Science.gov

Sample records for reverse genetic applications

  1. Flavivirus reverse genetic systems, construction techniques and applications: a historical perspective.

    PubMed

    Aubry, Fabien; Nougairède, Antoine; Gould, Ernest A; de Lamballerie, Xavier

    2015-02-01

    The study of flaviviruses, which cause some of the most important emerging tropical and sub-tropical human arbovirus diseases, has greatly benefited from the use of reverse genetic systems since its first development for yellow fever virus in 1989. Reverse genetics technology has completely revolutionized the study of these viruses, making it possible to manipulate their genomes and evaluate the direct effects of these changes on their biology and pathogenesis. The most commonly used reverse genetics system is the infectious clone technology. Whilst flavivirus infectious clones provide a powerful tool, their construction as full-length cDNA molecules in bacterial vectors can be problematic, laborious and time consuming, because they are often unstable, contain unwanted induced substitutions and may be toxic for bacteria due to viral protein expression. The incredible technological advances that have been made during the past 30years, such as the use of PCR or new sequencing methods, have allowed the development of new approaches to improve preexisting systems or elaborate new strategies that overcome these problems. This review summarizes the evolution and major technical breakthroughs in the development of flavivirus reverse genetics technologies and their application to the further understanding and control of these viruses and their diseases. PMID:25512228

  2. Influenza reverse genetics: dissecting immunity and pathogenesis.

    PubMed

    Ye, Siying; Evans, Justin G; Stambas, John

    2014-01-01

    Reverse genetics systems allow artificial generation of non-segmented and segmented negative-sense RNA viruses, like influenza viruses, entirely from cloned cDNA. Since the introduction of reverse genetics systems over a decade ago, the ability to generate 'designer' influenza viruses in the laboratory has advanced both basic and applied research, providing a powerful tool to investigate and characterise host-pathogen interactions and advance the development of novel therapeutic strategies. The list of applications for reverse genetics has expanded vastly in recent years. In this review, we discuss the development and implications of this technique, including the recent controversy surrounding the generation of a transmissible H5N1 influenza virus. We will focus on research involving the identification of viral protein function, development of live-attenuated influenza virus vaccines, host-pathogen interactions, immunity and the generation of recombinant influenza virus vaccine vectors for the prevention and treatment of infectious diseases and cancer. PMID:24528628

  3. RNA Virus Reverse Genetics and Vaccine Design

    PubMed Central

    Stobart, Christopher C.; Moore, Martin L.

    2014-01-01

    RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines. PMID:24967693

  4. Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals

    PubMed Central

    Barkley, N.A; Wang, M.L

    2008-01-01

    With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed. PMID:19452039

  5. Reverse genetics: Its origins and prospects

    SciTech Connect

    Berg, P. )

    1991-04-01

    The nucleotide sequence of a gene and its flanking segments alone will not tell us how its expression is regulated during development and differentiation, or in response to environmental changes. To comprehend the physiological significance of the molecular details requires biological analysis. Recombinant DNA techniques provide a powerful experimental approach. A strategy termed reverse genetics' utilizes the analysis of the activities of mutant and normal genes and experimentally constructed mutants to explore the relationship between gene structure and function thereby helping elucidate the relationship between genotype and phenotype.

  6. Arenavirus reverse genetics for vaccine development

    PubMed Central

    Ortiz-Riaño, Emilio; Cheng, Benson Yee Hin; Carlos de la Torre, Juan

    2013-01-01

    Arenaviruses are important human pathogens with no Food and Drug Administration (FDA)-licensed vaccines available and current antiviral therapy being limited to an off-label use of the nucleoside analogue ribavirin of limited prophylactic efficacy. The development of reverse genetics systems represented a major breakthrough in arenavirus research. However, rescue of recombinant arenaviruses using current reverse genetics systems has been restricted to rodent cells. In this study, we describe the rescue of recombinant arenaviruses from human 293T cells and Vero cells, an FDA-approved line for vaccine development. We also describe the generation of novel vectors that mediate synthesis of both negative-sense genome RNA and positive-sense mRNA species of lymphocytic choriomeningitis virus (LCMV) directed by the human RNA polymerases I and II, respectively, within the same plasmid. This approach reduces by half the number of vectors required for arenavirus rescue, which could facilitate virus rescue in cell lines approved for human vaccine production but that cannot be transfected at high efficiencies. We have shown the feasibility of this approach by rescuing both the Old World prototypic arenavirus LCMV and the live-attenuated vaccine Candid#1 strain of the New World arenavirus Junín. Moreover, we show the feasibility of using these novel strategies for efficient rescue of recombinant tri-segmented both LCMV and Candid#1. PMID:23364194

  7. Establishment of an entirely plasmid-based reverse genetics system for Bluetongue virus.

    PubMed

    Pretorius, Jakobus M; Huismans, Henk; Theron, Jacques

    2015-12-01

    Bluetongue virus (BTV), the type species of the genus Orbivirus within the family Reoviridae, has a genome consisting of 10 linear double-stranded RNA genome segments. Current reverse genetics approaches for engineering the BTV genome rely upon in vitro synthesis of capped RNA transcripts from cloned cDNA corresponding to viral genome segments. In an effort to expand the utility of BTV reverse genetics, we constructed a reverse genetics vector containing a T7 RNA polymerase promoter, hepatitis delta ribozyme sequence and T7 RNA polymerase terminator sequence. Viable virus was recovered following transfection of mammalian cells, expressing T7 RNA polymerase, with 10 plasmid constructs representing the cloned BTV-1 genome. Furthermore, the plasmid-based reverse genetics system was used successfully to isolate viable cross-serotype reassortant viruses and a mutant virus containing a defined mutation in the replicating viral genome. The new reverse genetics platform established here for BTV is likely applicable to other orbiviruses. PMID:26408855

  8. Reverse genetics approaches to combat pathogenic arenaviruses

    PubMed Central

    de la Torre, Juan C.

    2008-01-01

    Several arenaviruses cause hemorrhagic fever (HF) in humans, and evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. Moreover, arenaviruses pose a biodefense threat. No licensed anti-arenavirus vaccines are available, and current anti-arenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with anemia and other side effects. Therefore, it is important to develop effective vaccines and better antiviral drugs to combat the dual threats of naturally occurring and intentionally introduced arenavirus infections. The development of arenavirus reverse genetic systems is allowing investigators to conduct a detailed molecular characterization of the viral cis-acting signals and trans-acting factors that control each of the steps of the arenavirus life cycle, including RNA synthesis, packaging and budding. Knowledge derived from these studies is uncovering potential novel targets for therapeutic intervention, as well as facilitating the establishment of assays to identify and characterize candidate antiviral drugs capable of interfering with specific steps of the virus life cycle. Likewise, the ability to generate predetermined specific mutations within the arenavirus genome and analyze their phenotypic expression would significantly contribute to the elucidation of arenavirus-host interactions, including the basis of their ability to cause severe HF. This, in turn, could lead to the development of novel, potent and safe arenavirus vaccines. PMID:18782590

  9. Tackling feline infectious peritonitis via reverse genetics.

    PubMed

    Thiel, Volker; Thiel, Heinz-Jrgen; Tekes, Gergely

    2014-01-01

    Feline infectious peritonitis (FIP) is caused by feline coronaviruses (FCoVs) and represents one of the most important lethal infectious diseases of cats. To date, there is no efficacious prevention and treatment, and our limited knowledge on FIP pathogenesis is mainly based on analysis of experiments with field isolates. In a recent study, we reported a promising approach to study FIP pathogenesis using reverse genetics. We generated a set of recombinant FCoVs and investigated their pathogenicity in vivo. The set included the type I FCoV strain Black, a type I FCoV strain Black with restored accessory gene 7b, two chimeric type I/type II FCoVs and the highly pathogenic type II FCoV strain 79-1146. All recombinant FCoVs and the reference strain isolates were found to establish productive infections in cats. While none of the type I FCoVs and chimeric FCoVs induced FIP, the recombinant type II FCoV strain 79-1146 was as pathogenic as the parental isolate. Interestingly, an intact ORF 3c was confirmed to be restored in all viruses (re)isolated from FIP-diseased animals. PMID:25482087

  10. Tackling feline infectious peritonitis via reverse genetics

    PubMed Central

    Thiel, Volker; Thiel, Heinz-Jrgen; Tekes, Gergely

    2014-01-01

    Feline infectious peritonitis (FIP) is caused by feline coronaviruses (FCoVs) and represents one of the most important lethal infectious diseases of cats. To date, there is no efficacious prevention and treatment, and our limited knowledge on FIP pathogenesis is mainly based on analysis of experiments with field isolates. In a recent study, we reported a promising approach to study FIP pathogenesis using reverse genetics. We generated a set of recombinant FCoVs and investigated their pathogenicity in vivo. The set included the type I FCoV strain Black, a type I FCoV strain Black with restored accessory gene 7b, two chimeric type I/type II FCoVs and the highly pathogenic type II FCoV strain 791146. All recombinant FCoVs and the reference strain isolates were found to establish productive infections in cats. While none of the type I FCoVs and chimeric FCoVs induced FIP, the recombinant type II FCoV strain 791146 was as pathogenic as the parental isolate. Interestingly, an intact ORF 3c was confirmed to be restored in all viruses (re)isolated from FIP-diseased animals. PMID:25482087

  11. An inducible and reversible mouse genetic rescue system.

    PubMed

    Zeng, Hongkui; Horie, Kyoji; Madisen, Linda; Pavlova, Maria N; Gragerova, Galina; Rohde, Alex D; Schimpf, Brian A; Liang, Yuqiong; Ojala, Ethan; Kramer, Farah; Roth, Patricia; Slobodskaya, Olga; Dolka, Io; Southon, Eileen A; Tessarollo, Lino; Bornfeldt, Karin E; Gragerov, Alexander; Pavlakis, George N; Gaitanaris, George A

    2008-05-01

    Inducible and reversible regulation of gene expression is a powerful approach for uncovering gene function. We have established a general method to efficiently produce reversible and inducible gene knockout and rescue in mice. In this system, which we named iKO, the target gene can be turned on and off at will by treating the mice with doxycycline. This method combines two genetically modified mouse lines: a) a KO line with a tetracycline-dependent transactivator replacing the endogenous target gene, and b) a line with a tetracycline-inducible cDNA of the target gene inserted into a tightly regulated (TIGRE) genomic locus, which provides for low basal expression and high inducibility. Such a locus occurs infrequently in the genome and we have developed a method to easily introduce genes into the TIGRE site of mouse embryonic stem (ES) cells by recombinase-mediated insertion. Both KO and TIGRE lines have been engineered for high-throughput, large-scale and cost-effective production of iKO mice. As a proof of concept, we have created iKO mice in the apolipoprotein E (ApoE) gene, which allows for sensitive and quantitative phenotypic analyses. The results demonstrated reversible switching of ApoE transcription, plasma cholesterol levels, and atherosclerosis progression and regression. The iKO system shows stringent regulation and is a versatile genetic system that can easily incorporate other techniques and adapt to a wide range of applications. PMID:18464897

  12. Reversible gelation of genetically engineered macromolecules

    NASA Astrophysics Data System (ADS)

    Petka, Wendy Ann

    Genetic engineering of protein-based polymers offers distinct advantages over conventional synthesis of polymers. Microorganisms can synthesize high molecular weight materials, in relatively large quantities, that are inherently stereoregular, monodisperse, and of controlled sequence. In addition, specific secondary and higher order structures are determined by this protein sequence. As a result, scientists can design polymers to have unique structural features found in natural protein materials and functional properties that are inherent in certain peptide sequences. For this reason, genetic engineering principles were used to create a set of artificial genes that encode twelve macromolecules having both alpha-helical and disordered coil protein sequences with the last amino acid being cysteine (cys) or tryptophan (trp). Triblock copolymer sequences having coiled-coil protein ends, A or B, where A and B represent alpha-helical acidic and basic leucine zipper proteins, separated by a water soluble flexible spacer coil protein, C, where C represents ((AG)sb3PEG) sbn (n = 10 or 28), showed reversible physical gelation behavior. This behavior is believed to result from the aggregation of two or more helices that form physical crosslinks with the disordered coil domain retaining solvent and preventing precipitation of the chain. Diffising wave spectroscopy was used to investigate the gelation behavior of ACsb{10}Acys in buffer when environmental conditions such as pH, temperature, and concentration were varied. The dynamic intensity autocorrelation function recorded over time for 5% (w/v) ACsb{10}Acys showed that the protein behaved as a gel at pH 6.7-8.0 and that the melting point was between 40sp°C and 48sp°C. In addition to the triblock results, the incorporation of 5sp',5sp',5sp'-trifluoroleucine (Tfl) in place of leucine (Leu) in the A and B blocks was accomplished by synthesizing proteins in bacterial hosts auxotrophic for Leu. The substitution of Tfl for Leu in A and B was confirmed by electrospray mass spectrometry. Amino acid analyses performed on purified Tfl A and Tfl B populations suggested 66% and 38% levels of Tfl substitution, respectively. Thermal denaturation temperatures measured by circular dichroism of the Tfl containing helices were higher than those of the corresponding Leu containing helices by 8sp°C and 13sp°C for A and B respectively.

  13. Reverse Genetics for Functional Genomics of Phytopathogenic Fungi and Oomycetes

    PubMed Central

    Bhadauria, Vijai; Banniza, Sabine; Wei, Yangdou; Peng, You-Liang

    2009-01-01

    Sequencing of over 40 fungal and oomycete genomes has been completed. The next major challenge in modern fungal/oomycete biology is now to translate this plethora of genome sequence information into biological functions. Reverse genetics has emerged as a seminal tool for functional genomics investigations. Techniques utilized for reverse genetics like targeted gene disruption/replacement, gene silencing, insertional mutagenesis, and targeting induced local lesions in genomes will contribute greatly to the understanding of gene function of fungal and oomycete pathogens. This paper provides an overview on high-throughput reverse genetics approaches to decode fungal/oomycete genomes. PMID:19830245

  14. A novel reverse genetics system for human norovirus.

    PubMed

    Taube, Stefan; Wobus, Christiane E

    2014-11-01

    Human noroviruses cause significant morbidity, mortality, and economic losses worldwide. The inability to grow human noroviruses in cell culture has hampered our collective understanding of virus-host interactions and development of therapeutics. A newly described single-plasmid reverse genetics system for noroviruses has the potential to facilitate basic and applied research. PMID:25438616

  15. The reverse genetics applied to fish RNA viruses

    PubMed Central

    2011-01-01

    Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design. PMID:21314978

  16. Genetics and reverse epidemiology among patients on chronic hemodialysis.

    PubMed

    Balakrishnan, Vaidyanathapuram S; Rao, Madhumati

    2007-01-01

    A reversal in the association between traditional and nontraditional risk factors and clinical outcomes is often encountered in patients with chronic illness, including among those with advanced chronic kidney disease (CKD) on maintenance hemodialysis (MHD). The effects of the malnutrition-inflammation complex syndrome (MICS) may play a significant role in the reversal of this risk factor-outcomes association. the MICS, this syndrome complex is not universal in its prevalence among MHD patients. The significant inter- and intra-individual differences in the prevalence of inflammation, oxidative stress, and malnutrition, indicates the influence of genetic factors in this variability. In recent years, enormous advancement in the field of molecular genetics, genomics and bioinformatics, have revolutionized studies of the genetic epidemiology of several diseases. However, genetic association studies are at a preliminary stage in the population with advanced CKD (Table 1). Preliminary studies of the impact of polyphisms in inflammation and oxidative stress-related genes and genes affecting body composition and metabolism suggest that genetic variation may indeed affect the phenotype of the MHD population. Further, some of these gene polymorphisms may also contribute to a reversal of the association between traditional risk factors, such as BMI, blood pressure, and cholesterol and clinical outcomes in this vulnerable patient population. Genetic studies in patients with advanced CKD pose enormous challenges, including recruitment of sufficient numbers of patients to achieve adequate statistical power, resolution of immense genotypic and phenotypic heterogeneity, and gene-environment and gene-gene interactions. However, well-designed adequately powered studies with carefully defined phenotypes may potentially allow definition of risk profiles characterized by combinations of relevant Single nucleotide polymorphisms in the setting of given environmental factors. Accurate risk stratification that takes into account genetic information would allow more informed targeting of pharmacologic intervention and better refined clinical trial methodologies. PMID:17991207

  17. CORONAVIRUS REVERSE GENETIC SYSTEMS: INFECTIOUS CLONES AND REPLICONS

    PubMed Central

    Almazn, Fernando; Sola, Isabel; Zuiga, Sonia; Marquez-Jurado, Silvia; Morales, Lucia; Becares, Martina; Enjuanes, Luis

    2016-01-01

    Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last thirteen years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV). PMID:24930446

  18. Reverse genetics system for studying human rhinovirus infections.

    PubMed

    Lee, Wai-Ming; Wang, Wensheng; Bochkov, Yury A; Lee, Iris

    2015-01-01

    Human rhinovirus (HRV) contains a 7.2 kb messenger-sense RNA genome which is the template for reproducing progeny viruses after it enters the cytoplasm of a host cell. Reverse genetics refers to the regeneration of progeny viruses from an artificial cDNA copy of the RNA genome of an RNA virus. It has been a powerful molecular genetic tool for studying HRV and other RNA viruses because the artificial DNA stage makes it practical to introduce specific mutations into the viral RNA genome. This chapter uses HRV-16 as the model virus to illustrate the strategy and methods for constructing and cloning the artificial cDNA copy of a full-length HRV genome, identifying the infectious cDNA clone isolates, and selecting the most vigorous cDNA clone isolate to serve as the standard parental clone for future molecular genetic study of the virus. PMID:25261313

  19. Feline Genetics: Clinical Applications and Genetic Testing

    PubMed Central

    Lyons, Leslie A.

