive direct search and a real-coded genetic class of algorithms. The aim is to estimate the real-valued parameters and non-negative integer, correlated structure of stationary autoregressive moving average (ARMA) processes. The maximum likelihood function of the stationary ARMA process is embedded in Akaike's information criterion and the Bayesian information criterion, whereas the estimation procedure is based on Kalman filter recursions. The constraints imposed on the objective function enforce stability and invertibility. The best ARMA model is regarded as the global minimum of the non-convex MINLP problem. The robustness and computational performance of the MINLP solvers are compared with brute-force enumeration. Numerical experiments are done for existing time series and one new data set.

Carbon source-dependent expansion of the genetic code in bacteria

PubMed Central

Prat, Laure; Heinemann, Ilka U.; Aerni, Hans R.; Rinehart, Jesse; O’Donoghue, Patrick; Söll, Dieter

2012-01-01

Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNAPyl is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ∼5% of ORFs, whereas Pyl-decoding bacteria (∼20% of ORFs contain in-frame TAGs) regulate Pyl-tRNAPyl formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases. PMID:23185002

Question 6: coevolution theory of the genetic code: a proven theory.

PubMed

Wong, Jeffrey Tze-Fei

2007-10-01

The coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the four fundamental tenets of the theory, thus solving the riddle of the structure of the universal genetic code.

The RealGas and RealGasH2O options of the TOUGH+ code for the simulation of coupled fluid and heat flow in tight/shale gas systems

EPA Science Inventory

We developed two new EOS additions to the TOUGH+ family of codes, the RealGasH2O and RealGas. The RealGasH2O EOS option describes the non-isothermal two-phase flow of water and a real gas mixture in gas reservoirs, with a particular focus in ultra-tight (such as tight-sand and sh...

How Genetics Might Affect Real Property Rights: Currents in Contemporary Bioethics.

PubMed

Rothstein, Mark A; Rothstein, Laura

2016-03-01

New developments in genetics could affect a variety of real property rights. Mortgage lenders, mortgage insurers, real estate sellers, senior living centers, retirement communities, or other parties in residential real estate transactions begin requiring predictive genetic information as part of the application process. One likely use would be by retirement communities to learn an individual's genetic risk for Alzheimer's disease. The federal Fair Housing Act prohibits discrimination based on disability, but it is not clear that it would apply to genetic risk assessments. Only California law explicitly applies to this situation and there have been no reported cases. © 2016 American Society of Law, Medicine & Ethics.

Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal

NASA Astrophysics Data System (ADS)

Zamudio, Gabriel S.; José, Marco V.

2018-03-01

In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.

Evaluation of real-time PCR detection methods for detecting rice products contaminated by rice genetically modified with a CpTI-KDEL-T-nos transgenic construct.

PubMed

Nakamura, Kosuke; Akiyama, Hiroshi; Kawano, Noriaki; Kobayashi, Tomoko; Yoshimatsu, Kayo; Mano, Junichi; Kitta, Kazumi; Ohmori, Kiyomi; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko

2013-12-01

Genetically modified (GM) rice (Oryza sativa) lines, such as insecticidal Kefeng and Kemingdao, have been developed and found unauthorised in processed rice products in many countries. Therefore, qualitative detection methods for the GM rice are required for the GM food regulation. A transgenic construct for expressing cowpea (Vigna unguiculata) trypsin inhibitor (CpTI) was detected in some imported processed rice products contaminated with Kemingdao. The 3' terminal sequence of the identified transgenic construct for expression of CpTI included an endoplasmic reticulum retention signal coding sequence (KDEL) and nopaline synthase terminator (T-nos). The sequence was identical to that in a report on Kefeng. A novel construct-specific real-time polymerase chain reaction (PCR) detection method for detecting the junction region sequence between the CpTI-KDEL and T-nos was developed. The imported processed rice products were evaluated for the contamination of the GM rice using the developed construct-specific real-time PCR methods, and detection frequency was compared with five event-specific detection methods. The construct-specific detection methods detected the GM rice at higher frequency than the event-specific detection methods. Therefore, we propose that the construct-specific detection method is a beneficial tool for screening the contamination of GM rice lines, such as Kefeng, in processed rice products for the GM food regulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Performance optimization of PM-16QAM transmission system enabled by real-time self-adaptive coding.

PubMed

Qu, Zhen; Li, Yao; Mo, Weiyang; Yang, Mingwei; Zhu, Shengxiang; Kilper, Daniel C; Djordjevic, Ivan B

2017-10-15

We experimentally demonstrate self-adaptive coded 5×100  Gb/s WDM polarization multiplexed 16 quadrature amplitude modulation transmission over a 100 km fiber link, which is enabled by a real-time control plane. The real-time optical signal-to-noise ratio (OSNR) is measured using an optical performance monitoring device. The OSNR measurement is processed and fed back using control plane logic and messaging to the transmitter side for code adaptation, where the binary data are adaptively encoded with three types of low-density parity-check (LDPC) codes with code rates of 0.8, 0.75, and 0.7 of large girth. The total code-adaptation latency is measured to be 2273 ms. Compared with transmission without adaptation, average net capacity improvements of 102%, 36%, and 7.5% are obtained, respectively, by adaptive LDPC coding.

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records.

PubMed

Chen, Chia-Yen; Lee, Phil H; Castro, Victor M; Minnier, Jessica; Charney, Alexander W; Stahl, Eli A; Ruderfer, Douglas M; Murphy, Shawn N; Gainer, Vivian; Cai, Tianxi; Jones, Ian; Pato, Carlos N; Pato, Michele T; Landén, Mikael; Sklar, Pamela; Perlis, Roy H; Smoller, Jordan W

2018-04-18

Bipolar disorder (BD) is a heritable mood disorder characterized by episodes of mania and depression. Although genomewide association studies (GWAS) have successfully identified genetic loci contributing to BD risk, sample size has become a rate-limiting obstacle to genetic discovery. Electronic health records (EHRs) represent a vast but relatively untapped resource for high-throughput phenotyping. As part of the International Cohort Collection for Bipolar Disorder (ICCBD), we previously validated automated EHR-based phenotyping algorithms for BD against in-person diagnostic interviews (Castro et al. Am J Psychiatry 172:363-372, 2015). Here, we establish the genetic validity of these phenotypes by determining their genetic correlation with traditionally ascertained samples. Case and control algorithms were derived from structured and narrative text in the Partners Healthcare system comprising more than 4.6 million patients over 20 years. Genomewide genotype data for 3330 BD cases and 3952 controls of European ancestry were used to estimate SNP-based heritability (h 2 g ) and genetic correlation (r g ) between EHR-based phenotype definitions and traditionally ascertained BD cases in GWAS by the ICCBD and Psychiatric Genomics Consortium (PGC) using LD score regression. We evaluated BD cases identified using 4 EHR-based algorithms: an NLP-based algorithm (95-NLP) and three rule-based algorithms using codified EHR with decreasing levels of stringency-"coded-strict", "coded-broad", and "coded-broad based on a single clinical encounter" (coded-broad-SV). The analytic sample comprised 862 95-NLP, 1968 coded-strict, 2581 coded-broad, 408 coded-broad-SV BD cases, and 3 952 controls. The estimated h 2 g were 0.24 (p = 0.015), 0.09 (p = 0.064), 0.13 (p = 0.003), 0.00 (p = 0.591) for 95-NLP, coded-strict, coded-broad and coded-broad-SV BD, respectively. The h 2 g for all EHR-based cases combined except coded-broad-SV (excluded due to 0 h 2 g ) was 0.12 (p = 0.004). These h 2 g were lower or similar to the h 2 g observed by the ICCBD + PGCBD (0.23, p = 3.17E-80, total N = 33,181). However, the r g between ICCBD + PGCBD and the EHR-based cases were high for 95-NLP (0.66, p = 3.69 × 10 -5 ), coded-strict (1.00, p = 2.40 × 10 -4 ), and coded-broad (0.74, p = 8.11 × 10 -7 ). The r g between EHR-based BD definitions ranged from 0.90 to 0.98. These results provide the first genetic validation of automated EHR-based phenotyping for BD and suggest that this approach identifies cases that are highly genetically correlated with those ascertained through conventional methods. High throughput phenotyping using the large data resources available in EHRs represents a viable method for accelerating psychiatric genetic research.

Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672

The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

PubMed

Komar, Anton A

2016-01-01

Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

PubMed

Kubyshkin, Vladimir; Budisa, Nediljko

2017-08-01

The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Problem-Based Test: An "In Vitro" Experiment to Analyze the Genetic Code

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2010-01-01

Terms to be familiar with before you start to solve the test: genetic code, translation, synthetic polynucleotide, leucine, serine, filter precipitation, radioactivity measurement, template, mRNA, tRNA, rRNA, aminoacyl-tRNA synthesis, ribosomes, degeneration of the code, wobble, initiation, and elongation of protein synthesis, initiation codon.…

Evolutionary Computation with Spatial Receding Horizon Control to Minimize Network Coding Resources

PubMed Central

Leeson, Mark S.

2014-01-01

The minimization of network coding resources, such as coding nodes and links, is a challenging task, not only because it is a NP-hard problem, but also because the problem scale is huge; for example, networks in real world may have thousands or even millions of nodes and links. Genetic algorithms (GAs) have a good potential of resolving NP-hard problems like the network coding problem (NCP), but as a population-based algorithm, serious scalability and applicability problems are often confronted when GAs are applied to large- or huge-scale systems. Inspired by the temporal receding horizon control in control engineering, this paper proposes a novel spatial receding horizon control (SRHC) strategy as a network partitioning technology, and then designs an efficient GA to tackle the NCP. Traditional network partitioning methods can be viewed as a special case of the proposed SRHC, that is, one-step-wide SRHC, whilst the method in this paper is a generalized N-step-wide SRHC, which can make a better use of global information of network topologies. Besides the SRHC strategy, some useful designs are also reported in this paper. The advantages of the proposed SRHC and GA for the NCP are illustrated by extensive experiments, and they have a good potential of being extended to other large-scale complex problems. PMID:24883371

Real-time data compression of broadcast video signals

NASA Technical Reports Server (NTRS)

Shalkauser, Mary Jo W. (Inventor); Whyte, Wayne A., Jr. (Inventor); Barnes, Scott P. (Inventor)

1991-01-01

A non-adaptive predictor, a nonuniform quantizer, and a multi-level Huffman coder are incorporated into a differential pulse code modulation system for coding and decoding broadcast video signals in real time.

An extension of the coevolution theory of the origin of the genetic code

PubMed Central

Di Giulio, Massimo

2008-01-01

Background The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors. Results It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin. Conclusion All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses. Reviewers This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin. PMID:18775066

Gene-Auto: Automatic Software Code Generation for Real-Time Embedded Systems

NASA Astrophysics Data System (ADS)

Rugina, A.-E.; Thomas, D.; Olive, X.; Veran, G.

2008-08-01

This paper gives an overview of the Gene-Auto ITEA European project, which aims at building a qualified C code generator from mathematical models under Matlab-Simulink and Scilab-Scicos. The project is driven by major European industry partners, active in the real-time embedded systems domains. The Gene- Auto code generator will significantly improve the current development processes in such domains by shortening the time to market and by guaranteeing the quality of the generated code through the use of formal methods. The first version of the Gene-Auto code generator has already been released and has gone thought a validation phase on real-life case studies defined by each project partner. The validation results are taken into account in the implementation of the second version of the code generator. The partners aim at introducing the Gene-Auto results into industrial development by 2010.

Refactoring the Genetic Code for Increased Evolvability

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

Pines, Gur; Winkler, James D.; Pines, Assaf

ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of singlemore » nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology. IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.« less

Refactoring the Genetic Code for Increased Evolvability

DOE PAGES

Pines, Gur; Winkler, James D.; Pines, Assaf; ...

2017-11-14

ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of singlemore » nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology. IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.« less

Mitochondrial genetic codes evolve to match amino acid requirements of proteins.

PubMed

Swire, Jonathan; Judson, Olivia P; Burt, Austin

2005-01-01

Mitochondria often use genetic codes different from the standard genetic code. Now that many mitochondrial genomes have been sequenced, these variant codes provide the first opportunity to examine empirically the processes that produce new genetic codes. The key question is: Are codon reassignments the sole result of mutation and genetic drift? Or are they the result of natural selection? Here we present an analysis of 24 phylogenetically independent codon reassignments in mitochondria. Although the mutation-drift hypothesis can explain reassignments from stop to an amino acid, we found that it cannot explain reassignments from one amino acid to another. In particular--and contrary to the predictions of the mutation-drift hypothesis--the codon involved in such a reassignment was not rare in the ancestral genome. Instead, such reassignments appear to take place while the codon is in use at an appreciable frequency. Moreover, the comparison of inferred amino acid usage in the ancestral genome with the neutral expectation shows that the amino acid gaining the codon was selectively favored over the amino acid losing the codon. These results are consistent with a simple model of weak selection on the amino acid composition of proteins in which codon reassignments are selected because they compensate for multiple slightly deleterious mutations throughout the mitochondrial genome. We propose that the selection pressure is for reduced protein synthesis cost: most reassignments give amino acids that are less expensive to synthesize. Taken together, our results strongly suggest that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.

Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States▿

PubMed Central

Palacios, G.; Hui, J.; Quan, P. L.; Kalkstein, A.; Honkavuori, K. S.; Bussetti, A. V.; Conlan, S.; Evans, J.; Chen, Y. P.; vanEngelsdorp, D.; Efrat, H.; Pettis, J.; Cox-Foster, D.; Holmes, E. C.; Briese, T.; Lipkin, W. I.

2008-01-01

Israel acute paralysis virus (IAPV) is associated with colony collapse disorder of honey bees. Nonetheless, its role in the pathogenesis of the disorder and its geographic distribution are unclear. Here, we report phylogenetic analysis of IAPV obtained from bees in the United States, Canada, Australia, and Israel and the establishment of diagnostic real-time PCR assays for IAPV detection. Our data indicate the existence of at least three distinct IAPV lineages, two of them circulating in the United States. Analysis of representatives from each proposed lineage suggested the possibility of recombination events and revealed differences in coding sequences that may have implications for virulence. PMID:18434396

Population structure and covariate analysis based on pairwise microsatellite allele matching frequencies.

PubMed

Givens, Geof H; Ozaksoy, Isin

2007-01-01

We describe a general model for pairwise microsatellite allele matching probabilities. The model can be used for analysis of population substructure, and is particularly focused on relating genetic correlation to measurable covariates. The approach is intended for cases when the existence of subpopulations is uncertain and a priori assignment of samples to hypothesized subpopulations is difficult. Such a situation arises, for example, with western Arctic bowhead whales, where genetic samples are available only from a possibly mixed migratory assemblage. We estimate genetic structure associated with spatial, temporal, or other variables that may confound the detection of population structure. In the bowhead case, the model permits detection of genetic patterns associated with a temporally pulsed multi-population assemblage in the annual migration. Hypothesis tests for population substructure and for covariate effects can be carried out using permutation methods. Simulated and real examples illustrate the effectiveness and reliability of the approach and enable comparisons with other familiar approaches. Analysis of the bowhead data finds no evidence for two temporally pulsed subpopulations using the best available data, although a significant pattern found by other researchers using preliminary data is also confirmed here. Code in the R language is available from www.stat.colostate.edu/~geof/gammmp.html.

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization.

PubMed

Błażej, Paweł; Wnȩtrzak, Małgorzata; Mackiewicz, Paweł

2016-12-01

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure minimize the costs about 2.7 times better than the canonical genetic code. Interestingly, the optimal codes are dominated by amino acids characterized by polarity close to its average value for all amino acids. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg’s and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula

PubMed Central

Castro-Chavez, Fernando

2012-01-01

Background Three binary representations of the genetic code according to the ancient I Ching of Fu-Xi will be presented, depending on their defragging capabilities by pairing based on three biochemical properties of the nucleic acids: H-bonds, Purine/Pyrimidine rings, and the Keto-enol/Amino-imino tautomerism, yielding the last pair a 32/32 single-strand self-annealed genetic code and I Ching tables. Methods Our working tool is the ancient binary I Ching's resulting genetic code chromosomes defragged by vertical and by horizontal pairing, reverse engineered into non-binaries of 2D rotating 4×4×4 circles and 8×8 squares and into one 3D 100% symmetrical 16×4 tetrahedron coupled to a functional tetrahedron with apical signaling and central hydrophobicity (codon formula: 4[1(1)+1(3)+1(4)+4(2)]; 5:5, 6:6 in man) forming a stella octangula, and compared to Nirenberg's 16×4 codon table (1965) pairing the first two nucleotides of the 64 codons in axis y. Results One horizontal and one vertical defragging had the start Met at the center. Two, both horizontal and vertical pairings produced two pairs of 2×8×4 genetic code chromosomes naturally arranged (M and I), rearranged by semi-introversion of central purines or pyrimidines (M' and I') and by clustering hydrophobic amino acids; their quasi-identity was disrupted by amino acids with odd codons (Met and Tyr pairing to Ile and TGA Stop); in all instances, the 64-grid 90° rotational ability was restored. Conclusions We defragged three I Ching representations of the genetic code while emphasizing Nirenberg's historical finding. The synthetic genetic code chromosomes obtained reflect the protective strategy of enzymes with a similar function, having both humans and mammals a biased G-C dominance of three H-bonds in the third nucleotide of their most used codons per amino acid, as seen in one chromosome of the i, M and M' genetic codes, while a two H-bond A-T dominance was found in their complementary chromosome, as seen in invertebrates and plants. The reverse engineering of chromosome I' into 2D rotating circles and squares was undertaken, yielding a 100% symmetrical 3D geometry which was coupled to a previously obtained genetic code tetrahedron in order to differentiate the start methionine from the methionine that is acting as a codifying non-start codon. PMID:23431415

Quaternionic representation of the genetic code.

PubMed

Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

2016-03-01

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Simultaneous optimization of loading pattern and burnable poison placement for PWRs

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

Alim, F.; Ivanov, K.; Yilmaz, S.

2006-07-01

To solve in-core fuel management optimization problem, GARCO-PSU (Genetic Algorithm Reactor Core Optimization - Pennsylvania State Univ.) is developed. This code is applicable for all types and geometry of PWR core structures with unlimited number of fuel assembly (FA) types in the inventory. For this reason an innovative genetic algorithm is developed with modifying the classical representation of the genotype. In-core fuel management heuristic rules are introduced into GARCO. The core re-load design optimization has two parts, loading pattern (LP) optimization and burnable poison (BP) placement optimization. These parts depend on each other, but it is difficult to solve themore » combined problem due to its large size. Separating the problem into two parts provides a practical way to solve the problem. However, the result of this method does not reflect the real optimal solution. GARCO-PSU achieves to solve LP optimization and BP placement optimization simultaneously in an efficient manner. (authors)« less

Introduction to the Natural Anticipator and the Artificial Anticipator

NASA Astrophysics Data System (ADS)

Dubois, Daniel M.

2010-11-01

This short communication deals with the introduction of the concept of anticipator, which is one who anticipates, in the framework of computing anticipatory systems. The definition of anticipation deals with the concept of program. Indeed, the word program, comes from "pro-gram" meaning "to write before" by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes or behavioural responses, that is part of an organism. Any natural or artificial programs are thus related to anticipatory rewriting systems, as shown in this paper. All the cells in the body, and the neurons in the brain, are programmed by the anticipatory genetic code, DNA, in a low-level language with four signs. The programs in computers are also computing anticipatory systems. It will be shown, at one hand, that the genetic code DNA is a natural anticipator. As demonstrated by Nobel laureate McClintock [8], genomes are programmed. The fundamental program deals with the DNA genetic code. The properties of the DNA consist in self-replication and self-modification. The self-replicating process leads to reproduction of the species, while the self-modifying process leads to new species or evolution and adaptation in existing ones. The genetic code DNA keeps its instructions in memory in the DNA coding molecule. The genetic code DNA is a rewriting system, from DNA coding to DNA template molecule. The DNA template molecule is a rewriting system to the Messenger RNA molecule. The information is not destroyed during the execution of the rewriting program. On the other hand, it will be demonstrated that Turing machine is an artificial anticipator. The Turing machine is a rewriting system. The head reads and writes, modifying the content of the tape. The information is destroyed during the execution of the program. This is an irreversible process. The input data are lost.

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction

PubMed Central

Gallistel, C. R.; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

2014-01-01

We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer. PMID:24637442

Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction.

PubMed

Gallistel, C R; Balci, Fuat; Freestone, David; Kheifets, Aaron; King, Adam

2014-02-26

We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer.

Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms

PubMed Central

Telford, Maximilian J.; Herniou, Elisabeth A.; Russell, Robert B.; Littlewood, D. Timothy J.

2000-01-01

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate). PMID:11027335

Automated Detection and Analysis of Interplanetary Shocks with Real-Time Application

NASA Astrophysics Data System (ADS)

Vorotnikov, V.; Smith, C. W.; Hu, Q.; Szabo, A.; Skoug, R. M.; Cohen, C. M.

2006-12-01

The ACE real-time data stream provides web-based now-casting capabilities for solar wind conditions upstream of Earth. Our goal is to provide an automated code that finds and analyzes interplanetary shocks as they occur for possible real-time application to space weather nowcasting. Shock analysis algorithms based on the Rankine-Hugoniot jump conditions exist and are in wide-spread use today for the interactive analysis of interplanetary shocks yielding parameters such as shock speed and propagation direction and shock strength in the form of compression ratios. Although these codes can be automated in a reasonable manner to yield solutions not far from those obtained by user-directed interactive analysis, event detection presents an added obstacle and the first step in a fully automated analysis. We present a fully automated Rankine-Hugoniot analysis code that can scan the ACE science data, find shock candidates, analyze the events, obtain solutions in good agreement with those derived from interactive applications, and dismiss false positive shock candidates on the basis of the conservation equations. The intent is to make this code available to NOAA for use in real-time space weather applications. The code has the added advantage of being able to scan spacecraft data sets to provide shock solutions for use outside real-time applications and can easily be applied to science-quality data sets from other missions. Use of the code for this purpose will also be explored.

MARTe: A Multiplatform Real-Time Framework

NASA Astrophysics Data System (ADS)

Neto, André C.; Sartori, Filippo; Piccolo, Fabio; Vitelli, Riccardo; De Tommasi, Gianmaria; Zabeo, Luca; Barbalace, Antonio; Fernandes, Horacio; Valcarcel, Daniel F.; Batista, Antonio J. N.

2010-04-01

Development of real-time applications is usually associated with nonportable code targeted at specific real-time operating systems. The boundary between hardware drivers, system services, and user code is commonly not well defined, making the development in the target host significantly difficult. The Multithreaded Application Real-Time executor (MARTe) is a framework built over a multiplatform library that allows the execution of the same code in different operating systems. The framework provides the high-level interfaces with hardware, external configuration programs, and user interfaces, assuring at the same time hard real-time performances. End-users of the framework are required to define and implement algorithms inside a well-defined block of software, named Generic Application Module (GAM), that is executed by the real-time scheduler. Each GAM is reconfigurable with a set of predefined configuration meta-parameters and interchanges information using a set of data pipes that are provided as inputs and required as output. Using these connections, different GAMs can be chained either in series or parallel. GAMs can be developed and debugged in a non-real-time system and, only once the robustness of the code and correctness of the algorithm are verified, deployed to the real-time system. The software also supplies a large set of utilities that greatly ease the interaction and debugging of a running system. Among the most useful are a highly efficient real-time logger, HTTP introspection of real-time objects, and HTTP remote configuration. MARTe is currently being used to successfully drive the plasma vertical stabilization controller on the largest magnetic confinement fusion device in the world, with a control loop cycle of 50 ?s and a jitter under 1 ?s. In this particular project, MARTe is used with the Real-Time Application Interface (RTAI)/Linux operating system exploiting the new ?86 multicore processors technology.

Machine learning patterns for neuroimaging-genetic studies in the cloud.

PubMed

Da Mota, Benoit; Tudoran, Radu; Costan, Alexandru; Varoquaux, Gaël; Brasche, Goetz; Conrod, Patricia; Lemaitre, Herve; Paus, Tomas; Rietschel, Marcella; Frouin, Vincent; Poline, Jean-Baptiste; Antoniu, Gabriel; Thirion, Bertrand

2014-01-01

Brain imaging is a natural intermediate phenotype to understand the link between genetic information and behavior or brain pathologies risk factors. Massive efforts have been made in the last few years to acquire high-dimensional neuroimaging and genetic data on large cohorts of subjects. The statistical analysis of such data is carried out with increasingly sophisticated techniques and represents a great computational challenge. Fortunately, increasing computational power in distributed architectures can be harnessed, if new neuroinformatics infrastructures are designed and training to use these new tools is provided. Combining a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library), we design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data. End-users describe the statistical procedure to perform and can then test the model on their own computers before running the very same code in the cloud at a larger scale. We illustrate the potential of our approach on real data with an experiment showing how the functional signal in subcortical brain regions can be significantly fit with genome-wide genotypes. This experiment demonstrates the scalability and the reliability of our framework in the cloud with a 2 weeks deployment on hundreds of virtual machines.

William Friedman, Geneticist Turned Cryptographer.

PubMed

Goldman, Irwin L

2017-05-01

William Friedman (1891-1969), trained as a plant geneticist at Cornell University, was employed at Riverbank Laboratories by the eccentric millionaire George Fabyan to work on wheat breeding. Friedman, however, soon became intrigued by and started working on a pet project of Fabyan's involving the conjecture that Francis Bacon, a polymath known for the study of ciphers, was the real author of Shakespeare's plays. Thus, beginning in ∼1916, Friedman turned his attention to the so called "Baconian cipher," and developed decryption techniques that bore similarity to approaches for solving problems in population genetics. His most significant, indeed pathbreaking, work used ideas from genetics and statistics, focusing on analysis of the frequencies of letters in language use. Although he had transitioned from being a geneticist to a cryptographer, his earlier work had resonance in his later pursuits. He soon began working directly for the United States government and produced solutions used to solve complex military ciphers, in particular to break the Japanese Purple code during World War II. Another important legacy of his work was the establishment of the Signal Intelligence Service and eventually the National Security Agency. Copyright © 2017 by the Genetics Society of America.

Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing.

PubMed

Liang, Chanjuan; van Dijk, Jeroen P; Scholtens, Ingrid M J; Staats, Martijn; Prins, Theo W; Voorhuijzen, Marleen M; da Silva, Andrea M; Arisi, Ana Carolina Maisonnave; den Dunnen, Johan T; Kok, Esther J

2014-04-01

The growing number of biotech crops with novel genetic elements increasingly complicates the detection of genetically modified organisms (GMOs) in food and feed samples using conventional screening methods. Unauthorized GMOs (UGMOs) in food and feed are currently identified through combining GMO element screening with sequencing the DNA flanking these elements. In this study, a specific and sensitive qPCR assay was developed for vip3A element detection based on the vip3Aa20 coding sequences of the recently marketed MIR162 maize and COT102 cotton. Furthermore, SiteFinding-PCR in combination with Sanger, Illumina or Pacific BioSciences (PacBio) sequencing was performed targeting the flanking DNA of the vip3Aa20 element in MIR162. De novo assembly and Basic Local Alignment Search Tool searches were used to mimic UGMO identification. PacBio data resulted in relatively long contigs in the upstream (1,326 nucleotides (nt); 95 % identity) and downstream (1,135 nt; 92 % identity) regions, whereas Illumina data resulted in two smaller contigs of 858 and 1,038 nt with higher sequence identity (>99 % identity). Both approaches outperformed Sanger sequencing, underlining the potential for next-generation sequencing in UGMO identification.

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.

PubMed

Brunak, S; Engelbrecht, J

1996-06-01

A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome.

Real-time visual simulation of APT system based on RTW and Vega

NASA Astrophysics Data System (ADS)

Xiong, Shuai; Fu, Chengyu; Tang, Tao

2012-10-01

The Matlab/Simulink simulation model of APT (acquisition, pointing and tracking) system is analyzed and established. Then the model's C code which can be used for real-time simulation is generated by RTW (Real-Time Workshop). Practical experiments show, the simulation result of running the C code is the same as running the Simulink model directly in the Matlab environment. MultiGen-Vega is a real-time 3D scene simulation software system. With it and OpenGL, the APT scene simulation platform is developed and used to render and display the virtual scenes of the APT system. To add some necessary graphics effects to the virtual scenes real-time, GLSL (OpenGL Shading Language) shaders are used based on programmable GPU. By calling the C code, the scene simulation platform can adjust the system parameters on-line and get APT system's real-time simulation data to drive the scenes. Practical application shows that this visual simulation platform has high efficiency, low charge and good simulation effect.

File Compression and Expansion of the Genetic Code by the use of the Yin/Yang Directions to find its Sphered Cube

PubMed Central

Castro-Chavez, Fernando

2014-01-01

Objective The objective of this article is to demonstrate that the genetic code can be studied and represented in a 3-D Sphered Cube for bioinformatics and for education by using the graphical help of the ancient “Book of Changes” or I Ching for the comparison, pair by pair, of the three basic characteristics of nucleotides: H-bonds, molecular structure, and their tautomerism. Methods The source of natural biodiversity is the high plasticity of the genetic code, analyzable with a reverse engineering of its 2-D and 3-D representations (here illustrated), but also through the classical 64-hexagrams of the ancient I Ching, as if they were the 64-codons or words of the genetic code. Results In this article, the four elements of the Yin/Yang were found by correlating the 3×2=6 sets of Cartesian comparisons of the mentioned properties of nucleic acids, to the directionality of their resulting blocks of codons grouped according to their resulting amino acids and/or functions, integrating a 384-codon Sphered Cube whose function is illustrated by comparing six brain peptides and a promoter of osteoblasts from Humans versus Neanderthal, as well as to Negadi’s work on the importance of the number 384 within the genetic code. Conclusions Starting with the codon/anticodon correlation of Nirenberg, published in full here for the first time, and by studying the genetic code and its 3-D display, the buffers of reiteration within codons codifying for the same amino acid, displayed the two long (binary number one) and older Yin/Yang arrows that travel in opposite directions, mimicking the parental DNA strands, while annealing to the two younger and broken (binary number zero) Yin/Yang arrows, mimicking the new DNA strands; the graphic analysis of the of the genetic code and its plasticity was helpful to compare compatible sequences (human compatible to human versus neanderthal compatible to neanderthal), while further exploring the wondrous biodiversity of nature for educational purposes. PMID:25340175

Genetic Code Expansion of Mammalian Cells with Unnatural Amino Acids.

PubMed

Brown, Kalyn A; Deiters, Alexander

2015-09-01

The expansion of the genetic code of mammalian cells enables the incorporation of unnatural amino acids into proteins. This is achieved by adding components to the protein biosynthetic machinery, specifically an engineered aminoacyl-tRNA synthetase/tRNA pair. The unnatural amino acids are chemically synthesized and supplemented to the growth medium. Using this methodology, fundamental new chemistries can be added to the functional repertoire of the genetic code of mammalian cells. This protocol outlines the steps necessary to incorporate a photocaged lysine into proteins and showcases its application in the optical triggering of protein translocation to the nucleus. Copyright © 2015 John Wiley & Sons, Inc.

Possibilities for the evolution of the genetic code from a preceding form

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1973-01-01

Analysis of the interaction between mRNA codons and tRNA anticodons suggests a model for the evolution of the genetic code. Modification of the nucleic acid following the anticodon is at present essential in both eukaryotes and prokaryotes to ensure fidelity of translation of codons starting with A, and the amino acids which could be coded for before the evolution of the modifying enzymes can be deduced.

I-Ching, dyadic groups of binary numbers and the geno-logic coding in living bodies.

PubMed

Hu, Zhengbing; Petoukhov, Sergey V; Petukhova, Elena S

2017-12-01

The ancient Chinese book I-Ching was written a few thousand years ago. It introduces the system of symbols Yin and Yang (equivalents of 0 and 1). It had a powerful impact on culture, medicine and science of ancient China and several other countries. From the modern standpoint, I-Ching declares the importance of dyadic groups of binary numbers for the Nature. The system of I-Ching is represented by the tables with dyadic groups of 4 bigrams, 8 trigrams and 64 hexagrams, which were declared as fundamental archetypes of the Nature. The ancient Chinese did not know about the genetic code of protein sequences of amino acids but this code is organized in accordance with the I-Ching: in particularly, the genetic code is constructed on DNA molecules using 4 nitrogenous bases, 16 doublets, and 64 triplets. The article also describes the usage of dyadic groups as a foundation of the bio-mathematical doctrine of the geno-logic code, which exists in parallel with the known genetic code of amino acids but serves for a different goal: to code the inherited algorithmic processes using the logical holography and the spectral logic of systems of genetic Boolean functions. Some relations of this doctrine with the I-Ching are discussed. In addition, the ratios of musical harmony that can be revealed in the parameters of DNA structure are also represented in the I-Ching book. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the possible origin and evolution of the genetic code

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1974-01-01

The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

Summary of evidence for an anticodonic basis for the origin of the genetic code

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1981-01-01

This article summarizes data supporting the hypothesis that the genetic code origin was based on relationships (probably affinities) between amino acids and their anticodon nucleotides. Selective activation seems to follow from selective affinity and consequently, incorporation of amino acids into peptides can also be selective. It is suggested that these selectivities in affinity and activation, coupled with the base pairing specificities, allowed the origin of the code and the process of translation.

Gene-environment interaction on neural mechanisms of orthographic processing in Chinese children

PubMed Central

Su, Mengmeng; Wang, Jiuju; Maurer, Urs; Zhang, Yuping; Li, Jun; McBride-Chang, Catherine; Tardif, Twila; Liu, Youyi; Shu, Hua

2015-01-01

The ability to process and identify visual words requires efficient orthographic processing of print, consisting of letters in alphabetic languages or characters in Chinese. The N170 is a robust neural marker for orthographic processes. Both genetic and environmental factors, such as home literacy, have been shown to influence orthographic processing at the behavioral level, but their relative contributions and interactions are not well understood. The present study aimed to reveal possible gene-by-environment interactions on orthographic processing at the behavioral and neural level in a normal children sample. Sixty 12 year old Chinese children from a 10-year longitudinal sample underwent an implicit visual-word color decision task on real words and stroke combinations. The ERP analysis focused on the increase of the occipito-temporal N170 to words compared to stroke combinations. The genetic analysis focused on two SNPs (rs1419228, rs1091047) in the gene DCDC2 based on previous findings linking these 2 SNPs to orthographic coding. Home literacy was measured previously as the number of children's books at home, when the children were at the age of 3. Relative to stroke combinations, real words evoked greater N170 in bilateral posterior brain regions. A significant interaction between rs1091047 and home literacy was observed on the changes of N170 comparing real words to stroke combinations in the left hemisphere. Particularly, children carrying the major allele “G” showed a similar N170 effect irrespective of their environment, while children carrying the minor allele “C” showed a smaller N170 effect in low home-literacy environment than those in good environment. PMID:26294811

Nuclear fuel management optimization using genetic algorithms

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

DeChaine, M.D.; Feltus, M.A.

1995-07-01

The code independent genetic algorithm reactor optimization (CIGARO) system has been developed to optimize nuclear reactor loading patterns. It uses genetic algorithms (GAs) and a code-independent interface, so any reactor physics code (e.g., CASMO-3/SIMULATE-3) can be used to evaluate the loading patterns. The system is compared to other GA-based loading pattern optimizers. Tests were carried out to maximize the beginning of cycle k{sub eff} for a pressurized water reactor core loading with a penalty function to limit power peaking. The CIGARO system performed well, increasing the k{sub eff} after lowering the peak power. Tests of a prototype parallel evaluation methodmore » showed the potential for a significant speedup.« less

Clinical application of antenatal genetic diagnosis of osteogenesis imperfecta type IV.

PubMed

Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

2015-04-02

Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families.

Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods.

PubMed

Andrade, Xavier; Aspuru-Guzik, Alán

2013-10-08

We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs.

Genetic algorithms for adaptive real-time control in space systems

NASA Technical Reports Server (NTRS)

Vanderzijp, J.; Choudry, A.

1988-01-01

Genetic Algorithms that are used for learning as one way to control the combinational explosion associated with the generation of new rules are discussed. The Genetic Algorithm approach tends to work best when it can be applied to a domain independent knowledge representation. Applications to real time control in space systems are discussed.

Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection

USDA-ARS?s Scientific Manuscript database

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

[Direct genetic manipulation and criminal code in Venezuela: absolute criminal law void?].

PubMed

Cermeño Zambrano, Fernando G De J

2002-01-01

The judicial regulation of genetic biotechnology applied to the human genome is of big relevance currently in Venezuela due to the drafting of an innovative bioethical law in the country's parliament. This article will highlight the constitutional normative of Venezuela's 1999 Constitution regarding this subject, as it establishes the framework from which this matter will be legally regulated. The approach this article makes towards the genetic biotechnology applied to the human genome is made taking into account the Venezuelan penal law and by highlighting the violent genetic manipulations that have criminal relevance. The genetic biotechnology applied to the human genome has another important relevance as a consequence of the reformulation of the Venezuelan Penal Code discussed by the country's National Assembly. Therefore, a concise study of the country's penal code will be made in this article to better understand what judicial-penal properties have been protected by the Venezuelan penal legislation. This last step will enable us to identify the penal tools Venezuela counts on to face direct genetic manipulations. We will equally indicate the existing punitive loophole and that should be covered by the penal legislator. In conclusion, this essay concerns criminal policy, referred to the direct genetic manipulations on the human genome that haven't been typified in Venezuelan law, thus discovering a genetic biotechnology paradise.

A real-time simulator of a turbofan engine

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Delaat, John C.; Merrill, Walter C.

1989-01-01

A real-time digital simulator of a Pratt and Whitney F100 engine has been developed for real-time code verification and for actuator diagnosis during full-scale engine testing. This self-contained unit can operate in an open-loop stand-alone mode or as part of closed-loop control system. It can also be used for control system design and development. Tests conducted in conjunction with the NASA Advanced Detection, Isolation, and Accommodation program show that the simulator is a valuable tool for real-time code verification and as a real-time actuator simulator for actuator fault diagnosis. Although currently a small perturbation model, advances in microprocessor hardware should allow the simulator to evolve into a real-time, full-envelope, full engine simulation.

Decoding the genome beyond sequencing: the new phase of genomic research.

PubMed

Heng, Henry H Q; Liu, Guo; Stevens, Joshua B; Bremer, Steven W; Ye, Karen J; Abdallah, Batoul Y; Horne, Steven D; Ye, Christine J

2011-10-01

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing. Copyright © 2011 Elsevier Inc. All rights reserved.

Use of fluorescent proteins and color-coded imaging to visualize cancer cells with different genetic properties.

PubMed

Hoffman, Robert M

2016-03-01

Fluorescent proteins are very bright and available in spectrally-distinct colors, enable the imaging of color-coded cancer cells growing in vivo and therefore the distinction of cancer cells with different genetic properties. Non-invasive and intravital imaging of cancer cells with fluorescent proteins allows the visualization of distinct genetic variants of cancer cells down to the cellular level in vivo. Cancer cells with increased or decreased ability to metastasize can be distinguished in vivo. Gene exchange in vivo which enables low metastatic cancer cells to convert to high metastatic can be color-coded imaged in vivo. Cancer stem-like and non-stem cells can be distinguished in vivo by color-coded imaging. These properties also demonstrate the vast superiority of imaging cancer cells in vivo with fluorescent proteins over photon counting of luciferase-labeled cancer cells.

Computation of the Genetic Code

NASA Astrophysics Data System (ADS)

Kozlov, Nicolay N.; Kozlova, Olga N.

2018-03-01

One of the problems in the development of mathematical theory of the genetic code (summary is presented in [1], the detailed -to [2]) is the problem of the calculation of the genetic code. Similar problems in the world is unknown and could be delivered only in the 21st century. One approach to solving this problem is devoted to this work. For the first time provides a detailed description of the method of calculation of the genetic code, the idea of which was first published earlier [3]), and the choice of one of the most important sets for the calculation was based on an article [4]. Such a set of amino acid corresponds to a complete set of representations of the plurality of overlapping triple gene belonging to the same DNA strand. A separate issue was the initial point, triggering an iterative search process all codes submitted by the initial data. Mathematical analysis has shown that the said set contains some ambiguities, which have been founded because of our proposed compressed representation of the set. As a result, the developed method of calculation was limited to the two main stages of research, where the first stage only the of the area were used in the calculations. The proposed approach will significantly reduce the amount of computations at each step in this complex discrete structure.

Coding of Class I and II aminoacyl-tRNA synthetases

PubMed Central

Carter, Charles W.

2018-01-01

SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins. PMID:28828732

The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory.

PubMed

Di Giulio, Massimo

2016-06-21

I analyze the mechanism on which are based the majority of theories that put to the center of the origin of the genetic code the physico-chemical properties of amino acids. As this mechanism is based on excessive mutational steps, I conclude that it could not have been operative or if operative it would not have allowed a full realization of predictions of these theories, because this mechanism contained, evidently, a high indeterminacy. I make that disapproving the four-column theory of the origin of the genetic code (Higgs, 2009) and reply to the criticism that was directed towards the coevolution theory of the origin of the genetic code. In this context, I suggest a new hypothesis that clarifies the mechanism by which the domains of codons of the precursor amino acids would have evolved, as predicted by the coevolution theory. This mechanism would have used particular elongation factors that would have constrained the evolution of all amino acids belonging to a given biosynthetic family to the progenitor pre-tRNA, that for first recognized, the first codons that evolved in a certain codon domain of a determined precursor amino acid. This happened because the elongation factors recognized two characteristics of the progenitor pre-tRNAs of precursor amino acids, which prevented the elongation factors from recognizing the pre-tRNAs belonging to biosynthetic families of different precursor amino acids. Finally, I analyze by means of Fisher's exact test, the distribution, within the genetic code, of the biosynthetic classes of amino acids and the ones of polarity values of amino acids. This analysis would seem to support the biosynthetic classes of amino acids over the ones of polarity values, as the main factor that led to the structuring of the genetic code, with the physico-chemical properties of amino acids playing only a subsidiary role in this evolution. As a whole, the full analysis brings to the conclusion that the coevolution theory of the origin of the genetic code would be a theory highly corroborated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental program for real gas flow code validation at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Deiwert, George S.; Strawa, Anthony W.; Sharma, Surendra P.; Park, Chul

1989-01-01

The experimental program for validating real gas hypersonic flow codes at NASA Ames Rsearch Center is described. Ground-based test facilities used include ballistic ranges, shock tubes and shock tunnels, arc jet facilities and heated-air hypersonic wind tunnels. Also included are large-scale computer systems for kinetic theory simulations and benchmark code solutions. Flight tests consist of the Aeroassist Flight Experiment, the Space Shuttle, Project Fire 2, and planetary probes such as Galileo, Pioneer Venus, and PAET.

Real-Time Parallel Software Design Case Study: Implementation of the RASSP SAR Benchmark on the Intel Paragon.

DTIC Science & Technology

1996-01-01

Real-Time 19 5 Conclusion 23 List of References 25 ii LIST OF FIGURES FIGURE PAGE 3-1 Test Bench Pseudo Code 7 3-2 Fast Convolution...3-1 shows pseudo - code for a test bench with two application nodes. The outer test bench wrapper consists of three functions: pipeline_init, pipeline...exit_func); Figure 3-1. Test Bench Pseudo Code The application wrapper is contained in the pipeline routine and similarly consists of an

Survival in extreme environment by "preserve-expand-specialize" strategy: lessons from comparative genomics of an anhydrobiotic midge.

NASA Astrophysics Data System (ADS)

Gusev, Oleg; Sugimoto, Manabu; Novikova, Nataliya; Sychev, Vladimir; Okuda, Takashi; Kikawada, Takahiro

2012-07-01

Anhydrobiotic chironomid larvae of Polypedilum vanderplanki (Diptera) can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. Recent experiments showed that this insect is able to survive long-tern exposure to real outer space. At the same time, we found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Analysis of several remote populations of the chironomid in Africa that desiccation-related DNA damage might be a driving genetic force for rapid radiation within the species. First results of ongoing genome project suggest that origin and evolution of anhydrobiosis in this single insect species related to rapid duplication of the genes, coding late embryogenesis abundant proteins (LEA) and other molecular agents directly involved in desiccation resistance in the cells. Analysis of genome-wide mRNA expression profiles in the larvae subjected to desiccation shows that joint-activity of large multiple-genes coding regions in the genome involved in control of anhydrobiosis-related molecular adaptations in the chironomid.

Simulation of the detonation process of an ammonium nitrate based emulsion explosive using the lee-tarver reactive flow model

NASA Astrophysics Data System (ADS)

Ribeiro, José B.; Silva, Cristóvão; Mendes, Ricardo; Plaksin, I.; Campos, Jose

2012-03-01

The use of emulsion explosives [EEx] for processing materials (compaction, welding and forming) requires the ability to perform detailed simulations of its detonation process [DP]. Detailed numerical simulations of the DP of this kind of explosives, characterized by having a finite reaction zone thickness, are thought to be suitably performed using the Lee-Tarver reactive flow model. In this work a real coded genetic algorithm methodology was used to estimate the 15 parameters of the reaction rate equation [RRE] of that model for a particular EEx. This methodology allows, in a single optimization procedure, using only one experimental result and without the need of any starting solution, to seek for the 15 parameters of the RRE that fit the numerical to the experimental results. Mass averaging and the Plate-Gap Model have been used for the determination of the shock data used in the unreacted explosive JWL EoS assessment, and the thermochemical code THOR retrieved the data used in the detonation products JWL EoS assessment. The obtained parameters allow a reasonable description of the experimental data.

Genetic Recombination Between Stromal and Cancer Cells Results in Highly Malignant Cells Identified by Color-Coded Imaging in a Mouse Lymphoma Model.

PubMed

Nakamura, Miki; Suetsugu, Atsushi; Hasegawa, Kousuke; Matsumoto, Takuro; Aoki, Hitomi; Kunisada, Takahiro; Shimizu, Masahito; Saji, Shigetoyo; Moriwaki, Hisataka; Hoffman, Robert M

2017-12-01

The tumor microenvironment (TME) promotes tumor growth and metastasis. We previously established the color-coded EL4 lymphoma TME model with red fluorescent protein (RFP) expressing EL4 implanted in transgenic C57BL/6 green fluorescent protein (GFP) mice. Color-coded imaging of the lymphoma TME suggested an important role of stromal cells in lymphoma progression and metastasis. In the present study, we used color-coded imaging of RFP-lymphoma cells and GFP stromal cells to identify yellow-fluorescent genetically recombinant cells appearing only during metastasis. The EL4-RFP lymphoma cells were injected subcutaneously in C57BL/6-GFP transgenic mice and formed subcutaneous tumors 14 days after cell transplantation. The subcutaneous tumors were harvested and transplanted to the abdominal cavity of nude mice. Metastases to the liver, perigastric lymph node, ascites, bone marrow, and primary tumor were imaged. In addition to EL4-RFP cells and GFP-host cells, genetically recombinant yellow-fluorescent cells, were observed only in the ascites and bone marrow. These results indicate genetic exchange between the stromal and cancer cells. Possible mechanisms of genetic exchange are discussed as well as its ramifications for metastasis. J. Cell. Biochem. 118: 4216-4221, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The adaption and use of research codes for performance assessment

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

Liebetrau, A.M.

1987-05-01

Models of real-world phenomena are developed for many reasons. The models are usually, if not always, implemented in the form of a computer code. The characteristics of a code are determined largely by its intended use. Realizations or implementations of detailed mathematical models of complex physical and/or chemical processes are often referred to as research or scientific (RS) codes. Research codes typically require large amounts of computing time. One example of an RS code is a finite-element code for solving complex systems of differential equations that describe mass transfer through some geologic medium. Considerable computing time is required because computationsmore » are done at many points in time and/or space. Codes used to evaluate the overall performance of real-world physical systems are called performance assessment (PA) codes. Performance assessment codes are used to conduct simulated experiments involving systems that cannot be directly observed. Thus, PA codes usually involve repeated simulations of system performance in situations that preclude the use of conventional experimental and statistical methods. 3 figs.« less

A new coding system for metabolic disorders demonstrates gaps in the international disease classifications ICD-10 and SNOMED-CT, which can be barriers to genotype-phenotype data sharing.

PubMed

Sollie, Annet; Sijmons, Rolf H; Lindhout, Dick; van der Ploeg, Ans T; Rubio Gozalbo, M Estela; Smit, G Peter A; Verheijen, Frans; Waterham, Hans R; van Weely, Sonja; Wijburg, Frits A; Wijburg, Rudolph; Visser, Gepke

2013-07-01

Data sharing is essential for a better understanding of genetic disorders. Good phenotype coding plays a key role in this process. Unfortunately, the two most widely used coding systems in medicine, ICD-10 and SNOMED-CT, lack information necessary for the detailed classification and annotation of rare and genetic disorders. This prevents the optimal registration of such patients in databases and thus data-sharing efforts. To improve care and to facilitate research for patients with metabolic disorders, we developed a new coding system for metabolic diseases with a dedicated group of clinical specialists. Next, we compared the resulting codes with those in ICD and SNOMED-CT. No matches were found in 76% of cases in ICD-10 and in 54% in SNOMED-CT. We conclude that there are sizable gaps in the SNOMED-CT and ICD coding systems for metabolic disorders. There may be similar gaps for other classes of rare and genetic disorders. We have demonstrated that expert groups can help in addressing such coding issues. Our coding system has been made available to the ICD and SNOMED-CT organizations as well as to the Orphanet and HPO organizations for further public application and updates will be published online (www.ddrmd.nl and www.cineas.org). © 2013 WILEY PERIODICALS, INC.

DualSPHysics: A numerical tool to simulate real breakwaters

NASA Astrophysics Data System (ADS)

Zhang, Feng; Crespo, Alejandro; Altomare, Corrado; Domínguez, José; Marzeddu, Andrea; Shang, Shao-ping; Gómez-Gesteira, Moncho

2018-02-01

The open-source code DualSPHysics is used in this work to compute the wave run-up in an existing dike in the Chinese coast using realistic dimensions, bathymetry and wave conditions. The GPU computing power of the DualSPHysics allows simulating real-engineering problems that involve complex geometries with a high resolution in a reasonable computational time. The code is first validated by comparing the numerical free-surface elevation, the wave orbital velocities and the time series of the run-up with physical data in a wave flume. Those experiments include a smooth dike and an armored dike with two layers of cubic blocks. After validation, the code is applied to a real case to obtain the wave run-up under different incident wave conditions. In order to simulate the real open sea, the spurious reflections from the wavemaker are removed by using an active wave absorption technique.

Automated real-time software development

NASA Technical Reports Server (NTRS)

Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

1993-01-01

A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

Expanding the genetic code for site-specific labelling of tobacco mosaic virus coat protein and building biotin-functionalized virus-like particles.

PubMed

Wu, F C; Zhang, H; Zhou, Q; Wu, M; Ballard, Z; Tian, Y; Wang, J Y; Niu, Z W; Huang, Y

2014-04-18

A method for site-specific and high yield modification of tobacco mosaic virus coat protein (TMVCP) utilizing a genetic code expanding technology and copper free cycloaddition reaction has been established, and biotin-functionalized virus-like particles were built by the self-assembly of the protein monomers.

On origin of genetic code and tRNA before translation

PubMed Central

2011-01-01

Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule. Conclusion Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony. Reviewers This article was reviewed by Eugene V. Koonin, Wentao Ma (nominated by Juergen Brosius) and Anthony Poole. PMID:21342520

General Flow-Solver Code for Turbomachinery Applications

NASA Technical Reports Server (NTRS)

Dorney, Daniel; Sondak, Douglas

2006-01-01

Phantom is a computer code intended primarily for real-fluid turbomachinery problems. It is based on Corsair, an ideal-gas turbomachinery code, developed by the same authors, which evolved from the ROTOR codes from NASA Ames. Phantom is applicable to real and ideal fluids, both compressible and incompressible, flowing at subsonic, transonic, and supersonic speeds. It utilizes structured, overset, O- and H-type zonal grids to discretize flow fields and represent relative motions of components. Values on grid boundaries are updated at each time step by bilinear interpolation from adjacent grids. Inviscid fluxes are calculated to third-order spatial accuracy using Roe s scheme. Viscous fluxes are calculated using second-order-accurate central differences. The code is second-order accurate in time. Turbulence is represented by a modified Baldwin-Lomax algebraic model. The code offers two options for determining properties of fluids: One is based on equations of state, thermodynamic departure functions, and corresponding state principles. The other, which is more efficient, is based on splines generated from tables of properties of real fluids. Phantom currently contains fluid-property routines for water, hydrogen, oxygen, nitrogen, kerosene, methane, and carbon monoxide as well as ideal gases.

Genetic code mutations: the breaking of a three billion year invariance.

PubMed

Mat, Wai-Kin; Xue, Hong; Wong, J Tze-Fei

2010-08-20

The genetic code has been unchanging for some three billion years in its canonical ensemble of encoded amino acids, as indicated by the universal adoption of this ensemble by all known organisms. Code mutations beginning with the encoding of 4-fluoro-Trp by Bacillus subtilis, initially replacing and eventually displacing Trp from the ensemble, first revealed the intrinsic mutability of the code. This has since been confirmed by a spectrum of other experimental code alterations in both prokaryotes and eukaryotes. To shed light on the experimental conversion of a rigidly invariant code to a mutating code, the present study examined code mutations determining the propagation of Bacillus subtilis on Trp and 4-, 5- and 6-fluoro-tryptophans. The results obtained with the mutants with respect to cross-inhibitions between the different indole amino acids, and the growth effects of individual nutrient withdrawals rendering essential their biosynthetic pathways, suggested that oligogenic barriers comprising sensitive proteins which malfunction with amino acid analogues provide effective mechanisms for preserving the invariance of the code through immemorial time, and mutations of these barriers open up the code to continuous change.

26 CFR 22.0 - Certain elections under the Economic Recovery Tax Act of 1981.

Code of Federal Regulations, 2010 CFR

2010-04-01

... invalid. (b) Election of special use valuation for qualified real property. This paragraph applies to the election of special use valuation for qualified real property under section 2032A(d)(1) of the Code, as... the Code, (iii) Specifies the property with respect to which the election is made, and (iv) Provides...

Numerical solution of Space Shuttle Orbiter flow field including real gas effects

NASA Technical Reports Server (NTRS)

Prabhu, D. K.; Tannehill, J. C.

1984-01-01

The hypersonic, laminar flow around the Space Shuttle Orbiter has been computed for both an ideal gas (gamma = 1.2) and equilibrium air using a real-gas, parabolized Navier-Stokes code. This code employs a generalized coordinate transformation; hence, it places no restrictions on the orientation of the solution surfaces. The initial solution in the nose region was computed using a 3-D, real-gas, time-dependent Navier-Stokes code. The thermodynamic and transport properties of equilibrium air were obtained from either approximate curve fits or a table look-up procedure. Numerical results are presented for flight conditions corresponding to the STS-3 trajectory. The computed surface pressures and convective heating rates are compared with data from the STS-3 flight.

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

PubMed Central

José, Marco V.; Govezensky, Tzipe; García, José A.; Bobadilla, Juan R.

2009-01-01

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC. PMID:19183813

Effects of real fluid properties on axial turbine meanline design and off-design analysis

NASA Astrophysics Data System (ADS)

MacLean, Cameron

The effects of real fluid properties on axial turbine meanline analysis have been investigated employing two meanline analysis codes, namely Turbine Meanline Design (TMLD) and Turbine Meanline Off-Design (TMLO). The previously developed TMLD code assumed the working fluid was an ideal gas. Therefore it was modified to use real fluid properties. TMLO was then developed from TMLD Both codes can be run using either the ideal gas assumption or real fluid properties. TMLD was employed for the meanline design of several axial turbines for a range of inlet conditions, using both the ideal gas assumption and real fluid properties. The resulting designs were compared to see the effects of real fluid properties. Meanline designs, generated using the ideal gas assumption, were then analysed with TMLO using real fluid properties. This was done over a range of inlet conditions that correspond to varying degrees of departure from ideal gas conditions. The goal was to show how machines designed with the ideal gas assumption would perform with the real working fluid. The working fluid used in both investigations was supercritical carbon dioxide. Results from the investigation show that real fluid properties had a strong effect on the gas path areas of the turbine designs as well as the performance of turbines designed using the ideal gas assumption. Specifically, power output and the velocities of the working fluid were affected. It was found that accounting for losses tended to lessen the effects of the real fluid properties.

Blue Tigers, Black Tapirs, & the Pied Raven of the Faroe Islands: Teaching Genetic Drift Using Real-Life Animal Examples

ERIC Educational Resources Information Center

Robischon, Marcel

2015-01-01

Genetic drift is a concept of population genetics that is central to understanding evolutionary processes and aspects of conservation biology. It is frequently taught using rather abstract representations. I introduce three real-life zoological examples, based on historical and recent color morphs of tigers, tapirs, and ravens, that can complement…

Optimization of Straight Cylindrical Turning Using Artificial Bee Colony (ABC) Algorithm

NASA Astrophysics Data System (ADS)

Prasanth, Rajanampalli Seshasai Srinivasa; Hans Raj, Kandikonda

2017-04-01

Artificial bee colony (ABC) algorithm, that mimics the intelligent foraging behavior of honey bees, is increasingly gaining acceptance in the field of process optimization, as it is capable of handling nonlinearity, complexity and uncertainty. Straight cylindrical turning is a complex and nonlinear machining process which involves the selection of appropriate cutting parameters that affect the quality of the workpiece. This paper presents the estimation of optimal cutting parameters of the straight cylindrical turning process using the ABC algorithm. The ABC algorithm is first tested on four benchmark problems of numerical optimization and its performance is compared with genetic algorithm (GA) and ant colony optimization (ACO) algorithm. Results indicate that, the rate of convergence of ABC algorithm is better than GA and ACO. Then, the ABC algorithm is used to predict optimal cutting parameters such as cutting speed, feed rate, depth of cut and tool nose radius to achieve good surface finish. Results indicate that, the ABC algorithm estimated a comparable surface finish when compared with real coded genetic algorithm and differential evolution algorithm.

Enabling the extended compact genetic algorithm for real-parameter optimization by using adaptive discretization.

PubMed

Chen, Ying-ping; Chen, Chao-Hong

2010-01-01

An adaptive discretization method, called split-on-demand (SoD), enables estimation of distribution algorithms (EDAs) for discrete variables to solve continuous optimization problems. SoD randomly splits a continuous interval if the number of search points within the interval exceeds a threshold, which is decreased at every iteration. After the split operation, the nonempty intervals are assigned integer codes, and the search points are discretized accordingly. As an example of using SoD with EDAs, the integration of SoD and the extended compact genetic algorithm (ECGA) is presented and numerically examined. In this integration, we adopt a local search mechanism as an optional component of our back end optimization engine. As a result, the proposed framework can be considered as a memetic algorithm, and SoD can potentially be applied to other memetic algorithms. The numerical experiments consist of two parts: (1) a set of benchmark functions on which ECGA with SoD and ECGA with two well-known discretization methods: the fixed-height histogram (FHH) and the fixed-width histogram (FWH) are compared; (2) a real-world application, the economic dispatch problem, on which ECGA with SoD is compared to other methods. The experimental results indicate that SoD is a better discretization method to work with ECGA. Moreover, ECGA with SoD works quite well on the economic dispatch problem and delivers solutions better than the best known results obtained by other methods in existence.

Collaborative trial validation studies of real-time PCR-based GMO screening methods for detection of the bar gene and the ctp2-cp4epsps construct.

PubMed

Grohmann, Lutz; Brünen-Nieweler, Claudia; Nemeth, Anne; Waiblinger, Hans-Ulrich

2009-10-14

Polymerase Chain Reaction (PCR)-based screening methods targeting genetic elements commonly used in genetically modified (GM) plants are important tools for the detection of GM materials in food, feed, and seed samples. To expand and harmonize the screening capability of enforcement laboratories, the German Federal Office of Consumer Protection and Food Safety conducted collaborative trials for interlaboratory validation of real-time PCR methods for detection of the phosphinothricin acetyltransferase (bar) gene from Streptomyces hygroscopicus and a construct containing the 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens sp. strain CP4 (ctp2-cp4epsps), respectively. To assess the limit of detection, precision, and accuracy of the methods, laboratories had to analyze two sets of 18 coded genomic DNA samples of events LLRice62 and MS8 with the bar method and NK603 and GT73 with the ctp2-cp4epsps method at analyte levels of 0, 0.02, and 0.1% GM content, respectively. In addition, standard DNAs were provided to the laboratories to generate calibration curves for copy number quantification of the bar and ctp2-cp4epsps target sequences present in the test samples. The study design and the results obtained are discussed with respect to the difficult issue of developing general guidelines and concepts for the collaborative trial validation of qualitative PCR screening methods.

EEG Characteristic Extraction Method of Listening Music and Objective Estimation Method Based on Latency Structure Model in Individual Characteristics

NASA Astrophysics Data System (ADS)

Ito, Shin-Ichi; Mitsukura, Yasue; Nakamura Miyamura, Hiroko; Saito, Takafumi; Fukumi, Minoru

EEG is characterized by the unique and individual characteristics. Little research has been done to take into account the individual characteristics when analyzing EEG signals. Often the EEG has frequency components which can describe most of the significant characteristics. Then there is the difference of importance between the analyzed frequency components of the EEG. We think that the importance difference shows the individual characteristics. In this paper, we propose a new EEG extraction method of characteristic vector by a latency structure model in individual characteristics (LSMIC). The LSMIC is the latency structure model, which has personal error as the individual characteristics, based on normal distribution. The real-coded genetic algorithms (RGA) are used for specifying the personal error that is unknown parameter. Moreover we propose an objective estimation method that plots the EEG characteristic vector on a visualization space. Finally, the performance of the proposed method is evaluated using a realistic simulation and applied to a real EEG data. The result of our experiment shows the effectiveness of the proposed method.

Real-time single cell analysis of molecular mechanism of apoptosis and proliferation using FRET technique

NASA Astrophysics Data System (ADS)

Chen, Tongsheng; Xing, Da; Gao, Xuejuan; Wang, Fang

2006-09-01

Bcl-2 family proteins (such as Bid and Bak/Bax) and 14-3-3 proteins play a key role in the mitochondria-mediated cell apoptosis induced by cell death factors such as TNF-α and lower power laser irradiation (LPLI). In this report, fluorescence resonance energy transfer (FRET) has been used to study the molecular mechanism of apoptosis in living cells on a fluorescence scanning confocal microscope. Based on the genetic code technique and the green fluorescent proteins (GFPs), single-cell dynamic analysis of caspase3 activation, caspase8 activation, and PKCs activation are performed during apoptosis induced by laser irradiation in real-time. To investigate the cellular effect and mechanism of laser irradiation, human lung adenocarcinoma cells (ASTC-a-1) transfected with plasmid SCAT3 (pSCAT3)/ CKAR FRET reporter, were irradiated and monitored noninvasively with both FRET imaging. Our results show that high fluence lower power laser irradiation (HFLPLI) can induce an increase of caspase3 activation and a decrease of PKCs activation, and that LPLI induces the ASTC-a-1 cell proliferation by specifically activating PKCs.

[Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

PubMed

Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

2014-12-01

In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

Optimization of algorithm of coding of genetic information of Chlamydia

NASA Astrophysics Data System (ADS)

Feodorova, Valentina A.; Ulyanov, Sergey S.; Zaytsev, Sergey S.; Saltykov, Yury V.; Ulianova, Onega V.

2018-04-01

New method of coding of genetic information using coherent optical fields is developed. Universal technique of transformation of nucleotide sequences of bacterial gene into laser speckle pattern is suggested. Reference speckle patterns of the nucleotide sequences of omp1 gene of typical wild strains of Chlamydia trachomatis of genovars D, E, F, G, J and K and Chlamydia psittaci serovar I as well are generated. Algorithm of coding of gene information into speckle pattern is optimized. Fully developed speckles with Gaussian statistics for gene-based speckles have been used as criterion of optimization.

Translation and validation of a Spanish-language genetic health literacy screening tool.

PubMed

Rodríguez, Sally Ann; Roter, Debra L; Castillo-Salgado, Carlos; Hooker, Gillian W; Erby, Lori H

2015-02-01

Literacy deficits and underutilization of medical services have been linked to health disparities among minorities, and this appears especially relevant for the Latino population. Given the increasing importance of genetics, assessment of genetic health literacy may direct future efforts to better serve this vulnerable population. The current study was designed to contribute to this area by translating and validating a Spanish-language genetic health literacy measure. This was a cross-sectional study involving an interviewer-administered questionnaire. Eligible individuals were Latinos between the ages of 18 and 75 residing in Maryland, who self-reported Spanish as their primary language, recruited through convenience sampling. The genetic health literacy measure components were adapted from existing English-language measures [Erby, Roter, Larson, & Cho's (2008) Rapid Estimate of Adult Literacy in Genetics (REAL-G) and Hooker et al.'s (2014) Genetic Literacy and Comprehension]. An existing Spanish-language general health literacy measure was used to establish preliminary concurrent validity [Lee, Bender, Ruiz, & Cho's (2006) SAHLSA]. 116 individuals completed the assessment. The Spanish-language REAL-G (REAL-G-Sp) was found to correlate well with the SAHLSA (Pearson's r = .77, p < .01). A cut-off score of 59 (out of 62) distinguished low versus high genetic health literacy with a sensitivity of 86% and specificity of 71%, identifying 28% of participants as having inadequate genetic health literacy. The REAL-G-Sp was found to have preliminary concurrent validity with an existing health literacy measure in the Latino population residing in Maryland. Significant proportions of this population are predicted to have limitations in genetic health literacy, even when information is provided in Spanish.

Xenomicrobiology: a roadmap for genetic code engineering.

PubMed

Acevedo-Rocha, Carlos G; Budisa, Nediljko

2016-09-01

Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non-natural building blocks in living cells. In this context, genetic code engineering respectively enables the re-design of genes/genomes and proteins/proteomes with non-canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new-to-nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a 'genetic firewall' will also allow to study and understand the relation between code evolution and horizontal gene transfer. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Color Code: Using Hair Color to Make a Clear Connection between Genotype and Phenotype

ERIC Educational Resources Information Center

Bonner, J. Jose

2011-01-01

Students may wonder why they look the way they do. The answer lies in genetics, the branch of biology that deals with heredity and the variation of inherited traits. However, understanding how an organism's genetic code (i.e., genotype) affects its characteristics (i.e., phenotype) is more than a matter of idle curiosity: It's essential for…

Small non-coding RNAs (sncRNA) regulate gene silencing and modify homeostatic status in animals faced with porcine reproductive and respiratory syndrome virus (PRRSV)

USDA-ARS?s Scientific Manuscript database

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

The chemical basis for the origin of the genetic code and the process of protein synthesis

NASA Technical Reports Server (NTRS)

1982-01-01

The major thrust is to understand just how the process of protein synthesis, including that very important aspect, genetic coding, came to be. Two aspects of the problem: the chemistry of active aminoacyl species; and affinities between amino acids and nucleotides, and specifically, how these affinities might affect the chemistry between the two are stressed.

The impact of rare variation on gene expression across tissues.

PubMed

Li, Xin; Kim, Yungil; Tsang, Emily K; Davis, Joe R; Damani, Farhan N; Chiang, Colby; Hess, Gaelen T; Zappala, Zachary; Strober, Benjamin J; Scott, Alexandra J; Li, Amy; Ganna, Andrea; Bassik, Michael C; Merker, Jason D; Hall, Ira M; Battle, Alexis; Montgomery, Stephen B

2017-10-11

Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.

On the evolution of primitive genetic codes.

PubMed

Weberndorfer, Günter; Hofacker, Ivo L; Stadler, Peter F

2003-10-01

The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the present-day code came about we first need to explain how the language of the building plan can change without destroying the encoded information. In this work we introduce a minimal organism model that is based on biophysically reasonable descriptions of RNA and protein, namely secondary structure folding and knowledge based potentials. The evolution of a population of such organism under competition for a common resource is simulated explicitly at the level of individual replication events. Starting with very simple codes, and hence greatly reduced amino acid alphabets, we observe a diversification of the codes in most simulation runs. The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged.

Game-Based Learning Theory

NASA Technical Reports Server (NTRS)

Laughlin, Daniel

2008-01-01

Persistent Immersive Synthetic Environments (PISE) are not just connection points, they are meeting places. They are the new public squares, village centers, malt shops, malls and pubs all rolled into one. They come with a sense of 'thereness" that engages the mind like a real place does. Learning starts as a real code. The code defines "objects." The objects exist in computer space, known as the "grid." The objects and space combine to create a "place." A "world" is created, Before long, the grid and code becomes obscure, and the "world maintains focus.

Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod.

PubMed

Spies, Ingrid; Hauser, Lorenz; Jorde, Per Erik; Knutsen, Halvor; Punt, André E; Rogers, Lauren A; Stenseth, Nils Chr

2018-05-08

Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator F ST , such as Wright's equation, F ST ≈ 1/(4 N e m + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the N e / N t ratio (where N e is the effective and N t is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased N e / N t and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of F ST , particularly when genetic differentiation was low, F ST ≈ 10 -3 Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations. Copyright © 2018 the Author(s). Published by PNAS.

Genetics of Inflammatory Bowel Diseases

PubMed Central

McGovern, Dermot; Kugathasan, Subra; Cho, Judy H.

2015-01-01

In this Review, we provide an update on genome-wide association studies (GWAS) in inflammatory bowel disease (IBD). In addition, we summarize progress in defining the functional consequences of associated alleles for coding and non-coding genetic variation. In the small minority of loci where major association signals correspond to non-synonymous variation, we summarize studies defining their functional effects and implications for therapeutic targeting. Importantly, the large majority of GWAS-associated loci involve non-coding variation, many of which modulate levels of gene expression. Recent expression quantitative trait loci (eQTL) studies have established that expression of the large majority of human genes is regulated by non-coding genetic variation. Significant advances in defining the epigenetic landscape have demonstrated that IBD GWAS signals are highly enriched within cell-specific active enhancer marks. Studies in European ancestry populations have dominated the landscape of IBD genetics studies, but increasingly, studies in Asian and African-American populations are being reported. Common variation accounts for only a modest fraction of the predicted heritability and the role of rare genetic variation of higher effects (i.e. odds ratios markedly deviating from one) is increasingly being identified through sequencing efforts. These sequencing studies have been particularly productive in very-early onset, more severe cases. A major challenge in IBD genetics will be harnessing the vast array of genetic discovery for clinical utility, through emerging precision medicine initiatives. We discuss the rapidly evolving area of direct to consumer genetic testing, as well as the current utility of clinical exome sequencing, especially in very early onset, severe IBD cases. We summarize recent progress in the pharmacogenetics of IBD with respect of partitioning patient responses to anti-TNF and thiopurine therapies. Highly collaborative studies across research centers and across subspecialties and disciplines will be required to fully realize the promise of genetic discovery in IBD. PMID:26255561

Saturation of recognition elements blocks evolution of new tRNA identities

PubMed Central

Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

2016-01-01

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510

Conceptualisations of infinity by primary pre-service teachers

NASA Astrophysics Data System (ADS)

Date-Huxtable, Elizabeth; Cavanagh, Michael; Coady, Carmel; Easey, Michael

2018-05-01

As part of the Opening Real Science: Authentic Mathematics and Science Education for Australia project, an online mathematics learning module embedding conceptual thinking about infinity in science-based contexts, was designed and trialled with a cohort of 22 pre-service teachers during 1 week of intensive study. This research addressed the question: "How do pre-service teachers conceptualise infinity mathematically?" Participants argued the existence of infinity in a summative reflective task, using mathematical and empirical arguments that were coded according to five themes: definition, examples, application, philosophy and teaching; and 17 codes. Participants' reflections were differentiated as to whether infinity was referred to as an abstract (A) or a real (R) concept or whether both (B) codes were used. Principal component analysis of the reflections, using frequency of codings, revealed that A and R codes occurred at different frequencies in three groups of reflections. Distinct methods of argument were associated with each group of reflections: mathematical numerical examples and empirical measurement comparisons characterised arguments for infinity as an abstract concept, geometric and empirical dynamic examples and belief statements characterised arguments for infinity as a real concept and empirical measurement and mathematical examples and belief statements characterised arguments for infinity as both an abstract and a real concept. An implication of the results is that connections between mathematical and empirical applications of infinity may assist pre-service teachers to contrast finite with infinite models of the world.

Real-time minimal-bit-error probability decoding of convolutional codes

NASA Technical Reports Server (NTRS)

Lee, L.-N.

1974-01-01

A recursive procedure is derived for decoding of rate R = 1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit, subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e., fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications, such as in the inner coding system for concatenated coding.

Real-time minimal bit error probability decoding of convolutional codes

NASA Technical Reports Server (NTRS)

Lee, L. N.

1973-01-01

A recursive procedure is derived for decoding of rate R=1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e. fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications such as in the inner coding system for concatenated coding.

Evidence-Based Reading and Writing Assessment for Dyslexia in Adolescents and Young Adults

PubMed Central

Nielsen, Kathleen; Abbott, Robert; Griffin, Whitney; Lott, Joe; Raskind, Wendy; Berninger, Virginia W.

2016-01-01

The same working memory and reading and writing achievement phenotypes (behavioral markers of genetic variants) validated in prior research with younger children and older adults in a multi-generational family genetics study of dyslexia were used to study 81 adolescent and young adults (ages 16 to 25) from that study. Dyslexia is impaired word reading and spelling skills below the population mean and ability to use oral language to express thinking. These working memory predictor measures were given and used to predict reading and writing achievement: Coding (storing and processing) heard and spoken words (phonological coding), read and written words (orthographic coding), base words and affixes (morphological coding), and accumulating words over time (syntax coding); Cross-Code Integration (phonological loop for linking phonological name and orthographic letter codes and orthographic loop for linking orthographic letter codes and finger sequencing codes), and Supervisory Attention (focused and switching attention and self-monitoring during written word finding). Multiple regressions showed that most predictors explained individual difference in at least one reading or writing outcome, but which predictors explained unique variance beyond shared variance depended on outcome. ANOVAs confirmed that research-supported criteria for dyslexia validated for younger children and their parents could be used to diagnose which adolescents and young adults did (n=31) or did not (n=50) meet research criteria for dyslexia. Findings are discussed in reference to the heterogeneity of phenotypes (behavioral markers of genetic variables) and their application to assessment for accommodations and ongoing instruction for adolescents and young adults with dyslexia. PMID:26855554

On models of the genetic code generated by binary dichotomic algorithms.

PubMed

Gumbel, Markus; Fimmel, Elena; Danielli, Alberto; Strüngmann, Lutz

2015-02-01

In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

An Infrastructure for UML-Based Code Generation Tools

NASA Astrophysics Data System (ADS)

Wehrmeister, Marco A.; Freitas, Edison P.; Pereira, Carlos E.

The use of Model-Driven Engineering (MDE) techniques in the domain of distributed embedded real-time systems are gain importance in order to cope with the increasing design complexity of such systems. This paper discusses an infrastructure created to build GenERTiCA, a flexible tool that supports a MDE approach, which uses aspect-oriented concepts to handle non-functional requirements from embedded and real-time systems domain. GenERTiCA generates source code from UML models, and also performs weaving of aspects, which have been specified within the UML model. Additionally, this paper discusses the Distributed Embedded Real-Time Compact Specification (DERCS), a PIM created to support UML-based code generation tools. Some heuristics to transform UML models into DERCS, which have been implemented in GenERTiCA, are also discussed.

Enhancing Application Performance Using Mini-Apps: Comparison of Hybrid Parallel Programming Paradigms

NASA Technical Reports Server (NTRS)

Lawson, Gary; Sosonkina, Masha; Baurle, Robert; Hammond, Dana

2017-01-01

In many fields, real-world applications for High Performance Computing have already been developed. For these applications to stay up-to-date, new parallel strategies must be explored to yield the best performance; however, restructuring or modifying a real-world application may be daunting depending on the size of the code. In this case, a mini-app may be employed to quickly explore such options without modifying the entire code. In this work, several mini-apps have been created to enhance a real-world application performance, namely the VULCAN code for complex flow analysis developed at the NASA Langley Research Center. These mini-apps explore hybrid parallel programming paradigms with Message Passing Interface (MPI) for distributed memory access and either Shared MPI (SMPI) or OpenMP for shared memory accesses. Performance testing shows that MPI+SMPI yields the best execution performance, while requiring the largest number of code changes. A maximum speedup of 23 was measured for MPI+SMPI, but only 11 was measured for MPI+OpenMP.

Economic evaluation of Cardio inCode®, a clinical-genetic function for coronary heart disease risk assessment.

PubMed

Ramírez de Arellano, A; Coca, A; de la Figuera, M; Rubio-Terrés, C; Rubio-Rodríguez, D; Gracia, A; Boldeanu, A; Puig-Gilberte, J; Salas, E

2013-10-01

A clinical–genetic function (Cardio inCode®) was generated using genetic variants associated with coronary heart disease (CHD), but not with classical CHD risk factors, to achieve a more precise estimation of the CHD risk of individuals by incorporating genetics into risk equations [Framingham and REGICOR (Registre Gironí del Cor)]. The objective of this study was to conduct an economic analysis of the CHD risk assessment with Cardio inCode®, which incorporates the patient’s genetic risk into the functions of REGICOR and Framingham, compared with the standard method (using only the functions). A Markov model was developed with seven states of health (low CHD risk, moderate CHD risk, high CHD risk, CHD event, recurrent CHD, chronic CHD, and death). The reclassification of CHD risk derived from genetic information and transition probabilities between states was obtained from a validation study conducted in cohorts of REGICOR (Spain) and Framingham (USA). It was assumed that patients classified as at moderate risk by the standard method were the best candidates to test the risk reclassification with Cardio inCode®. The utilities and costs (€; year 2011 values) of Markov states were obtained from the literature and Spanish sources. The analysis was performed from the perspective of the Spanish National Health System, for a life expectancy of 82 years in Spain. An annual discount rate of 3.5 % for costs and benefits was applied. For a Cardio inCode® price of €400, the cost per QALY gained compared with the standard method [incremental cost-effectiveness ratio (ICER)] would be €12,969 and €21,385 in REGICOR and Framingham cohorts, respectively. The threshold price of Cardio inCode® to reach the ICER threshold generally accepted in Spain (€30,000/QALY) would range between €668 and €836. The greatest benefit occurred in the subgroup of patients with moderate–high risk, with a high-risk reclassification of 22.8 % and 12 % of patients and an ICER of €1,652/QALY and €5,884/QALY in the REGICOR and Framingham cohorts, respectively. Sensitivity analyses confirmed the stability of the study results. Cardio inCode® is a cost-effective risk score option in CHD risk assessment compared with the standard method.

Genetic Programming-based Phononic Bandgap Structure Design

DTIC Science & Technology

2011-09-01

derivative-based methods is that they require a good starting location to find the global minimum of a function. As can be seen from figure 2, there are many... FRANCHI CODE 7100 M H ORR CODE 7120 J A BUCARO CODE 7130 G J ORRIS 7140 J S PERKINS CODE 7140 S A CHIN BING CODE 7180 4555 OVERLOOK AVE SW WASHINGTON DC

Inter-individual variation in expression: a missing link in biomarker biology?