    2010-01-01

    DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately thirty-three genes contain fifty mutations that cause feline health problems or alterations in the cats appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab using a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cats internal genome. PMID:21147473

  20. Feline genetics: clinical applications and genetic testing.

    PubMed

    Lyons, Leslie A

    2010-11-01

    DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately 33 genes contain 50 mutations that cause feline health problems or alterations in the cat's appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab with a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cat's internal genome. PMID:21147473

  1. Development of an improved reverse genetics system for Akabane bunyavirus.

    PubMed

    Takenaka-Uema, Akiko; Sugiura, Keita; Bangphoomi, Norasuthi; Shioda, Chieko; Uchida, Kazuyuki; Kato, Kentaro; Haga, Takeshi; Murakami, Shin; Akashi, Hiroomi; Horimoto, Taisuke

    2016-06-01

    Akabane disease, caused by the insect-transmitted Akabane virus (AKAV), affects livestock by causing life-threatening deformities or mortality of fetuses. Therefore, Akabane disease has led to notable economic losses in numerous countries, including Japan. In this short communication, a new T7 RNA polymerase-based AKAV reverse genetics system was developed. Using this system, in which three plasmids transcribing antigenomic RNAs were transfected into cells stably expressing T7 polymerase, we successfully reconstituted the live attenuated vaccine TS-C2 strain (named rTTT), and also generated a mutant AKAV (rTTTΔNSs) that lacked the gene encoding the nonstructural NSs protein, which is regarded as a virulence factor. Analysis of growth kinetics revealed that rTTTΔNSs grew at a much slower rate than the rTTT and TS-C2 virus. These results suggest that our established reverse genetics system is a powerful tool that can be used for AKAV vaccine studies with gene-manipulated viruses. PMID:26927704

  2. Reverse Genetics System for Severe Fever with Thrombocytopenia Syndrome Virus

    PubMed Central

    Brennan, Benjamin; Li, Ping; Zhang, Shuo; Li, Aqian; Liang, Mifang; Li, Dexin

    2014-01-01

    ABSTRACT Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne pathogen that was first reported in China in 2009. Phylogenetic analysis of the viral genome showed that SFTS virus represents a new lineage within the Phlebovirus genus, distinct from the existing sandfly fever and Uukuniemi virus groups, in the family Bunyaviridae. SFTS disease is characterized by gastrointestinal symptoms, chills, joint pain, myalgia, thrombocytopenia, leukocytopenia, and some hemorrhagic manifestations with a case fatality rate of about 2 to 15%. Here we report the development of reverse genetics systems to study STFSV replication and pathogenesis. We developed and optimized functional T7 polymerase-based M- and S-segment minigenome assays, which revealed errors in the published terminal sequences of the S segment of the Hubei 29 strain of SFTSV. We then generated recombinant viruses from cloned cDNAs prepared to the antigenomic RNAs both of the minimally passaged virus (HB29) and of a cell culture-adapted strain designated HB29pp. The growth properties, pattern of viral protein synthesis, and subcellular localization of viral N and NSs proteins of wild-type HB29pp (wtHB29pp) and recombinant HB29pp viruses were indistinguishable. We also show that the viruses fail to shut off host cell polypeptide production. The robust reverse genetics system described will be a valuable tool for the design of therapeutics and the development of killed and attenuated vaccines against this important emerging pathogen. IMPORTANCE SFTSV and related tick-borne phleboviruses such as Heartland virus are emerging viruses shown to cause severe disease in humans in the Far East and the United States, respectively. Study of these novel pathogens would be facilitated by technology to manipulate these viruses in a laboratory setting using reverse genetics. Here, we report the generation of infectious SFTSV from cDNA clones and demonstrate that the behavior of recombinant viruses is similar to that of the wild type. This advance will allow for further dissection of the roles of each of the viral proteins in the context of virus infection, as well as help in the development of antiviral drugs and protective vaccines. PMID:25552716

  3. Rapid reverse genetic screening using CRISPR in zebrafish.

    PubMed

    Shah, Arish N; Davey, Crystal F; Whitebirch, Alex C; Miller, Adam C; Moens, Cecilia B

    2015-06-01

    Identifying genes involved in biological processes is critical for understanding the molecular building blocks of life. We used engineered CRISPR (clustered regularly interspaced short palindromic repeats) to efficiently mutate specific loci in zebrafish (Danio rerio) and screen for genes involved in vertebrate biological processes. We found that increasing CRISPR efficiency by injecting optimized amounts of Cas9-encoding mRNA and multiplexing single guide RNAs (sgRNAs) allowed for phenocopy of known mutants across many phenotypes in embryos. We performed a proof-of-concept screen in which we used intersecting, multiplexed pool injections to examine 48 loci and identified two new genes involved in electrical-synapse formation. By deep sequencing target loci, we found that 90% of the genes were effectively screened. We conclude that CRISPR can be used as a powerful reverse genetic screening strategy in vivo in a vertebrate system. PMID:25867848

  4. A Reverse Genetic Approach to Test Functional Redundancy During Embryogenesis

    PubMed Central

    Rikin, Amir; Rosenfeld, Gabriel E.; McCartin, Kellie; Evans, Todd

    2010-01-01

    Gene function during embryogenesis is typically defined by loss-of-function experiments, for example by targeted mutagenesis (knockout) in the mouse. In the zebrafish model, effective reverse genetic techniques have been developed using microinjection of gene-specific antisense morpholinos. Morpholinos target an mRNA through specific base-pairing and block gene function transiently by inhibiting translation or splicing for several days during embryogenesis (knockdown). However, in vertebrates such as mouse or zebrafish, some gene functions can be obscured by these approaches due to the presence of another gene that compensates for the loss. This is especially true for gene families containing sister genes that are co-expressed in the same developing tissues. In zebrafish, functional compensation can be tested in a relatively high-throughput manner, by co-injection of morpholinos that target knockdown of both genes simultaneously. Likewise, using morpholinos, a genetic interaction between any two genes can be demonstrated by knockdown of both genes together at sub-threshold levels. For example, morpholinos can be titrated such that neither individual knockdown generates a phenotype. If, under these conditions, co-injection of both morpholinos causes a phenotype, a genetic interaction is shown. Here we demonstrate how to show functional redundancy in the context of two related GATA transcription factors. GATA factors are essential for specification of cardiac progenitors, but this is revealed only by the loss of both Gata5 and Gata6. We show how to carry out microinjection experiments, validate the morpholinos, and evaluate the compensated phenotype for cardiogenesis. PMID:20736915

  5. Silver electrodes for reversible oxygen sensor applications

    NASA Astrophysics Data System (ADS)

    Kim, Taekyeong

    2015-09-01

    We report a single oxygen atomic sensor based on a scanning tunneling microscope break-junction (STM-BJ) technique by using silver electrodes at room temperature. The oxygen concentration was adjusted with argon gas in a glove box. An oxygen atom was inserted in the gap of the Ag electrodes after the Ag metal point contact had been ruptured during stretching of the Ag atomic junctions by moving a piezo. We successfully measured the conductance of a single oxygen atom by forming a series with the Ag contact, Ag-O-Ag bond. We found that the probability of Ag-O-Ag junction formation increased with increasing oxygen concentration. Furthermore, we observed that the peak height in the oxygen conductance histogram was changed reversibly depending on the oxygen concentration in a glove box. It confirms that our STM-BJ can be used for atomic sensor applications in the future.

  6. Respiratory Syncytial Virus: Virology, Reverse Genetics, and Pathogenesis of Disease

    PubMed Central

    Fearns, Rachel; Graham, Barney S.

    2016-01-01

    Human respiratory syncytial virus (RSV) is an enveloped, nonsegmented negative-strand RNA virus of family Paramyxoviridae. RSV is the most complex member of the family in terms of the number of genes and proteins. It is also relatively divergent and distinct from the prototype members of the family. In the past 30 years, we have seen a tremendous increase in our understanding of the molecular biology of RSV based on a succession of advances involving molecular cloning, reverse genetics, and detailed studies of protein function and structure. Much remains to be learned. RSV disease is complex and variable, and the host and viral factors that determine tropism and disease are poorly understood. RSV is notable for a historic vaccine failure in the 1960s involving a formalin-inactivated vaccine that primed for enhanced disease in RSV naïve recipients. Live vaccine candidates have been shown to be free of this complication. However, development of subunit or other protein-based vaccines for pediatric use is hampered by the possibility of enhanced disease and the difficulty of reliably demonstrating its absence in preclinical studies. PMID:24362682

  7. Live vaccines for human metapneumovirus designed by reverse genetics.

    PubMed

    Buchholz, Ursula J; Nagashima, Kunio; Murphy, Brian R; Collins, Peter L

    2006-10-01

    Human metapneumovirus (HMPV) was first described in 2001 and has quickly become recognized as an important cause of respiratory tract disease worldwide, especially in the pediatric population. A vaccine against HMPV is required to prevent severe disease associated with infection in infancy. The primary strategy is to develop a live-attenuated virus for intranasal immunization, which is particularly well suited against a respiratory virus. Reverse genetics provides a means of developing highly characterized 'designer' attenuated vaccine candidates. To date, several promising vaccine candidates have been developed, each using a different mode of attenuation. One candidate involves deletion of the G glycoprotein, providing attenuation that is probably based on reduced efficiency of attachment. A second candidate involves deletion of the M2-2 protein, which participates in regulating RNA synthesis and whose deletion has the advantageous property of upregulating transcription and increasing antigen synthesis. A third candidate involves replacing the P protein gene of HMPV with its counterpart from the related avian metapneumovirus, thereby introducing attenuation owing to its chimeric nature and host range restriction. Another live vaccine strategy involves using an attenuated parainfluenza virus as a vector to express HMPV protective antigens, providing a bivalent pediatric vaccine. Additional modifications to provide improved vaccines will also be discussed. PMID:17181442

  8. OryGenesDB: a database for rice reverse genetics.

    PubMed

    Droc, G; Ruiz, M; Larmande, P; Pereira, A; Piffanelli, P; Morel, J B; Dievart, A; Courtois, B; Guiderdoni, E; Prin, C

    2006-01-01

    Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an 'anchoring' option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors. PMID:16381969

  9. Rapid reverse genetic screening using CRISPR in zebrafish

    PubMed Central

    Shah, Arish N; Davey, Crystal F; Whitebirch, Alex C; Miller, Adam C; Moens, Cecilia B

    2015-01-01

    Identifying genes involved in biological processes is critical for understanding the molecular building blocks of life. The effectiveness of engineered CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) to efficiently mutate specific loci coupled with the accessibility of zebrafish (Danio rerio) provides an opportunity to screen for genes involved in vertebrate biological processes. Injection of Cas9-encoding mRNA and an engineered, single guide RNA (sgRNA) can cause biallelic mutations in injected embryos that phenocopy known mutant phenotypes. We found that increasing CRISPR efficiency and multiplexing sgRNAs allowed for phenocopy of known mutants across many phenotypes. We performed a proof-of-concept screen examining 48 loci by intersecting, multiplexed pool injections, and identified two new genes involved in electrical synapse formation. By deep-sequencing target loci we found that 90% of the genes were effectively screened. We conclude that CRISPR can be used as a powerful reverse genetic screening strategy in vivo in a vertebrate system. PMID:25867848

  10. Molecular studies of influenza B virus in the reverse genetics era.

    PubMed

    Jackson, David; Elderfield, Ruth A; Barclay, Wendy S

    2011-01-01

    Recovery of an infectious virus of defined genetic structure entirely from cDNA and the deduction of information about the virus resulting from phenotypic characterization of the mutant is the process of reverse genetics. This approach has been possible for a number of negative-strand RNA viruses since the recovery of rabies virus in 1994. However, the recovery of recombinant orthomyxoviruses posed a greater challenge due to the segmented nature of the genome. It was not until 1999 that such a system was reported for influenza A viruses, but since that time our knowledge of influenza A virus biology has grown dramatically. Annual influenza epidemics are caused not only by influenza A viruses but also by influenza B viruses. In 2002, two groups reported the successful recovery of influenza B virus entirely from cDNA. This has allowed greater depth of study into the biology of these viruses. This review will highlight the advances made in various areas of influenza B virus biology as a result of the development of reverse genetics techniques for these viruses, including (i) the importance of the non-coding regions of the influenza B virus genome; (ii) the generation of novel vaccine strains; (iii) studies into the mechanisms of drug resistance; (iv) the function(s) of viral proteins, both those analogous to influenza A virus proteins and those unique to influenza B viruses. The information generated by the application of influenza B virus reverse genetics systems will continue to contribute to our improved surveillance and control of human influenza. PMID:20926635

  11. Deletion-Based Reverse Genetics in Medicago truncatula1[W][OA

    PubMed Central

    Rogers, Christian; Wen, Jiangqi; Chen, Rujin; Oldroyd, Giles

    2009-01-01

    The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA. PMID:19759346

  12. Sperm-mediated 'reverse' gene transfer: a role of reverse transcriptase in the generation of new genetic information.

    PubMed

    Spadafora, Corrado

    2008-04-01

    Sperm-mediated gene transfer (SMGT) is a procedure through which new genetic traits are introduced in animals by exploiting the ability of spermatozoa to take up exogenous DNA molecules and deliver them to oocytes at fertilization. The interaction of exogenous DNA with sperm cells is a regulated process mediated by specific factors; among those, a reverse transcriptase (RT) activity plays a central role in SMGT. 'Retro-genes' are generated either through reverse transcription of exogenous RNA internalized in spermatozoa, or through sequential transcription, splicing and reverse transcription of exogenous DNA. The resulting retro-genes are delivered to oocytes and transmitted to embryos and born animals as low-copy, transcriptionally competent, extrachromosomal structures capable of determining new phenotypic traits. Retro-genes can be further transmitted through sexual reproduction from founders to their F1 progeny: new genetic and phenotypic features, unlinked to chromosomes, can thus be generated and inherited in a non-Mendelian ratio. We have called this phenomenon sperm-mediated 'reverse' gene transfer (SMRGT). Thus, a RT-mediated machinery operates in sperm cells and is responsible for the genesis and non-Mendelian propagation of new genetic information. The features of RT-generated traits elicited in SMRGT resemble those characterized in recent studies of RNA-mediated inheritance of extra-genomic information. PMID:18270183

  13. Generation of genetically stable recombinant rotaviruses containing novel genome rearrangements and heterologous sequences by reverse genetics.

    PubMed

    Navarro, Aitor; Trask, Shane D; Patton, John T

    2013-06-01

    The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5' and 3' untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3' UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>10(7) PFU/ml) and remained genetically stable during serial passage. Despite their longer 3' UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein in vivo. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents. PMID:23536662

  14. Reverse genetics of rabies virus: new strategies to attenuate virus virulence for vaccine development.

    PubMed

    Zhu, Shimao; Li, Hui; Wang, Chunhua; Luo, Farui; Guo, Caiping

    2015-08-01

    Rabies is an ancient neurological disease that is almost invariably fatal once the clinical symptoms develop. Currently, prompt wound cleansing after exposing to a potentially rabid animal and vaccination using rabies vaccine combined with administration of rabies immune globulin are the only effective methods for post-exposure prophylaxis against rabies. Reverse genetic technique is a novel approach to investigate the function of a specific gene by analyzing the phenotypic effects through directly manipulating the gene sequences. It has revolutionized and provided a powerful tool to study the molecular biology of RNA viruses and has been widely used in rabies virus research. The attenuation of rabies virus virulence is the prerequisite for rabies vaccine development. Given the current challenge that sufficient and affordable high-quality vaccines are limited and lacking for global rabies prevention and control, highly cell-adapted, stable, and attenuated rabies viruses with broad cross-reactivity against different viral variants are ideal candidates for consideration to meet the need for human rabies control in the future. A number of approaches have been pursued to reduce the virulence of the virus and improve the safety of rabies vaccines. The application of reverse genetic technique has greatly advanced the engineering of rabies virus and paves the avenue for utilizing rabies virus for vaccine against rabies, viral vectors for exogenous antigen expression, and gene therapy in the future. PMID:25994916

  15. A plasmid-based reverse genetics system for mammalian orthoreoviruses driven by a plasmid-encoded T7 RNA polymerase.

    PubMed

    Komoto, Satoshi; Kawagishi, Takahiro; Kobayashi, Takeshi; Ikizler, Mine; Iskarpatyoti, Jason; Dermody, Terence S; Taniguchi, Koki

    2014-02-01

    Mammalian orthoreoviruses (reoviruses) have served as highly useful models for studies of virus replication and pathogenesis. The development of a plasmid-based reverse genetics system represented a major breakthrough in reovirus research. The current reverse genetics systems for reoviruses rely on the expression of T7 RNA polymerase within cells transfected with reovirus gene-segment cDNA plasmids. In these systems, the T7 RNA polymerase is provided by using a recombinant vaccinia virus expressing T7 RNA polymerase or a cell line constitutively expressing T7 RNA polymerase. Here, we describe an alternative plasmid-based rescue system driven by a plasmid-encoded T7 RNA polymerase, which could increase the flexibility of such reverse genetics systems. Although this approach requires transfection of an additional plasmid, virus recovery was achieved when A549, BHK-21, or L929 cells were co-transfected with a reovirus 10-plasmid set together with a plasmid encoding T7 RNA polymerase. Theoretically, this system offers the possibility to generate reoviruses in any cell line, including those amenable to propagation of viral vectors for clinical use. Thus, this approach will increase the flexibility of reverse genetics for basic studies of reovirus biology and foster development of reoviruses for clinical applications. PMID:24183920

  16. Reversibility conditions for quantum channels and their applications

    SciTech Connect

    Shirokov, M E

    2013-08-31

    Conditions for a quantum channel (noncommutative Markov operator) to be reversible with respect to complete families of quantum states with bounded rank are obtained. A description of all quantum channels reversible with respect to a given (orthogonal or nonorthogonal) complete family of pure states is given. Some applications in quantum information theory are considered. Bibliography: 20 titles.

  17. Allele-specific chemical genetics: concept, strategies, and applications.

    PubMed

    Islam, Kabirul

    2015-02-20

    The relationship between DNA and protein sequences is well understood, yet because the members of a protein family/subfamily often carry out the same biochemical reaction, elucidating their individual role in cellular processes presents a challenge. Forward and reverse genetics have traditionally been employed to understand protein functions with considerable success. A fundamentally different approach that has gained widespread application is the use of small organic molecules, known as chemical genetics. However, the slow time-scale of genetics and inherent lack of specificity of small molecules used in chemical genetics have limited the applicability of these methods in deconvoluting the role of individual proteins involved in fast, dynamic biological events. Combining the advantages of both the techniques, the specificity achieved with genetics along with the reversibility and tunability of chemical genetics, has led to the development of a powerful approach to uncover protein functions in complex biological processes. This technique is known as allele-specific chemical genetics and is rapidly becoming an essential toolkit to shed light on proteins and their mechanism of action. The current review attempts to provide a comprehensive description of this approach by discussing the underlying principles, strategies, and successful case studies. Potential future implications of this technology in expanding the frontiers of modern biology are discussed. PMID:25436868

  18. Genetic Applications in Avian Conservation

    USGS Publications Warehouse

    Haig, Susan M.; Bronaugh, Whitcomb M.; Crowhurst, Rachel S.; D'Elia, Jesse; Eagles-Smith, Collin A.; Epps, Clinton W.; Knaus, Brian; Miller, Mark P.; Moses, Michael L.; Oyler-McCance, Sara; Robinson, W. Douglas; Sidlauskas, Brian

    2011-01-01

    A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems.

  19. Development of a reverse genetics system to generate a recombinant Ebola virus Makona expressing a green fluorescent protein.

    PubMed

    Albario, Csar G; Wiggleton Guerrero, Lisa; Lo, Michael K; Nichol, Stuart T; Towner, Jonathan S

    2015-10-01

    Previous studies have demonstrated the potential application of reverse genetics technology in studying a broad range of aspects of viral biology, including gene regulation, protein function, cell entry, and pathogenesis. Here, we describe a highly efficient reverse genetics system used to generate recombinant Ebola virus (EBOV) based on a recent isolate from a human patient infected during the 2014-2015 outbreak in Western Africa. We also rescued a recombinant EBOV expressing a fluorescent reporter protein from a cleaved VP40 protein fusion. Using this virus and an inexpensive method to quantitate the expression of the foreign gene, we demonstrate its potential usefulness as a tool for screening antiviral compounds and measuring neutralizing antibodies. PMID:26122472

  20. Yeast Genetics and Biotechnological Applications

    NASA Astrophysics Data System (ADS)

    Mishra, Saroj; Baranwal, Richa

    Yeast can be recognized as one of the very important groups of microorganisms on account of its extensive use in the fermentation industry and as a basic eukaryotic model cellular system. The yeast Saccharomyces cerevisiae has been extensively used to elucidate the genetics and regulation of several key functions in the cell such as cell mating, electron transport chain, protein trafficking, cell cycle events and others. Even before the genome sequence of the yeast was out, the structural organization and function of several of its genes was known. With the availability of the origin of replication from the 2 ?m plasmid and the development of transformation system, it became the host of choice for expression of a number of important proteins. A large number of episomal and integrative shuttle vectors are available for expression of mammalian proteins. The latest developments in genomics and micro-array technology have allowed investigations of individual gene function by site-specific deletion method. The application of metabolic profiling has also assisted in understanding the cellular network operating in this yeast. This chapter is aimed at reviewing the use of this system as an experimental tool for conducting classical genetics. Various vector systems available, foreign genes expressed and the limitations as a host will be discussed. Finally, the use of various yeast enzymes in biotechnology sector will be reviewed.

  1. Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.