PubMed

Little, Peter F R; Williams, Rohan B H; Wilkins, Marc R

2009-01-01

The past decade has seen an explosion of variation data demonstrating that diversity of both protein-coding sequences and of regulatory elements of protein-coding genes is common and of functional importance. In this article, we argue that genetic diversity can no longer be ignored in studies of human biology, even research projects without explicit genetic experimental design, and that this knowledge can, and must, inform research. By way of illustration, we focus on the potential role of genetic data in case-control studies to identify and validate cancer protein biomarkers. We argue that a consideration of genetics, in conjunction with proteomic biomarker discovery projects, should improve the proportion of biomarkers that can accurately classify patients.

Reliable Wireless Broadcast with Linear Network Coding for Multipoint-to-Multipoint Real-Time Communications

NASA Astrophysics Data System (ADS)

Kondo, Yoshihisa; Yomo, Hiroyuki; Yamaguchi, Shinji; Davis, Peter; Miura, Ryu; Obana, Sadao; Sampei, Seiichi

This paper proposes multipoint-to-multipoint (MPtoMP) real-time broadcast transmission using network coding for ad-hoc networks like video game networks. We aim to achieve highly reliable MPtoMP broadcasting using IEEE 802.11 media access control (MAC) that does not include a retransmission mechanism. When each node detects packets from the other nodes in a sequence, the correctly detected packets are network-encoded, and the encoded packet is broadcasted in the next sequence as a piggy-back for its native packet. To prevent increase of overhead in each packet due to piggy-back packet transmission, network coding vector for each node is exchanged between all nodes in the negotiation phase. Each user keeps using the same coding vector generated in the negotiation phase, and only coding information that represents which user signal is included in the network coding process is transmitted along with the piggy-back packet. Our simulation results show that the proposed method can provide higher reliability than other schemes using multi point relay (MPR) or redundant transmissions such as forward error correction (FEC). We also implement the proposed method in a wireless testbed, and show that the proposed method achieves high reliability in a real-world environment with a practical degree of complexity when installed on current wireless devices.

A SNP panel and online tool for checking genotype concordance through comparing QR codes.

PubMed

Du, Yonghong; Martin, Joshua S; McGee, John; Yang, Yuchen; Liu, Eric Yi; Sun, Yingrui; Geihs, Matthias; Kong, Xuejun; Zhou, Eric Lingfeng; Li, Yun; Huang, Jie

2017-01-01

In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

A SNP panel and online tool for checking genotype concordance through comparing QR codes

PubMed Central

Du, Yonghong; Martin, Joshua S.; McGee, John; Yang, Yuchen; Liu, Eric Yi; Sun, Yingrui; Geihs, Matthias; Kong, Xuejun; Zhou, Eric Lingfeng; Li, Yun

2017-01-01

In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine. PMID:28926565

Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding

PubMed Central

Carter, Charles W; Wills, Peter R

2018-01-01

Abstract Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. The resulting inversion symmetries in aaRS structural biology would have stabilized the initial and subsequent differentiation of coding specificities, rapidly promoting diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexive, nanoenvironmental sensing in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: 1) aaRS enzymes must be interdependent; 2) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; 3) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; and 4) the Central Dogma’s emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene–replicase–translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today. PMID:29077934

Genomic Editing of Non-Coding RNA Genes with CRISPR/Cas9 Ushers in a Potential Novel Approach to Study and Treat Schizophrenia

PubMed Central

Zhuo, Chuanjun; Hou, Weihong; Hu, Lirong; Lin, Chongguang; Chen, Ce; Lin, Xiaodong

2017-01-01

Schizophrenia is a genetically related mental illness, in which the majority of genetic alterations occur in the non-coding regions of the human genome. In the past decade, a growing number of regulatory non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified to be strongly associated with schizophrenia. However, the studies of these ncRNAs in the pathophysiology of schizophrenia and the reverting of their genetic defects in restoration of the normal phenotype have been hampered by insufficient technology to manipulate these ncRNA genes effectively as well as a lack of appropriate animal models. Most recently, a revolutionary gene editing technology known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9; CRISPR/Cas9) has been developed that enable researchers to overcome these challenges. In this review article, we mainly focus on the schizophrenia-related ncRNAs and the use of CRISPR/Cas9-mediated editing on the non-coding regions of the genomic DNA in proving causal relationship between the genetic defects and the pathophysiology of schizophrenia. We subsequently discuss the potential of translating this advanced technology into a clinical therapy for schizophrenia, although the CRISPR/Cas9 technology is currently still in its infancy and immature to put into use in the treatment of diseases. Furthermore, we suggest strategies to accelerate the pace from the bench to the bedside. This review describes the application of the powerful and feasible CRISPR/Cas9 technology to manipulate schizophrenia-associated ncRNA genes. This technology could help researchers tackle this complex health problem and perhaps other genetically related mental disorders due to the overlapping genetic alterations of schizophrenia with other mental illnesses. PMID:28217082

Universal Noiseless Coding Subroutines

NASA Technical Reports Server (NTRS)

Schlutsmeyer, A. P.; Rice, R. F.

1986-01-01

Software package consists of FORTRAN subroutines that perform universal noiseless coding and decoding of integer and binary data strings. Purpose of this type of coding to achieve data compression in sense that coded data represents original data perfectly (noiselessly) while taking fewer bits to do so. Routines universal because they apply to virtually any "real-world" data source.

An Internal Data Non-hiding Type Real-time Kernel and its Application to the Mechatronics Controller

NASA Astrophysics Data System (ADS)

Yoshida, Toshio

For the mechatronics equipment controller that controls robots and machine tools, high-speed motion control processing is essential. The software system of the controller like other embedded systems is composed of three layers software such as real-time kernel layer, middleware layer, and application software layer on the dedicated hardware. The application layer in the top layer is composed of many numbers of tasks, and application function of the system is realized by the cooperation between these tasks. In this paper we propose an internal data non-hiding type real-time kernel in which customizing the task control is possible only by change in the program code of the task side without any changes in the program code of real-time kernel. It is necessary to reduce the overhead caused by the real-time kernel task control for the speed-up of the motion control of the mechatronics equipment. For this, customizing the task control function is needed. We developed internal data non-cryptic type real-time kernel ZRK to evaluate this method, and applied to the control of the multi system automatic lathe. The effect of the speed-up of the task cooperation processing was able to be confirmed by combined task control processing on the task side program code using an internal data non-hiding type real-time kernel ZRK.

College Students’ Perceived Differences Between the Terms Real Meal, Meal, and Snack

PubMed Central

Banna, Jinan; Richards, Rickelle; Brown, Lora Beth

2017-01-01

Objective To assess qualitatively and quantitatively college students’ perceived differences between a real meal, meal, and snack. Design A descriptive study design was used to administer an 11-item online survey to college students. Setting Two university campuses in the western US. Participants Pilot testing was conducted with 20 students. The final survey was completed by 628 ethnically diverse students. Main Outcome Measures Students’ perceptions of the terms real meal, meal, and snack. Analysis Three researchers coded the data independently, reconciled differences via conference calls, and agreed on a final coding scheme. Data were reevaluated based on the coding scheme. Means, frequencies, Pearson chi-square, and t test statistics were used. Results More than half of students perceived a difference between the terms real meal and meal. Most (97.6%) perceived a difference between the terms meal and snack. A marked difference in the way students defined these terms was evident, with a real meal deemed nutritious and healthy and meeting dietary recommendations, compared with meals, which were considered anything to eat. Conclusions and Implications These findings suggest that the term real meal may provide nutrition educators with a simple phrase to use in educational campaigns to promote healthful food intake among college students. PMID:27993555

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

PubMed Central

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-01-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. PMID:27197221

TIP: protein backtranslation aided by genetic algorithms.

PubMed

Moreira, Andrés; Maass, Alejandro

2004-09-01

Several applications require the backtranslation of a protein sequence into a nucleic acid sequence. The degeneracy of the genetic code makes this process ambiguous; moreover, not every translation is equally viable. The usual answer is to mimic the codon usage of the target species; however, this does not capture all the relevant features of the 'genomic styles' from different taxa. The program TIP ' Traducción Inversa de Proteínas') applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target. http://www.cmm.uchile.cl/genoma/tip/

Expanding and reprogramming the genetic code.

PubMed

Chin, Jason W

2017-10-04

Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.

The Genetic Privacy Act and commentary

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

Annas, G.J.; Glantz, L.H.; Roche, P.A.

1995-02-28

The Genetic Privacy Act is a proposal for federal legislation. The Act is based on the premise that genetic information is different from other types of personal information in ways that require special protection. The DNA molecule holds an extensive amount of currently indecipherable information. The major goal of the Human Genome Project is to decipher this code so that the information it contains is accessible. The privacy question is, accessible to whom? The highly personal nature of the information contained in DNA can be illustrated by thinking of DNA as containing an individual`s {open_quotes}future diary.{close_quotes} A diary is perhapsmore » the most personal and private document a person can create. It contains a person`s innermost thoughts and perceptions, and is usually hidden and locked to assure its secrecy. Diaries describe the past. The information in one`s genetic code can be thought of as a coded probabilistic future diary because it describes an important part of a unique and personal future. This document presents an introduction to the proposal for federal legislation `the Genetic Privacy Act`; a copy of the proposed act; and comment.« less

Decay Of Bacterial Pathogens, Fecal Indicators, And Real-Time Quantitative PCR Genetic Markers In Manure-Amended Soils

EPA Science Inventory

This study examined persistence and decay of bacterial pathogens, fecal indicator bacteria (FIB), and emerging real-time quantitative PCR (qPCR) genetic markers for rapid detection of fecal pollution in manure-amended agricultural soils. Known concentrations of transformed green...

Decay Of Bacterial Pathogen, Fecal Indicators, And Real-Time Quantitative PCR Genetic Markers In Manure Amended Soils

EPA Science Inventory

This study examined persistence and decay of bacterial pathogens, fecal indicator bacteria, and emerging real-time quantitative PCR (qPCR) genetic markers for rapid detection of fecal pollution in manre-amended agricultural soils. Known concentrations of transformed green fluore...

Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment[OA

PubMed Central

2012-01-01

We have entered a new era in agricultural and biomedical science made possible by remarkable advances in DNA sequencing technologies. The complete sequence of an individual’s set of chromosomes (collectively, its genome) provides a primary genetic code for what makes that individual unique, just as the contents of every personal computer reflect the unique attributes of its owner. But a second code, composed of “epigenetic” layers of information, affects the accessibility of the stored information and the execution of specific tasks. Nature’s second code is enigmatic and must be deciphered if we are to fully understand and optimize the genetic potential of crop plants. The goal of the Epigenomics of Plants International Consortium is to crack this second code, and ultimately master its control, to help catalyze a new green revolution. PMID:22751210

A unified model of the standard genetic code.

PubMed

José, Marco V; Zamudio, Gabriel S; Morgado, Eberto R

2017-03-01

The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

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

Vassilevska, Tanya

This is the first code, designed to run on a desktop, which models the intracellular replication and the cell-to-cell infection and demonstrates virus evolution at the molecular level. This code simulates the infection of a population of "idealized biological cells" (represented as objects that do not divide or have metabolism) with "virus" (represented by its genetic sequence), the replication and simultaneous mutation of the virus which leads to evolution of the population of genetically diverse viruses. The code is built to simulate single-stranded RNA viruses. The input for the code is 1. the number of biological cells in the culture,more » 2. the initial composition of the virus population, 3. the reference genome of the RNA virus, 4. the coordinates of the genome regions and their significance and, 5. parameters determining the dynamics of virus replication, such as the mutation rate. The simulation ends when all cells have been infected or when no more infections occurs after a given number of attempts. The code has the ability to simulate the evolution of the virus in serial passage of cell "cultures", i.e. after the end of a simulation, a new one is immediately scheduled with a new culture of infected cells. The code outputs characteristics of the resulting virus population dynamics and genetic composition of the virus population, such as the top dominant genomes, percentage of a genome with specific characteristics.« less

Protecting quantum memories using coherent parity check codes

NASA Astrophysics Data System (ADS)

Roffe, Joschka; Headley, David; Chancellor, Nicholas; Horsman, Dominic; Kendon, Viv

2018-07-01

Coherent parity check (CPC) codes are a new framework for the construction of quantum error correction codes that encode multiple qubits per logical block. CPC codes have a canonical structure involving successive rounds of bit and phase parity checks, supplemented by cross-checks to fix the code distance. In this paper, we provide a detailed introduction to CPC codes using conventional quantum circuit notation. We demonstrate the implementation of a CPC code on real hardware, by designing a [[4, 2, 2

The "Wow! signal" of the terrestrial genetic code

NASA Astrophysics Data System (ADS)

shCherbak, Vladimir I.; Makukov, Maxim A.

2013-05-01

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like "signal" in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

Simulation of the detonation process of an ammonium nitrate based emulsion explosive using the Lee-Tarver reactive flow model

NASA Astrophysics Data System (ADS)

Ribeiro, Jose; Silva, Cristovao; Mendes, Ricardo; Plaksin, Igor; Campos, Jose

2011-06-01

The use of emulsion explosives [EEx] for processing materials (compaction, welding and forming) requires the ability to perform detailed simulations of its detonation process [DP]. Detailed numerical simulations of the DP of this kind of explosives, characterized by having a finite reaction zone thickness, are thought to be suitable performed using the Lee-Tarver reactive flow model. In this work a real coded genetic algorithm methodology was used to estimate the 15 parameters of the reaction rate equation [RRE] of that model for a particular EEx. This methodology allows, in a single optimization procedure, using only one experimental result and without the need of any starting solution, to seek for the 15 parameters of the RRE that fit the numerical to the experimental results. Mass averaging and the Plate-Gap Model have been used for the determination of the shock data used in the unreacted explosive JWL EoS assessment and the thermochemical code THOR retrieved the data used in the detonation products JWL EoS assessment. The obtained parameters allow a good description of the experimental data and show some peculiarities arising from the intrinsic nature of this kind of composite explosive.

Conservation of Shannon's redundancy for proteins. [information theory applied to amino acid sequences

NASA Technical Reports Server (NTRS)

Gatlin, L. L.

1974-01-01

Concepts of information theory are applied to examine various proteins in terms of their redundancy in natural originators such as animals and plants. The Monte Carlo method is used to derive information parameters for random protein sequences. Real protein sequence parameters are compared with the standard parameters of protein sequences having a specific length. The tendency of a chain to contain some amino acids more frequently than others and the tendency of a chain to contain certain amino acid pairs more frequently than other pairs are used as randomness measures of individual protein sequences. Non-periodic proteins are generally found to have random Shannon redundancies except in cases of constraints due to short chain length and genetic codes. Redundant characteristics of highly periodic proteins are discussed. A degree of periodicity parameter is derived.

Protocol vulnerability detection based on network traffic analysis and binary reverse engineering.

PubMed

Wen, Shameng; Meng, Qingkun; Feng, Chao; Tang, Chaojing

2017-01-01

Network protocol vulnerability detection plays an important role in many domains, including protocol security analysis, application security, and network intrusion detection. In this study, by analyzing the general fuzzing method of network protocols, we propose a novel approach that combines network traffic analysis with the binary reverse engineering method. For network traffic analysis, the block-based protocol description language is introduced to construct test scripts, while the binary reverse engineering method employs the genetic algorithm with a fitness function designed to focus on code coverage. This combination leads to a substantial improvement in fuzz testing for network protocols. We build a prototype system and use it to test several real-world network protocol implementations. The experimental results show that the proposed approach detects vulnerabilities more efficiently and effectively than general fuzzing methods such as SPIKE.

Complexes of polyadenylic acid and the methyl esters of amino acids

NASA Technical Reports Server (NTRS)

Khaled, M. A.; Mulins, D. W., Jr.; Swindle, M.; Lacey, J. C., Jr.

1983-01-01

A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

Fast Sparse Coding for Range Data Denoising with Sparse Ridges Constraint.

PubMed

Gao, Zhi; Lao, Mingjie; Sang, Yongsheng; Wen, Fei; Ramesh, Bharath; Zhai, Ruifang

2018-05-06

Light detection and ranging (LiDAR) sensors have been widely deployed on intelligent systems such as unmanned ground vehicles (UGVs) and unmanned aerial vehicles (UAVs) to perform localization, obstacle detection, and navigation tasks. Thus, research into range data processing with competitive performance in terms of both accuracy and efficiency has attracted increasing attention. Sparse coding has revolutionized signal processing and led to state-of-the-art performance in a variety of applications. However, dictionary learning, which plays the central role in sparse coding techniques, is computationally demanding, resulting in its limited applicability in real-time systems. In this study, we propose sparse coding algorithms with a fixed pre-learned ridge dictionary to realize range data denoising via leveraging the regularity of laser range measurements in man-made environments. Experiments on both synthesized data and real data demonstrate that our method obtains accuracy comparable to that of sophisticated sparse coding methods, but with much higher computational efficiency.

Distribution and differential expression of microRNAs in the intestinal mucosal layer of necrotic enteritis induced Fayoumi chickens

PubMed Central

Rengaraj, Deivendran; Truong, Anh Duc; Ban, Jihye; Lillehoj, Hyun S.; Hong, Yeong Ho

2017-01-01

Objective Despite an increasing number of investigations into the pathophysiology of necrotic enteritis (NE) disease, etiology of NE-associated diseases, and gene expression profiling of NE-affected tissues, the microRNA (miRNA) profiles of NE-affected poultry have been poorly studied. The aim of this study was to induce NE disease in the genetically disparate Fayoumi chicken lines, and to perform non-coding RNA sequencing in the intestinal mucosal layer. Methods NE disease was induced in the Fayoumi chicken lines (M5.1 and M15.2), and non-coding RNA sequencing was performed in the intestinal mucosal layer of both NE-affected and uninfected chickens to examine the differential expression of miRNAs. Next, quantitative real-time polymerase chain reaction (real-time qPCR) was performed to further examine four miRNAs that showed the highest fold differences. Finally, bioinformatics analyses were performed to examine the four miRNAs target genes involvement in the signaling pathways, and to examine their interaction. Results According to non-coding RNA sequencing, total 50 upregulated miRNAs and 26 downregulated miRNAs were detected in the NE-induced M5.1 chickens. While 32 upregulated miRNAs and 11 downregulated miRNAs were detected in the NE-induced M15.2 chickens. Results of real-time qPCR analysis on the four miRNAs (gga-miR-9-5p, gga-miR-20b-5p, gga-miR-196-5p, and gga-let-7d) were mostly correlated with the results of RNAseq. Overall, gga-miR-20b-5p was significantly downregulated in the NE-induced M5.1 chickens and this was associated with the upregulation of its top-ranking target gene, mitogen-activated protein kinase, kinase 2. Further bioinformatics analyses revealed that 45 of the gene targets of gga-miR-20b-5p were involved in signal transduction and immune system-related pathways, and 35 of these targets were predicted to interact with each other. Conclusion Our study is a novel report of miRNA expression in Fayoumi chickens, and could be very useful in understanding the role of differentially expressed miRNAs in a NE disease model. PMID:28111433

SETI in vivo: testing the we-are-them hypothesis

NASA Astrophysics Data System (ADS)

Makukov, Maxim A.; Shcherbak, Vladimir I.

2018-04-01

After it was proposed that life on Earth might descend from seeding by an earlier extraterrestrial civilization motivated to secure and spread life, some authors noted that this alternative offers a testable implication: microbial seeds could be intentionally supplied with a durable signature that might be found in extant organisms. In particular, it was suggested that the optimal location for such an artefact is the genetic code, as the least evolving part of cells. However, as the mainstream view goes, this scenario is too speculative and cannot be meaningfully tested because encoding/decoding a signature within the genetic code is something ill-defined, so any retrieval attempt is doomed to guesswork. Here we refresh the seeded-Earth hypothesis in light of recent observations, and discuss the motivation for inserting a signature. We then show that `biological SETI' involves even weaker assumptions than traditional SETI and admits a well-defined methodological framework. After assessing the possibility in terms of molecular and evolutionary biology, we formalize the approach and, adopting the standard guideline of SETI that encoding/decoding should follow from first principles and be convention-free, develop a universal retrieval strategy. Applied to the canonical genetic code, it reveals a non-trivial precision structure of interlocked logical and numerical attributes of systematic character (previously we found these heuristically). To assess this result in view of the initial assumption, we perform statistical, comparison, interdependence and semiotic analyses. Statistical analysis reveals no causal connection of the result to evolutionary models of the genetic code, interdependence analysis precludes overinterpretation, and comparison analysis shows that known variations of the code lack any precision-logic structures, in agreement with these variations being post-LUCA (i.e. post-seeding) evolutionary deviations from the canonical code. Finally, semiotic analysis shows that not only the found attributes are consistent with the initial assumption, but that they make perfect sense from SETI perspective, as they ultimately maintain some of the most universal codes of culture.

Aerodynamic Shape Optimization Using A Real-Number-Encoded Genetic Algorithm

NASA Technical Reports Server (NTRS)

Holst, Terry L.; Pulliam, Thomas H.

2001-01-01

A new method for aerodynamic shape optimization using a genetic algorithm with real number encoding is presented. The algorithm is used to optimize three different problems, a simple hill climbing problem, a quasi-one-dimensional nozzle problem using an Euler equation solver and a three-dimensional transonic wing problem using a nonlinear potential solver. Results indicate that the genetic algorithm is easy to implement and extremely reliable, being relatively insensitive to design space noise.

The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome

PubMed Central

Nedelcu, Aurora M.; Lee, Robert W.; Lemieux, Claude; Gray, Michael W.; Burger, Gertraud

2000-01-01

Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type. To determine if this unexpected dichotomy is real or is due to insufficient or biased sampling and to define trends in the evolution of the green algal mitochondrial genome, we sequenced and analyzed the mitochondrial DNA (mtDNA) of Scenedesmus obliquus. This genome is 42,919 bp in size and encodes 42 conserved genes (i.e., large and small subunit rRNA genes, 27 tRNA and 13 respiratory protein-coding genes), four additional free-standing open reading frames with no known homologs, and an intronic reading frame with endonuclease/maturase similarity. No 5S rRNA or ribosomal protein-coding genes have been identified in Scenedesmus mtDNA. The standard protein-coding genes feature a deviant genetic code characterized by the use of UAG (normally a stop codon) to specify leucine, and the unprecedented use of UCA (normally a serine codon) as a signal for termination of translation. The mitochondrial genome of Scenedesmus combines features of both green algal mitochondrial genome types: the presence of a more complex set of protein-coding and tRNA genes is shared with the ancestral type, whereas the lack of 5S rRNA and ribosomal protein-coding genes as well as the presence of fragmented and scrambled rRNA genes are shared with the reduced–derived type of mitochondrial genome organization. Furthermore, the gene content and the fragmentation pattern of the rRNA genes suggest that this genome represents an intermediate stage in the evolutionary process of mitochondrial genome streamlining in green algae. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF204057.] PMID:10854413

The chemical basis for the origin of the genetic code and the process of protein synthesis

NASA Technical Reports Server (NTRS)

1981-01-01

The principles upon which the process of protein synthesis and the genetic code were established are elucidated. Extensive work on nuclear magnetic resonance studies of both monomermonomer and monoamino acid polynucleotide interactions is included. A new method of general utility for studying any amino acid interacting with any polynucleotide was developed. This system involves the use of methyl esters of amino acids interacting with polynucleotides.

The genetic code as a periodic table: algebraic aspects.

PubMed

Bashford, J D; Jarvis, P D

2000-01-01

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

Emergence of Coding and its Specificity as a Physico-Informatic Problem

NASA Astrophysics Data System (ADS)

Wills, Peter R.; Nieselt, Kay; McCaskill, John S.

2015-06-01

We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. Genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term "quasispecies symmetry breaking" to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step.

The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

PubMed Central

Francis, Brian R.

2015-01-01

Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and polypeptides is proposed. The cell consists of an iron-sulfide particle enclosed by tholin, a heterogeneous organic material that is produced by Miller-Urey type experiments that simulate conditions on the early Earth. As the synthesis of nucleic acids evolved from β-linked polyesters, the singlet coding system for replication evolved into a four nucleotide/four amino acid process (AMP = aspartic acid, GMP = glycine, UMP = valine, CMP = alanine) and then into the triplet ribosomal process that permitted multiple copies of protein to be synthesized independent of replication. This hypothesis reconciles the “genetics first” and “metabolism first” approaches to the origin of life and explains why there are four bases in the genetic alphabet. PMID:25679748

EDGE 2017 R&D 100 Entry with Appendix

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

Chain, Patrick Sam Guy; Davenport, Karen Walston; Li, Po-E

Diabetes, infertility, cancer, and Alzheimer’s disease—the key to one day preventing or even curing such afflictions and diseases (both infectious and genetically driven) may be locked in our own genetic code and the code of microorganisms that inhabit our bodies. The study of this code, known as genomics, has recently become much more promising as a result of two things: (1) vast improvements in high-throughput, nextgeneration sequencing (NSG), and (2) an exponential decrease in the cost of such sequencing. For example, it originally cost approximately $3 billion to sequence the human genome; today, this genome could be resequenced for lessmore » than $1,000.« less

Real-world clinical applicability of pathogenicity predictors assessed on SERPINA1 mutations in alpha-1-antitrypsin deficiency.

PubMed

Giacopuzzi, Edoardo; Laffranchi, Mattia; Berardelli, Romina; Ravasio, Viola; Ferrarotti, Ilaria; Gooptu, Bibek; Borsani, Giuseppe; Fra, Annamaria

2018-06-07

The growth of publicly available data informing upon genetic variations, mechanisms of disease and disease sub-phenotypes offers great potential for personalised medicine. Computational approaches are likely required to assess large numbers of novel genetic variants. However, the integration of genetic, structural and pathophysiological data still represents a challenge for computational predictions and their clinical use. We addressed these issues for alpha-1-antitrypsin deficiency, a disease mediated by mutations in the SERPINA1 gene encoding alpha-1-antitrypsin. We compiled a comprehensive database of SERPINA1 coding mutations and assigned them apparent pathological relevance based upon available data. 'Benign' and 'Pathogenic' mutations were used to assess performance of 31 pathogenicity predictors. Well-performing algorithms clustered the subset of variants known to be severely pathogenic with high scores. Eight new mutations identified in the ExAC database and achieving high scores were selected for characterisation in cell models and showed secretory deficiency and polymer formation, supporting the predictive power of our computational approach. The behaviour of the pathogenic new variants and consistent outliers were rationalised by considering the protein structural context and residue conservation. These findings highlight the potential of computational methods to provide meaningful predictions of the pathogenic significance of novel mutations and identify areas for further investigation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

An alternative approach for neural network evolution with a genetic algorithm: crossover by combinatorial optimization.

PubMed

García-Pedrajas, Nicolás; Ortiz-Boyer, Domingo; Hervás-Martínez, César

2006-05-01

In this work we present a new approach to crossover operator in the genetic evolution of neural networks. The most widely used evolutionary computation paradigm for neural network evolution is evolutionary programming. This paradigm is usually preferred due to the problems caused by the application of crossover to neural network evolution. However, crossover is the most innovative operator within the field of evolutionary computation. One of the most notorious problems with the application of crossover to neural networks is known as the permutation problem. This problem occurs due to the fact that the same network can be represented in a genetic coding by many different codifications. Our approach modifies the standard crossover operator taking into account the special features of the individuals to be mated. We present a new model for mating individuals that considers the structure of the hidden layer and redefines the crossover operator. As each hidden node represents a non-linear projection of the input variables, we approach the crossover as a problem on combinatorial optimization. We can formulate the problem as the extraction of a subset of near-optimal projections to create the hidden layer of the new network. This new approach is compared to a classical crossover in 25 real-world problems with an excellent performance. Moreover, the networks obtained are much smaller than those obtained with classical crossover operator.

Genetic Code Expansion as a Tool to Study Regulatory Processes of Transcription

NASA Astrophysics Data System (ADS)

Schmidt, Moritz; Summerer, Daniel

2014-02-01

The expansion of the genetic code with noncanonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

PubMed Central

Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

2015-01-01

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

Joint Services Electronics Program Annual Progress Report.

DTIC Science & Technology

1985-11-01

one symbol memory) adaptive lHuffman codes were performed, and the compression achieved was compared with that of Ziv - Lempel coding. As was expected...MATERIALS 8 4. Information Systems 9 4.1 REAL TIME STATISTICAL DATA PROCESSING 9 -. 4.2 DATA COMPRESSION for COMPUTER DATA STRUCTURES 9 5. PhD...a. Real Time Statistical Data Processing (T. Kailatb) b. Data Compression for Computer Data Structures (J. Gill) Acces Fo NTIS CRA&I I " DTIC TAB

ARES: A System for Real-Time Operational and Tactical Decision Support

DTIC Science & Technology

1986-12-01

In B]LE LCLGf. 9 NAVAL POSTGRADUATE SCHOOL Monterey, California Vi,-. %*.. THESIS - ’ A RE S A SYSTEM -OR REAL- 1I I .-.. --- OPERATIONAL AND...able) aval Postgraduate School 54 Naval Postgraduate School NN DRESS (City,. State,. and ZIP Code) 7b ADDRESS (City,. State,. and ZIP Code...SUBJECT TERMS (Continue on reverse if necessaty and identify by block number) LD GROUP SUB-GROUP Decision Support System, Logistics Model, Operational

Some practical universal noiseless coding techniques

NASA Technical Reports Server (NTRS)

Rice, R. F.

1979-01-01

Some practical adaptive techniques for the efficient noiseless coding of a broad class of such data sources are developed and analyzed. Algorithms are designed for coding discrete memoryless sources which have a known symbol probability ordering but unknown probability values. A general applicability of these algorithms to solving practical problems is obtained because most real data sources can be simply transformed into this form by appropriate preprocessing. These algorithms have exhibited performance only slightly above all entropy values when applied to real data with stationary characteristics over the measurement span. Performance considerably under a measured average data entropy may be observed when data characteristics are changing over the measurement span.

Epigenetics: a new frontier in dentistry.

PubMed

Williams, S D; Hughes, T E; Adler, C J; Brook, A H; Townsend, G C

2014-06-01

In 2007, only four years after the completion of the Human Genome Project, the journal Science announced that epigenetics was the 'breakthrough of the year'. Time magazine placed it second in the top 10 discoveries of 2009. While our genetic code (i.e. our DNA) contains all of the information to produce the elements we require to function, our epigenetic code determines when and where genes in the genetic code are expressed. Without the epigenetic code, the genetic code is like an orchestra without a conductor. Although there is now a substantial amount of published research on epigenetics in medicine and biology, epigenetics in dental research is in its infancy. However, epigenetics promises to become increasingly relevant to dentistry because of the role it plays in gene expression during development and subsequently potentially influencing oral disease susceptibility. This paper provides a review of the field of epigenetics aimed specifically at oral health professionals. It defines epigenetics, addresses the underlying concepts and provides details about specific epigenetic molecular mechanisms. Further, we discuss some of the key areas where epigenetics is implicated, and review the literature on epigenetics research in dentistry, including its relevance to clinical disciplines. This review considers some implications of epigenetics for the future of dental practice, including a 'personalized medicine' approach to the management of common oral diseases. © 2014 Australian Dental Association.

GW/Bethe-Salpeter calculations for charged and model systems from real-space DFT

NASA Astrophysics Data System (ADS)

Strubbe, David A.

GW and Bethe-Salpeter (GW/BSE) calculations use mean-field input from density-functional theory (DFT) calculations to compute excited states of a condensed-matter system. Many parts of a GW/BSE calculation are efficiently performed in a plane-wave basis, and extensive effort has gone into optimizing and parallelizing plane-wave GW/BSE codes for large-scale computations. Most straightforwardly, plane-wave DFT can be used as a starting point, but real-space DFT is also an attractive starting point: it is systematically convergeable like plane waves, can take advantage of efficient domain parallelization for large systems, and is well suited physically for finite and especially charged systems. The flexibility of a real-space grid also allows convenient calculations on non-atomic model systems. I will discuss the interfacing of a real-space (TD)DFT code (Octopus, www.tddft.org/programs/octopus) with a plane-wave GW/BSE code (BerkeleyGW, www.berkeleygw.org), consider performance issues and accuracy, and present some applications to simple and paradigmatic systems that illuminate fundamental properties of these approximations in many-body perturbation theory.

Real-time chirp-coded imaging with a programmable ultrasound biomicroscope.

PubMed

Bosisio, Mattéo R; Hasquenoph, Jean-Michel; Sandrin, Laurent; Laugier, Pascal; Bridal, S Lori; Yon, Sylvain

2010-03-01

Ultrasound biomicroscopy (UBM) of mice can provide a testing ground for new imaging strategies. The UBM system presented in this paper facilitates the development of imaging and measurement methods with programmable design, arbitrary waveform coding, broad bandwidth (2-80 MHz), digital filtering, programmable processing, RF data acquisition, multithread/multicore real-time display, and rapid mechanical scanning (

A novel reverse genetics system for production of infectious West Nile virus using homologous recombination in mammalian cells.

PubMed

Kobayashi, Shintaro; Yoshii, Kentaro; Hirano, Minato; Muto, Memi; Kariwa, Hiroaki

2017-02-01

Reverse genetics systems facilitate investigation of many aspects of the life cycle and pathogenesis of viruses. However, genetic instability in Escherichia coli has hampered development of a reverse genetics system for West Nile virus (WNV). In this study, we developed a novel reverse genetics system for WNV based on homologous recombination in mammalian cells. Introduction of the DNA fragment coding for the WNV structural protein together with a DNA-based replicon resulted in the release of infectious WNV. The growth rate and plaque size of the recombinant virus were almost identical to those of the parent WNV. Furthermore, chimeric WNV was produced by introducing the DNA fragment coding for the structural protein and replicon plasmid derived from various strains. Here, we report development of a novel system that will facilitate research into WNV infection. Copyright © 2016 Elsevier B.V. All rights reserved.

The Human Proteome Project: Unlocking the Mysteries of Human Life and Unleashing Its Potential

DTIC Science & Technology

2011-02-16

Australasian Genetics Resource Book. June 2007. Accessed September 27, 2010. www.genetics.com.au/pdf/factsheets/fs24.pdf. 2 White House, Office of...Project and Beyond." The Australasian Genetics Resource Book. June 2007. Accessed September 27, 2010. www.genetics.com.au/pdf/factsheets/fs24.pdf...9 Centre for Genetics Education. "The Human Genetic Code – The Human Genome Project and Beyond." The Australasian Genetics Resource Book. June

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

PubMed

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-07-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. © 2016 Mühlhausen et al.; Published by Cold Spring Harbor Laboratory Press.

Does the Genetic Code Have A Eukaryotic Origin?

PubMed Central

Zhang, Zhang; Yu, Jun

2013-01-01

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core “house-keeping” functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables—GC and purine contents—of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern—the symmetric pattern—where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes. PMID:23402863

Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms.

PubMed

Schmidt, Markus; Pei, Lei; Budisa, Nediljko

The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.

Tuning of Kalman filter parameters via genetic algorithm for state-of-charge estimation in battery management system.

PubMed

Ting, T O; Man, Ka Lok; Lim, Eng Gee; Leach, Mark

2014-01-01

In this work, a state-space battery model is derived mathematically to estimate the state-of-charge (SoC) of a battery system. Subsequently, Kalman filter (KF) is applied to predict the dynamical behavior of the battery model. Results show an accurate prediction as the accumulated error, in terms of root-mean-square (RMS), is a very small value. From this work, it is found that different sets of Q and R values (KF's parameters) can be applied for better performance and hence lower RMS error. This is the motivation for the application of a metaheuristic algorithm. Hence, the result is further improved by applying a genetic algorithm (GA) to tune Q and R parameters of the KF. In an online application, a GA can be applied to obtain the optimal parameters of the KF before its application to a real plant (system). This simply means that the instantaneous response of the KF is not affected by the time consuming GA as this approach is applied only once to obtain the optimal parameters. The relevant workable MATLAB source codes are given in the appendix to ease future work and analysis in this area.

Tuning of Kalman Filter Parameters via Genetic Algorithm for State-of-Charge Estimation in Battery Management System

PubMed Central

Ting, T. O.; Lim, Eng Gee

2014-01-01

In this work, a state-space battery model is derived mathematically to estimate the state-of-charge (SoC) of a battery system. Subsequently, Kalman filter (KF) is applied to predict the dynamical behavior of the battery model. Results show an accurate prediction as the accumulated error, in terms of root-mean-square (RMS), is a very small value. From this work, it is found that different sets of Q and R values (KF's parameters) can be applied for better performance and hence lower RMS error. This is the motivation for the application of a metaheuristic algorithm. Hence, the result is further improved by applying a genetic algorithm (GA) to tune Q and R parameters of the KF. In an online application, a GA can be applied to obtain the optimal parameters of the KF before its application to a real plant (system). This simply means that the instantaneous response of the KF is not affected by the time consuming GA as this approach is applied only once to obtain the optimal parameters. The relevant workable MATLAB source codes are given in the appendix to ease future work and analysis in this area. PMID:25162041

William Friedman, Geneticist Turned Cryptographer

PubMed Central

Goldman, Irwin L.

2017-01-01

William Friedman (1891–1969), trained as a plant geneticist at Cornell University, was employed at Riverbank Laboratories by the eccentric millionaire George Fabyan to work on wheat breeding. Friedman, however, soon became intrigued by and started working on a pet project of Fabyan’s involving the conjecture that Francis Bacon, a polymath known for the study of ciphers, was the real author of Shakespeare’s plays. Thus, beginning in ∼1916, Friedman turned his attention to the so called “Baconian cipher,” and developed decryption techniques that bore similarity to approaches for solving problems in population genetics. His most significant, indeed pathbreaking, work used ideas from genetics and statistics, focusing on analysis of the frequencies of letters in language use. Although he had transitioned from being a geneticist to a cryptographer, his earlier work had resonance in his later pursuits. He soon began working directly for the United States government and produced solutions used to solve complex military ciphers, in particular to break the Japanese Purple code during World War II. Another important legacy of his work was the establishment of the Signal Intelligence Service and eventually the National Security Agency. PMID:28476859

Common spaceborne multicomputer operating system and development environment

NASA Technical Reports Server (NTRS)

Craymer, L. G.; Lewis, B. F.; Hayes, P. J.; Jones, R. L.

1994-01-01

A preliminary technical specification for a multicomputer operating system is developed. The operating system is targeted for spaceborne flight missions and provides a broad range of real-time functionality, dynamic remote code-patching capability, and system fault tolerance and long-term survivability features. Dataflow concepts are used for representing application algorithms. Functional features are included to ensure real-time predictability for a class of algorithms which require data-driven execution on an iterative steady state basis. The development environment supports the development of algorithm code, design of control parameters, performance analysis, simulation of real-time dataflow applications, and compiling and downloading of the resulting application.

[Genetic diversity of modern Russian durum wheat cultivars at the gliadin-coding loci].

PubMed

Kudriavtsev, A M; Dedova, L V; Mel'nik, V A; Shishkina, A A; Upelniek, V P; Novosel'skaia-Dragovich, A Iu

2014-05-01

The allelic diversity at four gliadin-coding loci was examined in modern cultivars of the spring and winter durum wheat Triticum durum Desf. Comparative analysis of the allelic diversity showed that the gene pools of these two types of durum wheat, having different life styles, were considerably different. For the modern spring durum wheat cultivars, a certain reduction of the genetic diversity was observed compared to the cultivars bred in the 20th century.

45 CFR 12.3 - General policies.

Code of Federal Regulations, 2012 CFR

2012-10-01

... with State or local zoning restrictions, building codes, or similar limitations. (e) Organizations...-exempt under section 501(c)(3) of the Internal Revenue Code of 1954. (c) Real property will be requested...

45 CFR 12.3 - General policies.

Code of Federal Regulations, 2014 CFR

2014-10-01

... with State or local zoning restrictions, building codes, or similar limitations. (e) Organizations...-exempt under section 501(c)(3) of the Internal Revenue Code of 1954. (c) Real property will be requested...

45 CFR 12.3 - General policies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... with State or local zoning restrictions, building codes, or similar limitations. (e) Organizations...-exempt under section 501(c)(3) of the Internal Revenue Code of 1954. (c) Real property will be requested...

45 CFR 12.3 - General policies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... with State or local zoning restrictions, building codes, or similar limitations. (e) Organizations...-exempt under section 501(c)(3) of the Internal Revenue Code of 1954. (c) Real property will be requested...

New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes.

PubMed

Xiao, P; Niu, L L; Zhao, Q J; Chen, X Y; Wang, L J; Li, L; Zhang, H P; Guo, J Z; Xu, H Y; Zhong, T

2017-11-16

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

Real-time software-based end-to-end wireless visual communications simulation platform

NASA Astrophysics Data System (ADS)

Chen, Ting-Chung; Chang, Li-Fung; Wong, Andria H.; Sun, Ming-Ting; Hsing, T. Russell

1995-04-01

Wireless channel impairments pose many challenges to real-time visual communications. In this paper, we describe a real-time software based wireless visual communications simulation platform which can be used for performance evaluation in real-time. This simulation platform consists of two personal computers serving as hosts. Major components of each PC host include a real-time programmable video code, a wireless channel simulator, and a network interface for data transport between the two hosts. The three major components are interfaced in real-time to show the interaction of various wireless channels and video coding algorithms. The programmable features in the above components allow users to do performance evaluation of user-controlled wireless channel effects without physically carrying out these experiments which are limited in scope, time-consuming, and costly. Using this simulation platform as a testbed, we have experimented with several wireless channel effects including Rayleigh fading, antenna diversity, channel filtering, symbol timing, modulation, and packet loss.

Real-time transmission of digital video using variable-length coding

NASA Technical Reports Server (NTRS)

Bizon, Thomas P.; Shalkhauser, Mary JO; Whyte, Wayne A., Jr.

1993-01-01

Huffman coding is a variable-length lossless compression technique where data with a high probability of occurrence is represented with short codewords, while 'not-so-likely' data is assigned longer codewords. Compression is achieved when the high-probability levels occur so frequently that their benefit outweighs any penalty paid when a less likely input occurs. One instance where Huffman coding is extremely effective occurs when data is highly predictable and differential coding can be applied (as with a digital video signal). For that reason, it is desirable to apply this compression technique to digital video transmission; however, special care must be taken in order to implement a communication protocol utilizing Huffman coding. This paper addresses several of the issues relating to the real-time transmission of Huffman-coded digital video over a constant-rate serial channel. Topics discussed include data rate conversion (from variable to a fixed rate), efficient data buffering, channel coding, recovery from communication errors, decoder synchronization, and decoder architectures. A description of the hardware developed to execute Huffman coding and serial transmission is also included. Although this paper focuses on matters relating to Huffman-coded digital video, the techniques discussed can easily be generalized for a variety of applications which require transmission of variable-length data.

An investigation of messy genetic algorithms

NASA Technical Reports Server (NTRS)

Goldberg, David E.; Deb, Kalyanmoy; Korb, Bradley

1990-01-01

Genetic algorithms (GAs) are search procedures based on the mechanics of natural selection and natural genetics. They combine the use of string codings or artificial chromosomes and populations with the selective and juxtapositional power of reproduction and recombination to motivate a surprisingly powerful search heuristic in many problems. Despite their empirical success, there has been a long standing objection to the use of GAs in arbitrarily difficult problems. A new approach was launched. Results to a 30-bit, order-three-deception problem were obtained using a new type of genetic algorithm called a messy genetic algorithm (mGAs). Messy genetic algorithms combine the use of variable-length strings, a two-phase selection scheme, and messy genetic operators to effect a solution to the fixed-coding problem of standard simple GAs. The results of the study of mGAs in problems with nonuniform subfunction scale and size are presented. The mGA approach is summarized, both its operation and the theory of its use. Experiments on problems of varying scale, varying building-block size, and combined varying scale and size are presented.

Application of a VLSI vector quantization processor to real-time speech coding

NASA Technical Reports Server (NTRS)

Davidson, G.; Gersho, A.

1986-01-01

Attention is given to a working vector quantization processor for speech coding that is based on a first-generation VLSI chip which efficiently performs the pattern-matching operation needed for the codebook search process (CPS). Using this chip, the CPS architecture has been successfully incorporated into a compact, single-board Vector PCM implementation operating at 7-18 kbits/sec. A real time Adaptive Vector Predictive Coder system using the CPS has also been implemented.

Intact coding region of the serotonin transporter gene in obsessive-compulsive disorder

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

Altemus, M.; Murphy, D.L.; Greenberg, B.

1996-07-26

Epidemiologic studies indicate that obsessive-compulsive disorder is genetically transmitted in some families, although no genetic abnormalities have been identified in individuals with this disorder. The selective response of obsessive-compulsive disorder to treatment with agents which block serotonin reuptake suggests the gene coding for the serotonin transporter as a candidate gene. The primary structure of the serotonin-transporter coding region was sequenced in 22 patients with obsessive-compulsive disorder, using direct PCR sequencing of cDNA synthesized from platelet serotonin-transporter mRNA. No variations in amino acid sequence were found among the obsessive-compulsive disorder patients or healthy controls. These results do not support a rolemore » for alteration in the primary structure of the coding region of the serotonin-transporter gene in the pathogenesis of obsessive-compulsive disorder. 27 refs.« less

On Francis Crick, the genetic code, and a clever kid.

PubMed

Goldstein, Bob

2018-04-02

A few years ago, Francis Crick's son told me a story that I can't get out of my mind. I had contacted Michael Crick by email while digging through the background of the researchers who had cracked the genetic code in the 1960s. Francis had died in 2004, and I was contacting some of the people who knew him when he was struggling to decipher the code. Francis didn't appear to struggle often - he is known mostly for his successes - and, as it turns out, this one well-known struggle may have had a clue sitting just barely out of sight. Copyright © 2018 Elsevier Ltd. All rights reserved.

Learning time-dependent noise to reduce logical errors: real time error rate estimation in quantum error correction

NASA Astrophysics Data System (ADS)

Huo, Ming-Xia; Li, Ying

2017-12-01

Quantum error correction is important to quantum information processing, which allows us to reliably process information encoded in quantum error correction codes. Efficient quantum error correction benefits from the knowledge of error rates. We propose a protocol for monitoring error rates in real time without interrupting the quantum error correction. Any adaptation of the quantum error correction code or its implementation circuit is not required. The protocol can be directly applied to the most advanced quantum error correction techniques, e.g. surface code. A Gaussian processes algorithm is used to estimate and predict error rates based on error correction data in the past. We find that using these estimated error rates, the probability of error correction failures can be significantly reduced by a factor increasing with the code distance.

Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.

PubMed

Kabra, Ritika; Kapil, Aditi; Attarwala, Kherunnisa; Rai, Piyush Kant; Shanker, Asheesh

2016-04-01

Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1-6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx. In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria.

Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry.

PubMed

Ronquillo, Jay G; Weng, Chunhua; Lester, William T

2017-11-17

  Precision medicine involves three major innovations currently taking place in healthcare:  electronic health records, genomics, and big data.  A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine.   To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats.   We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry.  Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC) database, and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT).  We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting. There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes.  Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring.  Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering.  Conclusion:  While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.

Selection and Evaluation of a Real Time Monitoring System for the Bigeye Bomb Fill/Close Production Facility. Phase 2

DTIC Science & Technology

1989-06-01

and ZIP Code ) 10 SOURCE OF FUNDING NU MBERS I O KUI PROGRAM PRO ECCT TASKWOKUI E L E M E N T N O . N O .I 1 2 0 N O A 5 A C C E S S I O N N OlI I1 TITLE... source of by-products formation. Generating Data for Mathematical Modeling of Real Vapor Phase Reaction Systems (tremendously speeds multi -level, multi ...SMCC-RI1 6c AD RS(Ciry,. State, and ZIP Code ) SCRRI 7b. ADDRESS (City, State, and ZIP Code ) IA!hrueýýt Proving Ground, MD 21010-54213 a.NMOFFUNI.DNG

Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.

PubMed

Dimitrieva, Slavica; Anisimova, Maria

2014-01-01

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To evaluate the extent and the nature of site-specific selection on synonymous codons, we computed the site-to-site synonymous rate variation (SRV) and identified gene properties that make SRV more likely in a large database of protein-coding gene families and protein domains. To our knowledge, this is the first study that explores the determinants and patterns of the SRV in real data. We show that the SRV is widespread in the evolution of protein-coding sequences, putting in doubt the validity of the synonymous rate as a standard neutral proxy. While protein domains rarely undergo adaptive evolution, the SRV appears to play important role in optimizing the domain function at the level of DNA. In contrast, protein families are more likely to evolve by positive selection, but are less likely to exhibit SRV. Stronger SRV was detected in genes with stronger codon bias and tRNA reusage, those coding for proteins with larger number of interactions or forming larger number of structures, located in intracellular components and those involved in typically conserved complex processes and functions. Genes with extreme SRV show higher expression levels in nearly all tissues. This indicates that codon bias in a gene, which often correlates with gene expression, may often be a site-specific phenomenon regulating the speed of translation along the sequence, consistent with the co-translational folding hypothesis. Strikingly, genes with SRV were strongly overrepresented for metabolic pathways and those associated with several genetic diseases, particularly cancers and diabetes.

Fast Sparse Coding for Range Data Denoising with Sparse Ridges Constraint

PubMed Central

Lao, Mingjie; Sang, Yongsheng; Wen, Fei; Zhai, Ruifang

2018-01-01

Light detection and ranging (LiDAR) sensors have been widely deployed on intelligent systems such as unmanned ground vehicles (UGVs) and unmanned aerial vehicles (UAVs) to perform localization, obstacle detection, and navigation tasks. Thus, research into range data processing with competitive performance in terms of both accuracy and efficiency has attracted increasing attention. Sparse coding has revolutionized signal processing and led to state-of-the-art performance in a variety of applications. However, dictionary learning, which plays the central role in sparse coding techniques, is computationally demanding, resulting in its limited applicability in real-time systems. In this study, we propose sparse coding algorithms with a fixed pre-learned ridge dictionary to realize range data denoising via leveraging the regularity of laser range measurements in man-made environments. Experiments on both synthesized data and real data demonstrate that our method obtains accuracy comparable to that of sophisticated sparse coding methods, but with much higher computational efficiency. PMID:29734793

Real-time speech encoding based on Code-Excited Linear Prediction (CELP)

NASA Technical Reports Server (NTRS)

Leblanc, Wilfrid P.; Mahmoud, S. A.

1988-01-01

This paper reports on the work proceeding with regard to the development of a real-time voice codec for the terrestrial and satellite mobile radio environments. The codec is based on a complexity reduced version of code-excited linear prediction (CELP). The codebook search complexity was reduced to only 0.5 million floating point operations per second (MFLOPS) while maintaining excellent speech quality. Novel methods to quantize the residual and the long and short term model filters are presented.

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

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

Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S.

1995-10-09

In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains amore » functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.« less

Quasi-real-time end-to-end simulations of ELT-scale adaptive optics systems on GPUs

NASA Astrophysics Data System (ADS)

Gratadour, Damien

2011-09-01

Our team has started the development of a code dedicated to GPUs for the simulation of AO systems at the E-ELT scale. It uses the CUDA toolkit and an original binding to Yorick (an open source interpreted language) to provide the user with a comprehensive interface. In this paper we present the first performance analysis of our simulation code, showing its ability to provide Shack-Hartmann (SH) images and measurements at the kHz scale for VLT-sized AO system and in quasi-real-time (up to 70 Hz) for ELT-sized systems on a single top-end GPU. The simulation code includes multiple layers atmospheric turbulence generation, ray tracing through these layers, image formation at the focal plane of every sub-apertures of a SH sensor using either natural or laser guide stars and centroiding on these images using various algorithms. Turbulence is generated on-the-fly giving the ability to simulate hours of observations without the need of loading extremely large phase screens in the global memory. Because of its performance this code additionally provides the unique ability to test real-time controllers for future AO systems under nominal conditions.

Design of thrust vectoring exhaust nozzles for real-time applications using neural networks

NASA Technical Reports Server (NTRS)

Prasanth, Ravi K.; Markin, Robert E.; Whitaker, Kevin W.

1991-01-01

Thrust vectoring continues to be an important issue in military aircraft system designs. A recently developed concept of vectoring aircraft thrust makes use of flexible exhaust nozzles. Subtle modifications in the nozzle wall contours produce a non-uniform flow field containing a complex pattern of shock and expansion waves. The end result, due to the asymmetric velocity and pressure distributions, is vectored thrust. Specification of the nozzle contours required for a desired thrust vector angle (an inverse design problem) has been achieved with genetic algorithms. This approach is computationally intensive and prevents the nozzles from being designed in real-time, which is necessary for an operational aircraft system. An investigation was conducted into using genetic algorithms to train a neural network in an attempt to obtain, in real-time, two-dimensional nozzle contours. Results show that genetic algorithm trained neural networks provide a viable, real-time alternative for designing thrust vectoring nozzles contours. Thrust vector angles up to 20 deg were obtained within an average error of 0.0914 deg. The error surfaces encountered were highly degenerate and thus the robustness of genetic algorithms was well suited for minimizing global errors.

A Genomic Selection Index Applied to Simulated and Real Data

PubMed Central

Ceron-Rojas, J. Jesus; Crossa, José; Arief, Vivi N.; Basford, Kaye; Rutkoski, Jessica; Jarquín, Diego; Alvarado, Gregorio; Beyene, Yoseph; Semagn, Kassa; DeLacy, Ian

2015-01-01

A genomic selection index (GSI) is a linear combination of genomic estimated breeding values that uses genomic markers to predict the net genetic merit and select parents from a nonphenotyped testing population. Some authors have proposed a GSI; however, they have not used simulated or real data to validate the GSI theory and have not explained how to estimate the GSI selection response and the GSI expected genetic gain per selection cycle for the unobserved traits after the first selection cycle to obtain information about the genetic gains in each subsequent selection cycle. In this paper, we develop the theory of a GSI and apply it to two simulated and four real data sets with four traits. Also, we numerically compare its efficiency with that of the phenotypic selection index (PSI) by using the ratio of the GSI response over the PSI response, and the PSI and GSI expected genetic gain per selection cycle for observed and unobserved traits, respectively. In addition, we used the Technow inequality to compare GSI vs. PSI efficiency. Results from the simulated data were confirmed by the real data, indicating that GSI was more efficient than PSI per unit of time. PMID:26290571

Development of a Novel and Rapid Fully Automated Genetic Testing System.

PubMed

Uehara, Masayuki

2016-01-01

We have developed a rapid genetic testing system integrating nucleic acid extraction, purification, amplification, and detection in a single cartridge. The system performs real-time polymerase chain reaction (PCR) after nucleic acid purification in a fully automated manner. RNase P, a housekeeping gene, was purified from human nasal epithelial cells using silica-coated magnetic beads and subjected to real-time PCR using a novel droplet-real-time-PCR machine. The process was completed within 13 min. This system will be widely applicable for research and diagnostic uses.

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks

PubMed Central

Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

2016-01-01

The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates. PMID:27918435

Biosamples, genomics, and human rights: context and content of Iceland's Biobanks Act.

PubMed

Winickoff, D E

2001-01-01

In recent years, human DNA sampling and collection has accelerated without the development of enforceable rules protecting the human rights of donors. The need for regulation of biobanking is especially acute in Iceland, whose parliament has granted a for-profit corporation, deCODE Genetics, an exclusive license to create a centralized database of health records for studies on human genetic variation. Until recently, how deCODE Genetics would get genetic material for its genotypic-phenotypic database remained unclear. However, in May 2000, the Icelandic Parliament passed the Icelandic Biobanks Act, the world's earliest attempt to construct binding rules for the use of biobanks in scientific research. Unfortunately, Iceland has lost an opportunity for bringing clear and ethically sound standards to the use of human biological samples in deCODE's database and in other projects: the Biobanks Act has extended a notion of "presumed consent" from the use of medical records to the use of patients' biological samples; worse, the act has made it possible--perhaps likely--that a donor's wish to withdraw his/her sample will be ignored. Inadequacies in the Act's legislative process help account for these deficiencies in the protection of donor autonomy.

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.

PubMed

Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

2016-12-02

The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.

Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.

PubMed

Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H; Gilissen, Christian; Reader, Rose H; Jara, Lillian; Echeverry, María Magdalena; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O'Hare, Anne; Bolton, Patrick F; Hennessy, Elizabeth R; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A; Cazier, Jean-Baptiste; De Barbieri, Zulema; Fisher, Simon E; Newbury, Dianne F

2015-03-01

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.

Concatenated coding systems employing a unit-memory convolutional code and a byte-oriented decoding algorithm

NASA Technical Reports Server (NTRS)

Lee, L.-N.

1977-01-01

Concatenated coding systems utilizing a convolutional code as the inner code and a Reed-Solomon code as the outer code are considered. In order to obtain very reliable communications over a very noisy channel with relatively modest coding complexity, it is proposed to concatenate a byte-oriented unit-memory convolutional code with an RS outer code whose symbol size is one byte. It is further proposed to utilize a real-time minimal-byte-error probability decoding algorithm, together with feedback from the outer decoder, in the decoder for the inner convolutional code. The performance of the proposed concatenated coding system is studied, and the improvement over conventional concatenated systems due to each additional feature is isolated.

Concatenated coding systems employing a unit-memory convolutional code and a byte-oriented decoding algorithm

NASA Technical Reports Server (NTRS)

Lee, L. N.

1976-01-01

Concatenated coding systems utilizing a convolutional code as the inner code and a Reed-Solomon code as the outer code are considered. In order to obtain very reliable communications over a very noisy channel with relatively small coding complexity, it is proposed to concatenate a byte oriented unit memory convolutional code with an RS outer code whose symbol size is one byte. It is further proposed to utilize a real time minimal byte error probability decoding algorithm, together with feedback from the outer decoder, in the decoder for the inner convolutional code. The performance of the proposed concatenated coding system is studied, and the improvement over conventional concatenated systems due to each additional feature is isolated.

Analysis of protein-coding genetic variation in 60,706 humans.

PubMed

Lek, Monkol; Karczewski, Konrad J; Minikel, Eric V; Samocha, Kaitlin E; Banks, Eric; Fennell, Timothy; O'Donnell-Luria, Anne H; Ware, James S; Hill, Andrew J; Cummings, Beryl B; Tukiainen, Taru; Birnbaum, Daniel P; Kosmicki, Jack A; Duncan, Laramie E; Estrada, Karol; Zhao, Fengmei; Zou, James; Pierce-Hoffman, Emma; Berghout, Joanne; Cooper, David N; Deflaux, Nicole; DePristo, Mark; Do, Ron; Flannick, Jason; Fromer, Menachem; Gauthier, Laura; Goldstein, Jackie; Gupta, Namrata; Howrigan, Daniel; Kiezun, Adam; Kurki, Mitja I; Moonshine, Ami Levy; Natarajan, Pradeep; Orozco, Lorena; Peloso, Gina M; Poplin, Ryan; Rivas, Manuel A; Ruano-Rubio, Valentin; Rose, Samuel A; Ruderfer, Douglas M; Shakir, Khalid; Stenson, Peter D; Stevens, Christine; Thomas, Brett P; Tiao, Grace; Tusie-Luna, Maria T; Weisburd, Ben; Won, Hong-Hee; Yu, Dongmei; Altshuler, David M; Ardissino, Diego; Boehnke, Michael; Danesh, John; Donnelly, Stacey; Elosua, Roberto; Florez, Jose C; Gabriel, Stacey B; Getz, Gad; Glatt, Stephen J; Hultman, Christina M; Kathiresan, Sekar; Laakso, Markku; McCarroll, Steven; McCarthy, Mark I; McGovern, Dermot; McPherson, Ruth; Neale, Benjamin M; Palotie, Aarno; Purcell, Shaun M; Saleheen, Danish; Scharf, Jeremiah M; Sklar, Pamela; Sullivan, Patrick F; Tuomilehto, Jaakko; Tsuang, Ming T; Watkins, Hugh C; Wilson, James G; Daly, Mark J; MacArthur, Daniel G

2016-08-18

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

Non-coding RNAs' partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling.

PubMed

Kotakis, Christos

2015-01-01

Ars longa, vita brevis -Hippocrates Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.

A New Design Method of Automotive Electronic Real-time Control System

NASA Astrophysics Data System (ADS)

Zuo, Wenying; Li, Yinguo; Wang, Fengjuan; Hou, Xiaobo

Structure and functionality of automotive electronic control system is becoming more and more complex. The traditional manual programming development mode to realize automotive electronic control system can't satisfy development needs. So, in order to meet diversity and speedability of development of real-time control system, combining model-based design approach and auto code generation technology, this paper proposed a new design method of automotive electronic control system based on Simulink/RTW. Fristly, design algorithms and build a control system model in Matlab/Simulink. Then generate embedded code automatically by RTW and achieve automotive real-time control system development in OSEK/VDX operating system environment. The new development mode can significantly shorten the development cycle of automotive electronic control system, improve program's portability, reusability and scalability and had certain practical value for the development of real-time control system.

Optimal sensor placement for spatial lattice structure based on genetic algorithms

NASA Astrophysics Data System (ADS)

Liu, Wei; Gao, Wei-cheng; Sun, Yi; Xu, Min-jian

2008-10-01

Optimal sensor placement technique plays a key role in structural health monitoring of spatial lattice structures. This paper considers the problem of locating sensors on a spatial lattice structure with the aim of maximizing the data information so that structural dynamic behavior can be fully characterized. Based on the criterion of optimal sensor placement for modal test, an improved genetic algorithm is introduced to find the optimal placement of sensors. The modal strain energy (MSE) and the modal assurance criterion (MAC) have been taken as the fitness function, respectively, so that three placement designs were produced. The decimal two-dimension array coding method instead of binary coding method is proposed to code the solution. Forced mutation operator is introduced when the identical genes appear via the crossover procedure. A computational simulation of a 12-bay plain truss model has been implemented to demonstrate the feasibility of the three optimal algorithms above. The obtained optimal sensor placements using the improved genetic algorithm are compared with those gained by exiting genetic algorithm using the binary coding method. Further the comparison criterion based on the mean square error between the finite element method (FEM) mode shapes and the Guyan expansion mode shapes identified by data-driven stochastic subspace identification (SSI-DATA) method are employed to demonstrate the advantage of the different fitness function. The results showed that some innovations in genetic algorithm proposed in this paper can enlarge the genes storage and improve the convergence of the algorithm. More importantly, the three optimal sensor placement methods can all provide the reliable results and identify the vibration characteristics of the 12-bay plain truss model accurately.

ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

PubMed

Engqvist, Martin K M; Nielsen, Jens

2015-08-21

The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

Physical Model for the Evolution of the Genetic Code

NASA Astrophysics Data System (ADS)

Yamashita, Tatsuro; Narikiyo, Osamu

2011-12-01

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

Color-coding cancer and stromal cells with genetic reporters in a patient-derived orthotopic xenograft (PDOX) model of pancreatic cancer enhances fluorescence-guided surgery

PubMed Central

Yano, Shuya; Hiroshima, Yukihiko; Maawy, Ali; Kishimoto, Hiroyuki; Suetsugu, Atsushi; Miwa, Shinji; Toneri, Makoto; Yamamoto, Mako; Katz, Matthew H.G.; Fleming, Jason B.; Urata, Yasuo; Tazawa, Hiroshi; Kagawa, Shunsuke; Bouvet, Michael; Fujiwara, Toshiyoshi; Hoffman, Robert M.

2015-01-01

Precise fluorescence-guided surgery (FGS) for pancreatic cancer has the potential to greatly improve the outcome in this recalcitrant disease. In order to achieve this goal, we have used genetic reporters to color code cancer and stroma cells in a patient-derived orthotopic xenograft (PDOX) model. The telomerase-dependent green fluorescent protein (GFP) containing adenovirus OBP401 was used to label the cancer cells of the pancreatic cancer PDOX. The PDOX was previously grown in a red fluorescent protein (RFP) transgenic mouse that stably labeled the PDOX stroma cells bright red. The color-coded PDOX model enabled FGS to completely resect the pancreatic tumors including stroma. Dual-colored FGS significantly prevented local recurrence, which bright-light surgery (BLS) or single color could not. FGS, with color-coded cancer and stroma cells has important potential for improving the outcome of recalcitrant cancer. PMID:26088297

Real Time Optima Tracking Using Harvesting Models of the Genetic Algorithm

NASA Technical Reports Server (NTRS)

Baskaran, Subbiah; Noever, D.

1999-01-01

Tracking optima in real time propulsion control, particularly for non-stationary optimization problems is a challenging task. Several approaches have been put forward for such a study including the numerical method called the genetic algorithm. In brief, this approach is built upon Darwinian-style competition between numerical alternatives displayed in the form of binary strings, or by analogy to 'pseudogenes'. Breeding of improved solution is an often cited parallel to natural selection in.evolutionary or soft computing. In this report we present our results of applying a novel model of a genetic algorithm for tracking optima in propulsion engineering and in real time control. We specialize the algorithm to mission profiling and planning optimizations, both to select reduced propulsion needs through trajectory planning and to explore time or fuel conservation strategies.

Prenatal Genetic Testing Chart

MedlinePlus

... www.acog.org/Patients/FAQs/Prenatal-Genetic-Diagnostic-Tests › › Resources & Publications Committee Opinions Practice Bulletins Patient Education Green Journal Clinical Updates Practice Management Coding Health Info Technology Professional Liability Managing Your Practice Patient Safety & Quality ...

Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

DTIC Science & Technology

2015-10-01

available, work will commence. Tau, genetics , susceptibility, MAPT, chronic traumatic encephalopathy, Alzheimer disease U U U U 1 USAMRMC Table of...AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John

An integrated, structure- and energy-based view of the genetic code.

PubMed

Grosjean, Henri; Westhof, Eric

2016-09-30

The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon-anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Verification Method of Inter-Task Cooperation in Embedded Real-time Systems and its Evaluation

NASA Astrophysics Data System (ADS)

Yoshida, Toshio

In software development process of embedded real-time systems, the design of the task cooperation process is very important. The cooperating process of such tasks is specified by task cooperation patterns. Adoption of unsuitable task cooperation patterns has fatal influence on system performance, quality, and extendibility. In order to prevent repetitive work caused by the shortage of task cooperation performance, it is necessary to verify task cooperation patterns in an early software development stage. However, it is very difficult to verify task cooperation patterns in an early software developing stage where task program codes are not completed yet. Therefore, we propose a verification method using task skeleton program codes and a real-time kernel that has a function of recording all events during software execution such as system calls issued by task program codes, external interrupts, and timer interrupt. In order to evaluate the proposed verification method, we applied it to the software development process of a mechatronics control system.

Rewiring protein synthesis: From natural to synthetic amino acids.

PubMed

Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

2017-11-01

The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Telemetry advances in data compression and channel coding

NASA Technical Reports Server (NTRS)

Miller, Warner H.; Morakis, James C.; Yeh, Pen-Shu

1990-01-01

Addressed in this paper is the dependence of telecommunication channel, forward error correcting coding and source data compression coding on integrated circuit technology. Emphasis is placed on real time high speed Reed Solomon (RS) decoding using full custom VLSI technology. Performance curves of NASA's standard channel coder and a proposed standard lossless data compression coder are presented.

ControlShell - A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Ullman, Marc A.; Chen, Vincent W.

1991-01-01

ControlShell is designed to enable modular design and impplementation of real-time software. It is an object-oriented tool-set for real-time software system programming. It provides a series of execution and data interchange mechansims that form a framework for building real-time applications. These mechanisms allow a component-based approach to real-time software generation and mangement. By defining a set of interface specifications for intermodule interaction, ControlShell provides a common platform that is the basis for real-time code development and exchange.

[Assisted reproduction and artificial insemination and genetic manipulation in the Criminal Code of the Federal District, Mexico].

PubMed

Brena Sesma, Ingrid

2004-01-01

The article that one presents has for purpose outline and comment on the recent modifications to the Penal Code for the Federal District of México which establish, for the first time, crimes related to the artificial procreation and to the genetic manipulation. Also one refers to the interaction of the new legal texts with the sanitary legislation of the country. Since it will be stated in some cases they present confrontations between the penal and the sanitary reglamentation and some points related to the legality or unlawfulness of a conduct that stayed without the enough development. These lacks will complicate the application of the new rules of the Penal Code of the Federal District.

Enabling complex genetic circuits to respond to extrinsic environmental signals.

PubMed

Hoynes-O'Connor, Allison; Shopera, Tatenda; Hinman, Kristina; Creamer, John Philip; Moon, Tae Seok

2017-07-01

Genetic circuits have the potential to improve a broad range of metabolic engineering processes and address a variety of medical and environmental challenges. However, in order to engineer genetic circuits that can meet the needs of these real-world applications, genetic sensors that respond to relevant extrinsic and intrinsic signals must be implemented in complex genetic circuits. In this work, we construct the first AND and NAND gates that respond to temperature and pH, two signals that have relevance in a variety of real-world applications. A previously identified pH-responsive promoter and a temperature-responsive promoter were extracted from the E. coli genome, characterized, and modified to suit the needs of the genetic circuits. These promoters were combined with components of the type III secretion system in Salmonella typhimurium and used to construct a set of AND gates with up to 23-fold change. Next, an antisense RNA was integrated into the circuit architecture to invert the logic of the AND gate and generate a set of NAND gates with up to 1168-fold change. These circuits provide the first demonstration of complex pH- and temperature-responsive genetic circuits, and lay the groundwork for the use of similar circuits in real-world applications. Biotechnol. Bioeng. 2017;114: 1626-1631. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Feasibility study for a realistic training dedicated to radiological protection improvement

NASA Astrophysics Data System (ADS)

Courageot, Estelle; Reinald, Kutschera; Gaillard-Lecanu, Emmanuelle; Sylvie, Jahan; Riedel, Alexandre; Therache, Benjamin

2014-06-01

Any personnel involved in activities within the controlled area of a nuclear facility must be provided with appropriate radiological protection training. An evident purpose of this training is to know the regulation dedicated to workplaces where ionizing radiation may be present, in order to properly carry out the radiation monitoring, to use suitable protective equipments and to behave correctly if unexpected working conditions happen. A major difficulty of this training consist in having the most realistic reading from the monitoring devices for a given exposure situation, but without using real radioactive sources. A new approach is developed at EDF R&D for radiological protection training. This approach combines different technologies, in an environment representative of the workplace but geographically separated from the nuclear power plant: a training area representative of a workplace, a Man Machine Interface used by the trainer to define the source configuration and the training scenario, a geolocalization system, fictive radiation monitoring devices and a particle transport code able to calculate in real time the dose map due to the virtual sources. In a first approach, our real-time particles transport code, called Moderato, used only an attenuation low in straight line. To improve the realism further, we would like to switch a code based on the Monte Carlo transport of particles method like Geant 4 or MCNPX instead of Moderato. The aim of our study is the evaluation of the code in our application, in particular, the possibility to keep a real time response of our architecture.

Real-time software receiver

NASA Technical Reports Server (NTRS)

Psiaki, Mark L. (Inventor); Kintner, Jr., Paul M. (Inventor); Ledvina, Brent M. (Inventor); Powell, Steven P. (Inventor)

2007-01-01

A real-time software receiver that executes on a general purpose processor. The software receiver includes data acquisition and correlator modules that perform, in place of hardware correlation, baseband mixing and PRN code correlation using bit-wise parallelism.

Real-time software receiver

NASA Technical Reports Server (NTRS)

Psiaki, Mark L. (Inventor); Ledvina, Brent M. (Inventor); Powell, Steven P. (Inventor); Kintner, Jr., Paul M. (Inventor)

2006-01-01

A real-time software receiver that executes on a general purpose processor. The software receiver includes data acquisition and correlator modules that perform, in place of hardware correlation, baseband mixing and PRN code correlation using bit-wise parallelism.

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

PubMed

Sanchez, Robersy; Grau, Ricardo

2005-09-01

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

Real-time video streaming using H.264 scalable video coding (SVC) in multihomed mobile networks: a testbed approach

NASA Astrophysics Data System (ADS)

Nightingale, James; Wang, Qi; Grecos, Christos

2011-03-01

Users of the next generation wireless paradigm known as multihomed mobile networks expect satisfactory quality of service (QoS) when accessing streamed multimedia content. The recent H.264 Scalable Video Coding (SVC) extension to the Advanced Video Coding standard (AVC), offers the facility to adapt real-time video streams in response to the dynamic conditions of multiple network paths encountered in multihomed wireless mobile networks. Nevertheless, preexisting streaming algorithms were mainly proposed for AVC delivery over multipath wired networks and were evaluated by software simulation. This paper introduces a practical, hardware-based testbed upon which we implement and evaluate real-time H.264 SVC streaming algorithms in a realistic multihomed wireless mobile networks environment. We propose an optimised streaming algorithm with multi-fold technical contributions. Firstly, we extended the AVC packet prioritisation schemes to reflect the three-dimensional granularity of SVC. Secondly, we designed a mechanism for evaluating the effects of different streamer 'read ahead window' sizes on real-time performance. Thirdly, we took account of the previously unconsidered path switching and mobile networks tunnelling overheads encountered in real-world deployments. Finally, we implemented a path condition monitoring and reporting scheme to facilitate the intelligent path switching. The proposed system has been experimentally shown to offer a significant improvement in PSNR of the received stream compared with representative existing algorithms.

Bats' avoidance of real and virtual objects: implications for the sonar coding of object size.

PubMed

Goerlitz, Holger R; Genzel, Daria; Wiegrebe, Lutz

2012-01-01

Fast movement in complex environments requires the controlled evasion of obstacles. Sonar-based obstacle evasion involves analysing the acoustic features of object-echoes (e.g., echo amplitude) that correlate with this object's physical features (e.g., object size). Here, we investigated sonar-based obstacle evasion in bats emerging in groups from their day roost. Using video-recordings, we first show that the bats evaded a small real object (ultrasonic loudspeaker) despite the familiar flight situation. Secondly, we studied the sonar coding of object size by adding a larger virtual object. The virtual object echo was generated by real-time convolution of the bats' calls with the acoustic impulse response of a large spherical disc and played from the loudspeaker. Contrary to the real object, the virtual object did not elicit evasive flight, despite the spectro-temporal similarity of real and virtual object echoes. Yet, their spatial echo features differ: virtual object echoes lack the spread of angles of incidence from which the echoes of large objects arrive at a bat's ears (sonar aperture). We hypothesise that this mismatch of spectro-temporal and spatial echo features caused the lack of virtual object evasion and suggest that the sonar aperture of object echoscapes contributes to the sonar coding of object size. Copyright © 2011 Elsevier B.V. All rights reserved.

OPAD-EDIFIS Real-Time Processing

NASA Technical Reports Server (NTRS)

Katsinis, Constantine

1997-01-01

The Optical Plume Anomaly Detection (OPAD) detects engine hardware degradation of flight vehicles through identification and quantification of elemental species found in the plume by analyzing the plume emission spectra in a real-time mode. Real-time performance of OPAD relies on extensive software which must report metal amounts in the plume faster than once every 0.5 sec. OPAD software previously written by NASA scientists performed most necessary functions at speeds which were far below what is needed for real-time operation. The research presented in this report improved the execution speed of the software by optimizing the code without changing the algorithms and converting it into a parallelized form which is executed in a shared-memory multiprocessor system. The resulting code was subjected to extensive timing analysis. The report also provides suggestions for further performance improvement by (1) identifying areas of algorithm optimization, (2) recommending commercially available multiprocessor architectures and operating systems to support real-time execution and (3) presenting an initial study of fault-tolerance requirements.

A real-time ionospheric model based on GNSS Precise Point Positioning

NASA Astrophysics Data System (ADS)

Tu, Rui; Zhang, Hongping; Ge, Maorong; Huang, Guanwen

2013-09-01

This paper proposes a method of real-time monitoring and modeling the ionospheric Total Electron Content (TEC) by Precise Point Positioning (PPP). Firstly, the ionospheric TEC and receiver’s Differential Code Biases (DCB) are estimated with the undifferenced raw observation in real-time, then the ionospheric TEC model is established based on the Single Layer Model (SLM) assumption and the recovered ionospheric TEC. In this study, phase observations with high precision are directly used instead of phase smoothed code observations. In addition, the DCB estimation is separated from the establishment of the ionospheric model which will limit the impacts of the SLM assumption impacts. The ionospheric model is established at every epoch for real time application. The method is validated with three different GNSS networks on a local, regional, and global basis. The results show that the method is feasible and effective, the real-time ionosphere and DCB results are very consistent with the IGS final products, with a bias of 1-2 TECU and 0.4 ns respectively.

17 CFR 210.3-15 - Special provisions as to real estate investment trusts.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Financial Statements § 210.3-15 Special provisions as to real estate investment trusts. (a)(1) The income... real estate investment trust under applicable provisions of the Internal Revenue Code as amended shall... estate investment trusts. 210.3-15 Section 210.3-15 Commodity and Securities Exchanges SECURITIES AND...

Self-Configuration and Localization in Ad Hoc Wireless Sensor Networks

DTIC Science & Technology

2010-08-31

Goddard I. SUMMARY OF CONTRIBUTIONS We explored the error mechanisms of iterative decoding of low-density parity-check ( LDPC ) codes . This work has resulted...important problems in the area of channel coding , as their unpredictable behavior has impeded the deployment of LDPC codes in many real-world applications. We...tree-based decoders of LDPC codes , including the extrinsic tree decoder, and an investigation into their performance and bounding capabilities [5], [6

Estimating the kinetic parameters of activated sludge storage using weighted non-linear least-squares and accelerating genetic algorithm.

PubMed

Fang, Fang; Ni, Bing-Jie; Yu, Han-Qing

2009-06-01

In this study, weighted non-linear least-squares analysis and accelerating genetic algorithm are integrated to estimate the kinetic parameters of substrate consumption and storage product formation of activated sludge. A storage product formation equation is developed and used to construct the objective function for the determination of its production kinetics. The weighted least-squares analysis is employed to calculate the differences in the storage product concentration between the model predictions and the experimental data as the sum of squared weighted errors. The kinetic parameters for the substrate consumption and the storage product formation are estimated to be the maximum heterotrophic growth rate of 0.121/h, the yield coefficient of 0.44 mg CODX/mg CODS (COD, chemical oxygen demand) and the substrate half saturation constant of 16.9 mg/L, respectively, by minimizing the objective function using a real-coding-based accelerating genetic algorithm. Also, the fraction of substrate electrons diverted to the storage product formation is estimated to be 0.43 mg CODSTO/mg CODS. The validity of our approach is confirmed by the results of independent tests and the kinetic parameter values reported in literature, suggesting that this approach could be useful to evaluate the product formation kinetics of mixed cultures like activated sludge. More importantly, as this integrated approach could estimate the kinetic parameters rapidly and accurately, it could be applied to other biological processes.

Decoding the non-coding genome: elucidating genetic risk outside the coding genome.

PubMed

Barr, C L; Misener, V L

2016-01-01

Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Genetics and culture: the geneticization thesis.