    PubMed

    Sunagawa, Genshiro A; Sumiyama, Kenta; Ukai-Tadenuma, Maki; Perrin, Dimitri; Fujishima, Hiroshi; Ukai, Hideki; Nishimura, Osamu; Shi, Shoi; Ohno, Rei-Ichiro; Narumi, Ryohei; Shimizu, Yoshihiro; Tone, Daisuke; Ode, Koji L; Kuraku, Shigehiro; Ueda, Hiroki R

    2016-01-26

    The identification of molecular networks at the system level in mammals is accelerated by next-generation mammalian genetics without crossing, which requires both the efficient production of whole-body biallelic knockout (KO) mice in a single generation and high-performance phenotype analyses. Here, we show that the triple targeting of a single gene using the CRISPR/Cas9 system achieves almost perfect KO efficiency (96%-100%). In addition, we developed a respiration-based fully automated non-invasive sleep phenotyping system, the Snappy Sleep Stager (SSS), for high-performance (95.3% accuracy) sleep/wake staging. Using the triple-target CRISPR and SSS in tandem, we reliably obtained sleep/wake phenotypes, even in double-KO mice. By using this system to comprehensively analyze all of the N-methyl-D-aspartate (NMDA) receptor family members, we found Nr3a as a short-sleeper gene, which is verified by an independent set of triple-target CRISPR. These results demonstrate the application of mammalian reverse genetics without crossing to organism-level systems biology in sleep research. PMID:26774482

  2. Potato genetics, genomics, and applications

    PubMed Central

    Watanabe, Kazuo

    2015-01-01

    Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding. PMID:25931980

  3. Experimental implementation of reverse time migration for nondestructive evaluation applications.

    PubMed

    Anderson, Brian E; Griffa, Michele; Bas, Pierre-Yves Le; Ulrich, Timothy J; Johnson, Paul A

    2011-01-01

    Reverse time migration (RTM) is a commonly employed imaging technique in seismic applications (e.g., to image reservoirs of oil). Its standard implementation cannot account for multiple scattering/reverberation. For this reason it has not yet found application in nondestructive evaluation (NDE). This paper applies RTM imaging to NDE applications in bounded samples, where reverberation is always present. This paper presents a fully experimental implementation of RTM, whereas in seismic applications, only part of the procedure is done experimentally. A modified RTM imaging condition is able to localize scatterers and locations of disbonding. Experiments are conducted on aluminum samples with controlled scatterers. PMID:21302980

  4. Clinical applications of melanoma genetics.

    PubMed

    Gabree, Michele; Patel, Devanshi; Rodgers, Linda

    2014-06-01

    Families that have several relatives with melanoma, multiple primary melanomas in one individual, younger than average ages of melanoma onset, and/or the presence of both pancreatic cancer and melanoma may be suggestive of a hereditary melanoma syndrome and are candidates for genetic counseling and risk assessment. Genetic counseling for hereditary melanoma presents many complexities. Only a minority of hereditary melanoma cases have been attributed to a single genetic factor, CDKN2A. Both the frequency and the penetrance of CDKN2A mutations has been shown to be dependent on multiple factors. The clinical utility of genetic testing for hereditary melanoma families is debatable because CDKN2A status may not impact medical management in patients with melanoma. No standard medical management guidelines exist for families with CDKN2A mutations; however, family history of melanoma and pancreatic cancer may warrant further discussion. Clinicians should discuss the clinical and psychological implications before genetic testing. Genetic counseling and pretest education regarding melanoma risk factors provides an opportunity to increase knowledge and understanding of melanoma risk, while addressing psychological risks and concerns. PMID:24652319

  5. Sex reversal triggers the rapid transition from genetic to temperature-dependent sex.

    PubMed

    Holleley, Clare E; O'Meally, Denis; Sarre, Stephen D; Marshall Graves, Jennifer A; Ezaz, Tariq; Matsubara, Kazumi; Azad, Bhumika; Zhang, Xiuwen; Georges, Arthur

    2015-07-01

    Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in amphibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change. PMID:26135451

  6. Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

    NASA Technical Reports Server (NTRS)

    Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

    1998-01-01

    Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

  7. Addition of exogenous polypeptides on the mammalian reovirus outer capsid using reverse genetics.

    PubMed

    Brochu-Lafontaine, Virginie; Lemay, Guy

    2012-02-01

    Addition of exogenous peptide sequences on viral capsids is a powerful approach to study the process of viral infection or to retarget viruses toward defined cell types. Until recently, it was not possible to manipulate the genome of mammalian reovirus and this was an obstacle to the addition of exogenous sequence tags onto the capsid of a replicating virus. This obstacle has now been overcome by the availability of the plasmid-based reverse genetics system. In the present study, reverse genetics was used to introduce different exogenous peptides, up to 40 amino acids long, at the carboxyl-terminal end of the ?1 outer capsid protein. The tagged viruses obtained were infectious, produce plaques of similar size, and could be easily propagated at high titers. However, attempts to introduce a 750 nucleotides-long sequence failed, even when it was added after the stop codon, suggesting a possible size limitation at the nucleic acid level. PMID:22155580

  8. A plasmid-based reverse genetics system for animal double-stranded RNA viruses.

    PubMed

    Kobayashi, Takeshi; Antar, Annukka A R; Boehme, Karl W; Danthi, Pranav; Eby, Elizabeth A; Guglielmi, Kristen M; Holm, Geoffrey H; Johnson, Elizabeth M; Maginnis, Melissa S; Naik, Sam; Skelton, Wesley B; Wetzel, J Denise; Wilson, Gregory J; Chappell, James D; Dermody, Terence S

    2007-04-19

    Mammalian orthoreoviruses (reoviruses) are highly tractable experimental models for studies of double-stranded (ds) RNA virus replication and pathogenesis. Reoviruses infect respiratory and intestinal epithelium and disseminate systemically in newborn animals. Until now, a strategy to rescue infectious virus from cloned cDNA has not been available for any member of the Reoviridae family of dsRNA viruses. We report the generation of viable reovirus following plasmid transfection of murine L929 (L) cells using a strategy free of helper virus and independent of selection. We used the reovirus reverse genetics system to introduce mutations into viral capsid proteins sigma1 and sigma3 and to rescue a virus that expresses a green fluorescent protein (GFP) transgene, thus demonstrating the tractability of this technology. The plasmid-based reverse genetics approach described here can be exploited for studies of reovirus replication and pathogenesis and used to develop reovirus as a vaccine vector. PMID:18005692

  9. UTILLdb, a Pisum sativum in silico forward and reverse genetics tool

    PubMed Central

    Dalmais, Marion; Schmidt, Julien; Le Signor, Christine; Moussy, Francoise; Burstin, Judith; Savois, Vincent; Aubert, Gregoire; Brunaud, Veronique; de Oliveira, Yannick; Guichard, Cecile; Thompson, Richard; Bendahmane, Abdelhafid

    2008-01-01

    The systematic characterization of gene functions in species recalcitrant to Agrobacterium-based transformation, like Pisum sativum, remains a challenge. To develop a high throughput forward and reverse genetics tool in pea, we have constructed a reference ethylmethane sulfonate mutant population and developed a database, UTILLdb, that contains phenotypic as well as sequence information on mutant genes. UTILLdb can be searched online for TILLING alleles, through the BLAST tool, or for phenotypic information about mutants by keywords. PMID:18302733

  10. Reversals.

    ERIC Educational Resources Information Center

    National Center on Educational Media and Materials for the Handicapped, Columbus, OH.

    Selected from the National Instructional Materials Information System (NIMIS)--a computer based on-line interactive retrieval system on special education materials--the bibliography covers nine materials for remediating reversals in handicapped students at the early childhood and elementary levels. Entries are presented in order of NIMIS accession

  11. An Assessment of Heavy Ion Irradiation Mutagenesis for Reverse Genetics in Wheat (Triticum aestivum L.)

    PubMed Central

    Fitzgerald, Timothy L.; Powell, Jonathan J.; Stiller, Jiri; Weese, Terri L.; Abe, Tomoko; Zhao, Guangyao; Jia, Jizeng; McIntyre, C. Lynne; Li, Zhongyi; Manners, John M.; Kazan, Kemal

    2015-01-01

    Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed. PMID:25719507

  12. Mobile Timekeeping Application Built on Reverse-Engineered JPL Infrastructure

    NASA Technical Reports Server (NTRS)

    Witoff, Robert J.

    2013-01-01

    Every year, non-exempt employees cumulatively waste over one man-year tracking their time and using the timekeeping Web page to save those times. This app eliminates this waste. The innovation is a native iPhone app. Libraries were built around a reverse- engineered JPL API. It represents a punch-in/punch-out paradigm for timekeeping. It is accessible natively via iPhones, and features ease of access. Any non-exempt employee can natively punch in and out, as well as save and view their JPL timecard. This app is built on custom libraries created by reverse-engineering the standard timekeeping application. Communication is through custom libraries that re-route traffic through BrowserRAS (remote access service). This has value at any center where employees track their time.

  13. Mouse Models of Cancer: Sleeping Beauty Transposons for Insertional Mutagenesis Screens and Reverse Genetic Studies

    PubMed Central

    Tschida, Barbara R.; Largaespada, David A.; Keng, Vincent W.

    2014-01-01

    The genetic complexity and heterogeneity of cancer has posed a problem in designing rationally targeted therapies effective in a large proportion of human cancer. Genomic characterization of many cancer types has provided a staggering amount of data that needs to be interpreted to further our understanding of this disease. Forward genetic screening in mice using Sleeping Beauty (SB) based insertional mutagenesis is an effective method for candidate cancer gene discovery that can aid in distinguishing driver from passenger mutations in human cancer. This system has been adapted for unbiased screens to identify drivers of multiple cancer types. These screens have already identified hundreds of candidate cancer-promoting mutations. These can be used to develop new mouse models for further study, which may prove useful for therapeutic testing. SB technology may also hold the key for rapid generation of reverse genetic mouse models of cancer, and has already been used to model glioblastoma and liver cancer. PMID:24468652

  14. [Applications of genetically modified animals].

    PubMed

    Houdebine, Louis-Marie

    2009-01-01

    The first transgenic animals, mice, were obtained in 1980. The techniques of gene transfer had to be adapted to obtain transgenic animals with an acceptable yield in about fifteen species. When the yield is low (low rate of random integration and targeted integration via homologous recombination), genetic modifications must be achieved in intermediate cells able to participate to the development of chimeric transgenic animals (ES cells, EG cells, iPS obtained by the dedifferentiation of somatic cells) or in somatic cells used as nuclear donor to generate transgenic clones. Various tools make possible a marked increase of homologous recombination efficiency (meganucleases and ZFN), or a gene inactivation at the genome level (direct or conditional knock out) or at the mRNA level (interfering RNAs). Vectors allow a more reliable transgene expression. Genetically modified animals are used mainly to obtain information on biological functions and human diseases. Transgenic animals produce recombinant pharmaceutical proteins in milk and soon in egg white. Pig organs adapted to be tolerated by patients might be tested in humans in five years. The projects based on the use of transgenesis to improve animal production are presently few. Transgenic salmon with accelerated growth might be on the market when their possible escape in oceans will be controlled. PMID:20122391

  15. Anisotropic Magnetic Confinement. Applications to Field-Reversed Configurations

    NASA Astrophysics Data System (ADS)

    Clemente, Roberto Antonio

    Introducing an auxiliary function of the usual poloidal magnetic stream function, it is possible to obtain axisymmetric solutions of the ideal anisotropic magnetohydrodynamic equations for steady rotating plasmas, in terms of solutions of the Maschke and Perrin equation for isotropic plasmas, with temperature as a surface function. For vanishing rotation, the problem is reduced to the classical Grad-Schlter-Shafranov equation for static equilibria. Some applications of the equilibrium models to the study of tilting stability and classical particle transport in field-reversed configurations are presented.

  16. Identification of plant genetic loci involved in a posttranscriptional mechanism for meiotically reversible transgene silencing.

    PubMed Central

    Dehio, C; Schell, J

    1994-01-01

    Numerous reports describe phenomena of transgene silencing in plants, yet the underlying genetic and molecular mechanisms are poorly understood. We observed that regeneration of Arabidopsis thaliana plants transgenic for the rolB gene of Agrobacterium rhizogenes results in a selection for transgene silencing. Transgene silencing could be monitored in this system by reversion of the visible RolB phenotype. We report a phenotypic, molecular, and genetic characterization of a meiotically reversible transgene silencing phenomenon observed in a rolB transgenic line. In this line, the rolB gene is expressed strongly and uniformly in seedlings, but in the course of further development, the rolB gene is silenced erratically at a frequency that depends on the dosage of rolB. The silenced state is mitotically stable, while complete resetting of rolB gene expression occurs in seedlings of the following generation. The silencing of rolB correlates with a dramatic reduction of steady-state rolB transcripts, while rolB nuclear run-off transcripts are only moderately reduced. Therefore, rolB gene silencing seems to act predominantly at the posttranscriptional level. The process of rolB gene silencing was found to be affected by two extragenic modifier loci that influence both the frequency and the timing of rolB gene silencing during plant development. These genetic data demonstrate a direct involvement of defined plant genes in this form of gene silencing. Images PMID:8202523

  17. Identification of Host Genes Involved in Geminivirus Infection Using a Reverse Genetics Approach

    PubMed Central

    Luna, Ana P.; Bejarano, Eduardo R.

    2011-01-01

    Geminiviruses, like all viruses, rely on the host cell machinery to establish a successful infection, but the identity and function of these required host proteins remain largely unknown. Tomato yellow leaf curl Sardinia virus (TYLCSV), a monopartite geminivirus, is one of the causal agents of the devastating Tomato yellow leaf curl disease (TYLCD). The transgenic 2IRGFP N. benthamiana plants, used in combination with Virus Induced Gene Silencing (VIGS), entail an important potential as a tool in reverse genetics studies to identify host factors involved in TYLCSV infection. Using these transgenic plants, we have made an accurate description of the evolution of TYLCSV replication in the host in both space and time. Moreover, we have determined that TYLCSV and Tobacco rattle virus (TRV) do not dramatically influence each other when co-infected in N. benthamiana, what makes the use of TRV-induced gene silencing in combination with TYLCSV for reverse genetic studies feasible. Finally, we have tested the effect of silencing candidate host genes on TYLCSV infection, identifying eighteen genes potentially involved in this process, fifteen of which had never been implicated in geminiviral infections before. Seven of the analyzed genes have a potential anti-viral effect, whereas the expression of the other eleven is required for a full infection. Interestingly, almost half of the genes altering TYLCSV infection play a role in postranslational modifications. Therefore, our results provide new insights into the molecular mechanisms underlying geminivirus infections, and at the same time reveal the 2IRGFP/VIGS system as a powerful tool for functional reverse genetics studies. PMID:21818318

  18. Applications of genetic engineering in veterinary medicine.

    PubMed

    Ciftci, K; Trovitch, P

    2000-09-15

    A mutation of just one gene will cause abnormal cell behavior leading to the synthesis of a dysfunctional protein. This mutation will inevitably result in the cell functioning only marginally or not at all. Other genetic mutations interfere with the cell's normal life cycle, especially the cell-division cycle. The goal behind recombinant DNA technology is to deliver the correct version of a mutated gene to the cell so that the expression will lead to the normal production of protein and the restoration of normal cell function. This can be considered qualitatively different from other conventional treatments due to genetic material being a putative therapeutic agent. By altering the genetic material of cells, gene therapy may correct, or one day cure, the specific disease pathophysiology. Genetic engineering has been used in veterinary medicine to diagnose, prevent and treat diseases, breed different species and produce transgenic animals for therapeutic proteins or xenografting. In this review the current status of recombinant DNA technology and its application in veterinary medicine together with the obstacles to, and applications of, genetic engineering in veterinary medicine are discussed. PMID:10967221

  19. Applications of Time-Reversal Processing for Planetary Surface Communications

    NASA Technical Reports Server (NTRS)

    Barton, Richard J.

    2007-01-01

    Due to the power constraints imposed on wireless sensor and communication networks deployed on a planetary surface during exploration, energy efficient transfer of data becomes a critical issue. In situations where groups of nodes within a network are located in relatively close proximity, cooperative communication techniques can be utilized to improve the range, data rate, power efficiency, and lifetime of the network. In particular, if the point-to-point communication channels on the network are well modeled as frequency non-selective, distributed or cooperative beamforming can employed. For frequency-selective channels, beamforming itself is not generally appropriate, but a natural generalization of it, time-reversal communication (TRC), can still be effective. Time-reversal processing has been proposed and studied previously for other applications, including acoustical imaging, electromagnetic imaging, underwater acoustic communication, and wireless communication channels. In this paper, we study both the theoretical advantages and the experimental performance of cooperative TRC for wireless communication on planetary surfaces. We give a brief introduction to TRC and present several scenarios where TRC could be profitably employed during planetary exploration. We also present simulation results illustrating the performance of cooperative TRC employed in a complex multipath environment and discuss the optimality of cooperative TRC for data aggregation in wireless sensor networks

  20. Establishment of a reverse genetics system for Schmallenberg virus, a newly emerged orthobunyavirus in Europe.

    PubMed

    Elliott, Richard M; Blakqori, Gjon; van Knippenberg, Ingeborg C; Koudriakova, Elina; Li, Ping; McLees, Angela; Shi, Xiaohong; Szemiel, Agnieszka M

    2013-04-01

    Schmallenberg virus (SBV) is a newly emerged orthobunyavirus that has caused widespread disease in cattle, sheep and goats in Europe. Like other orthobunyaviruses, SBV is characterized by a tripartite negative-sense RNA genome that encodes four structural and two non-structural proteins. This study showed that SBV has a wide in vitro host range, and that BHK-21 cells are a convenient host for both SBV propagation and assay by plaque titration. The SBV genome segments were cloned as cDNA and a three-plasmid rescue system was established to recover infectious virus. Recombinant virus behaved similarly in cell culture to authentic virus. The ORF for the non-structural NSs protein, encoded on the smallest genome segment, was disrupted by introduction of translation stop codons in the appropriate cDNA, and when this plasmid was used in reverse genetics, a recombinant virus that lacked NSs expression was recovered. This virus had reduced capacity to shut-off host-cell protein synthesis compared with the wild-type virus. In addition, the NSs-deleted virus induced interferon (IFN) in cells, indicating that, like other orthobunyaviruses, NSs functions as an IFN antagonist, most probably by globally inhibiting host-cell metabolism. The development of a robust reverse genetics system for SBV will facilitate investigation of its pathogenic mechanisms as well as the creation of attenuated strains that could be candidate vaccines. PMID:23255627

  1. Chronic kidney disease induced in mice by reversible unilateral ureteral obstruction is dependent on genetic background

    PubMed Central

    Shakaib, Mohammed I.; Chang, Anthony; Mathew, Liby; Olayinka, Oladunni; Minto, Andrew W. M.; Sarav, Menaka; Hack, Bradley K.; Quigg, Richard J.

    2010-01-01

    Chronic kidney disease (CKD) begins with renal injury; the progression thereafter depends upon a number of factors, including genetic background. Unilateral ureteral obstruction (UUO) is a well-described model of renal fibrosis and as such is considered a model of CKD. We used an improved reversible unilateral ureteral obstruction (rUUO) model in mice to study the strain dependence of development of CKD after obstruction-mediated injury. C57BL/6 mice developed CKD after reversal of three or more days of ureteral obstruction as assessed by blood urea nitrogen (BUN) measurements (>40 mg/dl). In contrast, BALB/c mice were resistant to CKD with up to 10 days ureteral obstruction. During rUUO, C57BL/6 mice exhibited pronounced inflammatory and intrinsic proliferative cellular responses, disruption of renal architecture, and ultimately fibrosis. By comparison, BALB/c mice had more controlled and measured extrinsic and intrinsic responses to injury with a return to normal within several weeks after release of ureteral obstruction. Our findings provide a model that allows investigation of the genetic basis of events during recovery from injury that contribute to the development of CKD. PMID:20089676

  2. Evolutionary reversion of live viral vaccines: Can genetic engineering subdue it?

    PubMed Central

    Bull, J. J.

    2016-01-01

    Attenuated, live viral vaccines have been extraordinarily successful in protecting against many diseases. The main drawbacks in their development and use have been reliance on an unpredictable method of attenuation and the potential for evolutionary reversion to high virulence. Methods of genetic engineering now provide many safer alternatives to live vaccines, so if live vaccines are to compete with these alternatives in the future, they must either have superior immunogenicity or they must be able to overcome these former disadvantages. Several live vaccine designs that were historically inaccessible are now feasible because of advances in genome synthesis. Some of those methods are addressed here, with an emphasis on whether they enable predictable levels of attenuation and whether they are stable against evolutionary reversion. These new designs overcome many of the former drawbacks and position live vaccines to be competitive with alternatives. Not only do new methods appear to retard evolutionary reversion enough to prevent vaccine-derived epidemics, but it may even be possible to permanently attenuate live vaccines that are transmissible but cannot evolve to higher virulence under prolonged adaptation.

  3. Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors

    PubMed Central

    Zhang, Wenheng; Steinmann, Victor W.; Nikolov, Lachezar; Kramer, Elena M.; Davis, Charles C.

    2013-01-01

    Malpighiaceae possess flowers with a unique bilateral symmetry (zygomorphy), which is a hypothesized adaptation associated with specialization on neotropical oil bee pollinators. Gene expression of two representatives of the CYC2 lineage of floral symmetry TCP genes, CYC2A and CYC2B, demarcate the adaxial (dorsal) region of the flower in the characteristic zygomorphic flowers of most Malpighiaceae. Several clades within the family, however, have independently lost their specialized oil bee pollinators and reverted to radial flowers (actinomorphy) like their ancestors. Here, we investigate CYC2 expression associated with four independent reversals to actinomorphy. We demonstrate that these reversals are always associated with alteration of the highly conserved CYC2 expression pattern observed in most New World (NW) Malpighiaceae. In NW Lasiocarpus and Old World (OW) Microsteria, the expression of CYC2-like genes has expanded to include the ventral region of the corolla. Thus, the pattern of gene expression in these species has become radialized, which is comparable to what has been reported in the radial flowered legume clade Cadia. In striking contrast, in NW Psychopterys and OW Sphedamnocarpus, CYC2-like expression is entirely absent or at barely detectable levels. This is more similar to the pattern of CYC2 expression observed in radial flowered Arabidopsis. These results collectively indicate that, regardless of geographic distribution, reversals to similar floral phenotypes in this large tropical angiosperm clade have evolved via different genetic changes from an otherwise highly conserved developmental program. PMID:23970887

  4. Application of Molecular Genetics and Transformation to Barley Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter of the new barley monograph summarizes current applications of molecular genetics and transformation to barley improvement. The chapter describes recent applications of molecular markers including association genetics, QTL mapping and marker assisted selection in barley programs, and in...