PubMed

ten Have, H A

2001-01-01

The concept of 'geneticization' has been introduced in the scholarly literature to describe the various interlocking and imperceptible mechanisms of interaction between medicine, genetics, society and culture. It is argued that Western culture currently is deeply involved in a process of geneticization. This process implies a redefinition of individuals in terms of DNA codes, a new language to describe and interpret human life and behavior in a genomic vocabulary of codes, blueprints, traits, dispositions, genetic mapping, and a gentechnological approach to disease, health and the body. This article analyses the thesis of 'geneticization'. Explaining the implications of the thesis, and discussing the critical refutations, it is argued that 'geneticization' primarily is a heuristic tool that can help to re-focus the moral debate on the implications of new genetic knowledge towards interpersonal relations, the power of medicine, the cultural context and social constraints, rather than emphasizing issues as personal autonomy and individual rights.

Genetically improved BarraCUDA.

PubMed

Langdon, W B; Lam, Brian Yee Hong

2017-01-01

BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.

tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

PubMed Central

Carter, Charles W.; Wolfenden, Richard

2016-01-01

abstract The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology. PMID:26595350

The VLBA correlator: Real-time in the distributed era

NASA Technical Reports Server (NTRS)

Wells, D. C.

1992-01-01

The correlator is the signal processing engine of the Very Long Baseline Array (VLBA). Radio signals are recorded on special wideband (128 Mb/s) digital recorders at the 10 telescopes, with sampling times controlled by hydrogen maser clocks. The magnetic tapes are shipped to the Array Operations Center in Socorro, New Mexico, where they are played back simultaneously into the correlator. Real-time software and firmware controls the playback drives to achieve synchronization, compute models of the wavefront delay, control the numerous modules of the correlator, and record FITS files of the fringe visibilities at the back-end of the correlator. In addition to the more than 3000 custom VLSI chips which handle the massive data flow of the signal processing, the correlator contains a total of more than 100 programmable computers, 8-, 16- and 32-bit CPUs. Code is downloaded into front-end CPU's dependent on operating mode. Low-level code is assembly language, high-level code is C running under a RT OS. We use VxWorks on Motorola MVME147 CPU's. Code development is on a complex of SPARC workstations connected to the RT CPU's by Ethernet. The overall management of the correlation process is dependent on a database management system. We use Ingres running on a Sparcstation-2. We transfer logging information from the database of the VLBA Monitor and Control System to our database using Ingres/NET. Job scripts are computed and are transferred to the real-time computers using NFS, and correlation job execution logs and status flow back by the route. Operator status and control displays use windows on workstations, interfaced to the real-time processes by network protocols. The extensive network protocol support provided by VxWorks is invaluable. The VLBA Correlator's dependence on network protocols is an example of the radical transformation of the real-time world over the past five years. Real-time is becoming more like conventional computing. Paradoxically, 'conventional' computing is also adopting practices from the real-time world: semaphores, shared memory, light-weight threads, and concurrency. This appears to be a convergence of thinking.

A New Model for Real-Time Regional Vertical Total Electron Content and Differential Code Bias Estimation Using IGS Real-Time Service (IGS-RTS) Products

NASA Astrophysics Data System (ADS)

Abdelazeem, Mohamed; Çelik, Rahmi N.; El-Rabbany, Ahmed

2016-04-01

The international global navigation satellite system (GNSS) real-time service (IGS-RTS) products have been used extensively for real-time precise point positioning and ionosphere modeling applications. In this study, we develop a regional model for real-time vertical total electron content (RT-VTEC) and differential code bias (RT-DCB) estimation over Europe using the IGS-RTS satellite orbit and clock products. The developed model has a spatial and temporal resolution of 1°×1° and 15 minutes, respectively. GPS observations from a regional network consisting of 60 IGS and EUREF reference stations are processed in the zero-difference mode using the Bernese-5.2 software package in order to extract the geometry-free linear combination of the smoothed code observations. The spherical harmonic expansion function is used to model the VTEC, the receiver and the satellite DCBs. To validate the proposed model, the RT-VTEC values are computed and compared with the final IGS-global ionospheric map (IGS-GIM) counterparts in three successive days under high solar activity including one of an extreme geomagnetic activity. The real-time satellite DCBs are also estimated and compared with the IGS-GIM counterparts. Moreover, the real-time receiver DCB for six IGS stations are obtained and compared with the IGS-GIM counterparts. The examined stations are located in different latitudes with different receiver types. The findings reveal that the estimated RT-VTEC values show agreement with the IGS-GIM counterparts with root mean-square-errors (RMSEs) values less than 2 TEC units. In addition, RMSEs of both the satellites and receivers DCBs are less than 0.85 ns and 0.65 ns, respectively in comparison with the IGS-GIM.

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

NASA Astrophysics Data System (ADS)

Andrade, Xavier; Strubbe, David; De Giovannini, Umberto; Larsen, Ask Hjorth; Oliveira, Micael J. T.; Alberdi-Rodriguez, Joseba; Varas, Alejandro; Theophilou, Iris; Helbig, Nicole; Verstraete, Matthieu J.; Stella, Lorenzo; Nogueira, Fernando; Aspuru-Guzik, Alán; Castro, Alberto; Marques, Miguel A. L.; Rubio, Angel

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schr\\"odinger equation for low-dimensionality systems.

Experimental demonstration of a real-time PAM-4 Q-band RoF system based on CMMA equalization and interleaved RS code

NASA Astrophysics Data System (ADS)

Deng, Rui; Yu, Jianjun; He, Jing; Wei, Yiran

2018-05-01

In this paper, we experimentally demonstrated a complete real-time 4-level pulse amplitude modulation (PAM-4) Q-band radio-over-fiber (RoF) system with optical heterodyning and envelope detector (ED) down-conversion. Meanwhile, a cost-efficient real-time implementation scheme of cascaded multi-modulus algorithm (CMMA) equalization is proposed in this paper. By using the proposed scheme, the CMMA equalization is applied in the system for signal recovery. In addition, to improve the transmission performance of the system, an interleaved Reed-Solomon (RS) code is applied in the real-time system. Although there is serious power impulse noise in the system, the system can still achieve a bit error rate (BER) at below 1 × 10-7 after 25 km standard single mode fiber (SSMF) transmission and 1-m wireless transmission.

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Analysis of Molecular Genetics Content in Spanish Secondary School Textbooks

ERIC Educational Resources Information Center

Martinez-Gracia, M. V.; Gil-Quilez, M. J.; Osada, J.

2006-01-01

The treatment of molecular biology in thirty-four Spanish high school biology textbooks has been analysed using a check-list made up of twenty-three items. The study showed a tendency to confuse the genetic code with genetic information. The treatment of DNA transcription, regulation of gene expression and translation were presented as masses of…

A field release of genetically engineered gypsy moth (Lymantria dispar L.) Nuclear Polyhedrosis Virus (LdNPV)

Treesearch

Vincent D' Amico; Joseph S. Elkinton; John D. Podgwaite; James M. Slavicek; Michael L. McManus; John P. Burand

1999-01-01

The gypsy moth (Lymantria dispar L.) nuclear polyhedrosis virus was genetically engineered for nonpersistence by removal of the gene coding for polyhedrin production and stabilized using a coocclusion process. A β-galactosidase marker gene was inserted into the genetically engineered virus (LdGEV) so that infected larvae could be tested for...

Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species

USDA-ARS?s Scientific Manuscript database

The aneupolyploidy genome of sugarcane (Saccharum hybrids spp.) and lack of a classical genetic linkage map make genetics research most difficult for sugarcane. Whole genome sequencing and genetic characterization of sugarcane and related taxa are far behind other crops. In this study, universal PCR...

The LENS Facilities and Experimental Studies to Evaluate the Modeling of Boundary Layer Transition, Shock/Boundary Layer Interaction, Real Gas, Radiation and Plasma Phenomena in Contemporary CFD Codes

DTIC Science & Technology

2010-04-01

Layer Interaction, Real Gas, Radiation and Plasma Phenomena in Contemporary CFD Codes Michael S. Holden, PhD CUBRC , Inc. 4455 Genesee Street Buffalo...NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) CUBRC , Inc. 4455 Genesee Street Buffalo, NY 14225, USA 8. PERFORMING...HyFly Navy EMRG Reentry-F Slide 2 X-43 HIFiRE-2 Figure 17: Transition in Hypervelocity Flows: CUBRC Focus – Fully Duplicated Ground Test

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools.

PubMed

D'Andrea, M; Dal Monego, S; Pallavicini, A; Modonut, M; Dreos, R; Stefanon, B; Pilla, F

2011-10-01

Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopolitan breeds, Large White (LW) and a crossbreed (CB; Duroc × Landrace × Large White). The results were validated by real-time PCR. All animals were of the same age and were raised under the same environmental conditions. Muscle tissues were collected at 3, 6, 9 and 11 months of age, and a total of 173 genes showed significant differential expression between CT and the cosmopolitan genetic types at 3 months of age. Time series cluster analysis indicated that the CT breed had a different pattern of gene expression compared with that of the LW and the CB. Four of the eight clusters highlighted the gene differences between CT and the other two breeds, which were further supported by statistical analyses: clusters 4 and 5 contained a total of 71 genes that were underexpressed at 3 months of age, and cluster 3 and cluster 7 included 28 and 42 genes respectively that were overexpressed at 3 months of age. As expected, differentially expressed genes belonged to the category of genes coding for contractile fibres and transcription factors involved in muscle development and differentiation. These findings highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Shannon information entropy in the canonical genetic code.

PubMed

Nemzer, Louis R

2017-02-21

The Shannon entropy measures the expected information value of messages. As with thermodynamic entropy, the Shannon entropy is only defined within a system that identifies at the outset the collections of possible messages, analogous to microstates, that will be considered indistinguishable macrostates. This fundamental insight is applied here for the first time to amino acid alphabets, which group the twenty common amino acids into families based on chemical and physical similarities. To evaluate these schemas objectively, a novel quantitative method is introduced based the inherent redundancy in the canonical genetic code. Each alphabet is taken as a separate system that partitions the 64 possible RNA codons, the microstates, into families, the macrostates. By calculating the normalized mutual information, which measures the reduction in Shannon entropy, conveyed by single nucleotide messages, groupings that best leverage this aspect of fault tolerance in the code are identified. The relative importance of properties related to protein folding - like hydropathy and size - and function, including side-chain acidity, can also be estimated. This approach allows the quantification of the average information value of nucleotide positions, which can shed light on the coevolution of the canonical genetic code with the tRNA-protein translation mechanism. Copyright © 2016 Elsevier Ltd. All rights reserved.

Revolutionize Situational Awareness in Emergencies

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

Hehlen, Markus Peter

This report describes an integrated system that provides real-time actionable information to first responders. LANL will integrate three technologies to form an advanced predictive real-time sensor network including compact chemical and wind sensor sin low cost rugged package for outdoor installation; flexible robust communication architecture linking sensors in near-real time to globally accessible servers; and the QUIC code which predicts contamination transport and dispersal in urban environments in near real time.

FitSKIRT: genetic algorithms to automatically fit dusty galaxies with a Monte Carlo radiative transfer code

NASA Astrophysics Data System (ADS)

De Geyter, G.; Baes, M.; Fritz, J.; Camps, P.

2013-02-01

We present FitSKIRT, a method to efficiently fit radiative transfer models to UV/optical images of dusty galaxies. These images have the advantage that they have better spatial resolution compared to FIR/submm data. FitSKIRT uses the GAlib genetic algorithm library to optimize the output of the SKIRT Monte Carlo radiative transfer code. Genetic algorithms prove to be a valuable tool in handling the multi- dimensional search space as well as the noise induced by the random nature of the Monte Carlo radiative transfer code. FitSKIRT is tested on artificial images of a simulated edge-on spiral galaxy, where we gradually increase the number of fitted parameters. We find that we can recover all model parameters, even if all 11 model parameters are left unconstrained. Finally, we apply the FitSKIRT code to a V-band image of the edge-on spiral galaxy NGC 4013. This galaxy has been modeled previously by other authors using different combinations of radiative transfer codes and optimization methods. Given the different models and techniques and the complexity and degeneracies in the parameter space, we find reasonable agreement between the different models. We conclude that the FitSKIRT method allows comparison between different models and geometries in a quantitative manner and minimizes the need of human intervention and biasing. The high level of automation makes it an ideal tool to use on larger sets of observed data.

SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis.

PubMed

Valdisser, Paula Arielle M R; Pappas, Georgios J; de Menezes, Ivandilson P P; Müller, Bárbara S F; Pereira, Wendell J; Narciso, Marcelo G; Brondani, Claudio; Souza, Thiago L P O; Borba, Tereza C O; Vianello, Rosana P

2016-06-01

Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00 %) and non-coding (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6 %, showing 73 % of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A slightly increased He (0.161, n = 21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype patterns spanning 310 Mb of the genome (60 %) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel of molecular tools for whole genome analysis, allowing integrating and better exploring the common bean breeding practices.

The generation of meaningful information in molecular systems.

PubMed

Wills, Peter R

2016-03-13

The physico-chemical processes occurring inside cells are under the computational control of genetic (DNA) and epigenetic (internal structural) programming. The origin and evolution of genetic information (nucleic acid sequences) is reasonably well understood, but scant attention has been paid to the origin and evolution of the molecular biological interpreters that give phenotypic meaning to the sequence information that is quite faithfully replicated during cellular reproduction. The near universality and age of the mapping from nucleotide triplets to amino acids embedded in the functionality of the protein synthetic machinery speaks to the early development of a system of coding which is still extant in every living organism. We take the origin of genetic coding as a paradigm of the emergence of computation in natural systems, focusing on the requirement that the molecular components of an interpreter be synthesized autocatalytically. Within this context, it is seen that interpreters of increasing complexity are generated by series of transitions through stepped dynamic instabilities (non-equilibrium phase transitions). The early phylogeny of the amino acyl-tRNA synthetase enzymes is discussed in such terms, leading to the conclusion that the observed optimality of the genetic code is a natural outcome of the processes of self-organization that produced it. © 2016 The Author(s).

Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

PubMed Central

Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H.; Gilissen, Christian; Reader, Rose H.; Jara, Lillian; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O’Hare, Anne; Bolton, Patrick F.; Hennessy, Elizabeth R.; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A.; Cazier, Jean-Baptiste; De Barbieri, Zulema

2015-01-01

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model. PMID:25781923

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

PubMed

Kimura, Yasumasa; Soma, Takahiro; Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J L; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

PubMed Central

Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J. L.; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download. PMID:26863543

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

A Comparison of Priority-based and Incremental Real-Time Garbage Collectors in the Implementation of the Shadow Design Pattern

DTIC Science & Technology

2008-08-15

running the real-time application we used in our previous study on IBM WebSphere Real Time. IBM WebSphere Real Time automatically sets Metronome , its...the experiment show that the modified code for the Shadow Design Pattern runs well under Metronome . 15. NUMBER OF PAGES 25 14. SUBJECT TERMS...includes the real-time garbage collector called the Metronome . Unlike the Sun RTGC, we cannot change the priority of the Metronome RTGC. Metronome is

Decoding the complex genetic causes of heart diseases using systems biology.

PubMed

Djordjevic, Djordje; Deshpande, Vinita; Szczesnik, Tomasz; Yang, Andrian; Humphreys, David T; Giannoulatou, Eleni; Ho, Joshua W K

2015-03-01

The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.

Harnessing epigenome modifications for better crops

USDA-ARS?s Scientific Manuscript database

Chemical DNA modifications such as methylation influence translation of the DNA code to specific genetic outcomes. While such modifications can be heritable, others are transient, and their overall contribution to plant genetic diversity remains intriguing but uncertain. The focus of this article is...

Transform coding for hardware-accelerated volume rendering.

PubMed

Fout, Nathaniel; Ma, Kwan-Liu

2007-01-01

Hardware-accelerated volume rendering using the GPU is now the standard approach for real-time volume rendering, although limited graphics memory can present a problem when rendering large volume data sets. Volumetric compression in which the decompression is coupled to rendering has been shown to be an effective solution to this problem; however, most existing techniques were developed in the context of software volume rendering, and all but the simplest approaches are prohibitive in a real-time hardware-accelerated volume rendering context. In this paper we present a novel block-based transform coding scheme designed specifically with real-time volume rendering in mind, such that the decompression is fast without sacrificing compression quality. This is made possible by consolidating the inverse transform with dequantization in such a way as to allow most of the reprojection to be precomputed. Furthermore, we take advantage of the freedom afforded by off-line compression in order to optimize the encoding as much as possible while hiding this complexity from the decoder. In this context we develop a new block classification scheme which allows us to preserve perceptually important features in the compression. The result of this work is an asymmetric transform coding scheme that allows very large volumes to be compressed and then decompressed in real-time while rendering on the GPU.

Informational structure of genetic sequences and nature of gene splicing

NASA Astrophysics Data System (ADS)

Trifonov, E. N.

1991-10-01

Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

Color-coded Live Imaging of Heterokaryon Formation and Nuclear Fusion of Hybridizing Cancer Cells.

PubMed

Suetsugu, Atsushi; Matsumoto, Takuro; Hasegawa, Kosuke; Nakamura, Miki; Kunisada, Takahiro; Shimizu, Masahito; Saji, Shigetoyo; Moriwaki, Hisataka; Bouvet, Michael; Hoffman, Robert M

2016-08-01

Fusion of cancer cells has been studied for over half a century. However, the steps involved after initial fusion between cells, such as heterokaryon formation and nuclear fusion, have been difficult to observe in real time. In order to be able to visualize these steps, we have established cancer-cell sublines from the human HT-1080 fibrosarcoma, one expressing green fluorescent protein (GFP) linked to histone H2B in the nucleus and a red fluorescent protein (RFP) in the cytoplasm and the other subline expressing RFP in the nucleus (mCherry) linked to histone H2B and GFP in the cytoplasm. The two reciprocal color-coded sublines of HT-1080 cells were fused using the Sendai virus. The fused cells were cultured on plastic and observed using an Olympus FV1000 confocal microscope. Multi-nucleate (heterokaryotic) cancer cells, in addition to hybrid cancer cells with single-or multiple-fused nuclei, including fused mitotic nuclei, were observed among the fused cells. Heterokaryons with red, green, orange and yellow nuclei were observed by confocal imaging, even in single hybrid cells. The orange and yellow nuclei indicate nuclear fusion. Red and green nuclei remained unfused. Cell fusion with heterokaryon formation and subsequent nuclear fusion resulting in hybridization may be an important natural phenomenon between cancer cells that may make them more malignant. The ability to image the complex processes following cell fusion using reciprocal color-coded cancer cells will allow greater understanding of the genetic basis of malignancy. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

PubMed Central

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-01

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

PubMed

Meringer, Markus; Cleaves, H James; Freeland, Stephen J

2013-11-25

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

Generation of a variety of stable Influenza A reporter viruses by genetic engineering of the NS gene segment

PubMed Central

Reuther, Peter; Göpfert, Kristina; Dudek, Alexandra H.; Heiner, Monika; Herold, Susanne; Schwemmle, Martin

2015-01-01

Influenza A viruses (IAV) pose a constant threat to the human population and therefore a better understanding of their fundamental biology and identification of novel therapeutics is of upmost importance. Various reporter-encoding IAV were generated to achieve these goals, however, one recurring difficulty was the genetic instability especially of larger reporter genes. We employed the viral NS segment coding for the non-structural protein 1 (NS1) and nuclear export protein (NEP) for stable expression of diverse reporter proteins. This was achieved by converting the NS segment into a single open reading frame (ORF) coding for NS1, the respective reporter and NEP. To allow expression of individual proteins, the reporter genes were flanked by two porcine Teschovirus-1 2A peptide (PTV-1 2A)-coding sequences. The resulting viruses encoding luciferases, fluorescent proteins or a Cre recombinase are characterized by a high genetic stability in vitro and in mice and can be readily employed for antiviral compound screenings, visualization of infected cells or cells that survived acute infection. PMID:26068081

Long noncoding RNAs and tumorigenesis: genetic associations, molecular mechanisms, and therapeutic strategies.

PubMed

Zhang, Fan; Zhang, Liang; Zhang, Caiguo

2016-01-01

The human genome contains a large number of nonprotein-coding sequences. Recently, new discoveries in the functions of nonprotein-coding sequences have demonstrated that the "Dark Genome" significantly contributes to human diseases, especially with regard to cancer. Of particular interest in this review are long noncoding RNAs (lncRNAs), which comprise a class of nonprotein-coding transcripts that are longer than 200 nucleotides. Accumulating evidence indicates that a large number of lncRNAs exhibit genetic associations with tumorigenesis, tumor progression, and metastasis. Our current understanding of the molecular bases of these lncRNAs that are associated with cancer indicate that they play critical roles in gene transcription, translation, and chromatin modification. Therapeutic strategies based on the targeting of lncRNAs to disrupt their expression or their functions are being developed. In this review, we briefly summarize and discuss the genetic associations and the aberrant expression of lncRNAs in cancer, with a particular focus on studies that have revealed the molecular mechanisms of lncRNAs in tumorigenesis. In addition, we also discuss different therapeutic strategies that involve the targeting of lncRNAs.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

PubMed

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-21

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

NASA Astrophysics Data System (ADS)

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-01

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Conservation genetics and geographic patterns of genetic variation of the endangered officinal herb Fritillaria pallidiflora

Treesearch

Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaolong Jiang; Mingli Zhang

2015-01-01

Fritillaria pallidiflora is an endangered officinal herb distributed in the Tianshan Mountains of northwestern China. We examined its phylogeography to study evolutionary processes and suggest implications for conservation. Six haplotypes were detected based on three chloroplast non-coding spacers (psbA-trnH, rps16, and trnS-trnG); genetic variation mainly occurred...

The Future of Genetics in Psychology and Psychiatry: Microarrays, Genome-Wide Association, and Non-Coding RNA

ERIC Educational Resources Information Center

Plomin, Robert; Davis, Oliver S. P.

2009-01-01

Background: Much of what we thought we knew about genetics needs to be modified in light of recent discoveries. What are the implications of these advances for identifying genes responsible for the high heritability of many behavioural disorders and dimensions in childhood? Methods: Although quantitative genetics such as twin studies will continue…

Development and validation of duplex, triplex, and pentaplex real-time PCR screening assays for the detection of genetically modified organisms in food and feed.

PubMed

Huber, Ingrid; Block, Annette; Sebah, Daniela; Debode, Frédéric; Morisset, Dany; Grohmann, Lutz; Berben, Gilbert; Stebih, Dejan; Milavec, Mojca; Zel, Jana; Busch, Ulrich

2013-10-30

Worldwide, qualitative methods based on PCR are most commonly used as screening tools for genetically modified material in food and feed. However, the increasing number and diversity of genetically modified organisms (GMO) require effective methods for simultaneously detecting several genetic elements marking the presence of transgenic events. Herein we describe the development and validation of a pentaplex, as well as complementary triplex and duplex real-time PCR assays, for the detection of the most common screening elements found in commercialized GMOs: P-35S, T-nos, ctp2-cp4-epsps, bar, and pat. The use of these screening assays allows the coverage of many GMO events globally approved for commercialization. Each multiplex real-time PCR assay shows high specificity and sensitivity with an absolute limit of detection below 20 copies for the targeted sequences. We demonstrate by intra- and interlaboratory tests that the assays are robust as well as cost- and time-effective for GMO screening if applied in routine GMO analysis.

Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

PubMed

Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

2009-01-14

We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

Identification and quantification of genetically modified Moonshade carnation lines using conventional and TaqMan real-time polymerase chain reaction methods.

PubMed

Li, Peng; Jia, Junwei; Bai, Lan; Pan, Aihu; Tang, Xueming

2013-07-01

Genetically modified carnation (Dianthus caryophyllus L.) Moonshade was approved for planting and commercialization in several countries from 2004. Developing methods for analyzing Moonshade is necessary for implementing genetically modified organism labeling regulations. In this study, the 5'-transgene integration sequence was isolated using thermal asymmetric interlaced (TAIL)-PCR. Based upon the 5'-transgene integration sequence, conventional and TaqMan real-time PCR assays were established. The relative limit of detection for the conventional PCR assay was 0.05 % for Moonshade using 100 ng total carnation genomic DNA, corresponding to approximately 79 copies of the carnation haploid genome, and the limits of detection and quantification of the TaqMan real-time PCR assay were estimated to be 51 and 254 copies of haploid carnation genomic DNA, respectively. These results are useful for identifying and quantifying Moonshade and its derivatives.

Development and Evaluation of Event-Specific Quantitative PCR Method for Genetically Modified Soybean MON87701.

PubMed

Tsukahara, Keita; Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Nishimaki-Mogami, Tomoko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2016-01-01

A real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) soybean event, MON87701. First, a standard plasmid for MON87701 quantification was constructed. The conversion factor (C f ) required to calculate the amount of genetically modified organism (GMO) was experimentally determined for a real-time PCR instrument. The determined C f for the real-time PCR instrument was 1.24. For the evaluation of the developed method, a blind test was carried out in an inter-laboratory trial. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr), respectively. The determined biases and the RSDr values were less than 30 and 13%, respectively, at all evaluated concentrations. The limit of quantitation of the method was 0.5%, and the developed method would thus be applicable for practical analyses for the detection and quantification of MON87701.

Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.

PubMed

Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J; Wu, Ying; Zhang, He; Zhou, Wei; Li, Jun; Tang, Clara Sze-Man; Dorajoo, Rajkumar; Li, Huaixing; Long, Jirong; Guo, Xiuqing; Xu, Ming; Spracklen, Cassandra N; Chen, Yang; Liu, Xuezhen; Zhang, Yan; Khor, Chiea Chuen; Liu, Jianjun; Sun, Liang; Wang, Laiyuan; Gao, Yu-Tang; Hu, Yao; Yu, Kuai; Wang, Yiqin; Cheung, Chloe Yu Yan; Wang, Feijie; Huang, Jianfeng; Fan, Qiao; Cai, Qiuyin; Chen, Shufeng; Shi, Jinxiu; Yang, Xueli; Zhao, Wanting; Sheu, Wayne H-H; Cherny, Stacey Shawn; He, Meian; Feranil, Alan B; Adair, Linda S; Gordon-Larsen, Penny; Du, Shufa; Varma, Rohit; Chen, Yii-Der Ida; Shu, Xiao-Ou; Lam, Karen Siu Ling; Wong, Tien Yin; Ganesh, Santhi K; Mo, Zengnan; Hveem, Kristian; Fritsche, Lars G; Nielsen, Jonas Bille; Tse, Hung-Fat; Huo, Yong; Cheng, Ching-Yu; Chen, Y Eugene; Zheng, Wei; Tai, E Shyong; Gao, Wei; Lin, Xu; Huang, Wei; Abecasis, Goncalo; Kathiresan, Sekar; Mohlke, Karen L; Wu, Tangchun; Sham, Pak Chung; Gu, Dongfeng; Willer, Cristen J

2017-12-01

Most genome-wide association studies have been of European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we used an exome array to examine protein-coding genetic variants in 47,532 East Asian individuals. We identified 255 variants at 41 loci that reached chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After a meta-analysis including >300,000 European samples, we identified an additional nine novel loci. Sixteen genes were identified by protein-altering variants in both East Asians and Europeans, and thus are likely to be functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population specific, and that examining genomic data across diverse ancestries may facilitate the identification of functional genes at associated loci.

Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants contributing to lipid levels and coronary artery disease

PubMed Central

Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J.; Wu, Ying; Zhang, He; Zhou, Wei; Li, Jun; Tang, Clara Sze-man; Dorajoo, Rajkumar; Li, Huaixing; Long, Jirong; Guo, Xiuqing; Xu, Ming; Spracklen, Cassandra N.; Chen, Yang; Liu, Xuezhen; Zhang, Yan; Khor, Chiea Chuen; Liu, Jianjun; Sun, Liang; Wang, Laiyuan; Gao, Yu-Tang; Hu, Yao; Yu, Kuai; Wang, Yiqin; Cheung, Chloe Yu Yan; Wang, Feijie; Huang, Jianfeng; Fan, Qiao; Cai, Qiuyin; Chen, Shufeng; Shi, Jinxiu; Yang, Xueli; Zhao, Wanting; Sheu, Wayne H.-H.; Cherny, Stacey Shawn; He, Meian; Feranil, Alan B.; Adair, Linda S.; Gordon-Larsen, Penny; Du, Shufa; Varma, Rohit; da Chen, Yii-Der I; Shu, XiaoOu; Lam, Karen Siu Ling; Wong, Tien Yin; Ganesh, Santhi K.; Mo, Zengnan; Hveem, Kristian; Fritsche, Lars; Nielsen, Jonas Bille; Tse, Hung-fat; Huo, Yong; Cheng, Ching-Yu; Chen, Y. Eugene; Zheng, Wei; Tai, E Shyong; Gao, Wei; Lin, Xu; Huang, Wei; Abecasis, Goncalo; Consortium, GLGC; Kathiresan, Sekar; Mohlke, Karen L.; Wu, Tangchun; Sham, Pak Chung; Gu, Dongfeng; Willer, Cristen J

2017-01-01

Most genome-wide association studies have been conducted in European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we examined protein-coding genetic variants in 47,532 East Asian individuals using an exome array. We identified 255 variants at 41 loci reaching chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After meta-analysis with > 300,000 European samples, we identified an additional 9 novel loci. The same 16 genes were identified by the protein-altering variants in both East Asians and Europeans, likely pointing to the functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population-specific, and that examining genomic data across diverse ancestries may facilitate the identification of functional genes at associated loci. PMID:29083407

Shannon Entropy of the Canonical Genetic Code

NASA Astrophysics Data System (ADS)

Nemzer, Louis

The probability that a non-synonymous point mutation in DNA will adversely affect the functionality of the resultant protein is greatly reduced if the substitution is conservative. In that case, the amino acid coded by the mutated codon has similar physico-chemical properties to the original. Many simplified alphabets, which group the 20 common amino acids into families, have been proposed. To evaluate these schema objectively, we introduce a novel, quantitative method based on the inherent redundancy in the canonical genetic code. By calculating the Shannon information entropy carried by 1- or 2-bit messages, groupings that best leverage the robustness of the code are identified. The relative importance of properties related to protein folding - like hydropathy and size - and function, including side-chain acidity, can also be estimated. In addition, this approach allows us to quantify the average information value of nucleotide codon positions, and explore the physiological basis for distinguishing between transition and transversion mutations. Supported by NSU PFRDG Grant #335347.

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy.

PubMed

Lee, Yi; El Andaloussi, Samir; Wood, Matthew J A

2012-10-15

Exosomes and microvesicles are extracellular nanovesicles released by most but not all cells. They are specifically equipped to mediate intercellular communication via the transfer of genetic information, including the transfer of both coding and non-coding RNAs, to recipient cells. As a result, both exosomes and microvesicles play a fundamental biological role in the regulation of normal physiological as well as aberrant pathological processes, via altered gene regulatory networks and/or via epigenetic programming. For example, microvesicle-mediated genetic transfer can regulate the maintenance of stem cell plasticity and induce beneficial cell phenotype modulation. Alternatively, such vesicles play a role in tumor pathogenesis and the spread of neurodegenerative diseases via the transfer of specific microRNAs and pathogenic proteins. Given this natural property for genetic information transfer, the possibility of exploiting these vesicles for therapeutic purposes is now being investigated. Stem cell-derived microvesicles appear to be naturally equipped to mediate tissue regeneration under certain conditions, while recent evidence suggests that exosomes might be harnessed for the targeted delivery of human genetic therapies via the introduction of exogenous genetic cargoes such as siRNA. Thus, extracellular vesicles are emerging as potent genetic information transfer agents underpinning a range of biological processes and with therapeutic potential.

The ASSERT Virtual Machine Kernel: Support for Preservation of Temporal Properties

NASA Astrophysics Data System (ADS)

Zamorano, J.; de la Puente, J. A.; Pulido, J. A.; Urueña

2008-08-01

A new approach to building embedded real-time software has been developed in the ASSERT project. One of its key elements is the concept of a virtual machine preserving the non-functional properties of the system, and especially real-time properties, all the way down from high- level design models down to executable code. The paper describes one instance of the virtual machine concept that provides support for the preservation of temporal properties both at the source code level —by accept- ing only "legal" entities, i.e. software components with statically analysable real-tim behaviour— and at run-time —by monitoring the temporal behaviour of the system. The virtual machine has been validated on several pilot projects carried out by aerospace companies in the framework of the ASSERT project.

The importance of immune gene variability (MHC) in evolutionary ecology and conservation

PubMed Central

Sommer, Simone

2005-01-01

Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs). However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC). MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I discuss the importance of adaptive genetic variability with respect to human impact and conservation, and implications for future studies. PMID:16242022

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Langhirt, Eric; Livny, Miron; Ramamurthy, Ravishankar; Soloman, Marvin; Traugott, Steve

2000-01-01

A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

Characterization and phylogenetic analysis of the swine leukocyte antigen 3 gene from Korean native pigs.

PubMed

Chung, H Y; Choi, Y C; Park, H N

2015-05-18

We investigated the phylogenetic relationships between pig breeds, compared the genetic similarity between humans and pigs, and provided basic genetic information on Korean native pigs (KNPs), using genetic variants of the swine leukocyte antigen 3 (SLA-3) gene. Primers were based on sequences from GenBank (accession Nos. AF464010 and AF464009). Polymerase chain reaction analysis amplified approximately 1727 bp of segments, which contained 1086 bp of coding regions and 641 bp of the 3'- and 5'-untranslated regions. Bacterial artificial chromosome clones of miniature pigs were used for sequencing the SLA-3 genomic region, which was 3114 bp in total length, including the coding (1086 bp) and non-coding (2028 bp) regions. Sequence analysis detected 53 single nucleotide polymorphisms (SNPs), based on a minor allele frequency greater than 0.01, which is low compared with other pig breeds, and the results suggest that there is low genetic variability in KNPs. Comparative analysis revealed that humans possess approximately three times more genetic variation than do pigs. Approximately 71% of SNPs in exons 2 and 3 were detected in KNPs, and exon 5 in humans is a highly polymorphic region. Newly identified sequences of SLA-3 using KNPs were submitted to GenBank (accession No. DQ992512-18). Cluster analysis revealed that KNPs were grouped according to three major alleles: SLA-3*0502 (DQ992518), SLA-3*0302 (DQ992513 and DQ992516), and SLA-3*0303 (DQ992512, DQ992514, DQ992515, and DQ992517). Alignments revealed that humans have a relatively close genetic relationship with pigs and chimpanzees. The information provided by this study may be useful in KNP management.

High-fidelity real-time maritime scene rendering

NASA Astrophysics Data System (ADS)

Shyu, Hawjye; Taczak, Thomas M.; Cox, Kevin; Gover, Robert; Maraviglia, Carlos; Cahill, Colin

2011-06-01

The ability to simulate authentic engagements using real-world hardware is an increasingly important tool. For rendering maritime environments, scene generators must be capable of rendering radiometrically accurate scenes with correct temporal and spatial characteristics. When the simulation is used as input to real-world hardware or human observers, the scene generator must operate in real-time. This paper introduces a novel, real-time scene generation capability for rendering radiometrically accurate scenes of backgrounds and targets in maritime environments. The new model is an optimized and parallelized version of the US Navy CRUISE_Missiles rendering engine. It was designed to accept environmental descriptions and engagement geometry data from external sources, render a scene, transform the radiometric scene using the electro-optical response functions of a sensor under test, and output the resulting signal to real-world hardware. This paper reviews components of the scene rendering algorithm, and details the modifications required to run this code in real-time. A description of the simulation architecture and interfaces to external hardware and models is presented. Performance assessments of the frame rate and radiometric accuracy of the new code are summarized. This work was completed in FY10 under Office of Secretary of Defense (OSD) Central Test and Evaluation Investment Program (CTEIP) funding and will undergo a validation process in FY11.

Utilization of genetic tests: analysis of gene-specific billing in Medicare claims data.

PubMed

Lynch, Julie A; Berse, Brygida; Dotson, W David; Khoury, Muin J; Coomer, Nicole; Kautter, John

2017-08-01

We examined the utilization of precision medicine tests among Medicare beneficiaries through analysis of gene-specific tier 1 and 2 billing codes developed by the American Medical Association in 2012. We conducted a retrospective cross-sectional study. The primary source of data was 2013 Medicare 100% fee-for-service claims. We identified claims billed for each laboratory test, the number of patients tested, expenditures, and the diagnostic codes indicated for testing. We analyzed variations in testing by patient demographics and region of the country. Pharmacogenetic tests were billed most frequently, accounting for 48% of the expenditures for new codes. The most common indications for testing were breast cancer, long-term use of medications, and disorders of lipid metabolism. There was underutilization of guideline-recommended tumor mutation tests (e.g., epidermal growth factor receptor) and substantial overutilization of a test discouraged by guidelines (methylenetetrahydrofolate reductase). Methodology-based tier 2 codes represented 15% of all claims billed with the new codes. The highest rate of testing per beneficiary was in Mississippi and the lowest rate was in Alaska. Gene-specific billing codes significantly improved our ability to conduct population-level research of precision medicine. Analysis of these data in conjunction with clinical records should be conducted to validate findings.Genet Med advance online publication 26 January 2017.

Analysis of typical WWER-1000 severe accident scenarios

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

Sorokin, Yu.S.; Shchekoldin, V.V.; Borisov, L.N.

2004-07-01

At present in EDO 'Gidropress' there is a certain experience of performing the analyses of severe accidents of reactor plant with WWER with application of domestic and foreign codes. Important data were also obtained by the results of calculation modeling of integrated experiments with fuel assembly melting comprising a real fuel. Systematization and consideration of these data in development and assimilation of codes are extremely important in connection with large uncertainty still existing in understanding and adequate description of phenomenology of severe accidents. The presented report gives a comparison of analysis results of severe accidents of reactor plant with WWER-1000more » for two typical scenarios made by using American MELCOR code and the Russian RATEG/SVECHA/HEFEST code. The results of calculation modeling are compared using above codes with the data of experiment FPT1 with fuel assembly melting comprising a real fuel, which has been carried out at the facility Phebus (France). The obtained results are considered in the report from the viewpoint of: - adequacy of results of calculation modeling of separate phenomena during severe accidents of RP with WWER by using the above codes; - influence of uncertainties (degree of details of calculation models, choice of parameters of models etc.); - choice of those or other setup variables (options) in the used codes; - necessity of detailed modeling of processes and phenomena as applied to design justification of safety of RP with WWER. (authors)« less

MicroRNAs in genetic disease: rethinking the dosage.

PubMed

Henrion-Caude, Alexandra; Girard, Muriel; Amiel, Jeanne

2012-08-01

To date, the general assumption was that most mutations interested protein-coding genes only. Thus, only few illustrations have mentioned here that mutations may occur in non-protein coding genes such as microRNAs (miRNAs). We thus report progress in delineating their contribution as phenotypic modulators, genetic switches and fine-tuners of gene expression. We reasoned that browsing their contribution to genetic disease may provide a framework for understanding the proper requirements to devise miRNA-based therapy strategies, in particular the relief of an appropriate dosage. Gain and loss of function of miRNA enforce the need to respectively antagonize or supply the miRNAs. We further categorized human disease according to the different ways in which the miRNA was altered arising either de novo, or inherited whether as a mendelian or as an epistatic trait, uncovering its role in epigenetics. We discuss how improving our knowledge on the contribution of miRNAs to genetic disease may be beneficial to devise appropriate gene therapy strategies.

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

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

Hasin-Brumshtein, Yehudit; Khan, Arshad H.; Hormozdiari, Farhad

2016-09-13

Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals bothlocalandtransexpression Quantitative Trait Loci (eQTLs) demonstrating 2transeQTL 'hotspots' associated with expression of hundreds of genes. We alsomore » report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.« less

Neural Codes for One's Own Position and Direction in a Real-World "Vista" Environment.

PubMed

Sulpizio, Valentina; Boccia, Maddalena; Guariglia, Cecilia; Galati, Gaspare

2018-01-01

Humans, like animals, rely on an accurate knowledge of one's spatial position and facing direction to keep orientated in the surrounding space. Although previous neuroimaging studies demonstrated that scene-selective regions (the parahippocampal place area or PPA, the occipital place area or OPA and the retrosplenial complex or RSC), and the hippocampus (HC) are implicated in coding position and facing direction within small-(room-sized) and large-scale navigational environments, little is known about how these regions represent these spatial quantities in a large open-field environment. Here, we used functional magnetic resonance imaging (fMRI) in humans to explore the neural codes of these navigationally-relevant information while participants viewed images which varied for position and facing direction within a familiar, real-world circular square. We observed neural adaptation for repeated directions in the HC, even if no navigational task was required. Further, we found that the amount of knowledge of the environment interacts with the PPA selectivity in encoding positions: individuals who needed more time to memorize positions in the square during a preliminary training task showed less neural attenuation in this scene-selective region. We also observed adaptation effects, which reflect the real distances between consecutive positions, in scene-selective regions but not in the HC. When examining the multi-voxel patterns of activity we observed that scene-responsive regions and the HC encoded both spatial information and that the RSC classification accuracy for positions was higher in individuals scoring higher to a self-reported questionnaire of spatial abilities. Our findings provide new insight into how the human brain represents a real, large-scale "vista" space, demonstrating the presence of neural codes for position and direction in both scene-selective and hippocampal regions, and revealing the existence, in the former regions, of a map-like spatial representation reflecting real-world distance between consecutive positions.

The conservation of forest genetic resources: case histories from Canada, Mexico, and the United States

Treesearch

F. Thomas Ledig; J. Jesús Vargas-Hernández; Kurt H. Johnsen

1998-01-01

The genetic codes of living organisms are natural resources no less than soil, air, and water. Genetic resources-from nucleotide sequences in DNA to selected genotypes, populations, and species-are the raw material in forestry: for breeders, for the forest manager who produces an economic crop, for society that reaps the environmental benefits provided by forests, and...

The detection of T-Nos, a genetic element present in GMOs, by cross-priming isothermal amplification with real-time fluorescence.

PubMed

Zhang, Fang; Wang, Liu; Fan, Kai; Wu, Jian; Ying, Yibin

2014-05-01

An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06 × 10(3) copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.

Compression performance comparison in low delay real-time video for mobile applications

NASA Astrophysics Data System (ADS)

Bivolarski, Lazar

2012-10-01

This article compares the performance of several current video coding standards in the conditions of low-delay real-time in a resource constrained environment. The comparison is performed using the same content and the metrics and mix of objective and perceptual quality metrics. The metrics results in different coding schemes are analyzed from a point of view of user perception and quality of service. Multiple standards are compared MPEG-2, MPEG4 and MPEG-AVC and well and H.263. The metrics used in the comparison include SSIM, VQM and DVQ. Subjective evaluation and quality of service are discussed from a point of view of perceptual metrics and their incorporation in the coding scheme development process. The performance and the correlation of results are presented as a predictor of the performance of video compression schemes.

Automated Detection and Analysis of Interplanetary Shocks Running Real-Time on the Web

NASA Astrophysics Data System (ADS)

Vorotnikov, V.; Smith, C. W.; Hu, Q.; Szabo, A.; Skoug, R. M.; Cohen, C. M.; Davis, A. J.

2008-05-01

The ACE real-time data stream provides web-based now-casting capabilities for solar wind conditions upstream of Earth. We have built a fully automated code that finds and analyzes interplanetary shocks as they occur and posts their solutions on the Web for possible real-time application to space weather nowcasting. Shock analysis algorithms based on the Rankine-Hugoniot jump conditions exist and are in wide-spread use today for the interactive analysis of interplanetary shocks yielding parameters such as shock speed and propagation direction and shock strength in the form of compression ratios. At a previous meeting we reported on efforts to develop a fully automated code that used ACE Level-2 (science quality) data to prove the applicability and correctness of the code and the associated shock-finder. We have since adapted the code to run ACE RTSW data provided by NOAA. This data lacks the full 3-dimensional velocity vector for the solar wind and contains only a single component wind speed. We show that by assuming the wind velocity to be radial strong shock solutions remain essentially unchanged and the analysis performs as well as it would if 3-D velocity components were available. This is due, at least in part, to the fact that strong shocks tend to have nearly radial shock normals and it is the strong shocks that are most effective in space weather applications. Strong shocks are the only shocks that concern us in this application. The code is now running on the Web and the results are available to all.

Prevalence of virulence genes in Escherichia coli strains isolated from Romanian adult urinary tract infection cases.

PubMed

Usein, C R; Damian, M; Tatu-Chitoiu, D; Capusa, C; Fagaras, R; Tudorache, D; Nica, M; Le Bouguénec, C

2001-01-01

A total of 78 E. coli strains isolated from adults with different types of urinary tract infections were screened by polymerase chain reaction for prevalence of genetic regions coding for virulence factors. The targeted genetic determinants were those coding for type 1 fimbriae (fimH), pili associated with pyelonephritis (pap), S and F1C fimbriae (sfa and foc), afimbrial adhesins (afa), hemolysin (hly), cytotoxic necrotizing factor (cnf), aerobactin (aer). Among the studied strains, the prevalence of genes coding for fimbrial adhesive systems was 86%, 36%, and 23% for fimH, pap, and sfa/foc,respectively. The operons coding for Afa afimbrial adhesins were identified in 14% of strains. The hly and cnf genes coding for toxins were amplified in 23% and 13% of strains, respectively. A prevalence of 54% was found for the aer gene. The various combinations of detected genes were designated as virulence patterns. The strains isolated from the hospitalized patients displayed a greater number of virulence genes and a diversity of gene associations compared to the strains isolated from the ambulatory subjects. A rapid assessment of the bacterial pathogenicity characteristics may contribute to a better medical approach of the patients with urinary tract infections.

Learning about the Benetic Code via Programming: Representing the Process of Translation.

ERIC Educational Resources Information Center

Ploger, Don

1991-01-01

This study examined the representations that a 16-year-old student made using the flexible computer system, "Boxer," in learning the genetic code. Results indicated that programing made it easier to build and explore flexible and useful representations and encouraged interdisciplinary collaboration between mathematics and biology…

Theory of epigenetic coding.

PubMed

Elder, D

1984-06-07

The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.

QOS-aware error recovery in wireless body sensor networks using adaptive network coding.

PubMed

Razzaque, Mohammad Abdur; Javadi, Saeideh S; Coulibaly, Yahaya; Hira, Muta Tah

2014-12-29

Wireless body sensor networks (WBSNs) for healthcare and medical applications are real-time and life-critical infrastructures, which require a strict guarantee of quality of service (QoS), in terms of latency, error rate and reliability. Considering the criticality of healthcare and medical applications, WBSNs need to fulfill users/applications and the corresponding network's QoS requirements. For instance, for a real-time application to support on-time data delivery, a WBSN needs to guarantee a constrained delay at the network level. A network coding-based error recovery mechanism is an emerging mechanism that can be used in these systems to support QoS at very low energy, memory and hardware cost. However, in dynamic network environments and user requirements, the original non-adaptive version of network coding fails to support some of the network and user QoS requirements. This work explores the QoS requirements of WBSNs in both perspectives of QoS. Based on these requirements, this paper proposes an adaptive network coding-based, QoS-aware error recovery mechanism for WBSNs. It utilizes network-level and user-/application-level information to make it adaptive in both contexts. Thus, it provides improved QoS support adaptively in terms of reliability, energy efficiency and delay. Simulation results show the potential of the proposed mechanism in terms of adaptability, reliability, real-time data delivery and network lifetime compared to its counterparts.

Heuristic rules embedded genetic algorithm for in-core fuel management optimization

NASA Astrophysics Data System (ADS)

Alim, Fatih

The objective of this study was to develop a unique methodology and a practical tool for designing loading pattern (LP) and burnable poison (BP) pattern for a given Pressurized Water Reactor (PWR) core. Because of the large number of possible combinations for the fuel assembly (FA) loading in the core, the design of the core configuration is a complex optimization problem. It requires finding an optimal FA arrangement and BP placement in order to achieve maximum cycle length while satisfying the safety constraints. Genetic Algorithms (GA) have been already used to solve this problem for LP optimization for both PWR and Boiling Water Reactor (BWR). The GA, which is a stochastic method works with a group of solutions and uses random variables to make decisions. Based on the theories of evaluation, the GA involves natural selection and reproduction of the individuals in the population for the next generation. The GA works by creating an initial population, evaluating it, and then improving the population by using the evaluation operators. To solve this optimization problem, a LP optimization package, GARCO (Genetic Algorithm Reactor Code Optimization) code is developed in the framework of this thesis. This code is applicable for all types of PWR cores having different geometries and structures with an unlimited number of FA types in the inventory. To reach this goal, an innovative GA is developed by modifying the classical representation of the genotype. To obtain the best result in a shorter time, not only the representation is changed but also the algorithm is changed to use in-core fuel management heuristics rules. The improved GA code was tested to demonstrate and verify the advantages of the new enhancements. The developed methodology is explained in this thesis and preliminary results are shown for the VVER-1000 reactor hexagonal geometry core and the TMI-1 PWR. The improved GA code was tested to verify the advantages of new enhancements. The core physics code used for VVER in this research is Moby-Dick, which was developed to analyze the VVER by SKODA Inc. The SIMULATE-3 code, which is an advanced two-group nodal code, is used to analyze the TMI-1.

Privacy rules for DNA databanks. Protecting coded 'future diaries'.

PubMed

Annas, G J

1993-11-17

In privacy terms, genetic information is like medical information. But the information contained in the DNA molecule itself is more sensitive because it contains an individual's probabilistic "future diary," is written in a code that has only partially been broken, and contains information about an individual's parents, siblings, and children. Current rules for protecting the privacy of medical information cannot protect either genetic information or identifiable DNA samples stored in DNA databanks. A review of the legal and public policy rationales for protecting genetic privacy suggests that specific enforceable privacy rules for DNA databanks are needed. Four preliminary rules are proposed to govern the creation of DNA databanks, the collection of DNA samples for storage, limits on the use of information derived from the samples, and continuing obligations to those whose DNA samples are in the databanks.

Association of genetic variants and expression levels of porcine FABP4 and FABP5 genes.

PubMed

Ballester, M; Puig-Oliveras, A; Castelló, A; Revilla, M; Fernández, A I; Folch, J M

2017-12-01

The FABP4 and FABP5 genes, coding for fatty acid transport proteins, have long been studied as positional candidate genes for SSC4 QTL affecting fat deposition and composition traits in pigs. Polymorphisms in these genes, FABP4:g.2634_2635insC and FABP5:g.3000T>G, have previously been associated with fatness traits in an Iberian by Landrace cross (IBMAP). The aim of the present work was to evaluate the functional implication of these genetic variants. For this purpose, FABP4 and FABP5 mRNA expression levels in 114 BC1_LD animals (25% Iberian × 75% Landrace) were analyzed using real-time quantitative PCR in backfat and muscle. FABP4 gene expression in backfat, but not in muscle, was associated with FABP4:g.2634_2635insC. In contrast, FABP5:g.3000T>G was not associated with gene expression levels. An expression-based genome-wide association study highlighted the FABP4:g.2634_2635insC polymorphism as the polymorphism most associated with FABP4 gene expression in backfat. Furthermore, other genomic regions associated in trans with the mRNA expression of FABP4 in backfat and FABP5 in muscle were also identified. Finally, two putative transcription binding sites for PPARG and NR4A2 may be affected by the FABP4:g.2634_2635insC polymorphism, modifying FABP4 gene expression. Our results reinforce FABP4 as a candidate gene for fatness traits on SSC4. © 2017 Stichting International Foundation for Animal Genetics.

SEQassembly: A Practical Tools Program for Coding Sequences Splicing

NASA Astrophysics Data System (ADS)

Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

Network Coded Cooperative Communication in a Real-Time Wireless Hospital Sensor Network.

PubMed

Prakash, R; Balaji Ganesh, A; Sivabalan, Somu

2017-05-01

The paper presents a network coded cooperative communication (NC-CC) enabled wireless hospital sensor network architecture for monitoring health as well as postural activities of a patient. A wearable device, referred as a smartband is interfaced with pulse rate, body temperature sensors and an accelerometer along with wireless protocol services, such as Bluetooth and Radio-Frequency transceiver and Wi-Fi. The energy efficiency of wearable device is improved by embedding a linear acceleration based transmission duty cycling algorithm (NC-DRDC). The real-time demonstration is carried-out in a hospital environment to evaluate the performance characteristics, such as power spectral density, energy consumption, signal to noise ratio, packet delivery ratio and transmission offset. The resource sharing and energy efficiency features of network coding technique are improved by proposing an algorithm referred as network coding based dynamic retransmit/rebroadcast decision control (LA-TDC). From the experimental results, it is observed that the proposed LA-TDC algorithm reduces network traffic and end-to-end delay by an average of 27.8% and 21.6%, respectively than traditional network coded wireless transmission. The wireless architecture is deployed in a hospital environment and results are then successfully validated.

Teaching Molecular Biology with Microcomputers.

ERIC Educational Resources Information Center

Reiss, Rebecca; Jameson, David

1984-01-01

Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

Propellant Chemistry for CFD Applications

NASA Technical Reports Server (NTRS)

Farmer, R. C.; Anderson, P. G.; Cheng, Gary C.

1996-01-01

Current concepts for reusable launch vehicle design have created renewed interest in the use of RP-1 fuels for high pressure and tri-propellant propulsion systems. Such designs require the use of an analytical technology that accurately accounts for the effects of real fluid properties, combustion of large hydrocarbon fuel modules, and the possibility of soot formation. These effects are inadequately treated in current computational fluid dynamic (CFD) codes used for propulsion system analyses. The objective of this investigation is to provide an accurate analytical description of hydrocarbon combustion thermodynamics and kinetics that is sufficiently computationally efficient to be a practical design tool when used with CFD codes such as the FDNS code. A rigorous description of real fluid properties for RP-1 and its combustion products will be derived from the literature and from experiments conducted in this investigation. Upon the establishment of such a description, the fluid description will be simplified by using the minimum of empiricism necessary to maintain accurate combustion analyses and including such empirical models into an appropriate CFD code. An additional benefit of this approach is that the real fluid properties analysis simplifies the introduction of the effects of droplet sprays into the combustion model. Typical species compositions of RP-1 have been identified, surrogate fuels have been established for analyses, and combustion and sooting reaction kinetics models have been developed. Methods for predicting the necessary real fluid properties have been developed and essential experiments have been designed. Verification studies are in progress, and preliminary results from these studies will be presented. The approach has been determined to be feasible, and upon its completion the required methodology for accurate performance and heat transfer CFD analyses for high pressure, tri-propellant propulsion systems will be available.

Scientific rationality, uncertainty and the governance of human genetics: an interview study with researchers at deCODE genetics.

PubMed

Hjörleifsson, Stefán; Schei, Edvin

2006-07-01

Technology development in human genetics is fraught with uncertainty, controversy and unresolved moral issues, and industry scientists are sometimes accused of neglecting the implications of their work. The present study was carried out to elicit industry scientists' reflections on the relationship between commercial, scientific and ethical dimensions of present day genetics and the resources needed for robust governance of new technologies. Interviewing scientists of the company deCODE genetics in Iceland, we found that in spite of optimism, the informants revealed ambiguity and uncertainty concerning the use of human genetic technologies for the prevention of common diseases. They concurred that uncritical marketing of scientific success might cause exaggerated public expectations of health benefits from genetics, with the risk of backfiring and causing resistance to genetics in the population. On the other hand, the scientists did not address dilemmas arising from the commercial nature of their own employer. Although the scientists tended to describe public fear as irrational, they identified issues where scepticism might be well founded and explored examples where they, despite expert knowledge, held ambiguous or tentative personal views on the use of predictive genetic technologies. The rationality of science was not seen as sufficient to ensure beneficial governance of new technologies. The reflexivity and suspension of judgement demonstrated in the interviews exemplify productive features of moral deliberation in complex situations. Scientists should take part in dialogues concerning the governance of genetic technologies, acknowledge any vested interests, and use their expertise to highlight, not conceal the technical and moral complexity involved.

Dynamic traffic assignment : genetic algorithms approach

DOT National Transportation Integrated Search

1997-01-01

Real-time route guidance is a promising approach to alleviating congestion on the nations highways. A dynamic traffic assignment model is central to the development of guidance strategies. The artificial intelligence technique of genetic algorithm...

The mathematical theory of signal processing and compression-designs

NASA Astrophysics Data System (ADS)

Feria, Erlan H.

2006-05-01

The mathematical theory of signal processing, named processor coding, will be shown to inherently arise as the computational time dual of Shannon's mathematical theory of communication which is also known as source coding. Source coding is concerned with signal source memory space compression while processor coding deals with signal processor computational time compression. Their combination is named compression-designs and referred as Conde in short. A compelling and pedagogically appealing diagram will be discussed highlighting Conde's remarkable successful application to real-world knowledge-aided (KA) airborne moving target indicator (AMTI) radar.

A novel neutron energy spectrum unfolding code using particle swarm optimization

NASA Astrophysics Data System (ADS)

Shahabinejad, H.; Sohrabpour, M.

2017-07-01

A novel neutron Spectrum Deconvolution using Particle Swarm Optimization (SDPSO) code has been developed to unfold the neutron spectrum from a pulse height distribution and a response matrix. The Particle Swarm Optimization (PSO) imitates the bird flocks social behavior to solve complex optimization problems. The results of the SDPSO code have been compared with those of the standard spectra and recently published Two-steps Genetic Algorithm Spectrum Unfolding (TGASU) code. The TGASU code have been previously compared with the other codes such as MAXED, GRAVEL, FERDOR and GAMCD and shown to be more accurate than the previous codes. The results of the SDPSO code have been demonstrated to match well with those of the TGASU code for both under determined and over-determined problems. In addition the SDPSO has been shown to be nearly two times faster than the TGASU code.

A hybrid genetic algorithm for resolving closely spaced objects

NASA Technical Reports Server (NTRS)

Abbott, R. J.; Lillo, W. E.; Schulenburg, N.

1995-01-01

A hybrid genetic algorithm is described for performing the difficult optimization task of resolving closely spaced objects appearing in space based and ground based surveillance data. This application of genetic algorithms is unusual in that it uses a powerful domain-specific operation as a genetic operator. Results of applying the algorithm to real data from telescopic observations of a star field are presented.

Nonlinear Real-Time Optical Signal Processing.

DTIC Science & Technology

1988-07-01

Principal Investigator B. K. Jenkins Signal and Image Processing Institute University of Southern California Mail Code 0272 Los Angeles, California...ADDRESS (09% SteW. Mnd ZIP Code ) 10. SOURC OF FUNONG NUMBERS Bldg. 410, Bolling AFB PROGAM CT TASK WORK UNIT Washington, D.C. 20332 EEETP.aso o 11...TAB Unmnnncced Justification By Distribution/ I O’ Availablility Codes I - ’_ ji and/or 2 I Summary During the period 1 July 1987 - 30 June 1988, the

Biophysics: Breaking the Nanometer Barrier

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

Block, Steven

2006-03-20

A new field of scientific exploration – single molecule biophysics – is currently reshaping and redefining our understanding of the mechanochemistry of life. The development of laser-based optical traps, or ‘optical tweezers,’ has allowed for physiological assessments of such precision that bio-molecules can now be measured and studied one at a time. In this colloquium, Professor Block will present findings based on his group’s construction of optical trapping instrumentation that has broken the nanometer barrier, allowing researchers to study single-molecule displacements on the Angstrom level. Focusing on RNA polymerase, the motor enzyme responsible for transcribing the genetic code contained inmore » DNA, Block’s group has been able to measure, in real time, the motion of a single molecule of RNA polymerase as it moves from base to base along the DNA template. A remarkable opportunity to gain insight into one of the most fundamental biological processes of life, this colloquium can not be missed!« less

Evolutionary pattern search algorithms

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

Hart, W.E.

1995-09-19

This paper defines a class of evolutionary algorithms called evolutionary pattern search algorithms (EPSAs) and analyzes their convergence properties. This class of algorithms is closely related to evolutionary programming, evolutionary strategie and real-coded genetic algorithms. EPSAs are self-adapting systems that modify the step size of the mutation operator in response to the success of previous optimization steps. The rule used to adapt the step size can be used to provide a stationary point convergence theory for EPSAs on any continuous function. This convergence theory is based on an extension of the convergence theory for generalized pattern search methods. An experimentalmore » analysis of the performance of EPSAs demonstrates that these algorithms can perform a level of global search that is comparable to that of canonical EAs. We also describe a stopping rule for EPSAs, which reliably terminated near stationary points in our experiments. This is the first stopping rule for any class of EAs that can terminate at a given distance from stationary points.« less

Isolation and Characterization of a microRNA-size Secretable Small RNA in Streptococcus sanguinis.

PubMed

Choi, Ji-Woong; Kwon, Tae-Yub; Hong, Su-Hyung; Lee, Heon-Jin

2018-06-01

MicroRNAs in eukaryotic cells are thought to control highly complex signal transduction and other biological processes by regulating coding transcripts, accounting for their important role in cellular events in eukaryotes. Recently, a novel class of bacterial RNAs similar in size [18-22 nucleotides (nt)] to microRNAs has been reported. Herein, we describe microRNAs, small RNAs from the oral pathogen Streptococcus sanguinis. The bacteria are normally present in the oral cavities and cause endocarditis by contaminating bloodstreams. Small RNAs were analyzed by deep sequencing. Selected highly expressed small RNAs were further validated by real-time polymerase chain reaction and northern blot analyses. We found that skim milk supplement changed the expression of small RNAs S.S-1964 in tandem with the nearby SSA_0513 gene involved in vitamin B 12 conversion. We furthermore observed small RNAs secreted via bacterial membrane vesicles. Although their precise function remains unclear, secretable small RNAs may represent an entirely new area of study in bacterial genetics.

Synthetic Genome Recoding: New genetic codes for new features

PubMed Central

Kuo, James; Stirling, Finn; Lau, Yu Heng; Shulgina, Yekaterina; Way, Jeffrey C.; Silver, Pamela A.

2018-01-01

Full genome recoding, or rewriting codon meaning, through chemical synthesis of entire bacterial chromosomes has become feasible in the past several years. Recoding an organism can impart new properties including non-natural amino acid incorporation, virus resistance, and biocontainment. The estimated cost of construction that includes DNA synthesis, assembly by recombination, and troubleshooting, is now comparable to costs of early stage development of drugs or other high-tech products. Here we discuss several recently published assembly methods and provide some thoughts on the future, including how synthetic efforts might benefit from analysis of natural recoding processes and organisms that use alternative genetic codes. PMID:28983660

Real-Time Precise Point Positioning (RTPPP) with raw observations and its application in real-time regional ionospheric VTEC modeling

NASA Astrophysics Data System (ADS)

Liu, Teng; Zhang, Baocheng; Yuan, Yunbin; Li, Min

2018-01-01

Precise Point Positioning (PPP) is an absolute positioning technology mainly used in post data processing. With the continuously increasing demand for real-time high-precision applications in positioning, timing, retrieval of atmospheric parameters, etc., Real-Time PPP (RTPPP) and its applications have drawn more and more research attention in recent years. This study focuses on the models, algorithms and ionospheric applications of RTPPP on the basis of raw observations, in which high-precision slant ionospheric delays are estimated among others in real time. For this purpose, a robust processing strategy for multi-station RTPPP with raw observations has been proposed and realized, in which real-time data streams and State-Space-Representative (SSR) satellite orbit and clock corrections are used. With the RTPPP-derived slant ionospheric delays from a regional network, a real-time regional ionospheric Vertical Total Electron Content (VTEC) modeling method is proposed based on Adjusted Spherical Harmonic Functions and a Moving-Window Filter. SSR satellite orbit and clock corrections from different IGS analysis centers are evaluated. Ten globally distributed real-time stations are used to evaluate the positioning performances of the proposed RTPPP algorithms in both static and kinematic modes. RMS values of positioning errors in static/kinematic mode are 5.2/15.5, 4.7/17.4 and 12.8/46.6 mm, for north, east and up components, respectively. Real-time slant ionospheric delays from RTPPP are compared with those from the traditional Carrier-to-Code Leveling (CCL) method, in terms of function model, formal precision and between-receiver differences of short baseline. Results show that slant ionospheric delays from RTPPP are more precise and have a much better convergence performance than those from the CCL method in real-time processing. 30 real-time stations from the Asia-Pacific Reference Frame network are used to model the ionospheric VTECs over Australia in real time, with slant ionospheric delays from both RTPPP and CCL methods for comparison. RMS of the VTEC differences between RTPPP/CCL method and CODE final products is 0.91/1.09 TECU, and RMS of the VTEC differences between RTPPP and CCL methods is 0.67 TECU. Slant Total Electron Contents retrieved from different VTEC models are also validated with epoch-differenced Geometry-Free combinations of dual-frequency phase observations, and mean RMS values are 2.14, 2.33 and 2.07 TECU for RTPPP method, CCL method and CODE final products, respectively. This shows the superiority of RTPPP-derived slant ionospheric delays in real-time ionospheric VTEC modeling.

Metabolic basis for the self-referential genetic code.

PubMed

Guimarães, Romeu Cardoso

2011-08-01

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine-this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.

Supporting Students' Knowledge Transfer in Modeling Activities

ERIC Educational Resources Information Center

Piksööt, Jaanika; Sarapuu, Tago

2014-01-01

This study investigates ways to enhance secondary school students' knowledge transfer in complex science domains by implementing question prompts. Two samples of students applied two web-based models to study molecular genetics--the model of genetic code (n = 258) and translation (n = 245). For each model, the samples were randomly divided into…

Using Economics and Genetics To Produce Leaner Pork.

ERIC Educational Resources Information Center

Welch, Mary A., Ed.

1994-01-01

The booklet describes the STAGES (Swine Testing and Genetic Evaluation System) program developed at Purdue University (Indiana), along with the USDA, National Pork Producers Council and swine breed associations. By selecting breeding stock from a coded catalogue developed by STAGES, producers are able to select the best breeding stock for more…

An Inquiry Activity for Genetics Using Chromosome Mapping.

ERIC Educational Resources Information Center

Leonard, William H.; Snodgrass, George

1982-01-01

Concepts to be developed, objectives, and student instructions are provided for an activity useful as an introduction to or review of Mendelian genetics and sex determination. Universal codes (read by optical scanners at supermarket checkout stands) from soup can labels are used as chromosome maps during the activity. (JN)

GENETIC DIVERSITY AS AN INDICATOR OF ECOSYSTEM CONDITION AND SUSTAINABILITY: UTILITY FOR REGIONAL ASSESSMENTS OF STREAM CONDITION IN THE EASTERN UNITED STATES

EPA Science Inventory

This report documents research undertaken to determine if the theoretical promise of genetic diversity as an ecological indicator is realized in real-world applications. Results of two case studies confirm that genetic diversity is a useful indicator of environmental condition. ...

Current and anticipated uses of thermal-hydraulic codes in Germany

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

Teschendorff, V.; Sommer, F.; Depisch, F.

1997-07-01

In Germany, one third of the electrical power is generated by nuclear plants. ATHLET and S-RELAP5 are successfully applied for safety analyses of the existing PWR and BWR reactors and possible future reactors, e.g. EPR. Continuous development and assessment of thermal-hydraulic codes are necessary in order to meet present and future needs of licensing organizations, utilities, and vendors. Desired improvements include thermal-hydraulic models, multi-dimensional simulation, computational speed, interfaces to coupled codes, and code architecture. Real-time capability will be essential for application in full-scope simulators. Comprehensive code validation and quantification of uncertainties are prerequisites for future best-estimate analyses.

Recent evidence for evolution of the genetic code

NASA Technical Reports Server (NTRS)

Osawa, S.; Jukes, T. H.; Watanabe, K.; Muto, A.

1992-01-01

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Achieving AFRL Universal FADEC Vision With Open Architecture Addressing Capability and Obsolescence for Military and Commercial Applications (Preprint)

DTIC Science & Technology

2006-11-01

engines will involve a family of common components. It will consist of a real - time operating system and partitioned application software (AS...system will employ a standard hardware and software architecture. It will consist of a real time operating system and partitioned application...Inputs - Enables Large Cost Reduction 3. Software - FAA Certified Auto Code - Real Time Operating System - Commercial

26 CFR 1.1033(g)-1 - Condemnation of real property held for productive use in trade or business or for investment.

Code of Federal Regulations, 2013 CFR

2013-04-01

... productive use in trade or business or for investment. 1.1033(g)-1 Section 1.1033(g)-1 Internal Revenue... (CONTINUED) Common Nontaxable Exchanges § 1.1033(g)-1 Condemnation of real property held for productive use... treat outdoor advertising displays as real property—(1) In general. Under section 1033(g)(3) of the Code...

26 CFR 1.1033(g)-1 - Condemnation of real property held for productive use in trade or business or for investment.

Code of Federal Regulations, 2011 CFR

2011-04-01

... productive use in trade or business or for investment. 1.1033(g)-1 Section 1.1033(g)-1 Internal Revenue... (CONTINUED) Common Nontaxable Exchanges § 1.1033(g)-1 Condemnation of real property held for productive use... treat outdoor advertising displays as real property—(1) In general. Under section 1033(g)(3) of the Code...

26 CFR 1.1033(g)-1 - Condemnation of real property held for productive use in trade or business or for investment.

Code of Federal Regulations, 2012 CFR

2012-04-01

... productive use in trade or business or for investment. 1.1033(g)-1 Section 1.1033(g)-1 Internal Revenue... (CONTINUED) Common Nontaxable Exchanges § 1.1033(g)-1 Condemnation of real property held for productive use... treat outdoor advertising displays as real property—(1) In general. Under section 1033(g)(3) of the Code...

26 CFR 1.1033(g)-1 - Condemnation of real property held for productive use in trade or business or for investment.

Code of Federal Regulations, 2014 CFR

2014-04-01

... productive use in trade or business or for investment. 1.1033(g)-1 Section 1.1033(g)-1 Internal Revenue... (CONTINUED) Common Nontaxable Exchanges § 1.1033(g)-1 Condemnation of real property held for productive use... treat outdoor advertising displays as real property—(1) In general. Under section 1033(g)(3) of the Code...

Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae).

PubMed

Liu, Ze-Xuan; Zhang, Yan; Liu, Yu-Ting; Chang, Qiao-Cheng; Su, Xin; Fu, Xue; Yue, Dong-Mei; Gao, Yuan; Wang, Chun-Ren

2016-04-01

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.

Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae)

PubMed Central

Liu, Ze-Xuan; Zhang, Yan; Liu, Yu-Ting; Chang, Qiao-Cheng; Su, Xin; Fu, Xue; Yue, Dong-Mei; Gao, Yuan; Wang, Chun-Ren

2016-01-01

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans. PMID:27180575

Development of Efficient Real-Fluid Model in Simulating Liquid Rocket Injector Flows

NASA Technical Reports Server (NTRS)

Cheng, Gary; Farmer, Richard

2003-01-01

The characteristics of propellant mixing near the injector have a profound effect on the liquid rocket engine performance. However, the flow features near the injector of liquid rocket engines are extremely complicated, for example supercritical-pressure spray, turbulent mixing, and chemical reactions are present. Previously, a homogeneous spray approach with a real-fluid property model was developed to account for the compressibility and evaporation effects such that thermodynamics properties of a mixture at a wide range of pressures and temperatures can be properly calculated, including liquid-phase, gas- phase, two-phase, and dense fluid regions. The developed homogeneous spray model demonstrated a good success in simulating uni- element shear coaxial injector spray combustion flows. However, the real-fluid model suffered a computational deficiency when applied to a pressure-based computational fluid dynamics (CFD) code. The deficiency is caused by the pressure and enthalpy being the independent variables in the solution procedure of a pressure-based code, whereas the real-fluid model utilizes density and temperature as independent variables. The objective of the present research work is to improve the computational efficiency of the real-fluid property model in computing thermal properties. The proposed approach is called an efficient real-fluid model, and the improvement of computational efficiency is achieved by using a combination of a liquid species and a gaseous species to represent a real-fluid species.

23 CFR 710.401 - General.

Code of Federal Regulations, 2012 CFR

2012-04-01

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41 CFR 102-75.1110 - What is the policy governing delegations of authority to the Secretary of the Interior, the...

Code of Federal Regulations, 2010 CFR

2010-07-01

... of Title 40 of the United States Code. ... Services, and the Secretary of Education for property used in the administration of any Native American... Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL PROPERTY 75-REAL...

The optimal code searching method with an improved criterion of coded exposure for remote sensing image restoration

NASA Astrophysics Data System (ADS)

He, Lirong; Cui, Guangmang; Feng, Huajun; Xu, Zhihai; Li, Qi; Chen, Yueting

2015-03-01

Coded exposure photography makes the motion de-blurring a well-posed problem. The integration pattern of light is modulated using the method of coded exposure by opening and closing the shutter within the exposure time, changing the traditional shutter frequency spectrum into a wider frequency band in order to preserve more image information in frequency domain. The searching method of optimal code is significant for coded exposure. In this paper, an improved criterion of the optimal code searching is proposed by analyzing relationship between code length and the number of ones in the code, considering the noise effect on code selection with the affine noise model. Then the optimal code is obtained utilizing the method of genetic searching algorithm based on the proposed selection criterion. Experimental results show that the time consuming of searching optimal code decreases with the presented method. The restoration image is obtained with better subjective experience and superior objective evaluation values.

Studying the genetic basis of speciation in high gene flow marine invertebrates

PubMed Central

2016-01-01

A growing number of genes responsible for reproductive incompatibilities between species (barrier loci) exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms (SNPs) in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying FST-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and non-coding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available. PMID:29491951

The Paraoxonase 1 Gene c.-108C>T SNP in the Promoter Is Associated with Risk for Glioma in Mexican Patients, but Not the p.L55M or p.Q192R Polymorphisms in the Coding Region.

PubMed

González-Herrera, Lizbeth; Gamas-Trujillo, Pablo Alejandro; Medina-Escobedo, Gilberto; Oaxaca-Castillo, David; Pérez-Mendoza, Gerardo; Williams-Jacquez, Dayana; Canto-Cetina, Thelma; Vargas-García, Rubén Darío

2015-09-01

To evaluate the association of the paraoxonase 1 (PON1) gene polymorphisms c.-108C>T, p.L55M, and p.Q192R with the risk of glioma in Southeast Mexico. Decreased PON1 activity caused by polymorphisms has been observed in gliomas, thus supporting the theory that PON1 is involved in tumorigenesis in the brain. Sixty-seven glioma patients and 58 control individuals were included. Three PON1 polymorphisms were genotyped by real-time PCR allelic discrimination using TaqMan probes: c.-108C>T in the promoter region, p.Q192R and p.L55M, both of which were in the coding region. Allele, genotype, and haplotype frequencies were assessed in cases and controls to test for statistical associations (STATA 10.2 package). Significant differences were found for the PON1 c.-108C>T polymorphism between the cases and controls. Compared to the controls the cases were more likely to be CT heterozygous (p =  0.002) or TT homozygous (p = 0.036); similarly cases were more likely to possess a T allele (p = 0.032). In contrast, the p.L55M and p.Q192R polymorphisms did not show significant differences between the glioma cases and controls (p > 0.05). The PON1 c.-108C>T polymorphism in the promoter region is associated with genetic risk for glioma. Conversely, p.L55M and p.Q192R polymorphisms in the coding region do not seem to have an influence in this population.

Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum.

PubMed

Prasad, Pushplata; Varshney, Deepti; Adholeya, Alok

2015-11-25

The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequence of P. lilacinum. The study aims to decipher the putative genetic components of the fungus involved in nematode pathogenesis by performing comparative genomic analysis with nine closely related fungal species in Hypocreales. de novo genomic assembly was done and a total of 301 scaffolds were constructed for P. lilacinum genomic DNA. By employing structural genome prediction models, 13, 266 genes coding for proteins were predicted in the genome. Approximately 73% of the predicted genes were functionally annotated using Blastp, InterProScan and Gene Ontology. A 14.7% fraction of the predicted genes shared significant homology with genes in the Pathogen Host Interactions (PHI) database. The phylogenomic analysis carried out using maximum likelihood RAxML algorithm provided insight into the evolutionary relationship of P. lilacinum. In congruence with other closely related species in the Hypocreales namely, Metarhizium spp., Pochonia chlamydosporia, Cordyceps militaris, Trichoderma reesei and Fusarium spp., P. lilacinum has large gene sets coding for G-protein coupled receptors (GPCRs), proteases, glycoside hydrolases and carbohydrate esterases that are required for degradation of nematode-egg shell components. Screening of the genome by Antibiotics & Secondary Metabolite Analysis Shell (AntiSMASH) pipeline indicated that the genome potentially codes for a variety of secondary metabolites, possibly required for adaptation to heterogeneous lifestyles reported for P. lilacinum. Significant up-regulation of subtilisin-like serine protease genes in presence of nematode eggs in quantitative real-time analyses suggested potential role of serine proteases in nematode pathogenesis. The data offer a better understanding of Purpureocillium lilacinum genome and will enhance our understanding on the molecular mechanism involved in nematophagy.

Complex Interplay among DNA Modification, Noncoding RNA Expression and Protein-Coding RNA Expression in Salvia miltiorrhiza Chloroplast Genome

PubMed Central

Chen, Haimei; Zhang, Jianhui; Yuan, George; Liu, Chang

2014-01-01

Salvia miltiorrhiza is one of the most widely used medicinal plants. As a first step to develop a chloroplast-based genetic engineering method for the over-production of active components from S. miltiorrhiza, we have analyzed the genome, transcriptome, and base modifications of the S. miltiorrhiza chloroplast. Total genomic DNA and RNA were extracted from fresh leaves and then subjected to strand-specific RNA-Seq and Single-Molecule Real-Time (SMRT) sequencing analyses. Mapping the RNA-Seq reads to the genome assembly allowed us to determine the relative expression levels of 80 protein-coding genes. In addition, we identified 19 polycistronic transcription units and 136 putative antisense and intergenic noncoding RNA (ncRNA) genes. Comparison of the abundance of protein-coding transcripts (cRNA) with and without overlapping antisense ncRNAs (asRNA) suggest that the presence of asRNA is associated with increased cRNA abundance (p<0.05). Using the SMRT Portal software (v1.3.2), 2687 potential DNA modification sites and two potential DNA modification motifs were predicted. The two motifs include a TATA box–like motif (CPGDMM1, “TATANNNATNA”), and an unknown motif (CPGDMM2 “WNYANTGAW”). Specifically, 35 of the 97 CPGDMM1 motifs (36.1%) and 91 of the 369 CPGDMM2 motifs (24.7%) were found to be significantly modified (p<0.01). Analysis of genes downstream of the CPGDMM1 motif revealed the significantly increased abundance of ncRNA genes that are less than 400 bp away from the significantly modified CPGDMM1motif (p<0.01). Taking together, the present study revealed a complex interplay among DNA modifications, ncRNA and cRNA expression in chloroplast genome. PMID:24914614

Complex interplay among DNA modification, noncoding RNA expression and protein-coding RNA expression in Salvia miltiorrhiza chloroplast genome.