  5. Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics.

    PubMed

    Wu, Jian-Li; Wu, Chanjian; Lei, Cailin; Baraoidan, Marietta; Bordeos, Alicia; Madamba, Ma Reina Suzette; Ramos-Pamplona, Marilou; Mauleon, Ramil; Portugal, Arlett; Ulat, Victor Jun; Bruskiewich, Richard; Wang, Guoliang; Leach, Jan; Khush, Gurdev; Leung, Hei

    2005-09-01

    IR64, the most widely grown indica rice in South and Southeast Asia, possesses many positive agronomic characteristics (e.g., wide adaptability, high yield potential, tolerance to multiple diseases and pests, and good eating quality,) that make it an ideal genotype for identifying mutational changes in traits of agronomic importance. We have produced a large collection of chemical and irradiation-induced IR64 mutants with different genetic lesions that are amenable to both forward and reverse genetics. About 60,000 IR64 mutants have been generated by mutagenesis using chemicals (diepoxybutane and ethylmethanesulfonate) and irradiation (fast neutron and gamma ray). More than 38,000 independent lines have been advanced to M4 generation enabling evaluation of quantitative traits by replicated trials. Morphological variations at vegetative and reproductive stages, including plant architecture, growth habit, pigmentation and various physiological characters, are commonly observed in the four mutagenized populations. Conditional mutants such as gain or loss of resistance to blast, bacterial blight, and tungro disease have been identified at frequencies ranging from 0.01% to 0.1%. Results from pilot experiments indicate that the mutant collections are suitable for reverse genetics through PCR-detection of deletions and TILLING. Furthermore, deletions can be detected using oligomer chips suggesting a general technique to pinpoint deletions when genome-wide oligomer chips are broadly available. M4 mutant seeds are available for users for screening of altered response to multiple stresses. So far, more than 15,000 mutant lines have been distributed. To facilitate broad usage of the mutants, a mutant database has been constructed in the International Rice Information System (IRIS; http: //www.iris.irri.org) to document the phenotypes and gene function discovered by users. PMID:16217604

  6. The Applications of Genetic Algorithms in Medicine

    PubMed Central

    Ghaheri, Ali; Shoar, Saeed; Naderan, Mohammad; Hoseini, Sayed Shahabuddin

    2015-01-01

    A great wealth of information is hidden amid medical research data that in some cases cannot be easily analyzed, if at all, using classical statistical methods. Inspired by nature, metaheuristic algorithms have been developed to offer optimal or near-optimal solutions to complex data analysis and decision-making tasks in a reasonable time. Due to their powerful features, metaheuristic algorithms have frequently been used in other fields of sciences. In medicine, however, the use of these algorithms are not known by physicians who may well benefit by applying them to solve complex medical problems. Therefore, in this paper, we introduce the genetic algorithm and its applications in medicine. The use of the genetic algorithm has promising implications in various medical specialties including radiology, radiotherapy, oncology, pediatrics, cardiology, endocrinology, surgery, obstetrics and gynecology, pulmonology, infectious diseases, orthopedics, rehabilitation medicine, neurology, pharmacotherapy, and health care management. This review introduces the applications of the genetic algorithm in disease screening, diagnosis, treatment planning, pharmacovigilance, prognosis, and health care management, and enables physicians to envision possible applications of this metaheuristic method in their medical career.] PMID:26676060

  7. Application of Genetic Algorithms in Seismic Tomography

    NASA Astrophysics Data System (ADS)

    Soupios, Pantelis; Akca, Irfan; Mpogiatzis, Petros; Basokur, Ahmet; Papazachos, Constantinos

    2010-05-01

    In the earth sciences several inverse problems that require data fitting and parameter estimation are nonlinear and can involve a large number of unknown parameters. Consequently, the application of analytical inversion or optimization techniques may be quite restrictive. In practice, most analytical methods are local in nature and rely on a linearized form of the problem in question, adopting an iterative procedure using partial derivatives to improve an initial model. This approach can lead to a dependence of the final model solution on the starting model and is prone to entrapment in local misfit minima. Moreover, the calculation of derivatives can be computationally inefficient and create instabilities when numerical approximations are used. In contrast to these local minimization methods, global techniques that do not rely on partial derivatives, are independent of the form of the data misfit criterion, and are computationally robust. Such methods often use random processes to sample a selected wider span of the model space. In this situation, randomly generated models are assessed in terms of their data-fitting quality and the process may be stopped after a certain number of acceptable models is identified or continued until a satisfactory data fit is achieved. A new class of methods known as genetic algorithms achieves the aforementioned approximation through novel model representation and manipulations. Genetic algorithms (GAs) were originally developed in the field of artificial intelligence by John Holland more than 20 years ago, but even in this field it is less than a decade that the methodology has been more generally applied and only recently did the methodology attract the attention of the earth sciences community. Applications have been generally concentrated in geophysics and in particular seismology. As awareness of genetic algorithms grows there surely will be many more and varied applications to earth science problems. In the present work, the application of hybrid genetic algorithms in seismic tomography is examined and the efficiency of least squares and genetic methods as representative of the local and global optimization, respectively, is presented and evaluated. The robustness of both optimization methods has been tested and compared for the same source-receiver geometry and characteristics of the model structure (anomalies, etc.). A set of seismic refraction synthetic (noise free) data was used for modeling. Specifically, cross-well, down-hole and typical refraction studies using 24 geophones and 5 shoots were used to confirm the applicability of the genetic algorithms in seismic tomography. To solve the forward modeling and estimate the traveltimes, the revisited ray bending method was used supplemented by an approximate computation of the first Fresnel volume. The root mean square (rms) error as the misfit function was used and calculated for the entire random velocity model for each generation. After the end of each generation and based on the misfit of the individuals (velocity models), the selection, crossover and mutation (typical process steps of genetic algorithms) were selected continuing the evolution theory and coding the new generation. To optimize the computation time, since the whole procedure is quite time consuming, the Matlab Distributed Computing Environment (MDCE) was used in a multicore engine. During the tests, we noticed that the fast convergence that the algorithm initially exhibits (first 5 generations) is followed by progressively slower improvements of the reconstructed velocity models. Thus, to improve the final tomographic models, a hybrid genetic algorithm (GA) approach was adopted by combining the GAs with a local optimization method after several generations, on the basis of the convergence of the resulting models. This approach is shown to be efficient, as it directs the solution search towards a model region close to the global minimum solution.

  8. Fractionation of bovine caseins by reverse phase high performance liquid chromatography: identification of a genetic variant.

    PubMed

    Carles, C

    1986-02-01

    Samples of reduced whole casein from genetically typed individual cows were quantitatively separated into their main components, alpha s1-, alpha s2-, beta- and kappa-caseins by reverse phase high performance liquid chromatography (RP-HPLC) using a mobile phase of phosphate-buffered aqueous propan-2-ol containing sodium dodecyl sulphate and an octadecylsilyl stationary phase. One casein sample was found to give two peaks of beta-casein of approximately equal areas. RP-HPLC of tryptic digests of the two separated peak fractions gave identical patterns with the exception of one peptide peak with different retention times. Amino acid analyses performed on both fractions showed that they corresponded to peptide 114-169 of beta-casein A1. The atypical beta-casein differed from the typical one by a Pro----Leu substitution in region 114-169. PMID:3958291

  9. Examination of a plasmid-based reverse genetics system for human astrovirus.

    PubMed

    Chapellier, Benoit; Tange, Shoichiro; Tasaki, Hidetaka; Yoshida, Kazuhiro; Zhou, Yan; Sakon, Naomi; Katayama, Kazuhiko; Nakanishi, Akira

    2015-10-01

    A plasmid-based reverse genetics system for human astrovirus type 1 (HAstV1) is examined. Upon transfection into 293T cells, the plasmid vector, which harbors a HAstV1 expression cassette, expressed astroviral RNA that appeared to be capable of viral RNA replication, as indicated by the production of subgenomic RNA and capsid protein expression irrespective of the heterologous 5' ends of the transcribed RNA. Particles infectious to Caco-2 cells were made in this system; however, their infectivity was much lower than would be expected from the amount of particles apparently produced. Using Huh-7 cells as the transfection host with the aim of improving viral capsid processing for virion maturation partially restored the efficiency of infectious particle formation. Our results support the possibility that the DNA transfection process induces a cellular response that targets late, but not early, stages of HAstV1 infection. PMID:26272702

  10. Detection of infectious bursal disease virus isolates with unknown antigenic properties by reverse genetics.

    PubMed

    Icard, Alan H; Sellers, Holly S; Mundt, Egbert

    2008-12-01

    Infectious bursal disease virus (IBDV) serotype 1 is the causative agent of a highly contagious immunosuppressive disease of young chickens. In the past, a number of antigenic, as well as pathogenic, subtypes have been described. The determination of the antigenic makeup of circulating strains is of vital interest to the poultry industry because changes in the antigenicity of circulating field strains have an impact on the use of vaccines. To obtain a more comprehensive overview of the relationship between the nucleotide and amino acid sequence and the antigenic makeup of field isolates, a system based on reverse genetics of IBDV was established. Using this approach, a database for field isolates from three different states in the United States (Georgia, Alabama, and Louisiana), consisting of nucleotide sequence, amino acid sequence, and a reaction pattern based on a panel of monoclonal antibodies, was established. The obtained results showed that phylogenic analysis, which is based on the similarity of sequences, would lead to false conclusions regarding a possible antigenic makeup of the particular isolate. Sequences of field samples were divided into three groups: 1) those that grouped with variant strain E/Del sequences but were antigenically different, 2) those that did not group with sequences of E/Del but were similar in their antigenic makeup, and 3) those that did not group with E/Del sequences and were antigenically different. In addition, using the reverse-genetics approach, a number of field isolates showed no reactivity with any of the used monoclonal antibodies, indicating that an unknown, antigenic subtype of IBDV serotype 1 is circulating in the field. PMID:19166049

  11. Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120.

    PubMed

    Zhou, Ying Shun; Zhang, Yi; Wang, Hong Ning; Fan, Wen Qiao; Yang, Xin; Zhang, An Yun; Zeng, Fan Ya; Zhang, Zhi Kun; Cao, Hai Peng; Zeng, Cheng

    2013-02-22

    Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. Thirteen 1.5-2.8 kb fragments contiguously spanning the virus genome were amplified and cloned into pMD19-T. Transcription grade complete length cDNA was acquired by a modified "No See'm" ligation strategy, which employed restriction enzyme Bsa I and BsmB I and ligated more than two fragments in one T4 ligase reaction. The full-length genomic cDNA was transcribed and its transcript was transfected by electroporation into BHK-21 together with the transcript of nucleocapsid gene. At 48 h post transfection, the medium to culture the transfected BHK-21 cells was harvested and inoculated into 10-days old SPF embryonated chicken eggs (ECE) to replicate the rescued virus. After passage of the virus in ECE five times, the rescued H120 virus (R-H120) was successfully recovered. R-H120 was subsequently identified to possess the introduced silent mutation site in its genome. Some biological characteristics of R-H120 such as growth curve, EID50 and HA titers, were tested and all of them were very similar to its parent strain H120. In addition, both R-H120 and H120 induced a comparable titer of HA inhibition (HI) antibody in immunized chickens and also provided up to 85% of immune protection to the chickens that were challenged with Mass41 IBV strain. The present study demonstrated that construction of infectious clone from IBV vaccine strain H120 is possible and IBV-H120 can be use as a vaccine vector for the development of novel vaccines through molecular recombination and the modified reverse genetics approach. PMID:22999521

  12. Machine learning applications in genetics and genomics.

    PubMed

    Libbrecht, Maxwell W; Noble, William Stafford

    2015-06-01

    The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning applications for the analysis of genome sequencing data sets, including the annotation of sequence elements and epigenetic, proteomic or metabolomic data. We present considerations and recurrent challenges in the application of supervised, semi-supervised and unsupervised machine learning methods, as well as of generative and discriminative modelling approaches. We provide general guidelines to assist in the selection of these machine learning methods and their practical application for the analysis of genetic and genomic data sets. PMID:25948244

  13. Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics.

    PubMed

    Zhou, Bin; Lin, Xudong; Wang, Wei; Halpin, Rebecca A; Bera, Jayati; Stockwell, Timothy B; Barr, Ian G; Wentworth, David E

    2014-05-01

    Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock. PMID:24501036

  14. A tunable and reversible platform for the intracellular formation of genetically engineered protein microdomains.

    PubMed

    Pastuszka, Martha K; Janib, Siti M; Weitzhandler, Isaac; Okamoto, Curtis T; Hamm-Alvarez, Sarah; Mackay, J Andrew

    2012-11-12

    From mitochondria to the nuclear envelope, the controlled assembly of micro- and nanostructures is essential for life; however, the level at which we can deliberately engineer the assembly of microstructures within intracellular environments remains primitive. To overcome this obstacle, we present a platform to reversibly assemble genetically engineered protein microdomains (GEPMs) on the time scale of minutes within living cells. Biologically inspired from the human protein tropoelastin, these protein polymers form a secondary aqueous phase above a tunable transition temperature. This assembly process is easily manipulated to occur at or near physiological temperature by adjusting molecular weight and hydrophobicity. We fused protein polymers to green fluorescent protein (GFP) to visualize their behavior within the cytoplasm. While soluble, these polymers have a similar intracellular diffusion constant as cytosolic proteins at 7.4 ?m(2)/s; however, above their phase transition temperature, the proteins form distinct microdomains (0.1-2 ?m) with a reduced diffusion coefficient of 1.1 ?m(2)/s. Microdomain assembly and disassembly are both rapid processes with half-lives of 3.8 and 1.0 min, respectively. Via selection of the protein polymer, the assembly temperature is tunable between 20 and 40 C. This approach may be useful to control intracellular formation of genetically engineered proteins and protein complexes into concentrated microdomains. PMID:23088632

  15. Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics

    PubMed Central

    Zhou, Bin; Lin, Xudong; Wang, Wei; Halpin, Rebecca A.; Bera, Jayati; Stockwell, Timothy B.; Barr, Ian G.

    2014-01-01

    Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock. PMID:24501036

  16. Clinical applications of molecular genetic discoveries.

    PubMed

    Marian, Ali J

    2016-02-01

    Genome-wide association studies of complex traits have mapped >15,000 common single nucleotide variants (SNVs). Likewise, applications of massively parallel nucleic acid sequencing technologies often referred to as next-generation sequencing to molecular genetic studies of complex traits have catalogued a large number of rare variants (population frequency of <0.01) in cases with complex traits. Moreover, high-throughput nucleic acid sequencing, variant burden analysis, and linkage studies are illuminating the presence of large number of SNVs in cases and families with single-gene disorders. The plethora of the genetic variants has exposed the formidable challenge of identifying the causal and pathogenic variants from the enormous number of innocuous common and rare variants that exist in the population and in an individual genome. The arduous task of identifying the causal and pathogenic variants is further compounded by the pleiotropic effects of the variants, complexity of cis and trans interactions in the genome, variability in phenotypic expression of the disease, as well as phenotypic plasticity, and the multifarious determinants of the phenotype. Population genetic studies offer the initial roadmaps and have the potential to elucidate novel pathways involved in the pathogenesis of the disease. However, the genome of an individual is unique, rendering unambiguous identification of the causal or pathogenic variant in a single individual exceedingly challenging. Yet, the focus of the practice of medicine is on the individual, as Sir William Osler elegantly expressed in his insightful quotation: "The good physician treats the disease; the great physician treats the patient who has the disease." The daunting task facing physicians, patients, and researchers alike is to apply the modern genetic discoveries to care of the individual with or at risk of the disease. PMID:26548329

  17. Genetically modified plants for tactical systems applications

    NASA Astrophysics Data System (ADS)

    Stewart, C. Neal, Jr.

    2002-08-01

    Plants are ubiquitous in the environment and have the ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green light when excited by blue or UV light. In addition, my group and collaborators have developed methods to detect GFP in plants by contact instruments and at a standoff. There are several tactical uses for this technology. Some obvious applications are using plants as sentinels for detecting biological and chemical warfare agents or their derivatives from a remote platform, as well as detecting explosives. Another tactical application is covert monitoring using individual plants. Different methods to detect GFP in transgenic plants will be discussed.

  18. Genetically modified plants for law enforcement applications

    NASA Astrophysics Data System (ADS)

    Stewart, C. Neal, Jr.

    2002-08-01

    Plants are ubiquitous in the environment and have the unique ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green light when excited by blue or UV light. In addition, my group and collaborators have developed methods to detect GFP in plants by contact instruments and at a standoff. There are several law enforcement applications for this technology. One involves using tagging and perhaps modifying drug plants genetically. In one instance, we could tag them for destruction. In another, we could adulterate them directly. Another application is one that falls into the chemical terrorism and bioterrorism countermeasures category. We are developing plants to sense toxins and whole organisms covertly. Plants are well adapted to monitor large geographic areas; biosurveillance. Some examples of research being performed focus on plants with plant pathogen inducible promoters fused to GFP for disease sensing, and algae biosensors for chemicals.

  19. Application of genetic algorithm to steganalysis

    NASA Astrophysics Data System (ADS)

    Knapik, Timothy; Lo, Ephraim; Marsh, John A.

    2006-05-01

    We present a novel application of genetic algorithm (GA) to optimal feature set selection in supervised learning using support vector machine (SVM) for steganalysis. Steganalysis attempts to determine whether a cover object (in our case an image file) contains hidden information. This is a bivariate classification problem: the image either does or does not contain hidden data. Our SVM classifier uses a training set of images with known classification to "learn" how to classify images with unknown classification. The SVM uses a feature set, essentially a set of statistical quantities extracted from the image. The performance of the SVM classifier is heavily dependent on the feature set used. Too many features not only increase computation time but decrease performance, and too few features do not provide enough information for accurate classification. Our steganalysis technique uses entropic features that yield up to 240 features per image. The selection of an optimum feature set is a problem that lends itself well to genetic algorithm optimization. We describe this technique in detail and present a "GA optimized" feature set of 48 features that, for our application, optimizes the tradeoff between computation time and classification accuracy.

  20. Deletion of liaR Reverses Daptomycin Resistance in Enterococcus faecium Independent of the Genetic Background.

    PubMed

    Panesso, Diana; Reyes, Jinnethe; Gaston, Elizabeth P; Deal, Morgan; Londoo, Alejandra; Nigo, Masayuki; Munita, Jose M; Miller, William R; Shamoo, Yousif; Tran, Truc T; Arias, Cesar A

    2015-12-01

    We have shown previously that changes in LiaFSR, a three-component regulatory system predicted to orchestrate the cell membrane stress response, are important mediators of daptomycin (DAP) resistance in enterococci. Indeed, deletion of the gene encoding the response regulator LiaR in a clinical strain of Enterococcus faecalis reversed DAP resistance (DAP-R) and produced a strain hypersusceptible to antimicrobial peptides. Since LiaFSR is conserved in Enterococcus faecium, we investigated the role of LiaR in a variety of clinical E. faecium strains representing the most common DAP-R genetic backgrounds. Deletion of liaR in DAP-R E. faecium R446F (DAP MIC of 16 ?g/ml) and R497F (MIC of 24 ?g/ml; harboring changes in LiaRS) strains fully reversed resistance (DAP MICs decreasing to 0.25 and 0.094 ?g/ml, respectively). Moreover, DAP at concentrations of 13 ?g/ml (achieved with human doses of 12 mg/kg body weight) retained bactericidal activity against the mutants. Furthermore, the liaR deletion derivatives of these two DAP-R strains exhibited increased binding of boron-dipyrromethene difluoride (BODIPY)-daptomycin, suggesting that high-level DAP-R mediated by LiaR in E. faecium involves repulsion of the calcium-DAP complex from the cell surface. In DAP-tolerant strains HOU503F and HOU515F (DAP MICs within the susceptible range but bacteria not killed by DAP concentrations of 5 the MIC), deletion of liaR not only markedly decreased the DAP MICs (0.064 and 0.047 ?g/ml, respectively) but also restored the bactericidal activity of DAP at concentrations as low as 4 ?g/ml (achieved with human doses of 4 mg/kg). Our results suggest that LiaR plays a relevant role in the enterococcal cell membrane adaptive response to antimicrobial peptides independent of the genetic background and emerges as an attractive target to restore the activity of DAP against multidrug-resistant strains. PMID:26369959

  1. Pharmacological and genetic reversal of age dependent cognitive deficits due to decreased presenilin function

    PubMed Central

    McBride, Sean M. J.; Choi, Catherine H.; Schoenfeld, Brian P.; Bell, Aaron J.; Liebelt, David A.; Ferreiro, David; Choi, Richard J.; Hinchey, Paul; Kollaros, Maria; Terlizzi, Allison M.; Ferrick, Neal J.; Koenigsberg, Eric; Rudominer, Rebecca L.; Sumida, Ai; Chiorean, Stephanie; Siwicki, Kathleen K.; Nguyen, Hanh T.; Fortini, Mark E.; McDonald, Thomas V.; Jongens, Thomas A.

    2010-01-01

    Alzheimer's disease is the leading cause of cognitive loss and neurodegeneration in the developed world. Although its genetic and environmental causes are not generally known, familial forms of the disease (FAD) are due to mutations in a single copy of the Presenilin (PS) and Amyloid Precursor Protein (APP) genes. The dominant inheritance pattern of FAD indicates that it may be due to gain or change of function mutations. Studies of FAD-linked forms of presenilin in model organisms, however, indicate that they are loss of function, leading to the possibility that a reduction in PS activity might contribute to FAD and that proper psn levels are important for maintaining normal cognition throughout life. To explore this issue further, we have tested the effect of reducing psn activity during aging in Drosophila melanogaster males. We have found that flies in which the dosage of psn function is reduced by 50% display age-onset impairments in learning and memory. Treatment with metabotropic glutamate receptor (mGluR) antagonists or lithium during the aging process prevented the onset of these deficits, and treatment of aged flies reversed the age-dependent deficits. Genetic reduction of DmGluRA, the inositol trisphosphate receptor (InsP3R) or IPPase also prevented these age-onset cognitive deficits. These findings suggest that reduced psn activity may contribute to the age onset cognitive loss observed with FAD. They also indicate that enhanced mGluR signaling and calcium release regulated by InsP3R as underlying causes of the age-dependent cognitive phenotypes observed when psn activity is reduced. PMID:20631179

  2. Association of genetic polymorphisms in the telomerase reverse transcriptase gene with prostate cancer aggressiveness.

    PubMed

    Wu, Dapeng; Yu, Hongjie; Sun, Jielin; Qi, Jun; Liu, Qiang; Li, Ruipeng; Zheng, Siqun Lily; Xu, Jianfeng; Kang, Jian

    2015-07-01

    Telomerase reverse transcriptase (TERT), encoded by the TERT gene, is an essential component of telomerase, essential for the maintenance of telomere DNA length, chromosomal stability and cellular immortality. The aim of the present study was to evaluate the association between common genetic variations across the TERT gene region and prostate cancer (PCa) aggressiveness in a Chinese population. A total of 12 TERT tagging single-nucleotide polymorphisms (SNPs) were genotyped on the Sequenom Mass-ARRAY iPLEX platform in a case-case study with 1,210 Chinese patients with PCa. Unconditional logistic regression was used to investigate the association of genotypes with PCa aggressiveness, Gleason grade and risk of developing early-onset PCa. It was observed that the C allele of the TERT intron 2 SNP (rs2736100) was significantly associated with reduced risk of PCa aggressiveness [odds ratio (OR)=0.81; 95% confidence interval (CI): 0.66-0.99; P=0.037]. This allele was also significantly correlated with a reduced risk of developing a tumor with a high Gleason score (>7; OR=0.83; 95% CI: 0.70-0.99; P=0.039). The T allele of the intron 4 SNP (rs10069690) was found to be significantly associated with a decreased risk for an aggressive form of PCa (OR=0.76; 95% CI: 0.59-0.97; P=0.030). In addition, the A allele of rs10078761 located at the 3' end of the TERT gene exhibited a statistically significant association with the reduced risk of developing a higher grade disease (OR=0.48; 95% CI: 0.28-0.81; P=0.006). However, no association between TERT polymorphisms and age at diagnosis was observed in the present study. The present findings demonstrated for the first time, to the best of our knowledge, that genetic variations across the TERT gene are associated with PCa aggressiveness in a Chinese Han population. PMID:25738283

  3. Static Performance of Six Innovative Thrust Reverser Concepts for Subsonic Transport Applications: Summary of the NASA Langley Innovative Thrust Reverser Test Program

    NASA Technical Reports Server (NTRS)

    Asbury, Scott C.; Yetter, Jeffrey A.

    2000-01-01

    The NASA Langley Configuration Aerodynamics Branch has conducted an experimental investigation to study the static performance of innovative thrust reverser concepts applicable to high-bypass-ratio turbofan engines. Testing was conducted on a conventional separate-flow exhaust system configuration, a conventional cascade thrust reverser configuration, and six innovative thrust reverser configurations. The innovative thrust reverser configurations consisted of a cascade thrust reverser with porous fan-duct blocker, a blockerless thrust reverser, two core-mounted target thrust reversers, a multi-door crocodile thrust reverser, and a wing-mounted thrust reverser. Each of the innovative thrust reverser concepts offer potential weight savings and/or design simplifications over a conventional cascade thrust reverser design. Testing was conducted in the Jet-Exit Test Facility at NASA Langley Research Center using a 7.9%-scale exhaust system model with a fan-to-core bypass ratio of approximately 9.0. All tests were conducted with no external flow and cold, high-pressure air was used to simulate core and fan exhaust flows. Results show that the innovative thrust reverser concepts achieved thrust reverser performance levels which, when taking into account the potential for system simplification and reduced weight, may make them competitive with, or potentially more cost effective than current state-of-the-art thrust reverser systems.

  4. Static Performance of Six Innovative Thrust Reverser Concepts for Subsonic Transport Applications: Summary of the NASA Langley Innovative Thrust Reverser Test Program

    NASA Technical Reports Server (NTRS)

    Asbury, Scott C.; Yetter, Jeffrey A.

    2000-01-01

    The NASA Langley Configuration Aerodynamics Branch has conducted an experimental investigation to study the static performance of innovative thrust reverser concepts applicable to high-bypass-ratio turbofan engines. Testing was conducted on a conventional separate-flow exhaust system configuration, a conventional cascade thrust reverser configuration, and six innovative thrust reverser configurations. The innovative thrust reverser configurations consisted of a cascade thrust reverser with porous fan-duct blocker, a blockerless thrust reverser, two core-mounted target thrust reversers, a multi-door crocodile thrust reverser, and a wing-mounted thrust reverser. Each of the innovative thrust reverser concepts offer potential weight savings and/or design simplifications over a conventional cascade thrust reverser design. Testing was conducted in the Jet-Exit Test Facility at NASA Langley Research Center using a 7.9%-scale exhaust system model with a fan-to-core bypass ratio of approximately 9.0. All tests were conducted with no external flow and cold, high-pressure air was used to simulate core and fan exhaust flows. Results show that the innovative thrust reverser concepts achieved thrust reverser performance levels which, when taking into account the potential for system simplification and reduced weight, may make them competitive with, or potentially more cost effective than current state-of-the-art thrust reverser systems. All data gathered in this investigation are contained in the CD-ROM.

  5. Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

    NASA Technical Reports Server (NTRS)

    Dhaeseleer, Patrik; Liang, Shoudan; Somogyi, Roland

    2000-01-01

    Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

  6. Reverse genetics of Mononegavirales: How they work, new vaccines, and new cancer therapeutics

    PubMed Central

    Pfaller, Christian K.; Cattaneo, Roberto; Schnell, Matthias J.

    2015-01-01

    The order Mononegavirales includes five families: Bornaviridae, Filoviridae, Nyamaviridae, Paramyxoviridae, and Rhabdoviridae. The genome of these viruses is one molecule of negative-sense single strand RNA coding for five to ten genes in a conserved order. The RNA is not infectious until packaged by the nucleocapsid protein and transcribed by the polymerase and co-factors. Reverse genetics approaches have answered fundamental questions about the biology of Mononegavirales. The lack of icosahedral symmetry and modular organization in the genome of these viruses has facilitated engineering of viruses expressing fluorescent proteins, and these fluorescent proteins have provided important insights about the molecular and cellular basis of tissue tropism and pathogenesis. Studies have assessed the relevance for virulence of different receptors and the interactions with cellular proteins governing the innate immune responses. Research has also analyzed the mechanisms of attenuation. Based on these findings, ongoing clinical trials are exploring new live attenuated vaccines and the use of viruses re-engineered as cancer therapeutics. PMID:25702088

  7. Development of reverse genetics for Ibaraki virus to produce viable VP6-tagged IBAV

    PubMed Central

    Matsuo, Eiko; Saeki, Keiichi; Roy, Polly; Kawano, Junichi

    2015-01-01

    Ibaraki virus (IBAV) is a member of the epizootic hemorrhagic disease virus (EHDV) serogroup, which belongs to the Orbivirus genus of the Reoviridae family. Although EHDV, including IBAV, represents an ongoing threat to livestock in the world, molecular mechanisms of EHDV replication and pathogenesis have been unclear. The reverse genetics (RG) system is one of the strong tools to understand molecular mechanisms of virus replication. Here, we developed a RG system for IBAV to identify the nonessential region of a minor structural protein, VP6, by generating VP6-truncated IBAV. Moreover, several tags were inserted into the truncated region to produce VP6-tagged IBAV. We demonstrated that all VP6-tagged IBAV could replicate in BHK cells in the absence of any helper VP6 protein. Further, tagged-VP6 proteins were first assembled into puncta in cells infected with VP6-tagged IBAV. Our data suggests that, in order to initiate primary replication, IBAV VP6 is likely to accumulate in some parts of infected cells to assemble efficiently into the primary replication complex (subcore). PMID:26101741

  8. Plasmid-Based Reverse Genetics for Animal Double-Stranded RNA Viruses

    PubMed Central

    Kobayashi, Takeshi; Antar, Annukka A. R.; Boehme, Karl W.; Danthi, Pranav; Eby, Elizabeth A.; Guglielmi, Kristen M.; Holm, Geoffrey H.; Johnson, Elizabeth M.; Maginnis, Melissa S.; Naik, Sam; Skelton, Wesley B.; Wetzel, J. Denise; Wilson, Gregory J.; Chappell, James D.; Dermody, Terence S.

    2007-01-01

    SUMMARY Mammalian orthoreoviruses (reoviruses) are highly tractable experimental models for studies of double-stranded (ds) RNA virus replication and pathogenesis. Reoviruses infect respiratory and intestinal epithelium and disseminate systemically in newborn animals. Until now, a strategy to rescue infectious virus from cloned cDNA has not been available for any member of the Reoviridae family of dsRNA viruses. We report the generation of viable reovirus following plasmid transfection of murine L929 (L) cells using a strategy free of helper virus and independent of selection. Point mutations introduced into viral capsid proteins ?1 and ?3 were used to define sequences that govern susceptibility to cleavage by intestinal proteases. We recovered a recombinant virus that expresses green fluorescent protein (GFP) by replacement of the ?3 open-reading frame with GFP. The plasmid-based reverse genetics approach described here can be exploited for studies of reovirus replication and pathogenesis and used to develop reovirus as a vaccine vector. PMID:18005692

  9. APPLICATIONS OF MIXED LINEAR MODEL APPROACHES ON COTTON QUANTITATIVE GENETICS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many practical genetic models have been developed based on the idea of analysis of variance (ANOVA) proposed by Fisher (1925). These genetic models include NC I, NC II designs, and diallele crossed models. The application of the ANOVA approach in quantitative genetic analyses greatly facilitated the...

  10. Community genetics: a new discipline and its application in Brazil.

    PubMed

    Ramalho, A S; Silva, R B

    2000-01-01

    Community genetics is a new discipline which aims to provide genetic services to the community as a whole. As a science, community genetics encompasses all research needed to develop and evaluate its application. There is no question that the development of community genetics is necessary in Brazil. The implementation of such programs in our country, especially for hemoglobinopathies, has been recommended by the World Health Organization and other international organizations. Apart from the need for and appeal of community genetics programs, some aspects require serious review. This article discusses various cultural, social, psychological, and economic factors that can make genetic screening an invasion of individual privacy. PMID:10738173

  11. Development and characterization of reverse genetics system for the Indian West Nile virus lineage 1 strain 68856.

    PubMed

    Pavitrakar, Daya V; Ayachit, Vijay M; Mundhra, Sonal; Bondre, Vijay P

    2015-12-15

    Our previous studies on West Nile virus (WNV) strains isolated from human patients in India suggested substantial variation at the genetic level reflecting their variable pathogenesis. This study describes the development of reverse genetics system for a neurovirulent WNV isolate 68856 and its characterization. Full length viral cDNA was cloned into bacterial artificial chromosome (BAC) under the transcription control of T7 promoter. The RNA transcripts obtained by in vitro transcription were infectious in mammalian cells upon transfection. Cytopathic effect caused by synthetic RNA transcripts in mammalian cells, detection of cell associated viral protein after transfection and recovery of genetic markers in the progeny virus genome marked the successful development of reverse genetics system for WNV. Replication potential and plaque morphology of newly expressed virus along with its antigenic cross reactivity with the parental virus suggests synthesis of biologically identical replicative virus. Comparative neuropathogenesis studies in murine model indicated that the three genetic changes occurred in the recombinant virus during in vitro transcription has no impact on viral pathogenesis. The stable infectious cDNA clone generated from the neurovirulent Indian WNV strain will serve as a valuable experimental tool to study the viral factors contributing towards pathogenesis, host-virus interaction and immune evasion. PMID:26388421

  12. Reverse osmosis application for butanol-acetone fermentation

    SciTech Connect

    Garcia, A.; Iannotti, E.L.; Fischer, J.R.

    1984-01-01

    The problems of dilute solvent concentration in butanol-acetone fermentation can be solved by using reverse osmosis to dewater the fermentation liquor. Polyamide membranes exhibited butanol rejection rates as high as 85%. Optimum rejection of butanol occurs at a pressure of approximately 5.5 to 6.5 MPa and hydraulic recoveries of 50-70%. Flux ranged from 0.5 to 1.8 l.

  13. Ontogenic and morphological study of gonadal formation in genetically-modified sex reversal XYPOS mice

    PubMed Central

    UMEMURA, Yuria; MIYAMOTO, Ryosuke; HASHIMOTO, Rie; KINOSHITA, Kyoko; OMOTEHARA, Takuya; NAGAHARA, Daichi; HIRANO, Tetsushi; KUBOTA, Naoto; MINAMI, Kiichi; YANAI, Shogo; MASUDA, Natsumi; YUASA, Hideto; MANTANI, Youhei; MATSUO, Eiko; YOKOYAMA, Toshifumi; KITAGAWA, Hiroshi; HOSHI, Nobuhiko

    2015-01-01

    Mammalian sexual fate is determined by the presence or absence of sex determining region of the Y chromosome (Sry) in the bipotential gonads. Recent studies have demonstrated that both male and female sexual development are induced by distinct and active genetic pathways. Breeding the Y chromosome from Mus m. domesticus poschiavinus (POS) strains into C57BL/6J (B6J) mice (B6J-XYPOS) has been shown to induce sex reversal (75%: bilateral ovary, 25%: true hermaphrodites). However, our B6N-XYPOS mice, which were generated by backcrossing of B6J-XYPOS on an inbred B6N-XX, develop as males (36%: bilateral testis with fertility as well as bilateral ovary (34%), and the remainder develop as true hermaphrodites. Here, we investigated in detail the expressions of essential sex-related genes and histological features in B6N-XYPOS mice from the fetal period to adulthood. The onsets of both Sry and SRY-box 9 (Sox9) expressions as determined spatiotemporally by whole-mount immunohistochemistry in the B6N-XYPOS gonads occurred 23 tail somites later than those in B6N-XYB6 gonads, but earlier than those in B6J-XYPOS, respectively. It is possible that such a small difference in timing of the Sry expression underlies testicular development in our B6N-XYPOS. Our study is the first to histologically show the expression and ectopic localization of a female-related gene in the XYPOS testes and a male-related gene in the XYPOS ovaries. The results from these and previous experiments indicate that the interplay between genome variants, epigenetics and developmental gene regulation is crucial for testis development. PMID:26194606

  14. Reverse osmosis applications to low-level radioactive waste

    SciTech Connect

    Garrett, L.

    1990-09-01

    The Hanford Site at Richland, Washington, is operated for the US Department of Energy (DOE) by Westinghouse Hanford Company. Since the Hanford Site was established in the 1940's, the operation of the various facilities has resulted in the contamination of liquid effluents and some groundwater with radioactive constituents. Westinghouse Hanford Company has been testing various technologies to determine their effectiveness in decontaminating these two types of liquids. Reverse osmosis (RO) has been applied to two process effluents and two groundwaters. Rejection data have been collected for uranium, technetium, tritium, strontium, cesium, and total alpha and beta. 4 refs., 1 fig., 8 tabs.

  15. Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird

    PubMed Central

    Harrison, Xavier A; York, Jennifer E; Young, Andrew J

    2014-01-01

    Sex-biased dispersal is pervasive and has diverse evolutionary implications, but the fundamental drivers of dispersal sex biases remain unresolved. This is due in part to limited diversity within taxonomic groups in the direction of dispersal sex biases, which leaves hypothesis testing critically dependent upon identifying rare reversals of taxonomic norms. Here, we use a combination of observational and genetic data to demonstrate a rare reversal of the avian sex bias in dispersal in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). Direct observations revealed that (i) natal philopatry was rare, with both sexes typically dispersing locally to breed, and (ii), unusually for birds, males bred at significantly greater distances from their natal group than females. Population genetic analyses confirmed these patterns, as (i) corrected Assignment index (AIc), FST tests and isolation-by-distance metrics were all indicative of longer dispersal distances among males than females, and (ii) spatial autocorrelation analysis indicated stronger within-group genetic structure among females than males. Examining the spatial scale of extra-group mating highlighted that the resulting ‘sperm dispersal’ could have acted in concert with individual dispersal to generate these genetic patterns, but gamete dispersal alone cannot account entirely for the sex differences in genetic structure observed. That leading hypotheses for the evolution of dispersal sex biases cannot readily account for these sex-reversed patterns of dispersal in white-browed sparrow weavers highlights the continued need for attention to alternative explanations for this enigmatic phenomenon. We highlight the potential importance of sex differences in the distances over which dispersal opportunities can be detected. PMID:25346189

  16. Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.

    PubMed

    Fetzner, S; Lingens, F

    1994-12-01

    This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail. PMID:7854251

  17. Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.

    PubMed Central

    Fetzner, S; Lingens, F

    1994-01-01

    This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail. PMID:7854251

  18. Transmission-reflection tomography: Application to reverse VSP data

    SciTech Connect

    Mao, W.; Stuart, G.W.

    1997-05-01

    A multiphase tomographic algorithm is presented that allows 2-D and 3-D slowness (inverse of velocity) and variable reflector depth to be reconstructed simultaneously from both transmission and reflection traveltimes. The authors analyze the ambiguity in the determination of velocity and depth in transmission and reflection data and realize that depth in transmission and reflection data and realize that depth perturbation is more sensitive to reflection traveltime anomalies than slowness perturbation, whereas the reverse is true of transmission traveltime anomalies. Because of the constraints on velocity and depth provided by the different wave types, this algorithm reduces the ambiguity substantially between velocity and depth prevalent in reflection tomography and also avoids the undetermined problem in transmission tomography. The linearized inversion was undertaken iteratively by decoupling velocity parameters from reflector depths. A rapid 2-D and 3-D ray-tracing algorithm is used to compute transmission and reflection traveltimes and partial derivatives with respect to slowness and reflector depth. Both depth and velocity are parameterized in terms of cubic B-spline functions. The method has been applied to a reverse vertical seismic profile (VSP) data set recorded on the British coal measures along a crossed-linear array.