PubMed

Chen, Haimei; Zhang, Jianhui; Yuan, George; Liu, Chang

2014-01-01

Salvia miltiorrhiza is one of the most widely used medicinal plants. As a first step to develop a chloroplast-based genetic engineering method for the over-production of active components from S. miltiorrhiza, we have analyzed the genome, transcriptome, and base modifications of the S. miltiorrhiza chloroplast. Total genomic DNA and RNA were extracted from fresh leaves and then subjected to strand-specific RNA-Seq and Single-Molecule Real-Time (SMRT) sequencing analyses. Mapping the RNA-Seq reads to the genome assembly allowed us to determine the relative expression levels of 80 protein-coding genes. In addition, we identified 19 polycistronic transcription units and 136 putative antisense and intergenic noncoding RNA (ncRNA) genes. Comparison of the abundance of protein-coding transcripts (cRNA) with and without overlapping antisense ncRNAs (asRNA) suggest that the presence of asRNA is associated with increased cRNA abundance (p<0.05). Using the SMRT Portal software (v1.3.2), 2687 potential DNA modification sites and two potential DNA modification motifs were predicted. The two motifs include a TATA box-like motif (CPGDMM1, "TATANNNATNA"), and an unknown motif (CPGDMM2 "WNYANTGAW"). Specifically, 35 of the 97 CPGDMM1 motifs (36.1%) and 91 of the 369 CPGDMM2 motifs (24.7%) were found to be significantly modified (p<0.01). Analysis of genes downstream of the CPGDMM1 motif revealed the significantly increased abundance of ncRNA genes that are less than 400 bp away from the significantly modified CPGDMM1motif (p<0.01). Taking together, the present study revealed a complex interplay among DNA modifications, ncRNA and cRNA expression in chloroplast genome.

The design of dual-mode complex signal processors based on quadratic modular number codes

NASA Astrophysics Data System (ADS)

Jenkins, W. K.; Krogmeier, J. V.

1987-04-01

It has been known for a long time that quadratic modular number codes admit an unusual representation of complex numbers which leads to complete decoupling of the real and imaginary channels, thereby simplifying complex multiplication and providing error isolation between the real and imaginary channels. This paper first presents a tutorial review of the theory behind the different types of complex modular rings (fields) that result from particular parameter selections, and then presents a theory for a 'dual-mode' complex signal processor based on the choice of augmented power-of-2 moduli. It is shown how a diminished-1 binary code, used by previous designers for the realization of Fermat number transforms, also leads to efficient realizations for dual-mode complex arithmetic for certain augmented power-of-2 moduli. Then a design is presented for a recursive complex filter based on a ROM/ACCUMULATOR architecture and realized in an augmented power-of-2 quadratic code, and a computer-generated example of a complex recursive filter is shown to illustrate the principles of the theory.

MPEG-compliant joint source/channel coding using discrete cosine transform and substream scheduling for visual communication over packet networks

NASA Astrophysics Data System (ADS)

Kim, Seong-Whan; Suthaharan, Shan; Lee, Heung-Kyu; Rao, K. R.

2001-01-01

Quality of Service (QoS)-guarantee in real-time communication for multimedia applications is significantly important. An architectural framework for multimedia networks based on substreams or flows is effectively exploited for combining source and channel coding for multimedia data. But the existing frame by frame approach which includes Moving Pictures Expert Group (MPEG) cannot be neglected because it is a standard. In this paper, first, we designed an MPEG transcoder which converts an MPEG coded stream into variable rate packet sequences to be used for our joint source/channel coding (JSCC) scheme. Second, we designed a classification scheme to partition the packet stream into multiple substreams which have their own QoS requirements. Finally, we designed a management (reservation and scheduling) scheme for substreams to support better perceptual video quality such as the bound of end-to-end jitter. We have shown that our JSCC scheme is better than two other two popular techniques by simulation and real video experiments on the TCP/IP environment.

Lifting scheme-based method for joint coding 3D stereo digital cinema with luminace correction and optimized prediction

NASA Astrophysics Data System (ADS)

Darazi, R.; Gouze, A.; Macq, B.

2009-01-01

Reproducing a natural and real scene as we see in the real world everyday is becoming more and more popular. Stereoscopic and multi-view techniques are used for this end. However due to the fact that more information are displayed requires supporting technologies such as digital compression to ensure the storage and transmission of the sequences. In this paper, a new scheme for stereo image coding is proposed. The original left and right images are jointly coded. The main idea is to optimally exploit the existing correlation between the two images. This is done by the design of an efficient transform that reduces the existing redundancy in the stereo image pair. This approach was inspired by Lifting Scheme (LS). The novelty in our work is that the prediction step is been replaced by an hybrid step that consists in disparity compensation followed by luminance correction and an optimized prediction step. The proposed scheme can be used for lossless and for lossy coding. Experimental results show improvement in terms of performance and complexity compared to recently proposed methods.

Increased apomixis expression concurrent with genetic and epigenetic variation in a newly synthesized Eragrostis curvula polyploid

NASA Astrophysics Data System (ADS)

Zappacosta, Diego C.; Ochogavía, Ana C.; Rodrigo, Juan M.; Romero, José R.; Meier, Mauro S.; Garbus, Ingrid; Pessino, Silvina C.; Echenique, Viviana C.

2014-04-01

Eragrostis curvula includes biotypes reproducing through obligate and facultative apomixis or, rarely, full sexuality. We previously generated a ``tetraploid-dihaploid-tetraploid'' series of plants consisting of a tetraploid apomictic plant (T), a sexual dihaploid plant (D) and a tetraploid artificial colchiploid (C). Initially, plant C was nearly 100% sexual. However, its capacity to form non-reduced embryo sacs dramatically increased over a four year period (2003-2007) to reach levels of 85-90%. Here, we confirmed high rates of apomixis in plant C, and used AFLPs and MSAPs to characterize the genetic and epigenetic variation observed in this plant in 2007 as compared to 2003. Of the polymorphic sequences, some had no coding potential whereas others were homologous to retrotransposons and/or protein-coding-like sequences. Our results suggest that in this particular plant system increased apomixis expression is concurrent with genetic and epigenetic modifications, possibly involving transposable elements.

Inverting the parameters of an earthquake-ruptured fault with a genetic algorithm

NASA Astrophysics Data System (ADS)

Yu, Ting-To; Fernàndez, Josè; Rundle, John B.

1998-03-01

Natural selection is the spirit of the genetic algorithm (GA): by keeping the good genes in the current generation, thereby producing better offspring during evolution. The crossover function ensures the heritage of good genes from parent to offspring. Meanwhile, the process of mutation creates a special gene, the character of which does not exist in the parent generation. A program based on genetic algorithms using C language is constructed to invert the parameters of an earthquake-ruptured fault. The verification and application of this code is shown to demonstrate its capabilities. It is determined that this code is able to find the global extreme and can be used to solve more practical problems with constraints gathered from other sources. It is shown that GA is superior to other inverting schema in many aspects. This easy handling and yet powerful algorithm should have many suitable applications in the field of geosciences.

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity.

PubMed

Ishikawa, Sohta A; Inagaki, Yuji; Hashimoto, Tetsuo

2012-01-01

In phylogenetic analyses of nucleotide sequences, 'homogeneous' substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, 'RY-coding' and 'non-homogeneous' models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.

Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

PubMed

Peng, Cheng; Wang, Pengfei; Xu, Xiaoli; Wang, Xiaofu; Wei, Wei; Chen, Xiaoyun; Xu, Junfeng

2016-01-01

As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

Parallelization of Lower-Upper Symmetric Gauss-Seidel Method for Chemically Reacting Flow

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Jost, Gabriele; Chang, Sherry

2005-01-01

Development of technologies for exploration of the solar system has revived an interest in computational simulation of chemically reacting flows since planetary probe vehicles exhibit non-equilibrium phenomena during the atmospheric entry of a planet or a moon as well as the reentry to the Earth. Stability in combustion is essential for new propulsion systems. Numerical solution of real-gas flows often increases computational work by an order-of-magnitude compared to perfect gas flow partly because of the increased complexity of equations to solve. Recently, as part of Project Columbia, NASA has integrated a cluster of interconnected SGI Altix systems to provide a ten-fold increase in current supercomputing capacity that includes an SGI Origin system. Both the new and existing machines are based on cache coherent non-uniform memory access architecture. Lower-Upper Symmetric Gauss-Seidel (LU-SGS) relaxation method has been implemented into both perfect and real gas flow codes including Real-Gas Aerodynamic Simulator (RGAS). However, the vectorized RGAS code runs inefficiently on cache-based shared-memory machines such as SGI system. Parallelization of a Gauss-Seidel method is nontrivial due to its sequential nature. The LU-SGS method has been vectorized on an oblique plane in INS3D-LU code that has been one of the base codes for NAS Parallel benchmarks. The oblique plane has been called a hyperplane by computer scientists. It is straightforward to parallelize a Gauss-Seidel method by partitioning the hyperplanes once they are formed. Another way of parallelization is to schedule processors like a pipeline using software. Both hyperplane and pipeline methods have been implemented using openMP directives. The present paper reports the performance of the parallelized RGAS code on SGI Origin and Altix systems.

Efficient computation of kinship and identity coefficients on large pedigrees.

PubMed

Cheng, En; Elliott, Brendan; Ozsoyoglu, Z Meral

2009-06-01

With the rapidly expanding field of medical genetics and genetic counseling, genealogy information is becoming increasingly abundant. An important computation on pedigree data is the calculation of identity coefficients, which provide a complete description of the degree of relatedness of a pair of individuals. The areas of application of identity coefficients are numerous and diverse, from genetic counseling to disease tracking, and thus, the computation of identity coefficients merits special attention. However, the computation of identity coefficients is not done directly, but rather as the final step after computing a set of generalized kinship coefficients. In this paper, we first propose a novel Path-Counting Formula for calculating generalized kinship coefficients, which is motivated by Wright's path-counting method for computing inbreeding coefficient. We then present an efficient and scalable scheme for calculating generalized kinship coefficients on large pedigrees using NodeCodes, a special encoding scheme for expediting the evaluation of queries on pedigree graph structures. Furthermore, we propose an improved scheme using Family NodeCodes for the computation of generalized kinship coefficients, which is motivated by the significant improvement of using Family NodeCodes for inbreeding coefficient over the use of NodeCodes. We also perform experiments for evaluating the efficiency of our method, and compare it with the performance of the traditional recursive algorithm for three individuals. Experimental results demonstrate that the resulting scheme is more scalable and efficient than the traditional recursive methods for computing generalized kinship coefficients.

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

PubMed Central

Carlile, Thomas M.; Rojas-Duran, Maria F.; Zinshteyn, Boris; Shin, Hakyung; Bartoli, Kristen M.; Gilbert, Wendy V.

2014-01-01

Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs1, enhances the function of transfer RNA and ribosomal RNA by stabilizing RNA structure2–8. mRNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function – it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding center9,10. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological was unclear. Here we present a comprehensive analysis of pseudouridylation in yeast and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as 100 novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1–4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease11–13. PMID:25192136

Neuroscience and behavioral genetics in US criminal law: an empirical analysis

PubMed Central

Farahany, Nita A.

2016-01-01

The goal of this study was to examine the growing use of neurological and behavioral genetic evidence by criminal defendants in US criminal law. Judicial opinions issued between 2005–12 that discussed the use of neuroscience or behavioral genetics by criminal defendants were identified, coded and analysed. Criminal defendants are increasingly introducing such evidence to challenge defendants’ competency, the effectiveness of defense counsel at trial, and to mitigate punishment. PMID:27774210

Low-level processing for real-time image analysis

NASA Technical Reports Server (NTRS)

Eskenazi, R.; Wilf, J. M.

1979-01-01

A system that detects object outlines in television images in real time is described. A high-speed pipeline processor transforms the raw image into an edge map and a microprocessor, which is integrated into the system, clusters the edges, and represents them as chain codes. Image statistics, useful for higher level tasks such as pattern recognition, are computed by the microprocessor. Peak intensity and peak gradient values are extracted within a programmable window and are used for iris and focus control. The algorithms implemented in hardware and the pipeline processor architecture are described. The strategy for partitioning functions in the pipeline was chosen to make the implementation modular. The microprocessor interface allows flexible and adaptive control of the feature extraction process. The software algorithms for clustering edge segments, creating chain codes, and computing image statistics are also discussed. A strategy for real time image analysis that uses this system is given.

Vectors a Fortran 90 module for 3-dimensional vector and dyadic arithmetic

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

Brock, B.C.

1998-02-01

A major advance contained in the new Fortran 90 language standard is the ability to define new data types and the operators associated with them. Writing computer code to implement computations with real and complex three-dimensional vectors and dyadics is greatly simplified if the equations can be implemented directly, without the need to code the vector arithmetic explicitly. The Fortran 90 module described here defines new data types for real and complex 3-dimensional vectors and dyadics, along with the common operations needed to work with these objects. Routines to allow convenient initialization and output of the new types are alsomore » included. In keeping with the philosophy of data abstraction, the details of the implementation of the data types are maintained private, and the functions and operators are made generic to simplify the combining of real, complex, single- and double-precision vectors and dyadics.« less

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants

PubMed Central

Khan, Abdur Rahim; Park, Gun-Seok; Asaf, Sajjad; Hong, Sung-Jun; Jung, Byung Kwon

2017-01-01

Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants. PMID:28187139

Creation of the Naturalistic Engagement in Secondary Tasks (NEST) distracted driving dataset.

PubMed

Owens, Justin M; Angell, Linda; Hankey, Jonathan M; Foley, James; Ebe, Kazutoshi

2015-09-01

Distracted driving has become a topic of critical importance to driving safety research over the past several decades. Naturalistic driving data offer a unique opportunity to study how drivers engage with secondary tasks in real-world driving; however, the complexities involved with identifying and coding relevant epochs of naturalistic data have limited its accessibility to the general research community. This project was developed to help address this problem by creating an accessible dataset of driver behavior and situational factors observed during distraction-related safety-critical events and baseline driving epochs, using the Strategic Highway Research Program 2 (SHRP2) naturalistic dataset. The new NEST (Naturalistic Engagement in Secondary Tasks) dataset was created using crashes and near-crashes from the SHRP2 dataset that were identified as including secondary task engagement as a potential contributing factor. Data coding included frame-by-frame video analysis of secondary task and hands-on-wheel activity, as well as summary event information. In addition, information about each secondary task engagement within the trip prior to the crash/near-crash was coded at a higher level. Data were also coded for four baseline epochs and trips per safety-critical event. 1,180 events and baseline epochs were coded, and a dataset was constructed. The project team is currently working to determine the most useful way to allow broad public access to the dataset. We anticipate that the NEST dataset will be extraordinarily useful in allowing qualified researchers access to timely, real-world data concerning how drivers interact with secondary tasks during safety-critical events and baseline driving. The coded dataset developed for this project will allow future researchers to have access to detailed data on driver secondary task engagement in the real world. It will be useful for standalone research, as well as for integration with additional SHRP2 data to enable the conduct of more complex research. Copyright © 2015 Elsevier Ltd and National Safety Council. All rights reserved.

Selecting the Perfect Baby: The Ethics of Embryo Design.

ERIC Educational Resources Information Center

Omarzu, Julia

2002-01-01

Presents the real life story of Molly, who was born with a rare genetic disorder, and her parents' hope to cure her by having another child with specific genetic markers and using his/her stem cells to cure Molly. Addresses the ethical issues of genetic manipulation and fertility treatment. Includes teaching notes and classroom management…

Food Control and a Citizen Science Approach for Improving Teaching of Genetics in Universities

ERIC Educational Resources Information Center

Borrell, Y. J.; Muñoz-Colmenero, A. M.; Dopico, E.; Miralles, L.; Garcia-Vazquez, E.

2016-01-01

A Citizen Science approach was implemented in the laboratory practices of Genetics at the University of Oviedo, related with the engaging topic of Food Control. Real samples of food products consumed by students at home ("students as samplers") were employed as teaching material in three different courses of Genetics during the academic…

Fleet DNA Brings Fleet Data to Life, Informs R&D | News | NREL

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over 11.5 million miles of real-world data from more than 1,700 medium- and heavy-duty vehicles -cycle summaries and visualizations similar to real-world genetics, helping users understand the broad real-world data is a national resource that enables insight critical to the successful development of

Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains.

PubMed

Argemi, Xavier; Nanoukon, Chimène; Affolabi, Dissou; Keller, Daniel; Hansmann, Yves; Riegel, Philippe; Baba-Moussa, Lamine; Prévost, Gilles

2018-02-25

Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus ; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8-89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes ( hsrA and dfrG , respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus . Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis .

Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains

PubMed Central

Nanoukon, Chimène; Affolabi, Dissou; Keller, Daniel; Hansmann, Yves; Riegel, Philippe; Baba-Moussa, Lamine; Prévost, Gilles

2018-01-01

Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8–89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis. PMID:29495323

A Cytogenetic Abnormality and Rare Coding Variants Identify ABCA13 as a Candidate Gene in Schizophrenia, Bipolar Disorder, and Depression

PubMed Central

Knight, Helen M.; Pickard, Benjamin S.; Maclean, Alan; Malloy, Mary P.; Soares, Dinesh C.; McRae, Allan F.; Condie, Alison; White, Angela; Hawkins, William; McGhee, Kevin; van Beck, Margaret; MacIntyre, Donald J.; Starr, John M.; Deary, Ian J.; Visscher, Peter M.; Porteous, David J.; Cannon, Ronald E.; St Clair, David; Muir, Walter J.; Blackwood, Douglas H.R.

2009-01-01

Schizophrenia and bipolar disorder are leading causes of morbidity across all populations, with heritability estimates of ∼80% indicating a substantial genetic component. Population genetics and genome-wide association studies suggest an overlap of genetic risk factors between these illnesses but it is unclear how this genetic component is divided between common gene polymorphisms, rare genomic copy number variants, and rare gene sequence mutations. We report evidence that the lipid transporter gene ABCA13 is a susceptibility factor for both schizophrenia and bipolar disorder. After the initial discovery of its disruption by a chromosome abnormality in a person with schizophrenia, we resequenced ABCA13 exons in 100 cases with schizophrenia and 100 controls. Multiple rare coding variants were identified including one nonsense and nine missense mutations and compound heterozygosity/homozygosity in six cases. Variants were genotyped in additional schizophrenia, bipolar, depression (n > 1600), and control (n > 950) cohorts and the frequency of all rare variants combined was greater than controls in schizophrenia (OR = 1.93, p = 0.0057) and bipolar disorder (OR = 2.71, p = 0.00007). The population attributable risk of these mutations was 2.2% for schizophrenia and 4.0% for bipolar disorder. In a study of 21 families of mutation carriers, we genotyped affected and unaffected relatives and found significant linkage (LOD = 4.3) of rare variants with a phenotype including schizophrenia, bipolar disorder, and major depression. These data identify a candidate gene, highlight the genetic overlap between schizophrenia, bipolar disorder, and depression, and suggest that rare coding variants may contribute significantly to risk of these disorders. PMID:19944402

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

PubMed

Mascarenhas, Roshan; Pietrzak, Maciej; Smith, Ryan M; Webb, Amy; Wang, Danxin; Papp, Audrey C; Pinsonneault, Julia K; Seweryn, Michal; Rempala, Grzegorz; Sadee, Wolfgang

2015-01-01

mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids.

PubMed

José, Marco V; Morgado, Eberto R; Guimarães, Romeu Cardoso; Zamudio, Gabriel S; de Farías, Sávio Torres; Bobadilla, Juan R; Sosa, Daniela

2014-08-11

Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state.

7 CFR 457.112 - Hybrid sorghum seed crop insurance provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... produced by crossing a male and female parent plant, each having a different genetic character. This... formula for establishing the value must be based on data provided by a public third party that establishes..., number or code assigned to a specific genetic cross by the seed company or the Special Provisions for the...

Two Aspects of Meaningful Problem Solving in Science.

ERIC Educational Resources Information Center

Stewart, James

1982-01-01

Presents a model for solving genetics problems when problem statements include information on which alleles are dominant/recessive and on what forms of a trait are coded for by the alleles. Includes procedural steps employed in a solution and conceptual knowledge of genetics/meiosis allowing students to justify what they have done. (Author/JN)

DNA as information: at the crossroads between biology, mathematics, physics and chemistry

PubMed Central

2016-01-01

On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems—or parts of them—within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate. PMID:26857674

Biological Information Transfer Beyond the Genetic Code: The Sugar Code

NASA Astrophysics Data System (ADS)

Gabius, H.-J.

In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i.e., contributions of bidentate or cooperative hydrogen bonds, dispersion forces, stacking, and solvent rearrangement, will enable the design of high-affinity ligands or mimetics thereof. They embody clinical applications reaching from receptor localization in diagnostic pathology to cell type-selective targeting of drugs and inhibition of undesired cell adhesion in bacterial/viral infections, inflammation, or metastasis.

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture

PubMed Central

Zheng, Hou-Feng; Forgetta, Vincenzo; Hsu, Yi-Hsiang; Estrada, Karol; Rosello-Diez, Alberto; Leo, Paul J; Dahia, Chitra L; Park-Min, Kyung Hyun; Tobias, Jonathan H; Kooperberg, Charles; Kleinman, Aaron; Styrkarsdottir, Unnur; Liu, Ching-Ti; Uggla, Charlotta; Evans, Daniel S; Nielson, Carrie M; Walter, Klaudia; Pettersson-Kymmer, Ulrika; McCarthy, Shane; Eriksson, Joel; Kwan, Tony; Jhamai, Mila; Trajanoska, Katerina; Memari, Yasin; Min, Josine; Huang, Jie; Danecek, Petr; Wilmot, Beth; Li, Rui; Chou, Wen-Chi; Mokry, Lauren E; Moayyeri, Alireza; Claussnitzer, Melina; Cheng, Chia-Ho; Cheung, Warren; Medina-Gómez, Carolina; Ge, Bing; Chen, Shu-Huang; Choi, Kwangbom; Oei, Ling; Fraser, James; Kraaij, Robert; Hibbs, Matthew A; Gregson, Celia L; Paquette, Denis; Hofman, Albert; Wibom, Carl; Tranah, Gregory J; Marshall, Mhairi; Gardiner, Brooke B; Cremin, Katie; Auer, Paul; Hsu, Li; Ring, Sue; Tung, Joyce Y; Thorleifsson, Gudmar; Enneman, Anke W; van Schoor, Natasja M; de Groot, Lisette C.P.G.M.; van der Velde, Nathalie; Melin, Beatrice; Kemp, John P; Christiansen, Claus; Sayers, Adrian; Zhou, Yanhua; Calderari, Sophie; van Rooij, Jeroen; Carlson, Chris; Peters, Ulrike; Berlivet, Soizik; Dostie, Josée; Uitterlinden, Andre G; Williams, Stephen R.; Farber, Charles; Grinberg, Daniel; LaCroix, Andrea Z; Haessler, Jeff; Chasman, Daniel I; Giulianini, Franco; Rose, Lynda M; Ridker, Paul M; Eisman, John A; Nguyen, Tuan V; Center, Jacqueline R; Nogues, Xavier; Garcia-Giralt, Natalia; Launer, Lenore L; Gudnason, Vilmunder; Mellström, Dan; Vandenput, Liesbeth; Karlsson, Magnus K; Ljunggren, Östen; Svensson, Olle; Hallmans, Göran; Rousseau, François; Giroux, Sylvie; Bussière, Johanne; Arp, Pascal P; Koromani, Fjorda; Prince, Richard L; Lewis, Joshua R; Langdahl, Bente L; Hermann, A Pernille; Jensen, Jens-Erik B; Kaptoge, Stephen; Khaw, Kay-Tee; Reeve, Jonathan; Formosa, Melissa M; Xuereb-Anastasi, Angela; Åkesson, Kristina; McGuigan, Fiona E; Garg, Gaurav; Olmos, Jose M; Zarrabeitia, Maria T; Riancho, Jose A; Ralston, Stuart H; Alonso, Nerea; Jiang, Xi; Goltzman, David; Pastinen, Tomi; Grundberg, Elin; Gauguier, Dominique; Orwoll, Eric S; Karasik, David; Davey-Smith, George; Smith, Albert V; Siggeirsdottir, Kristin; Harris, Tamara B; Zillikens, M Carola; van Meurs, Joyce BJ; Thorsteinsdottir, Unnur; Maurano, Matthew T; Timpson, Nicholas J; Soranzo, Nicole; Durbin, Richard; Wilson, Scott G; Ntzani, Evangelia E; Brown, Matthew A; Stefansson, Kari; Hinds, David A; Spector, Tim; Cupples, L Adrienne; Ohlsson, Claes; Greenwood, Celia MT; Jackson, Rebecca D; Rowe, David W; Loomis, Cynthia A; Evans, David M; Ackert-Bicknell, Cheryl L; Joyner, Alexandra L; Duncan, Emma L; Kiel, Douglas P; Rivadeneira, Fernando; Richards, J Brent

2016-01-01

SUMMARY The extent to which low-frequency (minor allele frequency [MAF] between 1–5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is largely unknown. Bone mineral density (BMD) is highly heritable, is a major predictor of osteoporotic fractures and has been previously associated with common genetic variants1–8, and rare, population-specific, coding variants9. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n=2,882 from UK10K), whole-exome sequencing (n= 3,549), deep imputation of genotyped samples using a combined UK10K/1000Genomes reference panel (n=26,534), and de-novo replication genotyping (n= 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size 4-fold larger than the mean of previously reported common variants for lumbar spine BMD8 (rs11692564[T], MAF = 1.7%, replication effect size = +0.20 standard deviations [SD], Pmeta = 2×10−14), which was also associated with a decreased risk of fracture (OR = 0.85; P = 2×10−11; ncases = 98,742 and ncontrols = 409,511). Using an En1Cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, likely as a consequence of high bone turn-over. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817[T], MAF = 1.1%, replication effect size = +0.39 SD, Pmeta = 1×10−11). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population. PMID:26367794

Categorical data processing for real estate objects valuation using statistical analysis

NASA Astrophysics Data System (ADS)

Parygin, D. S.; Malikov, V. P.; Golubev, A. V.; Sadovnikova, N. P.; Petrova, T. M.; Finogeev, A. G.

2018-05-01

Theoretical and practical approaches to the use of statistical methods for studying various properties of infrastructure objects are analyzed in the paper. Methods of forecasting the value of objects are considered. A method for coding categorical variables describing properties of real estate objects is proposed. The analysis of the results of modeling the price of real estate objects using regression analysis and an algorithm based on a comparative approach is carried out.

Real Time Data System (RTDS)

NASA Technical Reports Server (NTRS)

Muratore, John F.

1991-01-01

Lessons learned from operational real time expert systems are examined. The basic system architecture is discussed. An expert system is any software that performs tasks to a standard that would normally require a human expert. An expert system implies knowledge contained in data rather than code. And an expert system implies the use of heuristics as well as algorithms. The 15 top lessons learned by the operation of a real time data system are presented.

Most Used Codons per Amino Acid and per Genome in the Code of Man Compared to Other Organisms According to the Rotating Circular Genetic Code

PubMed Central

Castro-Chavez, Fernando

2011-01-01

My previous theoretical research shows that the rotating circular genetic code is a viable tool to make easier to distinguish the rules of variation applied to the amino acid exchange; it presents a precise and positional bio-mathematical balance of codons, according to the amino acids they codify. Here, I demonstrate that when using the conventional or classic circular genetic code, a clearer pattern for the human codon usage per amino acid and per genome emerges. The most used human codons per amino acid were the ones ending with the three hydrogen bond nucleotides: C for 12 amino acids and G for the remaining 8, plus one codon for arginine ending in A that was used approximately with the same frequency than the one ending in G for this same amino acid (plus *). The most used codons in man fall almost all the time at the rightmost position, clockwise, ending either in C or in G within the circular genetic code. The human codon usage per genome is compared to other organisms such as fruit flies (Drosophila melanogaster), squid (Loligo pealei), and many others. The biosemiotic codon usage of each genomic population or ‘Theme’ is equated to a ‘molecular language’. The C/U choice or difference, and the G/A difference in the third nucleotide of the most used codons per amino acid are illustrated by comparing the most used codons per genome in humans and squids. The human distribution in the third position of most used codons is a 12-8-2, C-G-A, nucleotide ending signature, while the squid distribution in the third position of most used codons was an odd, or uneven, distribution in the third position of its most used codons: 13-6-3, U-A-G, as its nucleotide ending signature. These findings may help to design computational tools to compare human genomes, to determine the exchangeability between compatible codons and amino acids, and for the early detection of incompatible changes leading to hereditary diseases. PMID:22997484

Software and Hardware Description of the Helicopter Motion Equations for VAX Computers

DTIC Science & Technology

1989-08-01

17. COSATI CODES 18 SUBJECT TERMS (Continue on reverse if r:".essary and identify by block number) FIELD GROUP SUB-GROUP human engineering flight eq...global section’s name is HACSEC. d. The name of the disk file opened to map the pages is HACSEC.DAT. VAX FORTRAN common statements are used in all...MOZ(1O) INTEGER*2 ATYPE(10) INTECER*2 AGAT( 10) INTEGER*2 AGRQUP(10) REAL*4 MOUC 10) REAL*4 MOHEAD(10) REAL*4 MOPHI(10) REAL*4 MOTHET(10) GOMMO4N

Surveying multidisciplinary aspects in real-time distributed coding for Wireless Sensor Networks.

PubMed

Braccini, Carlo; Davoli, Franco; Marchese, Mario; Mongelli, Maurizio

2015-01-27

Wireless Sensor Networks (WSNs), where a multiplicity of sensors observe a physical phenomenon and transmit their measurements to one or more sinks, pertain to the class of multi-terminal source and channel coding problems of Information Theory. In this category, "real-time" coding is often encountered for WSNs, referring to the problem of finding the minimum distortion (according to a given measure), under transmission power constraints, attainable by encoding and decoding functions, with stringent limits on delay and complexity. On the other hand, the Decision Theory approach seeks to determine the optimal coding/decoding strategies or some of their structural properties. Since encoder(s) and decoder(s) possess different information, though sharing a common goal, the setting here is that of Team Decision Theory. A more pragmatic vision rooted in Signal Processing consists of fixing the form of the coding strategies (e.g., to linear functions) and, consequently, finding the corresponding optimal decoding strategies and the achievable distortion, generally by applying parametric optimization techniques. All approaches have a long history of past investigations and recent results. The goal of the present paper is to provide the taxonomy of the various formulations, a survey of the vast related literature, examples from the authors' own research, and some highlights on the inter-play of the different theories.

EO/IR scene generation open source initiative for real-time hardware-in-the-loop and all-digital simulation

NASA Astrophysics Data System (ADS)

Morris, Joseph W.; Lowry, Mac; Boren, Brett; Towers, James B.; Trimble, Darian E.; Bunfield, Dennis H.

2011-06-01

The US Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) and the Redstone Test Center (RTC) has formed the Scene Generation Development Center (SGDC) to support the Department of Defense (DoD) open source EO/IR Scene Generation initiative for real-time hardware-in-the-loop and all-digital simulation. Various branches of the DoD have invested significant resources in the development of advanced scene and target signature generation codes. The SGDC goal is to maintain unlimited government rights and controlled access to government open source scene generation and signature codes. In addition, the SGDC provides development support to a multi-service community of test and evaluation (T&E) users, developers, and integrators in a collaborative environment. The SGDC has leveraged the DoD Defense Information Systems Agency (DISA) ProjectForge (https://Project.Forge.mil) which provides a collaborative development and distribution environment for the DoD community. The SGDC will develop and maintain several codes for tactical and strategic simulation, such as the Joint Signature Image Generator (JSIG), the Multi-spectral Advanced Volumetric Real-time Imaging Compositor (MAVRIC), and Office of the Secretary of Defense (OSD) Test and Evaluation Science and Technology (T&E/S&T) thermal modeling and atmospherics packages, such as EOView, CHARM, and STAR. Other utility packages included are the ContinuumCore for real-time messaging and data management and IGStudio for run-time visualization and scenario generation.

Computerized Systems for Collecting Real-Time Observational Data.

ERIC Educational Resources Information Center

Kahng, SungWoo; Iwata, Brian

1998-01-01

A survey of 15 developers of computerized real-time observation systems found many systems have incorporated laptop or handheld computers as well as bar-code scanners. Most systems used IBM-compatible software, and ranged from free to complete systems costing more than $1,500. Data analysis programs were included with most programs. (Author/CR)

14 CFR 1214.403 - Code of Conduct for the International Space Station Crew.

Code of Federal Regulations, 2010 CFR

2010-01-01

... responsible for directing the mission. A Flight Director will be in charge of directing real-time ISS... advance of the mission and are designed to minimize the amount of real-time discussion required during... and impose disciplinary measures. (4) “ETOV” means Earth-to-Orbit Vehicle travelling between Earth and...

How to establish, maintain and use timber depletion accounts

Treesearch

William C. Siegel

2001-01-01

Section 1221 of the Internal Revenue Code defines capital expenditures. In general, these are amounts spent to acquire real estate or equipment, or to make improvements that increase the value of real estate or equipment already owned. Forestry examples include land, buildings, standing timber, reforestation costs, and tractors and trucks. Property owners who incur...

Fast interrupt platform for extended DOS

NASA Technical Reports Server (NTRS)

Duryea, T. W.

1995-01-01

Extended DOS offers the unique combination of a simple operating system which allows direct access to the interrupt tables, 32 bit protected mode access to 4096 MByte address space, and the use of industry standard C compilers. The drawback is that fast interrupt handling requires both 32 bit and 16 bit versions of each real-time process interrupt handler to avoid mode switches on the interrupts. A set of tools has been developed which automates the process of transforming the output of a standard 32 bit C compiler to 16 bit interrupt code which directly handles the real mode interrupts. The entire process compiles one set of source code via a make file, which boosts productivity by making the management of the compile-link cycle very simple. The software components are in the form of classes written mostly in C. A foreground process written as a conventional application which can use the standard C libraries can communicate with the background real-time classes via a message passing mechanism. The platform thus enables the integration of high performance real-time processing into a conventional application framework.

The analysis of a nonsimilar laminar boundary layer

NASA Technical Reports Server (NTRS)

Stalmach, D. D.; Bertin, J. J.

1978-01-01

A computer code is described which yields accurate solutions for a broad range of laminar, nonsimilar boundary layers, providing the inviscid flow field is known. The boundary layer may be subject to mass injection for perfect-gas, nonreacting flows. If no mass injection is present, the code can be used with either perfect-gas or real-gas thermodynamic models. Solutions, ranging from two-dimensional similarity solutions to solutions for the boundary layer on the Space Shuttle Orbiter during reentry conditions, have been obtained with the code. Comparisons of these solutions, and others, with solutions presented in the literature; and with solutions obtained from other codes, demonstrate the accuracy of the present code.

Analysis of a two-dimensional type 6 shock-interference pattern using a perfect-gas code and a real-gas code

NASA Technical Reports Server (NTRS)

Bertin, J. J.; Graumann, B. W.

1973-01-01

Numerical codes were developed to calculate the two dimensional flow field which results when supersonic flow encounters double wedge configurations whose angles are such that a type 4 pattern occurs. The flow field model included the shock interaction phenomena for a delta wing orbiter. Two numerical codes were developed, one which used the perfect gas relations and a second which incorporated a Mollier table to define equilibrium air properties. The two codes were used to generate theoretical surface pressure and heat transfer distributions for velocities from 3,821 feet per second to an entry condition of 25,000 feet per second.

A real-time chirp-coded imaging system with tissue attenuation compensation.

PubMed

Ramalli, A; Guidi, F; Boni, E; Tortoli, P

2015-07-01

In ultrasound imaging, pulse compression methods based on the transmission (TX) of long coded pulses and matched receive filtering can be used to improve the penetration depth while preserving the axial resolution (coded-imaging). The performance of most of these methods is affected by the frequency dependent attenuation of tissue, which causes mismatch of the receiver filter. This, together with the involved additional computational load, has probably so far limited the implementation of pulse compression methods in real-time imaging systems. In this paper, a real-time low-computational-cost coded-imaging system operating on the beamformed and demodulated data received by a linear array probe is presented. The system has been implemented by extending the firmware and the software of the ULA-OP research platform. In particular, pulse compression is performed by exploiting the computational resources of a single digital signal processor. Each image line is produced in less than 20 μs, so that, e.g., 192-line frames can be generated at up to 200 fps. Although the system may work with a large class of codes, this paper has been focused on the test of linear frequency modulated chirps. The new system has been used to experimentally investigate the effects of tissue attenuation so that the design of the receive compression filter can be accordingly guided. Tests made with different chirp signals confirm that, although the attainable compression gain in attenuating media is lower than the theoretical value expected for a given TX Time-Bandwidth product (BT), good SNR gains can be obtained. For example, by using a chirp signal having BT=19, a 13 dB compression gain has been measured. By adapting the frequency band of the receiver to the band of the received echo, the signal-to-noise ratio and the penetration depth have been further increased, as shown by real-time tests conducted on phantoms and in vivo. In particular, a 2.7 dB SNR increase has been measured through a novel attenuation compensation scheme, which only requires to shift the demodulation frequency by 1 MHz. The proposed method characterizes for its simplicity and easy implementation. Copyright © 2015 Elsevier B.V. All rights reserved.

The minimal autopoietic unit.

PubMed

Luisi, Pier Luigi

2014-12-01

It is argued that closed, cell-like compartments, may have existed in prebiotic time, showing a simplified metabolism which was bringing about a primitive form of stationary state- a kind of homeostasis. The autopoietic primitive cell can be taken as an example and there are preliminary experimental data supporting the possible existence of this primitive form of cell activity. The genetic code permits, among other things, the continuous self-reproduction of proteins; enzymic proteins permit the synthesis of nucleic acids, and in this way there is a perfect recycling between the two most important classes of biopolymers in our life. On the other hand, the genetic code is a complex machinery, which cannot be posed at the very early time of the origin of life. And the question then arises, whether some form of alternative beginning, prior to the genetic code, would have been possible: and this is the core of the question asked. Is something with the flavor of early life conceivable, prior to the genetic code? My answer is positive, although I am too well aware that the term "conceivable" does not mean that this something is easily to be performed experimentally. To illustrate my answer, I would first go back to the operational description of cellular life as given by the theory of autopoiesis. Accordingly, a living cell is an open system capable of self-maintenance, due to a process of internal self-regeneration of the components, all within a boundary which is itself product from within. This is a universal code, valid not only for a cell, but for any living macroscopic entity, as no living system exists on Earth which does not obey this principle. In this definition (or better operational description) there is no mention of DNA or genetic code. I added in that definition the term "open system"-which is not present in the primary literature (Varela, et al., 1974) to make clear that every living system is indeed an open system-without this addition, it may seem that with autopoiesis we are dealing with a perpetuum mobile, against the second principle of thermodynamics. Now consider the following figure (Fig. 1). It represents in a very schematic form a cell, as an open system, with a semipermeable membrane constituted by the chemical S, which permits the entrance of the nutrient A and the elimination of the decay product P. A is transformed inside the cell into S by a chemical reaction characterized by kgen, and S can be transformed into P by the reaction kdec. The two reactions actually may represent two entire families of reaction, in the sense that one can envisage several A and several S and several P.

Progressive fracture of fiber composites

NASA Technical Reports Server (NTRS)

Irvin, T. B.; Ginty, C. A.

1983-01-01

Refined models and procedures are described for determining progressive composite fracture in graphite/epoxy angleplied laminates. Lewis Research Center capabilities are utilized including the Real Time Ultrasonic C Scan (RUSCAN) experimental facility and the Composite Durability Structural Analysis (CODSTRAN) computer code. The CODSTRAN computer code is used to predict the fracture progression based on composite mechanics, finite element stress analysis, and fracture criteria modules. The RUSCAN facility, CODSTRAN computer code, and scanning electron microscope are used to determine durability and identify failure mechanisms in graphite/epoxy composites.

High data rate coding for the space station telemetry links.

NASA Technical Reports Server (NTRS)

Lumb, D. R.; Viterbi, A. J.