  19. Imaging-Genetics Applications in Child Psychiatry

    ERIC Educational Resources Information Center

    Pine, Daniel S.; Ernst, Monique; Leibenluft, Ellen

    2010-01-01

    Objective: To place imaging-genetics research in the context of child psychiatry. Method: A conceptual overview is provided, followed by discussion of specific research examples. Results: Imaging-genetics research is described linking brain function to two specific genes, for the serotonin-reuptake-transporter protein and a monoamine oxidase…

  20. Imaging-Genetics Applications in Child Psychiatry

    ERIC Educational Resources Information Center

    Pine, Daniel S.; Ernst, Monique; Leibenluft, Ellen

    2010-01-01

    Objective: To place imaging-genetics research in the context of child psychiatry. Method: A conceptual overview is provided, followed by discussion of specific research examples. Results: Imaging-genetics research is described linking brain function to two specific genes, for the serotonin-reuptake-transporter protein and a monoamine oxidase

  1. A strategy for the identification of new abiotic stress determinants in Arabidopsis using web-based data mining and reverse genetics.

    PubMed

    Azevedo, Herlnder; Silva-Correia, Joana; Oliveira, Juliana; Laranjeira, Sara; Barbeta, Ctia; Amorim-Silva, Vitor; Botella, Miguel A; Lino-Neto, Teresa; Tavares, Rui M

    2011-12-01

    Since the sequencing of the Arabidopsis thaliana genome in 2000, plant researchers have faced the complex challenge of assigning function to thousands of genes. Functional discovery by in silico prediction or homology search resolved a significant number of genes, but only a minor part has been experimentally validated. Arabidopsis entry into the post-genomic era signified a massive increase in high-throughput approaches to functional discovery, which have since become available through publicly-available web-based resources. The present work focuses on an easy and straightforward strategy that couples data-mining to reverse genetics principles, to allow for the identification of new abiotic stress determinant genes. The strategy explores systematic microarray-based transcriptomics experiments, involving Arabidopsis abiotic stress responses. An overview of the most significant resources and databases for functional discovery in Arabidopsis is presented. The successful application of the outlined strategy is illustrated by the identification of a new abiotic stress determinant gene, HRR, which displays a heat-stress-related phenotype after a loss-of-function reverse genetics approach. PMID:22136640

  2. Plasmid-based human norovirus reverse genetics system produces reporter-tagged progeny virus containing infectious genomic RNA

    PubMed Central

    Katayama, Kazuhiko; Murakami, Kosuke; Sharp, Tyler M.; Guix, Susana; Oka, Tomoichiro; Takai-Todaka, Reiko; Nakanishi, Akira; Crawford, Sue E.; Atmar, Robert L.; Estes, Mary K.

    2014-01-01

    Human norovirus (HuNoV) is the leading cause of gastroenteritis worldwide. HuNoV replication studies have been hampered by the inability to grow the virus in cultured cells. The HuNoV genome is a positive-sense single-stranded RNA (ssRNA) molecule with three open reading frames (ORFs). We established a reverse genetics system driven by a mammalian promoter that functions without helper virus. The complete genome of the HuNoV genogroup II.3 U201 strain was cloned downstream of an elongation factor-1α (EF-1α) mammalian promoter. Cells transfected with plasmid containing the full-length genome (pHuNoVU201F) expressed the ORF1 polyprotein, which was cleaved by the viral protease to produce the mature nonstructural viral proteins, and the capsid proteins. Progeny virus produced from the transfected cells contained the complete NoV genomic RNA (VP1, VP2, and VPg) and exhibited the same density in isopycnic cesium chloride gradients as native infectious NoV particles from a patient’s stool. This system also was applied to drive murine NoV RNA replication and produced infectious progeny virions. A GFP reporter construct containing the GFP gene in ORF1 produced complete virions that contain VPg-linked RNA. RNA from virions containing the encapsidated GFP-genomic RNA was successfully transfected back into cells producing fluorescent puncta, indicating that the encapsidated RNA is replication-competent. The EF-1α mammalian promoter expression system provides the first reverse genetics system, to our knowledge, generalizable for human and animal NoVs that does not require a helper virus. Establishing a complete reverse genetics system expressed from cDNA for HuNoVs now allows the manipulation of the viral genome and production of reporter virions. PMID:25192933

  3. Polyglot programming in applications used for genetic data analysis.

    PubMed

    Nowak, Robert M

    2014-01-01

    Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

  4. Polyglot Programming in Applications Used for Genetic Data Analysis

    PubMed Central

    Nowak, Robert M.

    2014-01-01

    Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

  5. Application and evaluation of genetic programming for aim point selection

    NASA Astrophysics Data System (ADS)

    Schwartz, Carey; Keyes, Charles; van Bronkhorst, Erik

    1996-11-01

    We report on the application of genetic programming to the determination of a desired output vector from an input vector. Genetic programming is an emerging technique similar in spirit to genetic algorithms which employ a metric to drive a parallel search of the solution space. In contrast to genetic algorithms which yield a single encoded string as the solution, genetic programming yields a computer program which can be examined and understood. Genetic programming also offers the possibility of enabling a technique whereby feature vectors can be automatically developed. We have applied the technique to the determination of ship aimpoints from segmented imagery using input from a sensor. The raw imagery is then processed and a feature vector extracted, as was done in a previous problem. The feature vectors are then used as input to the genetic programming technique. We will report on the sensitivity of performance of the genetic programming technique as a function of the metric employed. In addition we will compare the performance of the computer program obtained by genetic programming to the performance of a back propagation neural networks developed for our problem. Furthermore we will report on the performance results obtained using genetic programming with and without the presence of automatically created subroutines as well as the determination of critical inputs.

  6. Reversibility of a quantum channel: General conditions and their applications to Bosonic linear channels

    SciTech Connect

    Shirokov, M. E.

    2013-11-15

    The method of complementary channel for analysis of reversibility (sufficiency) of a quantum channel with respect to families of input states (pure states for the most part) are considered and applied to Bosonic linear (quasi-free) channels, in particular, to Bosonic Gaussian channels. The obtained reversibility conditions for Bosonic linear channels have clear physical interpretation and their sufficiency is also shown by explicit construction of reversing channels. The method of complementary channel gives possibility to prove necessity of these conditions and to describe all reversed families of pure states in the Schrodinger representation. Some applications in quantum information theory are considered. Conditions for existence of discrete classical-quantum subchannels and of completely depolarizing subchannels of a Bosonic linear channel are presented.

  7. Stable transformation and reverse genetic analysis of Penium margaritaceum: a platform for studies of charophyte green algae, the immediate ancestors of land plants.

    PubMed

    Sørensen, Iben; Fei, Zhangjun; Andreas, Amanda; Willats, William G T; Domozych, David S; Rose, Jocelyn K C

    2014-02-01

    The charophyte green algae (CGA, Streptophyta, Viridiplantae) occupy a key phylogenetic position as the immediate ancestors of land plants but, paradoxically, are less well-studied than the other major plant lineages. This is particularly true in the context of functional genomic studies, where the lack of an efficient protocol for their stable genetic transformation has been a major obstacle. Observations of extant CGA species suggest the existence of some of the evolutionary adaptations that had to occur for land colonization; however, to date, there has been no robust experimental platform to address this genetically. We present a protocol for high-throughput Agrobacterium tumefaciens-mediated transformation of Penium margaritaceum, a unicellular CGA species. The versatility of Penium as a model for studying various aspects of plant cell biology and development was illustrated through non-invasive visualization of protein localization and dynamics in living cells. In addition, the utility of RNA interference (RNAi) for reverse genetic studies was demonstrated by targeting genes associated with cell wall modification (pectin methylesterase) and biosynthesis (cellulose synthase). This provided evidence supporting current models of cell wall assembly and inter-polymer interactions that were based on studies of land plants, but in this case using direct observation in vivo. This new functional genomics platform has broad potential applications, including studies of plant organismal biology and the evolutionary innovations required for transition from aquatic to terrestrial habitats. PMID:24308430

  8. Clinical applications of schizophrenia genetics: genetic diagnosis, risk, and counseling in the molecular era

    PubMed Central

    Costain, Gregory; Bassett, Anne S

    2012-01-01

    Schizophrenia is a complex neuropsychiatric disease with documented clinical and genetic heterogeneity, and evidence for neurodevelopmental origins. Driven by new genetic technologies and advances in molecular medicine, there has recently been concrete progress in understanding some of the specific genetic causes of this serious psychiatric illness. In particular, several large rare structural variants have been convincingly associated with schizophrenia, in targeted studies over two decades with respect to 22q11.2 microdeletions, and more recently in large-scale, genome-wide case-control studies. These advances promise to help many families afflicted with this disease. In this review, we critically appraise recent developments in the field of schizophrenia genetics through the lens of immediate clinical applicability. Much work remains in translating the recent surge of genetic research discoveries into the clinic. The epidemiology and basic genetic parameters (such as penetrance and expression) of most genomic disorders associated with schizophrenia are not yet well characterized. To date, 22q11.2 deletion syndrome is the only established genetic subtype of schizophrenia of proven clinical relevance. We use this well-established association as a model to chart the pathway for translating emerging genetic discoveries into clinical practice. We also propose new directions for research involving general genetic risk prediction and counseling in schizophrenia. PMID:23144566

  9. Genetic Inactivation of D-Amino Acid Oxidase Enhances Extinction and Reversal Learning in Mice

    ERIC Educational Resources Information Center

    Labrie, Viviane; Duffy, Steven; Wang, Wei; Barger, Steven W.; Baker, Glen B.; Roder, John C.

    2009-01-01

    Activation of the N-methyl-d-aspartate receptor (NMDAR) glycine site has been shown to accelerate adaptive forms of learning that may benefit psychopathologies involving cognitive and perseverative disturbances. In this study, the effects of increasing the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic

  10. High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis

    SciTech Connect

    Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T.

    1994-09-01

    The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

  11. The reverse two-hybrid system: a genetic scheme for selection against specific protein/protein interactions.

    PubMed Central

    Leanna, C A; Hannink, M

    1996-01-01

    The yeast two-hybrid system is a powerful experimental approach for the characterization of protein/ protein interactions. A unique strength of the yeast two-hybrid system is the provision for genetic selection techniques that enable the identification of specific protein/protein interactions. We now report the development of a modified yeast two-hybrid system which enables genetic selection against a specific protein/protein interaction. This reverse two-hybrid system utilizes a yeast strain which is resistant to cycloheximide due to the presence of a mutant cyh2 gene. This strain also contains the wild-type CYH2 allele under the transcriptional control of the Gal1 promoter. Expression of the wild-type Gal4 protein is sufficient to restore growth sensitivity to cycloheximide. Growth sensitivity towards cycloheximide is also restored by the coexpression of the avian c-Rel protein and its I kappa B alpha counterpart, p40, as Gal4 fusion proteins. Restoration of growth sensitivity towards cycloheximide requires the association of c-Rel and p40 at the Gal1 promoter and correlates with the ability of the c-Rel/p40 interaction to activate expression from the Gal1 promoter. A genetic selection scheme against specific protein/protein interactions may be a valuable tool for the analysis of protein/protein interactions. PMID:8811088

  12. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system.

    PubMed Central

    Vidal, M; Braun, P; Chen, E; Boeke, J D; Harlow, E

    1996-01-01

    Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that allow single amino acid changes that disrupt protein-protein interactions to be selected from large libraries of randomly generated mutant alleles. The strategy, based on a yeast reverse two-hybrid system, involves a first-step negative selection for mutations that affect interaction, followed by a second-step positive selection for a subset of these mutations that maintain expression of full-length protein (two-step selection). We have selected such mutations in the transcription factor E2F1 that affect its ability to heterodimerize with DP1. The mutations obtained identified a putative helix in the marked box, a region conserved among E2F family members, as an important determinant for interaction. This two-step selection procedure can be used to characterize any interaction domain that can be tested in the two-hybrid system. Images Fig. 1 Fig. 2 PMID:8816798

  13. Genetic data simulators and their applications: an overview

    PubMed Central

    Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E.; Racine, Ben; Clarke, John; Gillanders, Elizabeth; Feuer, Eric J.

    2016-01-01

    Computer simulations have played an indispensable role in the development and application of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the Genetic Simulation Resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators. PMID:25504286

  14. Genetically engineered antibody molecules and their application.

    PubMed

    Morrison, S L; Wims, L; Wallick, S; Tan, L; Oi, V T

    1987-01-01

    Immunoglobulin genes can be efficiently expressed following transfection into myeloma cells. Using protoplast fusion, transfection frequencies greater than 10(-3) can be achieved. Compatible plasmids containing two different selectible markers are used to simultaneously deliver heavy and light chain genes to the same cell. To produce molecules with differing specificities the rearranged and expressed variable regions can be cloned from the appropriate hybridoma. In some cases, variable regions from cDNAs can be inserted into the expression vectors. It is possible to manipulate the immunoglobulin genes and produce novel antibody molecules. Antibodies have been produced in which the variable regions from mouse antibodies have been joined to human constant regions. In addition, antibodies with altered constant regions have been produced. These genetically engineered antibodies provide a unique set of reagents to study structure-function relationships within the molecule. They also can potentially be used in the diagnosis and therapy of human disease. PMID:3327412

  15. Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides.

    PubMed

    Sztainberg, Yehezkel; Chen, Hong-mei; Swann, John W; Hao, Shuang; Tang, Bin; Wu, Zhenyu; Tang, Jianrong; Wan, Ying-Wooi; Liu, Zhandong; Rigo, Frank; Zoghbi, Huda Y

    2015-12-01

    Copy number variations have been frequently associated with developmental delay, intellectual disability and autism spectrum disorders. MECP2 duplication syndrome is one of the most common genomic rearrangements in males and is characterized by autism, intellectual disability, motor dysfunction, anxiety, epilepsy, recurrent respiratory tract infections and early death. The broad range of deficits caused by methyl-CpG-binding protein 2 (MeCP2) overexpression poses a daunting challenge to traditional biochemical-pathway-based therapeutic approaches. Accordingly, we sought strategies that directly target MeCP2 and are amenable to translation into clinical therapy. The first question that we addressed was whether the neurological dysfunction is reversible after symptoms set in. Reversal of phenotypes in adult symptomatic mice has been demonstrated in some models of monogenic loss-of-function neurological disorders, including loss of MeCP2 in Rett syndrome, indicating that, at least in some cases, the neuroanatomy may remain sufficiently intact so that correction of the molecular dysfunction underlying these disorders can restore healthy physiology. Given the absence of neurodegeneration in MECP2 duplication syndrome, we propose that restoration of normal MeCP2 levels in MECP2 duplication adult mice would rescue their phenotype. By generating and characterizing a conditional Mecp2-overexpressing mouse model, here we show that correction of MeCP2 levels largely reverses the behavioural, molecular and electrophysiological deficits. We also reduced MeCP2 using an antisense oligonucleotide strategy, which has greater translational potential. Antisense oligonucleotides are small, modified nucleic acids that can selectively hybridize with messenger RNA transcribed from a target gene and silence it, and have been successfully used to correct deficits in different mouse models. We find that antisense oligonucleotide treatment induces a broad phenotypic rescue in adult symptomatic transgenic MECP2 duplication mice (MECP2-TG), and corrected MECP2 levels in lymphoblastoid cells from MECP2 duplication patients in a dose-dependent manner. PMID:26605526

  16. Retrospective on reverse genetics in mice around the world and in Japan.

    PubMed

    Aizawa, Shinichi

    2008-06-01

    The 2007 Nobel Prize for Physiology or Medicine was awarded to Mario R. Capecchi, Martin J. Evans and Oliver Smithies for their contribution in generating mutant mice by gene targeting in embryonic stem (ES) cells. Although there are many experimental animals, it is yet only in mouse that one can genetically examine functions of genes at will. It was merely a dream in the early 1980s that genetic studies with mutants would one day become a reality in mammals. The story began with tetratocarcinoma/embryonal carcinoma cells. Now, through the successes of cloning in mammals, somatic cells such as our skin cells will shortly be transformed into ES-like (induced pluripotent stem) cells by the proper activation of endogenous genes such as Oct4 and Sox2 with chemicals. How have times changed? PMID:18430168

  17. On some contrast reversals in SEM: application to metal/insulator systems.

    PubMed

    Cazaux, Jacques

    2008-11-01

    Contrast changes of SEM images with experimental conditions (beam energy, angle of detection, etc.) are analyzed by combining physical arguments based on secondary electron emission (SEE) to instrumental arguments involving detection. Possible occurrences of contrast reversals are explored to illustrate these changes in a striking manner. Deduced from SEE yield data, simulated SEM images show a material contrast reversal for a Pt/quartz specimen, a result partly supported by real images of a Cr/quartz integrated circuit. A shift of reversal energy with the detector's position is deduced from a difference in secondary electrons (SE) angular distributions between metals and insulators. Similarly, changes of topographic contrast with detection conditions, specimen composition and angle of tilt are investigated and a possible contrast reversal is again indicated. Finally, it is shown how charging contrast deduced from the expected evolution of SEE yield during irradiation is amplified by in-lens detection: a point illustrated by a contrast reversal of images of SiC particles. The main application concerns a proper interpretation of SEM images that is essential in the investigation of devices obtained from lithographic processes. The discussion on material contrast outlines the difficulty in generalizing the present analysis based on published data and experimental strategies based on implementing specific attachments in the SEM or on biasing the specimen holder are suggested. PMID:18692317

  18. Reversal of diet-induced obesity and insulin resistance by inducible genetic ablation of GRK2

    PubMed Central

    Vila-Bedmar, Rocio; Cruces-Sande, Marta; Lucas, Elisa; Willemen, Hanneke L.D.M.; Heijnen, Cobi J.; Kavelaars, Annemieke; Mayor, Federico; Murga, Cristina

    2015-01-01

    Insulin resistance is a common feature of obesity and predisposes individuals to various prevalent pathological conditions. G protein-coupled receptor kinase 2 (GRK2) integrates several signal transduction pathways and is emerging as a physiologically relevant inhibitor of insulin signaling. GRK2 abundanceis increased in humans with metabolic syndrome and in different murine models of insulin resistance. To support GRK2 as a potential drug target in type 2 diabetes and obesity, we investigated whether lowering GRK2 abundance reversed an ongoing systemic insulin-resistant phenotype, using a mouse model of tamoxifen-induced GRK2 ablation after high fat diet-dependent obesity and insulin resistance. Tamoxifen-triggered GRK2 deletion impeded further body weight gain, normalized fa sting glycemia, improved glucose tolerance and was associated with preserved insulin sensitivity in skeletal muscle and liver, thereby maintaining whole body glucose homeostasis. Moreover, when continued to be fed a high fat diet, these animals displayed reduced fat mass and smaller adipocytes, were resistant to the development of liver steatosis, and showed reduced expression of pro-inflammatory markers in the liver. Our results indicate that GRK2 acts as a hub to control metabolic functions in different tissues, which is key to controlling insulin resistance development in vivo. These data suggest that inhibiting GRK2 could reverse an established insulin-resistant and obese phenotype, thereby putting forward this enzyme as a potential therapeutic target linking glucose homeostasis and regulation of adiposity. PMID:26198359

  19. The Reverse Cholesterol Transport Pathway Improves Understanding of Genetic Networks for Fat Deposition and Muscle Growth in Beef Cattle

    PubMed Central

    Daniels, Tyler F.; Wu, Xiao-Lin; Pan, Zengxiang; Michal, Jennifer J.; Wright, Raymond W.; Killinger, Karen M.; MacNeil, Michael D.; Jiang, Zhihua

    2010-01-01

    In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F1 bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production. PMID:21151936

  20. Reverse genetics in the tide pool: knock-down of target gene expression via RNA interference in the copepod Tigriopus californicus.

    PubMed

    Barreto, Felipe S; Schoville, Sean D; Burton, Ronald S

    2015-07-01

    Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are susceptible to RNAi-mediated gene knock-down, we developed a simple method for delivery of gene-specific double-stranded RNA that results in significant suppression of target gene transcription levels. The protocol was examined on five genes of interest, and for each, at least 50% knock-down in expression was achieved. While knock-down levels did not reach 100% in any trial, a well-controlled experiment with one heat-shock gene showed unambiguously that such partial gene suppression may cause dramatic changes in phenotype. Copepods with suppressed expression of heat-shock protein beta 1 (hspb1) exhibited dramatically decreased tolerance to high temperatures, validating the importance of this gene during thermal stress, as proposed by a previous study. The application of this RNAi protocol in T. californicus will be invaluable for examining the role of genes putatively involved in reproductive isolation, mitochondrial function and local adaptation. PMID:25487181

  1. Reverse genetic engineering of the human rhinovirus serotype 16 genome to introduce an antibody-detectable tag.

    PubMed

    Walker, Erin J; Jensen, Lora M; Ghildyal, Reena

    2015-01-01

    The ability to accurately detect viral proteins during infection is essential for virology research, and the lack of specific antibodies can make this detection difficult. Reverse genetic engineering of virus genomes to alter the wild-type genome is a powerful technique to introduce a detectable tag onto a viral protein. Here we outline a method to incorporate an influenza hemagglutinin epitope tag onto the 2A protease of HRV16. The method uses site-directed mutagenesis PCR to introduce the sequence for the HA antigen onto either the C or N termini of 2A protease while keeping the relevant internal cleavage sites intact. The new viral product is then cloned into a wild-type HRV16 plasmid and transfected into Ohio Hela cells to produce recombinant virus. PMID:25261314

  2. Development of a reverse genetics system for the aG strain of rabies virus in China.

    PubMed

    Wenqiang, Jiao; Yin, Xiangping; Lan, Xi; Li, Xuerui; Liu, Jixing

    2014-05-01

    The aG rabies virus strain has been attenuated through multiple passages in cells and is now used as a vaccine strain in China. We attempted to develop a reverse genetics system using the aG strain. Recombinant full-length genomic cDNA was flanked by a hammerhead ribozyme and the hepatitis delta virus ribozyme. Three helper plasmids encoding the nucleoprotein, the phosphoprotein, and the large protein were produced and introduced together with a plasmid containing the full-length aG viral genome into BHK-21 cells by transfection. Recombinant virus was successfully recovered from the cloned cDNA under the control of a CMV promoter driven by RNA polymerase II. The recombinant virus was confirmed by RT-PCR, and the titer of the recombinant virus was 6.2 log LD50. PMID:24272786

  3. SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement

    PubMed Central

    2013-01-01

    Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

  4. Adaptable Constrained Genetic Programming: Extensions and Applications

    NASA Technical Reports Server (NTRS)

    Janikow, Cezary Z.

    2005-01-01

    An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.

  5. Genetic Algorithm Application in Optimization of Wireless Sensor Networks

    PubMed Central

    Norouzi, Ali; Zaim, A. Halim

    2014-01-01

    There are several applications known for wireless sensor networks (WSN), and such variety demands improvement of the currently available protocols and the specific parameters. Some notable parameters are lifetime of network and energy consumption for routing which play key role in every application. Genetic algorithm is one of the nonlinear optimization methods and relatively better option thanks to its efficiency for large scale applications and that the final formula can be modified by operators. The present survey tries to exert a comprehensive improvement in all operational stages of a WSN including node placement, network coverage, clustering, and data aggregation and achieve an ideal set of parameters of routing and application based WSN. Using genetic algorithm and based on the results of simulations in NS, a specific fitness function was achieved, optimized, and customized for all the operational stages of WSNs. PMID:24693235

  6. Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen.

    PubMed

    Liakath-Ali, Kifayathullah; Vancollie, Valerie E; Heath, Emma; Smedley, Damian P; Estabel, Jeanne; Sunter, David; Ditommaso, Tia; White, Jacqueline K; Ramirez-Solis, Ramiro; Smyth, Ian; Steel, Karen P; Watt, Fiona M

    2014-01-01

    Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous gland and interfollicular epidermal abnormalities using ontology terms from the Mammalian Phenotype Ontology. Of the 50 mutants with an epidermal phenotype, 9 map to human genetic conditions with skin abnormalities. Some mutant genes are expressed in the skin, whereas others are not, indicating systemic effects. One phenotype is affected by diet and several are incompletely penetrant. In-depth analysis of three mutants, Krt76, Myo5a (a model of human Griscelli syndrome) and Mysm1, provides validation of the screen. Our study is the first large-scale genome-wide tissue phenotype screen from the International Knockout Mouse Consortium and provides an open access resource for the scientific community. PMID:24721909

  7. Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen

    PubMed Central

    Liakath-Ali, Kifayathullah; Vancollie, Valerie E.; Heath, Emma; Smedley, Damian P.; Estabel, Jeanne; Sunter, David; DiTommaso, Tia; White, Jacqueline K.; Ramirez-Solis, Ramiro; Smyth, Ian; Steel, Karen P.; Watt, Fiona M.

    2014-01-01

    Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous gland and interfollicular epidermal abnormalities using ontology terms from the Mammalian Phenotype Ontology. Of the 50 mutants with an epidermal phenotype, 9 map to human genetic conditions with skin abnormalities. Some mutant genes are expressed in the skin, whereas others are not, indicating systemic effects. One phenotype is affected by diet and several are incompletely penetrant. In-depth analysis of three mutants, Krt76, Myo5a (a model of human Griscelli syndrome) and Mysm1, provides validation of the screen. Our study is the first large-scale genome-wide tissue phenotype screen from the International Knockout Mouse Consortium and provides an open access resource for the scientific community. PMID:24721909

  8. "Reverse-staining" of biomolecules in electrophoresis gels: analytical and micropreparative applications.

    PubMed

    Hardy, Eugenio; Castellanos-Serra, Lila R

    2004-05-01

    Negative or reverse staining using imidazole and zinc salts for protein detection in electrophoresis gels was originally introduced in 1990. The method is based on the selective precipitation of zinc imidazolate in the gel except in the zones where proteins are located. The method was later adapted to allow high-sensitivity negative detection of nucleic acids and bacterial lipopolysaccharides. It provides a practically quantitative recovery of intact biomolecules and is a method of choice for micropreparative applications of gel electrophoresis to proteomics and similar structural studies. Zinc-mediated protein fixation in the gel is fully reversible and the eluted biomolecules are neither chemically modified nor contaminated with organic dyes. Here we present a detailed compilation of practical methods for implementing these techniques with emphasis in their analytical or micropreparative applications. PMID:15081901

  9. Genetic algorithms and their applications in accelerator physics

    SciTech Connect

    Hofler, Alicia S.

    2013-12-01

    Multi-objective optimization techniques are widely used in an extremely broad range of fields. Genetic optimization for multi-objective optimization was introduced in the accelerator community in relatively recent times and quickly spread becoming a fundamental tool in multi-dimensional optimization problems. This discussion introduces the basics of the technique and reviews applications in accelerator problems.

  10. Applications of Genetic Methods to NASA Design and Operations Problems

    NASA Technical Reports Server (NTRS)

    Laird, Philip D.

    1996-01-01

    We review four recent NASA-funded applications in which evolutionary/genetic methods are important. In the process we survey: the kinds of problems being solved today with these methods; techniques and tools used; problems encountered; and areas where research is needed. The presentation slides are annotated briefly at the top of each page.

  11. Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.

    PubMed

    DiTommaso, Tia; Jones, Lynelle K; Cottle, Denny L; Gerdin, Anna-Karin; Vancollie, Valerie E; Watt, Fiona M; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P; Sundberg, John P; White, Jacqueline K; Smyth, Ian M

    2014-10-01

    The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

  12. Identification of Genes Important for Cutaneous Function Revealed by a Large Scale Reverse Genetic Screen in the Mouse

    PubMed Central

    DiTommaso, Tia; Jones, Lynelle K.; Cottle, Denny L.; Gerdin, Anna-Karin; Vancollie, Valerie E.; Watt, Fiona M.; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P.; Sundberg, John P.; White, Jacqueline K.; Smyth, Ian M.

    2014-01-01

    The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

  13. [The application of genetic risk score in genetic studies of complex human diseases].

    PubMed

    Dayan, Niu; Weili, Yan

    2015-12-01

    Complex diseases such as cardiovascular disease, type 2 diabetes, essential hypertension, asthma, obesity and cancer have spread across the globe and become the predominant cause of death. There are growing concerns over the role of genetic susceptibility in pathogenesis of complex diseases. However, the related susceptibility genes and sequence variations are still unknown. To elucidate the genetic basis of complex diseases, researchers have identified a large number of genetic variants associated with complex diseases through genome-wide association studies (GWAS) and candidate gene studies recently. The identification of these causal and/or associated variants promotes the development of approaches for complex diseases prediction and prevention. Genetic risk score (GRS), an emerging method for exploring correlation between single nucleotide polymorphisms (SNPs) and clinical phenotypes of complex diseases, integrates weak effects of multiple SNPs and dramatically enhances predictability of complex diseases by gene polymorphisms. This method has been applied successfully in genetic studies of many complex diseases. Here we focus on the introduction of the computational methods and evaluation criteria of GRS, enumerate a series of achievements through GRS application, discuss some limitations during application, and finally prospect the future of GRS. PMID:26704945

  14. Quantitative genetic versions of Hamilton's rule with empirical applications

    PubMed Central

    McGlothlin, Joel W.; Wolf, Jason B.; Brodie, Edmund D.; Moore, Allen J.

    2014-01-01

    Hamilton's theory of inclusive fitness revolutionized our understanding of the evolution of social interactions. Surprisingly, an incorporation of Hamilton's perspective into the quantitative genetic theory of phenotypic evolution has been slow, despite the popularity of quantitative genetics in evolutionary studies. Here, we discuss several versions of Hamilton's rule for social evolution from a quantitative genetic perspective, emphasizing its utility in empirical applications. Although evolutionary quantitative genetics offers methods to measure each of the critical parameters of Hamilton's rule, empirical work has lagged behind theory. In particular, we lack studies of selection on altruistic traits in the wild. Fitness costs and benefits of altruism can be estimated using a simple extension of phenotypic selection analysis that incorporates the traits of social interactants. We also discuss the importance of considering the genetic influence of the social environment, or indirect genetic effects (IGEs), in the context of Hamilton's rule. Research in social evolution has generated an extensive body of empirical work focusingwith good reasonalmost solely on relatedness. We argue that quantifying the roles of social and non-social components of selection and IGEs, in addition to relatedness, is now timely and should provide unique additional insights into social evolution. PMID:24686930

  15. Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish.

    PubMed

    Jones, A G; Walker, D; Avise, J C

    2001-12-22

    Due to the phenomenon of male pregnancy, the fish family Syngnathidae (seahorses and pipefishes) has historically been considered an archetypal example of a group in which sexual selection should act more strongly on females than on males. However, more recent work has called into question the idea that all species with male pregnancy are sex-role reversed with respect to the intensity of sexual selection. Furthermore, no studies have formally quantified the opportunity for sexual selection in any natural breeding assemblage of pipefishes or seahorses in order to demonstrate conclusively that sexual selection acts most strongly on females. Here, we use a DNA-based study of parentage in the Gulf pipefish Syngnathus scovelli in order to show that sexual selection indeed acts more strongly on females than on males in this species. Moreover, the Gulf pipefish exhibits classical polyandry with the greatest asymmetry in reproductive roles (as quantified by variances in mating success) between males and females yet documented in any system. Thus, the intensity of sexual selection on females in pipefish rivals that of any other taxon yet studied. PMID:11749706

  16. Genetic correction using engineered nucleases for gene therapy applications.

    PubMed

    Li, Hongmei Lisa; Nakano, Takao; Hotta, Akitsu

    2014-01-01

    Genetic mutations in humans are associated with congenital disorders and phenotypic traits. Gene therapy holds the promise to cure such genetic disorders, although it has suffered from several technical limitations for decades. Recent progress in gene editing technology using tailor-made nucleases, such as meganucleases (MNs), zinc finger nucleases (ZFNs), TAL effector nucleases (TALENs) and, more recently, CRISPR/Cas9, has significantly broadened our ability to precisely modify target sites in the human genome. In this review, we summarize recent progress in gene correction approaches of the human genome, with a particular emphasis on the clinical applications of gene therapy. PMID:24329887

  17. Reversible Thermal Denaturation of a 60-kDa Genetically Engineered β-Sheet Polypeptide

    PubMed Central

    Lednev, Igor K.; Ermolenkov, Vladimir V.; Higashiya, Seiichiro; Popova, Ludmila A.; Topilina, Natalya I.; Welch, John T.

    2006-01-01

    A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)3GY(GA)3GE(GA)3GH(GA)3GK, forms large β-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of β-sheet formation yielding intimate folding information that is otherwise difficult to obtain and may inform folding studies of naturally occurring materials. The polypeptide assumes a fully folded antiparallel β-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125°C, adopting a predominant polyproline II conformation. Deep ultraviolet Raman spectroscopy indicated that melting/refolding occurred without any spectroscopically distinct intermediates, yet the relaxation kinetics depend on the initial polypeptide state, as would be indicative of a non-two-state process. Thermal denaturation and refolding on cooling appeared to be monoexponential with characteristic times of ∼1 and ∼60 min, respectively, indicating no detectable formation of hairpin-type nuclei in the millisecond timescale that could be attributed to nonlocal “nonnative” interactions. The polypeptide folding dynamics agree with a general property of β-sheet proteins, i.e., initial collapse precedes secondary structure formation. The observed folding is much faster than expected for a protein of this size and could be attributed to a less frustrated free-energy landscape funnel for folding. The polypeptide sequence suggests an important balance between the absence of strong nonnative contacts (salt bridges or hydrophobic collapse) and limited repulsion of charged side chains. PMID:16891363

  18. SEQUENCE ANALYSIS OF THE COMPLETE GENOME OF AVIAN METAPNEUMOVIRUS SUBGROUP C COLORADO STRAIN: DEVELOPMENT OF A REVERSE GENETICS SYSTEM FOR THIS VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of the complete genome information is essential for development of a reverse genetics system to study the molecular biology and rescue infectious avian metapneumovirus from cloned DNA. Therefore, we determined the nucleotide (nt) sequence of the complete genome of aMPV-C Colorado s...

  19. Cross flow filtration for radwaste applications reverse osmosis demonstration case studies

    SciTech Connect

    Malkmus, D.

    1995-05-01

    Today`s radwaste economic and regulatory scenarios signify the importance in the improvement of operational practices to reduce generator liabilities. This action is largely due to the rising cost dealing with burial sites and the imposed waste volume restriction. To control the economical burdens associated with waste burial and to comply with stricter environmental regulations, NPP`s are attempting to modify their radwaste system(s) design and operating philosophy by placing a major emphasis on waste volume reduction and processing techniques. The utilization of reverse osmosis technology as a means for treatment of process and wastewater streams in the nuclear power industry has been investigated for many years. This paper will outline reverse osmosis theory and highlight performance data for process and waste stream purification applications. Case studies performed at 5 nuclear plants have been outlined. The demonstrations were performed on a widely variety of process stream for both a PWR and BWR application. The data provided by the pilot systems, the equipment design, and the economical impact a reverse osmosis unit will have on producing treated (high purity) are as follows.

  20. The application of genetic knowledge: ethical and policy implications.

    PubMed

    Driscoll, K M

    1998-11-01

    This article explores societal ethical concerns about the application of the rapidly developing knowledge in the field of genetics. The article calls for nurses to reflect on these ethical concerns not only in the care of patients but also in professional and societal discussion, so that sound ethical and societally acceptable public policy can be adopted. A brief summary introduces the concepts of ethics and policy. The text than offers discussion of genetic testing for adults and children, testing in relation to behavioral attributes, and genetics and reproduction. Hypothetical cases using fictional names are used to illustrate each section. Recommendations for nurse action are cited. Finally, the article poses questions that require public awareness and discussion. PMID:9855870

  1. [The genetic control of mouse coat color and its applications in genetics teaching].

    PubMed

    Xing, Wanjin; Morigen, Morigen

    2014-10-01

    Mice are the most commonly used mammalian model. The coat colors of mice are typical Mendelian traits, which have various colors such as white, black, yellow and agouti. The inheritance of mouse coat color is usually stated as an example only in teaching the knowledge of recessive lethal alleles. After searched the related literatures and summarized the molecular mechanisms of mouse coat color inheritance, we further expanded the application of this example into the introduction of the basic concepts of alleles and Mendelian laws, demonstration of the gene structure and function, regulation of gene expression, gene interaction, epigenetic modification, quantitative genetics, as well as evolutionary genetics. By running this example through the whole genetics-teaching lectures, we help the student to form a systemic and developmental view of genetic analysis. At the same time, this teaching approach not only highlights the advancement and integrity of genetics, but also results in a good teaching effect on inspiring the students' interest and attracting students' attention. PMID:25406255

  2. A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications

    PubMed Central

    Chang, Hao; Zhang, Mingshu; Ji, Wei; Chen, Juanjuan; Zhang, Yongdeng; Liu, Bei; Lu, Jingze; Zhang, Junlong; Xu, Pingyong; Xu, Tao

    2012-01-01

    Reversibly switchable fluorescent proteins (RSFPs) have attracted widespread interest for emerging techniques including repeated tracking of protein behavior and superresolution microscopy. Among the limited number of RSFPs available, only Dronpa is widely employed for most cell biology applications due to its monomeric and other favorable photochemical properties. Here we developed a series of monomeric green RSFPs with beneficial optical characteristics such as high photon output per switch, high photostability, a broad range of switching rate, and pH-dependence, which make them potentially useful for various applications. One member of this series, mGeos-M, exhibits the highest photon budget and localization precision potential among all green RSFPs. We propose mGeos-M as a candidate to replace Dronpa for applications such as dynamic tracking, dual-color superresolution imaging, and optical lock-in detection. PMID:22375034

  3. Genetic engineering of cytokinins and their application to agriculture.

    PubMed

    Ma, Qing-Hu

    2008-01-01

    Cytokinins are master regulators of plant growth and development. They are involved in the regulation of many important physiological and metabolic processes. Recent progress in cytokinin research at the molecular level, including identification of related genes and cytokinin receptors, plus elucidation of signal transduction, has greatly increased our understanding of cytokinin actions. Although still in its infant stage, molecular breeding of crops with altered cytokinin metabolism, when combined with the transgenic approach, has shown very promising potential for application to agriculture. In this review we briefly introduce recent progress in cytokinin molecular biology, discuss applications of cytokinin genetic engineering to agriculture, and present implications and future research directions. PMID:18855152

  4. Time-reversal symmetry in nonstationary Markov processes with application to some fluctuation theorems.

    PubMed

    Van Vliet, Carolyne M

    2012-11-01

    Nonequilibrium processes require that the density operator of an interacting system with Hamiltonian H(t) = H(0)(t)+?V converges and produces entropy. Employing projection operators in the state space, the density operator is developed to all orders of perturbation and then resummed. In contrast to earlier treatments by Van Hove [Physica 21, 517 (1955)] and others [U. Fano, Rev. Mod. Phys. 29, 74 (1959); U. Fano, in Lectures on the Many-Body Problem, Vol 2, edited by E. R. Caniello (Academic Press, New York, 1964); R. Zwanzig, in Lectures in Theoretical Physics, Vol. III, edited by W. E. Britten, B. W. Downs, and J. Downs (Wiley Interscience, New York, 1961), pp. 116-141; K. M. Van Vliet, J. Math. Phys. 19, 1345 (1978); K. M. Van Vliet, Can. J. Phys. 56, 1206 (1978)], closed expressions are obtained. From these we establish the time-reversal symmetry property P(?,t|?',t') = P?',t'|?,t), where the tilde refers to the time-reversed protocol; also a nonstationary Markovian master equation is derived. Time-reversal symmetry is then applied to thermostatted systems yielding the Crooks-Tasaki fluctuation theorem (FT) and the quantum Jarzynski work-energy theorem, as well as the general entropy FT. The quantum mechanical concepts of work and entropy are discussed in detail. Finally, we present a nonequilibrium extension of Mazo's lemma of linear response theory, obtaining some applications via this alternate route. PMID:23214737

  5. Novel and potential application of cryopreservation to plant genetic transformation.

    PubMed

    Wang, Biao; Zhang, Zhibo; Yin, Zhenfang; Feng, Chaohong; Wang, Qiaochun

    2012-01-01

    The world population now is 6.7 billion and is predicted to reach 9 billion by 2050. Such a rapid growing population has tremendously increased the challenge for food security. Obviously, it is impossible for traditional agriculture to ensure the food security, while plant biotechnology offers considerable potential to realize this goal. Over the last 15 years, great benefits have been brought to sustainable agriculture by commercial cultivation of genetically modified (GM) crops. Further development of new GM crops will with no doubt contribute to meeting the requirements for food by the increasing population. The present article provides updated comprehensive information on novel and potential application of cryopreservation to genetic transformation. The major progresses that have been achieved in this subject include (1), long-term storage of a large number of valuable plant genes, which offers a good potential for further development of novel cultivars by genetic transformation; (2), retention of regenerative capacity of embryogenic tissues and protoplasts, which ensures efficient plant regeneration system for genetic transformation; (3), improvement of transformation efficiency and plant regeneration of transformed cells; (4), long-term preservation of transgenic materials with stable expression of transgenes and productive ability of recombinant proteins, which allows transgenic materials to be stored in a safe manner before being analyzed and evaluated, and allows establishment of stable seed stocks for commercial production of homologous proteins. Data provided in this article clearly demonstrate that cryo-technique has an important role to play in the whole chain of genetic transformation. Further studies coupling cryotechnique and genetic transformation are expected to significantly improve development of new GM crops. PMID:22079800

  6. Application of Ionic Liquids in High Performance Reversed-Phase Chromatography

    PubMed Central

    Wang, Ye; Tian, Minglei; Bi, Wentao; Row, Kyung Ho

    2009-01-01

    Ionic liquids, considered “green” chemicals, are widely used in many areas of analytical chemistry due to their unique properties. Recently, ionic liquids have been used as a kind of novel additive in separation and combined with silica to synthesize new stationary phase as separation media. This review will focus on the properties and mechanisms of ionic liquids and their potential applications as mobile phase modifier and surface-bonded stationary phase in reversed-phase high performance liquid chromatography (RP-HPLC). Ionic liquids demonstrate advantages and potential in chromatographic field. PMID:19582220

  7. Application of genetic algorithms to tuning fuzzy control systems

    NASA Technical Reports Server (NTRS)

    Espy, Todd; Vombrack, Endre; Aldridge, Jack

    1993-01-01

    Real number genetic algorithms (GA) were applied for tuning fuzzy membership functions of three controller applications. The first application is our 'Fuzzy Pong' demonstration, a controller that controls a very responsive system. The performance of the automatically tuned membership functions exceeded that of manually tuned membership functions both when the algorithm started with randomly generated functions and with the best manually-tuned functions. The second GA tunes input membership functions to achieve a specified control surface. The third application is a practical one, a motor controller for a printed circuit manufacturing system. The GA alters the positions and overlaps of the membership functions to accomplish the tuning. The applications, the real number GA approach, the fitness function and population parameters, and the performance improvements achieved are discussed. Directions for further research in tuning input and output membership functions and in tuning fuzzy rules are described.