1971-01-01

Coding systems for high data rates were examined from the standpoint of potential application in space-station telemetry links. Approaches considered included convolutional codes with sequential, Viterbi, and cascaded-Viterbi decoding. It was concluded that a high-speed (40 Mbps) sequential decoding system best satisfies the requirements for the assumed growth potential and specified constraints. Trade-off studies leading to this conclusion are viewed, and some sequential (Fano) algorithm improvements are discussed, together with real-time simulation results.

Report on corrections and future considerations for Appendices II–VIII of the International Code of Nomenclature for Algae, Fungi, and Plants

USDA-ARS?s Scientific Manuscript database

For the first time, the main text and Appendices II–VIII of the International Code of Nomenclature were separately published following decisions of the Melbourne Nomenclature Section, which contributed to subsequent development of an online resource capable of producing the Appendices in real time. ...

Engineering High Assurance Distributed Cyber Physical Systems

DTIC Science & Technology

2015-01-15

decisions: number of interacting agents and co-dependent decisions made in real-time without causing interference . To engineer a high assurance DART...environment specification, architecture definition, domain-specific languages, design patterns, code - generation, analysis, test-generation, and simulation...include synchronization between the models and source code , debugging at the model level, expression of the design intent, and quality of service

GenInfoGuard--a robust and distortion-free watermarking technique for genetic data.

PubMed

Iftikhar, Saman; Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

2015-01-01

Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique-GenInfoGuard-ensures its robustness through the "watermark encoding" in permuted values, and exhibits high decoding accuracy against various malicious attacks.

JSPAM: A restricted three-body code for simulating interacting galaxies

NASA Astrophysics Data System (ADS)

Wallin, J. F.; Holincheck, A. J.; Harvey, A.

2016-07-01

Restricted three-body codes have a proven ability to recreate much of the disturbed morphology of actual interacting galaxies. As more sophisticated n-body models were developed and computer speed increased, restricted three-body codes fell out of favor. However, their supporting role for performing wide searches of parameter space when fitting orbits to real systems demonstrates a continuing need for their use. Here we present the model and algorithm used in the JSPAM code. A precursor of this code was originally described in 1990, and was called SPAM. We have recently updated the software with an alternate potential and a treatment of dynamical friction to more closely mimic the results from n-body tree codes. The code is released publicly for use under the terms of the Academic Free License ("AFL") v. 3.0 and has been added to the Astrophysics Source Code Library.

Stochastic many-body problems in ecology, evolution, neuroscience, and systems biology

NASA Astrophysics Data System (ADS)

Butler, Thomas C.

Using the tools of many-body theory, I analyze problems in four different areas of biology dominated by strong fluctuations: The evolutionary history of the genetic code, spatiotemporal pattern formation in ecology, spatiotemporal pattern formation in neuroscience and the robustness of a model circadian rhythm circuit in systems biology. In the first two research chapters, I demonstrate that the genetic code is extremely optimal (in the sense that it manages the effects of point mutations or mistranslations efficiently), more than an order of magnitude beyond what was previously thought. I further show that the structure of the genetic code implies that early proteins were probably only loosely defined. Both the nature of early proteins and the extreme optimality of the genetic code are interpreted in light of recent theory [1] as evidence that the evolution of the genetic code was driven by evolutionary dynamics that were dominated by horizontal gene transfer. I then explore the optimality of a proposed precursor to the genetic code. The results show that the precursor code has only limited optimality, which is interpreted as evidence that the precursor emerged prior to translation, or else never existed. In the next part of the dissertation, I introduce a many-body formalism for reaction-diffusion systems described at the mesoscopic scale with master equations. I first apply this formalism to spatially-extended predator-prey ecosystems, resulting in the prediction that many-body correlations and fluctuations drive population cycles in time, called quasicycles. Most of these results were previously known, but were derived using the system size expansion [2, 3]. I next apply the analytical techniques developed in the study of quasi-cycles to a simple model of Turing patterns in a predator-prey ecosystem. This analysis shows that fluctuations drive the formation of a new kind of spatiotemporal pattern formation that I name "quasi-patterns." These quasi-patterns exist over a much larger range of physically accessible parameters than the patterns predicted in mean field theory and therefore account for the apparent observations in ecology of patterns in regimes where Turing patterns do not occur. I further show that quasi-patterns have statistical properties that allow them to be distinguished empirically from mean field Turing patterns. I next analyze a model of visual cortex in the brain that has striking similarities to the activator-inhibitor model of ecosystem quasi-pattern formation. Through analysis of the resulting phase diagram, I show that the architecture of the neural network in the visual cortex is configured to make the visual cortex robust to unwanted internally generated spatial structure that interferes with normal visual function. I also predict that some geometric visual hallucinations are quasi-patterns and that the visual cortex supports a new phase of spatially scale invariant behavior present far from criticality. In the final chapter, I explore the effects of fluctuations on cycles in systems biology, specifically the pervasive phenomenon of circadian rhythms. By exploring the behavior of a generic stochastic model of circadian rhythms, I show that the circadian rhythm circuit exploits leaky mRNA production to safeguard the cycle from failure. I also show that this safeguard mechanism is highly robust to changes in the rate of leaky mRNA production. Finally, I explore the failure of the deterministic model in two different contexts, one where the deterministic model predicts cycles where they do not exist, and another context in which cycles are not predicted by the deterministic model.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

PubMed

Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Kelley, Scott T

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .

A Molecular Genetic Lab to Generate Inclusive and Exclusive Forensic Evidence: Two Suspects, a Victim, and a Bloodstained T-Shirt

ERIC Educational Resources Information Center

Smit, Julie; Heath, Daniel D.; Walter, Ryan P.

2014-01-01

Molecular genetic laboratory exercises can be ineffective due the student's lack of connection to the complex and sequential protocols. In this inquiry-based molecular genetic laboratory exercise, we harness students' fascination with human forensics and provide a real-life scenario using biomolecular techniques to identify "whose…

Coding for parallel execution of hardware-in-the-loop millimeter-wave scene generation models on multicore SIMD processor architectures

NASA Astrophysics Data System (ADS)

Olson, Richard F.

2013-05-01

Rendering of point scatterer based radar scenes for millimeter wave (mmW) seeker tests in real-time hardware-in-the-loop (HWIL) scene generation requires efficient algorithms and vector-friendly computer architectures for complex signal synthesis. New processor technology from Intel implements an extended 256-bit vector SIMD instruction set (AVX, AVX2) in a multi-core CPU design providing peak execution rates of hundreds of GigaFLOPS (GFLOPS) on one chip. Real world mmW scene generation code can approach peak SIMD execution rates only after careful algorithm and source code design. An effective software design will maintain high computing intensity emphasizing register-to-register SIMD arithmetic operations over data movement between CPU caches or off-chip memories. Engineers at the U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) applied two basic parallel coding methods to assess new 256-bit SIMD multi-core architectures for mmW scene generation in HWIL. These include use of POSIX threads built on vector library functions and more portable, highlevel parallel code based on compiler technology (e.g. OpenMP pragmas and SIMD autovectorization). Since CPU technology is rapidly advancing toward high processor core counts and TeraFLOPS peak SIMD execution rates, it is imperative that coding methods be identified which produce efficient and maintainable parallel code. This paper describes the algorithms used in point scatterer target model rendering, the parallelization of those algorithms, and the execution performance achieved on an AVX multi-core machine using the two basic parallel coding methods. The paper concludes with estimates for scale-up performance on upcoming multi-core technology.

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs.

PubMed

Pena, Ramona Natacha; Ros-Freixedes, Roger; Tor, Marc; Estany, Joan

2016-12-14

Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker ( PCK1 c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase ( SCD ) gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.

Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1.

PubMed

Reschen, Michael E; Lin, Da; Chalisey, Anil; Soilleux, Elizabeth J; O'Callaghan, Christopher A

2016-07-01

Coronary artery disease (CAD) risk is associated with non-coding genetic variants at the phosphatase and actin regulating protein 1(PHACTR1) gene locus. The PHACTR1 gene encodes an actin-binding protein with phosphatase regulating activity. The mechanism whereby PHACTR1 influences CAD risk is unknown. We hypothesized that PHACTR1 would be expressed in human cell types relevant to CAD and regulated by atherogenic or genetic factors. Using immunohistochemistry, we demonstrate that PHACTR1 protein is expressed strongly in human atherosclerotic plaque macrophages, lipid-laden foam cells, adventitial lymphocytes and endothelial cells. Using a combination of genomic analysis and molecular techniques, we demonstrate that PHACTR1 is expressed as multiple previously uncharacterized transcripts in macrophages, foam cells, lymphocytes and endothelial cells. Immunoblotting confirmed a total absence of PHACTR1 in vascular smooth muscle cells. Real-time quantitative PCR showed that PHACTR1 is regulated by atherogenic and inflammatory stimuli. In aortic endothelial cells, oxLDL and TNF-alpha both upregulated an intermediate length transcript. A short transcript expressed only in immune cells was upregulated in macrophages by oxidized low-density lipoprotein, and oxidized phospholipids but suppressed by lipopolysaccharide or TNF-alpha. In primary human macrophages, we identified a novel expression quantitative trait locus (eQTL) specific for this short transcript, whereby the risk allele at CAD risk SNP rs9349379 is associated with reduced PHACTR1 expression, similar to the effect of an inflammatory stimulus. Our data demonstrate that PHACTR1 is a key atherosclerosis candidate gene since it is regulated by atherogenic stimuli in macrophages and endothelial cells and we identify an effect of the genetic risk variant on PHACTR1 expression in macrophages that is similar to that of an inflammatory stimulus. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

PubMed

Seligmann, Hervé; Warthi, Ganesh

2017-01-01

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment.

PubMed

Biddle, Wil; Schmitt, Margaret A; Fisk, John D

2016-12-01

Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNA Opt We suspected a modification of the tRNA Opt AUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNA Opt AUG is converted to inosine. We identified tRNA Opt AUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Real Time Updating Genetic Network Programming for Adapting to the Change of Stock Prices

NASA Astrophysics Data System (ADS)

Chen, Yan; Mabu, Shingo; Shimada, Kaoru; Hirasawa, Kotaro

The key in stock trading model is to take the right actions for trading at the right time, primarily based on the accurate forecast of future stock trends. Since an effective trading with given information of stock prices needs an intelligent strategy for the decision making, we applied Genetic Network Programming (GNP) to creating a stock trading model. In this paper, we propose a new method called Real Time Updating Genetic Network Programming (RTU-GNP) for adapting to the change of stock prices. There are three important points in this paper: First, the RTU-GNP method makes a stock trading decision considering both the recommendable information of technical indices and the candlestick charts according to the real time stock prices. Second, we combine RTU-GNP with a Sarsa learning algorithm to create the programs efficiently. Also, sub-nodes are introduced in each judgment and processing node to determine appropriate actions (buying/selling) and to select appropriate stock price information depending on the situation. Third, a Real Time Updating system has been firstly introduced in our paper considering the change of the trend of stock prices. The experimental results on the Japanese stock market show that the trading model with the proposed RTU-GNP method outperforms other models without real time updating. We also compared the experimental results using the proposed method with Buy&Hold method to confirm its effectiveness, and it is clarified that the proposed trading model can obtain much higher profits than Buy&Hold method.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

Exome sequencing of a multigenerational human pedigree.

PubMed

Hedges, Dale J; Hedges, Dale; Burges, Dan; Powell, Eric; Almonte, Cherylyn; Huang, Jia; Young, Stuart; Boese, Benjamin; Schmidt, Mike; Pericak-Vance, Margaret A; Martin, Eden; Zhang, Xinmin; Harkins, Timothy T; Züchner, Stephan

2009-12-14

Over the next few years, the efficient use of next-generation sequencing (NGS) in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or approximately 180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of > or = 3, 86% at a read depth of > or = 10, and over 50% of all targets were covered with > or = 20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at > or = 10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect >99% of SNPs covered > or = 8x. Our results offer guidance for "real-world" applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments.

Phylogenetic Network for European mtDNA

PubMed Central

Finnilä, Saara; Lehtonen, Mervi S.; Majamaa, Kari

2001-01-01

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms. PMID:11349229

Unnatural reactive amino acid genetic code additions

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

Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

2013-01-22

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Genetic Diversity of Toscana Virus

PubMed Central

Collao, Ximena; Palacios, Gustavo; Sanbonmatsu-Gámez, Sara; Pérez-Ruiz, Mercedes; Negredo, Ana I.; Navarro-Marí, José-María; Grandadam, Marc; Aransay, Ana Maria; Lipkin, W. Ian; Tenorio, Antonio

2009-01-01

Distribution of Toscana virus (TOSV) is evolving with climate change, and pathogenicity may be higher in nonexposed populations outside areas of current prevalence (Mediterranean Basin). To characterize genetic diversity of TOSV, we determined the coding sequences of isolates from Spain and France. TOSV is more diverse than other well-studied phleboviruses (e.g.,Rift Valley fever virus). PMID:19331735

Expanding the eukaryotic genetic code

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

Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W [Cambridge, GB; Cropp, T Ashton [Bethesda, MD; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2009-10-27

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G

2015-02-03

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W [Cambridge, GB; Cropp, T Ashton [Bethesda, MD; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2009-12-01

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W [Cambridge, GB; Cropp, T Ashton [Bethesda, MD; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2012-02-14

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W [Cambridge, GB; Cropp, T Ashton [Bethesda, MD; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2009-11-17

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

2010-09-14

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Unnatural reactive amino acid genetic code additions

DOEpatents

Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G

2013-05-21

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Expanding the eukaryotic genetic code

DOEpatents

Chin, Jason W [Cambridge, GB; Cropp, T Ashton [Bethesda, MD; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2012-05-08

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Unnatural reactive amino acid genetic code additions

DOEpatents

Deiters, Alexander [La Jolla, CA; Cropp, T Ashton [San Diego, CA; Chin, Jason W [Cambridge, GB; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2011-02-15

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Unnatural reactive amino acid genetic code additions

DOEpatents

Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

2014-08-26

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Unnatural reactive amino acid genetic code additions

DOEpatents

Deiters, Alexander [La Jolla, CA; Cropp, T Ashton [Bethesda, MD; Chin, Jason W [Cambridge, GB; Anderson, J Christopher [San Francisco, CA; Schultz, Peter G [La Jolla, CA

2011-08-09

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNAsyn-thetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Genetic variants in long non-coding RNA MIAT contribute to risk of paranoid schizophrenia in a Chinese Han population.

PubMed

Rao, Shu-Quan; Hu, Hui-Ling; Ye, Ning; Shen, Yan; Xu, Qi

2015-08-01

The heritability of schizophrenia has been reported to be as high as ~80%, but the contribution of genetic variants identified to this heritability remains to be estimated. Long non-coding RNAs (LncRNAs) are involved in multiple processes critical to normal cellular function and dysfunction of lncRNA MIAT may contribute to the pathophysiology of schizophrenia. However, the genetic evidence of lncRNAs involved in schizophrenia has not been documented. Here, we conducted a two-stage association analysis on 8 tag SNPs that cover the whole MIAT locus in two independent Han Chinese schizophrenia case-control cohorts (discovery sample from Shanxi Province: 1093 patients with paranoid schizophrenia and 1180 control subjects; replication cohort from Jilin Province: 1255 cases and 1209 healthy controls). In discovery stage, significant genetic association with paranoid schizophrenia was observed for rs1894720 (χ(2)=74.20, P=7.1E-18), of which minor allele (T) had an OR of 1.70 (95% CI=1.50-1.91). This association was confirmed in the replication cohort (χ(2)=22.66, P=1.9E-06, OR=1.32, 95%CI 1.18-1.49). Besides, a weak genotypic association was detected for rs4274 (χ(2)=4.96, df=2, P=0.03); the AA carriers showed increased disease risk (OR=1.30, 95%CI=1.03-1.64). No significant association was found between any haplotype and paranoid schizophrenia. The present studies showed that lncRNA MIAT was a novel susceptibility gene for paranoid schizophrenia in the Chinese Han population. Considering that most lncRNAs locate in non-coding regions, our result may explain why most susceptibility loci for schizophrenia identified by genome wide association studies were out of coding regions. Copyright © 2015 Elsevier B.V. All rights reserved.

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

PubMed

Qian, Jing; Nunez, Sara; Reed, Eric; Reilly, Muredach P; Foulkes, Andrea S

2016-01-01

Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs. We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT), to identify protein-coding gene association with 14 cardiometabolic (CMD) related traits across 6 publicly available genome wide association (GWA) meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1. We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes. We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and adds significant value with respect to its potential for identifying multiple novel and clinically relevant trait associations.

Representation mutations from standard genetic codes

NASA Astrophysics Data System (ADS)

Aisah, I.; Suyudi, M.; Carnia, E.; Suhendi; Supriatna, A. K.

2018-03-01

Graph is widely used in everyday life especially to describe model problem and describe it concretely and clearly. In addition graph is also used to facilitate solve various kinds of problems that are difficult to be solved by calculation. In Biology, graph can be used to describe the process of protein synthesis in DNA. Protein has an important role for DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). Proteins are composed of amino acids. In this study, amino acids are related to genetics, especially the genetic code. The genetic code is also known as the triplet or codon code which is a three-letter arrangement of DNA nitrogen base. The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). While on RNA thymine (T) is replaced with Urasil (U). The set of all Nitrogen bases in RNA is denoted by N = {C U, A, G}. This codon works at the time of protein synthesis inside the cell. This codon also encodes the stop signal as a sign of the stop of protein synthesis process. This paper will examine the process of protein synthesis through mathematical studies and present it in three-dimensional space or graph. The study begins by analysing the set of all codons denoted by NNN such that to obtain geometric representations. At this stage there is a matching between the sets of all nitrogen bases N with Z 2 × Z 2; C=(\\overline{0},\\overline{0}),{{U}}=(\\overline{0},\\overline{1}),{{A}}=(\\overline{1},\\overline{0}),{{G}}=(\\overline{1},\\overline{1}). By matching the algebraic structure will be obtained such as group, group Klein-4,Quotien group etc. With the help of Geogebra software, the set of all codons denoted by NNN can be presented in a three-dimensional space as a multicube NNN and also can be represented as a graph, so that can easily see relationship between the codon.

Toward Real-Time Infoveillance of Twitter Health Messages.

PubMed

Colditz, Jason B; Chu, Kar-Hai; Emery, Sherry L; Larkin, Chandler R; James, A Everette; Welling, Joel; Primack, Brian A

2018-06-21

There is growing interest in conducting public health research using data from social media. In particular, Twitter "infoveillance" has demonstrated utility across health contexts. However, rigorous and reproducible methodologies for using Twitter data in public health are not yet well articulated, particularly those related to content analysis, which is a highly popular approach. In 2014, we gathered an interdisciplinary team of health science researchers, computer scientists, and methodologists to begin implementing an open-source framework for real-time infoveillance of Twitter health messages (RITHM). Through this process, we documented common challenges and novel solutions to inform future work in real-time Twitter data collection and subsequent human coding. The RITHM framework allows researchers and practitioners to use well-planned and reproducible processes in retrieving, storing, filtering, subsampling, and formatting data for health topics of interest. Further considerations for human coding of Twitter data include coder selection and training, data representation, codebook development and refinement, and monitoring coding accuracy and productivity. We illustrate methodological considerations through practical examples from formative work related to hookah tobacco smoking, and we reference essential methods literature related to understanding and using Twitter data. (Am J Public Health. Published online ahead of print June 21, 2018: e1-e6. doi:10.2105/AJPH.2018.304497).

Long Non-Coding RNAs Regulating Immunity in Insects

PubMed Central

Satyavathi, Valluri; Ghosh, Rupam; Subramanian, Srividya

2017-01-01

Recent advances in modern technology have led to the understanding that not all genetic information is coded into protein and that the genomes of each and every organism including insects produce non-coding RNAs that can control different biological processes. Among RNAs identified in the last decade, long non-coding RNAs (lncRNAs) represent a repertoire of a hidden layer of internal signals that can regulate gene expression in physiological, pathological, and immunological processes. Evidence shows the importance of lncRNAs in the regulation of host–pathogen interactions. In this review, an attempt has been made to view the role of lncRNAs regulating immune responses in insects. PMID:29657286

Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analysis analyses of pooled RNA-Seq samples in rainbow trout

USDA-ARS?s Scientific Manuscript database

Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, mus...

[Genetic research with stored human tissue: a coding procedure with optimal use of information and protection of privacy].

PubMed

Schmidt, M K; van Leeuwen, F E; Klaren, H M; Tollenaar, R A; van 't Veer, L J

2004-03-20

To answer research questions concerning the course of disease and the optimal treatment of hereditary breast cancer, genetic typing together with the clinical and tumour characteristics of breast cancer patients are an important source of information. Part of the incidence of breast cancer can be explained by BRCA1 and BRCA2 germline mutations, which with current techniques can be retrospectively analysed in stored, paraffin-embedded tissue samples. In view of the implications of BRCA1- or BRCA2-carrier status for patients and other family members and the lack of clear legal regulations regarding the procedures to be followed when analysis is performed on historical material and no individual informed consent can be asked from the patients, an appropriate procedure for coding such data or rendering it anonymous is of great importance. By using the coding procedure described in this article, it becomes possible to follow and to work out in greater detail the guidelines of the code for 'Proper secondary use of human tissue' of the Federation of Biomedical Scientific Societies and to use these valuable databases again in the future.

Human fecal source identification with real-time quantitative PCR

EPA Science Inventory

Waterborne diseases represent a significant public health risk worldwide, and can originate from contact with water contaminated with human fecal material. We describe a real-time quantitative PCR (qPCR) method that targets a Bacteroides dori human-associated genetic marker for...

A Real-Time Plagiarism Detection Tool for Computer-Based Assessments

ERIC Educational Resources Information Center

Jeske, Heimo J.; Lall, Manoj; Kogeda, Okuthe P.

2018-01-01

Aim/Purpose: The aim of this article is to develop a tool to detect plagiarism in real time amongst students being evaluated for learning in a computer-based assessment setting. Background: Cheating or copying all or part of source code of a program is a serious concern to academic institutions. Many academic institutions apply a combination of…

Real-time distributed video coding for 1K-pixel visual sensor networks

NASA Astrophysics Data System (ADS)

Hanca, Jan; Deligiannis, Nikos; Munteanu, Adrian

2016-07-01

Many applications in visual sensor networks (VSNs) demand the low-cost wireless transmission of video data. In this context, distributed video coding (DVC) has proven its potential to achieve state-of-the-art compression performance while maintaining low computational complexity of the encoder. Despite their proven capabilities, current DVC solutions overlook hardware constraints, and this renders them unsuitable for practical implementations. This paper introduces a DVC architecture that offers highly efficient wireless communication in real-world VSNs. The design takes into account the severe computational and memory constraints imposed by practical implementations on low-resolution visual sensors. We study performance-complexity trade-offs for feedback-channel removal, propose learning-based techniques for rate allocation, and investigate various simplifications of side information generation yielding real-time decoding. The proposed system is evaluated against H.264/AVC intra, Motion-JPEG, and our previously designed DVC prototype for low-resolution visual sensors. Extensive experimental results on various data show significant improvements in multiple configurations. The proposed encoder achieves real-time performance on a 1k-pixel visual sensor mote. Real-time decoding is performed on a Raspberry Pi single-board computer or a low-end notebook PC. To the best of our knowledge, the proposed codec is the first practical DVC deployment on low-resolution VSNs.

A Non-Degenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

PubMed Central

Blair, David R.; Lyttle, Christopher S.; Mortensen, Jonathan M.; Bearden, Charles F.; Jensen, Anders Boeck; Khiabanian, Hossein; Melamed, Rachel; Rabadan, Raul; Bernstam, Elmer V.; Brunak, Søren; Jensen, Lars Juhl; Nicolae, Dan; Shah, Nigam H.; Grossman, Robert L.; Cox, Nancy J.; White, Kevin P.; Rzhetsky, Andrey

2013-01-01

Summary Whereas countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. Here, we examine the extent to which Mendelian variation contributes to complex disease risk by mining the medical records of over 110 million patients. We detect thousands of associations between Mendelian and complex diseases, revealing a non-degenerate, phenotypic code that links each complex disorder to a unique collection of Mendelian loci. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this “Mendelian code.” Finally, we detect hundreds of comorbidity associations among Mendelian disorders, and we use probabilistic genetic modeling to demonstrate that Mendelian variants likely contribute non-additively to the risk for a subset of complex diseases. Overall, this study illustrates a complementary approach for mapping complex disease loci and provides unique predictions concerning the etiologies of specific diseases. PMID:24074861

Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.

PubMed

Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

2012-01-03

Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg(2+) concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon-anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

A contourlet transform based algorithm for real-time video encoding

NASA Astrophysics Data System (ADS)

Katsigiannis, Stamos; Papaioannou, Georgios; Maroulis, Dimitris

2012-06-01

In recent years, real-time video communication over the internet has been widely utilized for applications like video conferencing. Streaming live video over heterogeneous IP networks, including wireless networks, requires video coding algorithms that can support various levels of quality in order to adapt to the network end-to-end bandwidth and transmitter/receiver resources. In this work, a scalable video coding and compression algorithm based on the Contourlet Transform is proposed. The algorithm allows for multiple levels of detail, without re-encoding the video frames, by just dropping the encoded information referring to higher resolution than needed. Compression is achieved by means of lossy and lossless methods, as well as variable bit rate encoding schemes. Furthermore, due to the transformation utilized, it does not suffer from blocking artifacts that occur with many widely adopted compression algorithms. Another highly advantageous characteristic of the algorithm is the suppression of noise induced by low-quality sensors usually encountered in web-cameras, due to the manipulation of the transform coefficients at the compression stage. The proposed algorithm is designed to introduce minimal coding delay, thus achieving real-time performance. Performance is enhanced by utilizing the vast computational capabilities of modern GPUs, providing satisfactory encoding and decoding times at relatively low cost. These characteristics make this method suitable for applications like video-conferencing that demand real-time performance, along with the highest visual quality possible for each user. Through the presented performance and quality evaluation of the algorithm, experimental results show that the proposed algorithm achieves better or comparable visual quality relative to other compression and encoding methods tested, while maintaining a satisfactory compression ratio. Especially at low bitrates, it provides more human-eye friendly images compared to algorithms utilizing block-based coding, like the MPEG family, as it introduces fuzziness and blurring instead of artificial block artifacts.

Reeds computer code

NASA Technical Reports Server (NTRS)

Bjork, C.

1981-01-01

The REEDS (rocket exhaust effluent diffusion single layer) computer code is used for the estimation of certain rocket exhaust effluent concentrations and dosages and their distributions near the Earth's surface following a rocket launch event. Output from REEDS is used in producing near real time air quality and environmental assessments of the effects of certain potentially harmful effluents, namely HCl, Al2O3, CO, and NO.

Channel coding/decoding alternatives for compressed TV data on advanced planetary missions.

NASA Technical Reports Server (NTRS)

Rice, R. F.

1972-01-01

The compatibility of channel coding/decoding schemes with a specific TV compressor developed for advanced planetary missions is considered. Under certain conditions, it is shown that compressed data can be transmitted at approximately the same rate as uncompressed data without any loss in quality. Thus, the full gains of data compression can be achieved in real-time transmission.

Coding Instructions, Worksheets, and Keypunch Sheets for M.E.T.R.O.-APEX Simulation.

ERIC Educational Resources Information Center

Michigan Univ., Ann Arbor. Environmental Simulation Lab.

Compiled in this resource are coding instructions, worksheets, and keypunch sheets for use in the M.E.T.R.O.-APEX simulation, described in detail in documents ED 064 530 through ED 064 550. Air Pollution Exercise (APEX) is a computerized college and professional level "real world" simulation of a community with urban and rural problems, industrial…

On initial Brain Activity Mapping of episodic and semantic memory code in the hippocampus.

PubMed

Tsien, Joe Z; Li, Meng; Osan, Remus; Chen, Guifen; Lin, Longian; Wang, Phillip Lei; Frey, Sabine; Frey, Julietta; Zhu, Dajiang; Liu, Tianming; Zhao, Fang; Kuang, Hui

2013-10-01

It has been widely recognized that the understanding of the brain code would require large-scale recording and decoding of brain activity patterns. In 2007 with support from Georgia Research Alliance, we have launched the Brain Decoding Project Initiative with the basic idea which is now similarly advocated by BRAIN project or Brain Activity Map proposal. As the planning of the BRAIN project is currently underway, we share our insights and lessons from our efforts in mapping real-time episodic memory traces in the hippocampus of freely behaving mice. We show that appropriate large-scale statistical methods are essential to decipher and measure real-time memory traces and neural dynamics. We also provide an example of how the carefully designed, sometime thinking-outside-the-box, behavioral paradigms can be highly instrumental to the unraveling of memory-coding cell assembly organizing principle in the hippocampus. Our observations to date have led us to conclude that the specific-to-general categorical and combinatorial feature-coding cell assembly mechanism represents an emergent property for enabling the neural networks to generate and organize not only episodic memory, but also semantic knowledge and imagination. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

On Initial Brain Activity Mapping of Associative Memory Code in the Hippocampus

PubMed Central

Tsien, Joe Z.; Li, Meng; Osan, Remus; Chen, Guifen; Lin, Longian; Lei Wang, Phillip; Frey, Sabine; Frey, Julietta; Zhu, Dajiang; Liu, Tianming; Zhao, Fang; Kuang, Hui

2013-01-01

It has been widely recognized that the understanding of the brain code would require large-scale recording and decoding of brain activity patterns. In 2007 with support from Georgia Research Alliance, we have launched the Brain Decoding Project Initiative with the basic idea which is now similarly advocated by BRAIN project or Brain Activity Map proposal. As the planning of the BRAIN project is currently underway, we share our insights and lessons from our efforts in mapping real-time episodic memory traces in the hippocampus of freely behaving mice. We show that appropriate large-scale statistical methods are essential to decipher and measure real-time memory traces and neural dynamics. We also provide an example of how the carefully designed, sometime thinking-outside-the-box, behavioral paradigms can be highly instrumental to the unraveling of memory-coding cell assembly organizing principle in the hippocampus. Our observations to date have led us to conclude that the specific-to-general categorical and combinatorial feature-coding cell assembly mechanism represents an emergent property for enabling the neural networks to generate and organize not only episodic memory, but also semantic knowledge and imagination. PMID:23838072

Image compression using quad-tree coding with morphological dilation

NASA Astrophysics Data System (ADS)

Wu, Jiaji; Jiang, Weiwei; Jiao, Licheng; Wang, Lei

2007-11-01

In this paper, we propose a new algorithm which integrates morphological dilation operation to quad-tree coding, the purpose of doing this is to compensate each other's drawback by using quad-tree coding and morphological dilation operation respectively. New algorithm can not only quickly find the seed significant coefficient of dilation but also break the limit of block boundary of quad-tree coding. We also make a full use of both within-subband and cross-subband correlation to avoid the expensive cost of representing insignificant coefficients. Experimental results show that our algorithm outperforms SPECK and SPIHT. Without using any arithmetic coding, our algorithm can achieve good performance with low computational cost and it's more suitable to mobile devices or scenarios with a strict real-time requirement.

Dynamic code block size for JPEG 2000

NASA Astrophysics Data System (ADS)

Tsai, Ping-Sing; LeCornec, Yann

2008-02-01

Since the standardization of the JPEG 2000, it has found its way into many different applications such as DICOM (digital imaging and communication in medicine), satellite photography, military surveillance, digital cinema initiative, professional video cameras, and so on. The unified framework of the JPEG 2000 architecture makes practical high quality real-time compression possible even in video mode, i.e. motion JPEG 2000. In this paper, we present a study of the compression impact using dynamic code block size instead of fixed code block size as specified in the JPEG 2000 standard. The simulation results show that there is no significant impact on compression if dynamic code block sizes are used. In this study, we also unveil the advantages of using dynamic code block sizes.

Learning dictionaries of sparse codes of 3D movements of body joints for real-time human activity understanding.

PubMed

Qi, Jin; Yang, Zhiyong

2014-01-01

Real-time human activity recognition is essential for human-robot interactions for assisted healthy independent living. Most previous work in this area is performed on traditional two-dimensional (2D) videos and both global and local methods have been used. Since 2D videos are sensitive to changes of lighting condition, view angle, and scale, researchers begun to explore applications of 3D information in human activity understanding in recently years. Unfortunately, features that work well on 2D videos usually don't perform well on 3D videos and there is no consensus on what 3D features should be used. Here we propose a model of human activity recognition based on 3D movements of body joints. Our method has three steps, learning dictionaries of sparse codes of 3D movements of joints, sparse coding, and classification. In the first step, space-time volumes of 3D movements of body joints are obtained via dense sampling and independent component analysis is then performed to construct a dictionary of sparse codes for each activity. In the second step, the space-time volumes are projected to the dictionaries and a set of sparse histograms of the projection coefficients are constructed as feature representations of the activities. Finally, the sparse histograms are used as inputs to a support vector machine to recognize human activities. We tested this model on three databases of human activities and found that it outperforms the state-of-the-art algorithms. Thus, this model can be used for real-time human activity recognition in many applications.

Nanotechnology Infrared Optics for Astronomy Missions

NASA Technical Reports Server (NTRS)

Frogel, Jay (Technical Monitor); Smith, Howard A.

2004-01-01

We have used the "MicroStripes" code (Flomerics, Inc.) to perform full-, near- and far-field diffraction modeling of metal mesh performance on substrates. Our Miles Code software, which approximates the full calculation in a quick, gui-based window, is useful as an iterative device by adjusting the input parameters (index of refraction, thickness, etc.) to provide agreement with the full calculation. However, despite the somewhat extravagant claims by the MicroStripes manufacturer, this code is also not perfect because numerous free parameters must be set. Key among these, as identified in our earlier papers and proposal documents, is the high frequency (i.e., far IR) character of the real and imaginary parts of the index of refraction of the metal mesh, the high frequency character of the real and imaginary parts of the index of refraction of the substrate, and the character of the interface between the mesh and the substrate material, and in particular the suppression (or possible enhancement) of surface effects at the interface.

An Energy-Efficient Compressive Image Coding for Green Internet of Things (IoT).

PubMed

Li, Ran; Duan, Xiaomeng; Li, Xu; He, Wei; Li, Yanling

2018-04-17

Aimed at a low-energy consumption of Green Internet of Things (IoT), this paper presents an energy-efficient compressive image coding scheme, which provides compressive encoder and real-time decoder according to Compressive Sensing (CS) theory. The compressive encoder adaptively measures each image block based on the block-based gradient field, which models the distribution of block sparse degree, and the real-time decoder linearly reconstructs each image block through a projection matrix, which is learned by Minimum Mean Square Error (MMSE) criterion. Both the encoder and decoder have a low computational complexity, so that they only consume a small amount of energy. Experimental results show that the proposed scheme not only has a low encoding and decoding complexity when compared with traditional methods, but it also provides good objective and subjective reconstruction qualities. In particular, it presents better time-distortion performance than JPEG. Therefore, the proposed compressive image coding is a potential energy-efficient scheme for Green IoT.

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

A Software Development Platform for Wearable Medical Applications.

PubMed

Zhang, Ruikai; Lin, Wei

2015-10-01

Wearable medical devices have become a leading trend in healthcare industry. Microcontrollers are computers on a chip with sufficient processing power and preferred embedded computing units in those devices. We have developed a software platform specifically for the design of the wearable medical applications with a small code footprint on the microcontrollers. It is supported by the open source real time operating system FreeRTOS and supplemented with a set of standard APIs for the architectural specific hardware interfaces on the microcontrollers for data acquisition and wireless communication. We modified the tick counter routine in FreeRTOS to include a real time soft clock. When combined with the multitasking features in the FreeRTOS, the platform offers the quick development of wearable applications and easy porting of the application code to different microprocessors. Test results have demonstrated that the application software developed using this platform are highly efficient in CPU usage while maintaining a small code foot print to accommodate the limited memory space in microcontrollers.

Operational rate-distortion performance for joint source and channel coding of images.

PubMed

Ruf, M J; Modestino, J W

1999-01-01

This paper describes a methodology for evaluating the operational rate-distortion behavior of combined source and channel coding schemes with particular application to images. In particular, we demonstrate use of the operational rate-distortion function to obtain the optimum tradeoff between source coding accuracy and channel error protection under the constraint of a fixed transmission bandwidth for the investigated transmission schemes. Furthermore, we develop information-theoretic bounds on performance for specific source and channel coding systems and demonstrate that our combined source-channel coding methodology applied to different schemes results in operational rate-distortion performance which closely approach these theoretical limits. We concentrate specifically on a wavelet-based subband source coding scheme and the use of binary rate-compatible punctured convolutional (RCPC) codes for transmission over the additive white Gaussian noise (AWGN) channel. Explicit results for real-world images demonstrate the efficacy of this approach.

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294

Learning directed acyclic graphs from large-scale genomics data.

PubMed

Nikolay, Fabio; Pesavento, Marius; Kritikos, George; Typas, Nassos

2017-09-20

In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactions-Detector (GENIE) to identify the complex biological dependencies among genes and to compute the DAG topology that matches the DK measurements best. Furthermore, we extend the GENIE program by incorporating genetic interaction profile (GI-profile) data to further enhance the detection performance. In addition, we propose a sequential scalability technique for large sets of genes under study, in order to provide statistically significant results for real measurement data. Finally, we show via numeric simulations that the GENIE program and the GI-profile data extended GENIE (GI-GENIE) program clearly outperform the conventional techniques and present real data results for our proposed sequential scalability technique.

Automated real time peg and tool detection for the FLS trainer box.

PubMed

Nemani, Arun; Sankaranarayanan, Ganesh

2012-01-01

This study proposes a method that effectively tracks trocar tool and peg positions in real time to allow real time assessment of the peg transfer task of the Fundamentals of Laparoscopic Surgery (FLS). By utilizing custom code along with OpenCV libraries, tool and peg positions can be accurately tracked without altering the original setup conditions of the FLS trainer box. This is achieved via a series of image filtration sequences, thresholding functions, and Haar training methods.

Real-time optical holographic tracking of multiple objects

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin; Liu, Hua-Kuang

1989-01-01

A coherent optical correlation technique for real-time simultaneous tracking of several different objects making independent movements is described, and experimental results are presented. An evaluation of this system compared with digital computing systems is made. The real-time processing capability is obtained through the use of a liquid crystal television spatial light modulator and a dichromated gelatin multifocus hololens. A coded reference beam is utilized in the separation of the output correlation plane associated with each input target so that independent tracking can be achieved.

Towards defining the role of glycans as hardware in information storage and transfer: basic principles, experimental approaches and recent progress.

PubMed

Solís, D; Jiménez-Barbero, J; Kaltner, H; Romero, A; Siebert, H C; von der Lieth, C W; Gabius, H J

2001-01-01

The term 'code' in biological information transfer appears to be tightly and hitherto exclusively connected with the genetic code based on nucleotides and translated into functional activities via proteins. However, the recent appreciation of the enormous coding capacity of oligosaccharide chains of natural glycoconjugates has spurred to give heed to a new concept: versatile glycan assembly by the genetically encoded glycosyltransferases endows cells with a probably not yet fully catalogued array of meaningful messages. Enciphered by sugar receptors such as endogenous lectins the information of code words established by a series of covalently linked monosaccharides as letters for example guides correct intra- and intercellular routing of glycoproteins, modulates cell proliferation or migration and mediates cell adhesion. Evidently, the elucidation of the structural frameworks and the recognition strategies within the operation of the sugar code poses a fascinating conundrum. The far-reaching impact of this recognition mode on the level of cells, tissues and organs has fueled vigorous investigations to probe the subtleties of protein-carbohydrate interactions. This review presents information on the necessarily concerted approach using X-ray crystallography, molecular modeling, nuclear magnetic resonance spectroscopy, thermodynamic analysis and engineered ligands and receptors. This part of the treatise is flanked by exemplarily chosen insights made possible by these techniques. Copyright 2001 S. Karger AG, Basel