  8. Broadening the application of evolutionarily based genetic pest management.

    PubMed

    Gould, Fred

    2008-02-01

    Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems. PMID:17999722

  9. Ontogenic and morphological study of gonadal formation in genetically-modified sex reversal XY(POS) mice.

    PubMed

    Umemura, Yuria; Miyamoto, Ryosuke; Hashimoto, Rie; Kinoshita, Kyoko; Omotehara, Takuya; Nagahara, Daichi; Hirano, Tetsushi; Kubota, Naoto; Minami, Kiichi; Yanai, Shogo; Masuda, Natsumi; Yuasa, Hideto; Mantani, Youhei; Matsuo, Eiko; Yokoyama, Toshifumi; Kitagawa, Hiroshi; Hoshi, Nobuhiko

    2016-01-01

    Mammalian sexual fate is determined by the presence or absence of sex determining region of the Y chromosome (Sry) in the "bipotential" gonads. Recent studies have demonstrated that both male and female sexual development are induced by distinct and active genetic pathways. Breeding the Y chromosome from Mus m. domesticus poschiavinus (POS) strains into C57BL/6J (B6J) mice (B6J-XY(POS)) has been shown to induce sex reversal (75%: bilateral ovary, 25%: true hermaphrodites). However, our B6N-XY(POS) mice, which were generated by backcrossing of B6J-XY(POS) on an inbred B6N-XX, develop as males (36%: bilateral testis with fertility as well as bilateral ovary (34%), and the remainder develop as true hermaphrodites. Here, we investigated in detail the expressions of essential sex-related genes and histological features in B6N-XY(POS) mice from the fetal period to adulthood. The onsets of both Sry and SRY-box 9 (Sox9) expressions as determined spatiotemporally by whole-mount immunohistochemistry in the B6N-XY(POS) gonads occurred 2-3 tail somites later than those in B6N-XY(B6) gonads, but earlier than those in B6J-XY(POS), respectively. It is possible that such a small difference in timing of the Sry expression underlies testicular development in our B6N-XY(POS). Our study is the first to histologically show the expression and ectopic localization of a female-related gene in the XY(POS) testes and a male-related gene in the XY(POS) ovaries. The results from these and previous experiments indicate that the interplay between genome variants, epigenetics and developmental gene regulation is crucial for testis development. PMID:26194606

  10. Applications of a formal approach to decipher discrete genetic networks

    PubMed Central

    2010-01-01

    Background A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. Results In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach, offers a wide variety of functionalities, going beyond simple simulations, such as proof of consistency, model revision, prediction of properties, search for minimal models relatively to specified criteria. Conclusions The formal approach proposed here deeply changes the way to proceed in the exploration of genetic and biochemical networks, first by avoiding the usual trial-and-error procedure, and second by placing the emphasis on sets of solutions, rather than a single solution arbitrarily chosen among many others. Last, the constraint approach promotes an integration of model and experimental data in a single framework. PMID:20646302

  11. Reverse Genetics for Fusogenic Bat-Borne Orthoreovirus Associated with Acute Respiratory Tract Infections in Humans: Role of Outer Capsid Protein ?C in Viral Replication and Pathogenesis.

    PubMed

    Kawagishi, Takahiro; Kanai, Yuta; Tani, Hideki; Shimojima, Masayuki; Saijo, Masayuki; Matsuura, Yoshiharu; Kobayashi, Takeshi

    2016-02-01

    Nelson Bay orthoreoviruses (NBVs) are members of the fusogenic orthoreoviruses and possess 10-segmented double-stranded RNA genomes. NBV was first isolated from a fruit bat in Australia more than 40 years ago, but it was not associated with any disease. However, several NBV strains have been recently identified as causative agents for respiratory tract infections in humans. Isolation of these pathogenic bat reoviruses from patients suggests that NBVs have evolved to propagate in humans in the form of zoonosis. To date, no strategy has been developed to rescue infectious viruses from cloned cDNA for any member of the fusogenic orthoreoviruses. In this study, we report the development of a plasmid-based reverse genetics system free of helper viruses and independent of any selection for NBV isolated from humans with acute respiratory infection. cDNAs corresponding to each of the 10 full-length RNA gene segments of NBV were cotransfected into culture cells expressing T7 RNA polymerase, and viable NBV was isolated using a plaque assay. The growth kinetics and cell-to-cell fusion activity of recombinant strains, rescued using the reverse genetics system, were indistinguishable from those of native strains. We used the reverse genetics system to generate viruses deficient in the cell attachment protein ?C to define the biological function of this protein in the viral life cycle. Our results with ?C-deficient viruses demonstrated that ?C is dispensable for cell attachment in several cell lines, including murine fibroblast L929 cells but not in human lung epithelial A549 cells, and plays a critical role in viral pathogenesis. We also used the system to rescue a virus that expresses a yellow fluorescent protein. The reverse genetics system developed in this study can be applied to study the propagation and pathogenesis of pathogenic NBVs and in the generation of recombinant NBVs for future vaccines and therapeutics. PMID:26901882

  12. Time-reversal symmetry in nonstationary Markov processes with application to some fluctuation theorems

    NASA Astrophysics Data System (ADS)

    Van Vliet, Carolyne M.

    2012-11-01

    Nonequilibrium processes require that the density operator of an interacting system with Hamiltonian H(t)=H0(t)+?V converges and produces entropy. Employing projection operators in the state space, the density operator is developed to all orders of perturbation and then resummed. In contrast to earlier treatments by Van Hove [Physica0031-891410.1016/S0031-8914(54)92646-4 21, 517 (1955)] and others [U. Fano, Rev. Mod. Phys.0034-686110.1103/RevModPhys.29.74 29, 74 (1959); U. Fano, in Lectures on the Many-Body Problem, Vol 2, edited by E. R. Caniello (Academic Press, New York, 1964); R. Zwanzig, in Lectures in Theoretical Physics, Vol. III, edited by W. E. Britten, B. W. Downs, and J. Downs (Wiley Interscience, New York, 1961), pp. 116-141; K. M. Van Vliet, J. Math. Phys.0022-248810.1063/1.523833 19, 1345 (1978); K. M. Van Vliet, Can. J. Phys. 56, 1206 (1978)], closed expressions are obtained. From these we establish the time-reversal symmetry property P(?,t|?',t')=P(?',t'|?,t), where the tilde refers to the time-reversed protocol; also a nonstationary Markovian master equation is derived. Time-reversal symmetry is then applied to thermostatted systems yielding the Crooks-Tasaki fluctuation theorem (FT) and the quantum Jarzynski work-energy theorem, as well as the general entropy FT. The quantum mechanical concepts of work and entropy are discussed in detail. Finally, we present a nonequilibrium extension of Mazo's lemma of linear response theory, obtaining some applications via this alternate route.

  13. Celiac disease genetics: current concepts and practical applications.

    PubMed

    Sollid, Ludvig M; Lie, Benedicte A

    2005-09-01

    Celiac disease is a multifactorial disease with complex genetics. Both HLA and non-HLA genes contribute to the genetic component, but recent findings suggest that the importance of non-HLA genes might have been overestimated. No susceptibility genes other than HLA-DQ have yet been identified in celiac disease. In contrast to the meager knowledge regarding non-HLA genes, we have acquired a detailed understanding about which HLA genes are predisposing for disease, and how they are involved in the pathogenesis. This knowledge might pave the road for novel treatments for the disease. The role of HLA as a necessary, but not sufficient, genetic factor can moreover be used for diagnostic purposes to exclude a celiac disease diagnosis. The applicability of HLA genotyping is particularly useful for excluding celiac disease in family members or risk groups with fairly unbiased distribution of HLA alleles (ie, patients with Turner syndrome and patients with Down syndrome) and in patients with a clinical suspicion of celiac disease. PMID:16234020

  14. Molecular scissors and their application in genetically modified farm animals.

    PubMed

    Petersen, Bjoern; Niemann, Heiner

    2015-06-01

    Molecular scissors (MS), incl. Zinc Finger Nucleases (ZFN), Transcription-activator like endoncleases (TALENS) and meganucleases possess long recognition sites and are thus capable of cutting DNA in a very specific manner. These molecular scissors mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination based gene targeting, MS can increase the targeting rate 10,000-fold, and gene disruption via mutagenic DNA repair is stimulated at a similar frequency. The successful application of different MS has been shown in different organisms, including insects, amphibians, plants, nematodes, and mammals, including humans. Recently, another novel class of molecular scissors was described that uses RNAs to target a specific genomic site. The CRISPR/Cas9 system is capable of targeting even multiple genomic sites in one shot and thus could be superior to ZFNs or TALEN, especially by its easy design. MS can be successfully employed for improving the understanding of complex physiological systems, producing transgenic animals, incl. creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on molecular scissors, their underlying mechanism and focuses on new opportunities for generating genetically modified farm animals. PMID:25603988

  15. Two applications of time reversal mirrors: seismic radio and seismic radar.

    PubMed

    Hanafy, Sherif M; Schuster, Gerard T

    2011-10-01

    Two seismic applications of time reversal mirrors (TRMs) are introduced and tested with field experiments. The first one is sending, receiving, and decoding coded messages similar to a radio except seismic waves are used. The second one is, similar to radar surveillance, detecting and tracking a moving object(s) in a remote area, including the determination of the objects speed of movement. Both applications require the prior recording of calibration Green's functions in the area of interest. This reference Green's function will be used as a codebook to decrypt the coded message in the first application and as a moving sensor for the second application. Field tests show that seismic radar can detect the moving coordinates (x(t), y(t), z(t)) of a person running through a calibration site. This information also allows for a calculation of his velocity as a function of location. Results with the seismic radio are successful in seismically detecting and decoding coded pulses produced by a hammer. Both seismic radio and radar are highly robust to signals in high noise environments due to the super-stacking property of TRMs. PMID:21973353

  16. Application of chromosomal microdissection, polymerase chain reaction (PCR), and reverse chromosome painting in prenatal diagnosis

    SciTech Connect

    Wang, N.; Xu, J.; Cedrone, E.

    1994-09-01

    De novo marker chromosomes have been found in about 0.04% of amniotic fluid cultures. The origin of these marker chromosomes is difficult to identify by routine chromosome banding analysis. In the present study, we applied microdissection, PCR, and reverse chromosome painting to two amniotic fluid cases with a karyotype of 47,XX,+mar, and 47,XX,+?i(9p), respectively. Fluorescence in situ hybridization of the biotin-labeled DNA probe generated from 5 copies of the dissected marker chromosomes was applied to the normal metaphase spreads and revealed that the marker originated from the p arm of chromosomes 14 and 22, while the ?i(9p) was actually i(4p). Reverse painting of the same probe to the metaphase spreads of the patients completely painted the marker chromosomes in question, which confirms the accuracy of the analysis. Our study provides an example of the application of chromosome microdissection and molecular cytogenetics in prenatal diagnosis for the identification of marker chromosomes unidentifiable by routine analysis.

  17. Genetic markers and their application in poultry breeding.

    PubMed

    Emara, M G; Kim, H

    2003-06-01

    The current chicken genetic map contains at least 1,965 loci within 50 linkage groups, and it covers about 4,000 cM. About 235 of these loci have homology with known human or mammalian genes. The remaining loci are anonymous molecular DNA markers, including microsatellites, amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), CR1 elements, and others. A third generation genetic map for human uses single nucleotide polymorphisms (SNP), which have allowed the mapping of complex traits by linkage disequilibrium. One advantage of SNP is that they are usually linked to the gene of interest, and association of the SNP with traits of economic importance can be analyzed using candidate gene approaches. With the tremendous advancements in characterizing chicken expressed sequence tags (EST), the identification of genetic polymorphisms such as SNP in chicken genes has become a reality. Our laboratory has undertaken an in silico analysis of the chicken EST at the University of Delaware by using a Phred/Phrap/Polyphred/Consed pipeline to identify candidate chicken SNP. Initial scanning of 23,427 chicken EST identified a total of 1,209 candidate SNP, with at least 182 non-synonymous SNP that result in an amino acid change observed. Validation of these candidate chicken SNP is ongoing. Placement of the SNP on the chicken genetic map will enhance marker density, thus allowing for mapping of complex traits through linkage analysis and linkage disequilibrium. Application of SNP to identify disease resistance genes in chickens is of special interest to our laboratory, especially in regards to Marek's disease and coccidiosis. PMID:12817450

  18. A theoretical model of reversible adhesion in shape memory surface relief structures and its application in transfer printing

    NASA Astrophysics Data System (ADS)

    Xue, Yeguang; Zhang, Yihui; Feng, Xue; Kim, Seok; Rogers, John A.; Huang, Yonggang

    2015-04-01

    Transfer printing is an important and versatile tool for deterministic assembly and integration of micro/nanomaterials on unusual substrates, with promising applications in fabrication of stretchable and flexible electronics. The shape memory polymers (SMP) with triangular surface relief structures are introduced to achieve large, reversible adhesion, thereby with potential applications in temperature-controlled transfer printing. An analytic model is established, and it identifies two mechanisms to increase the adhesion: (1) transition of contact mode from the triangular to trapezoidal configurations, and (2) explicit enhancement in the contact area. The surface relief structures are optimized to achieve reversible adhesion and transfer printing. The theoretical model and results presented can be exploited as design guidelines for future applications of SMP in reversible adhesion and stretchable electronics.

  19. Trends in genetic patent applications: the commercialization of academic intellectual property.

    PubMed

    Kers, Jannigje G; Van Burg, Elco; Stoop, Tom; Cornel, Martina C

    2014-10-01

    We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications data from the PATSTAT database from 1990 until 2009 were analyzed for time trends and regional distribution. Overall, the number of patent applications has been growing. In 2009, 152?000 patent applications were submitted under the Patent Cooperation Treaty (PCT) and within the EP (European Patent) system of the European Patent Office (EPO). The number of genetic patent applications increased until a peak was reached in the year 2000, with >8000 applications, after which it declined by almost 50%. Continents show different patterns over time, with the global peak in 2000 mainly explained by the USA and Europe, while Asia shows a stable number of >1000 per year. Nine countries together account for 98.9% of the total number of genetic patent applications. In The Netherlands, 26.7% of the genetic patent applications originate from public research institutions. After the year 2000, the number of genetic patent applications dropped significantly. Academic leadership and policy as well as patent regulations seem to have an important role in the trend differences. The ongoing investment in genetic research in the past decade is not reflected by an increase of patent applications. PMID:24448546

  20. Trends in genetic patent applications: the commercialization of academic intellectual property

    PubMed Central

    Kers, Jannigje G; Van Burg, Elco; Stoop, Tom; Cornel, Martina C

    2014-01-01

    We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications data from the PATSTAT database from 1990 until 2009 were analyzed for time trends and regional distribution. Overall, the number of patent applications has been growing. In 2009, 152?000 patent applications were submitted under the Patent Cooperation Treaty (PCT) and within the EP (European Patent) system of the European Patent Office (EPO). The number of genetic patent applications increased until a peak was reached in the year 2000, with >8000 applications, after which it declined by almost 50%. Continents show different patterns over time, with the global peak in 2000 mainly explained by the USA and Europe, while Asia shows a stable number of >1000 per year. Nine countries together account for 98.9% of the total number of genetic patent applications. In The Netherlands, 26.7% of the genetic patent applications originate from public research institutions. After the year 2000, the number of genetic patent applications dropped significantly. Academic leadership and policy as well as patent regulations seem to have an important role in the trend differences. The ongoing investment in genetic research in the past decade is not reflected by an increase of patent applications. PMID:24448546

  1. Time Reversal Ocean Acoustic Experiments At 3.5 kHz: Applications To Active Sonar And Undersea Communications

    NASA Astrophysics Data System (ADS)

    Song, Heechun; Roux, P.; Akal, T.; Edelmann, G.; Higley, W.; Hodgkiss, W. S.; Kuperman, W. A.; Raghukumar, K.; Stevenson, M.

    2004-11-01

    We have conducted a series of time-reversal experiments at a center frequency of 3.5 kHz with a 1 kHz bandwidth. These experiments and follow-up analysis suggest applications to active sonar and undersea communications. In the area of active sonar, time reversal physics points to procedures to minimize reverberation and therefore enhance the echo-to-reverberation ratio. These ideas have been confirmed under limited circumstances in our shallow-water acoustic experiments. For undersea communications, time reversal provides an opportunity to implement space-time multiplexing in complex environments. Our experiments indicate that vertical aperture provides a capability for implementing multiple input/multiple output (MIMO) communications. We also have demonstrated experimentally that a moving source and/or receiver can communicate by establishing a synthesized horizontal aperture time-reversal mirror.

  2. The multi-niche crowding genetic algorithm: Analysis and applications

    SciTech Connect

    Cedeno, W.

    1995-09-01

    The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

  3. Ormosil approach toward developing a completely reversible hydrogen sensor for aerospace applications

    NASA Astrophysics Data System (ADS)

    Kazemi, Alex A.; Goswami, Kisholoy; Sampathkumaran, Uma

    2006-08-01

    Optical hydrogen sensors are intrinsically safe since they produce no arc or spark in an explosive environment caused by the leakage of hydrogen. Safety remains a top priority since leakage of hydrogen in air during production, storage, transfer and distribution creates an explosive atmosphere for concentrations between 4% (v/v) - the lower explosive limit (LEL) and 74.5% (v/v) - the upper explosive limit (UEL) at room temperature and pressure. Being a very small molecule, hydrogen is prone to leakage through seals and micro-cracks. Hydrogen detection in space application is very challenging; public acceptance of hydrogen fuel would require the integration of a reliable hydrogen safety sensor. For detecting leakage of cryogenic fluids in spaceport facilities, Launch vehicle industry and NASA are currently relying heavily on the bulky mass spectrometers, which fill one or more equipment racks, and weigh several hundred kilograms. An optical sensor system can decrease pay load while monitoring multiple leak locations in situ and in real time. In this paper design of ormsoil approach for developing a completely reversible optical hydrogen sensors for aerospace application is being discussed.

  4. Reversibility and stability of ZnO-Sb₂Te₃ nanocomposite films for phase change memory applications.

    PubMed

    Wang, Guoxiang; Chen, Yimin; Shen, Xiang; Li, Junjian; Wang, Rongping; Lu, Yegang; Dai, Shixun; Xu, Tiefeng; Nie, Qiuhua

    2014-06-11

    (ZnO)x(Sb2Te3)1-x materials with different ZnO contents have been systemically studied with an aim of finding the most suitable composition for phase change memory applications. It was found that ZnO-doping could improve thermal stability and electrical behavior of Sb2Te3 film. Sb2Te3-rich nanocrystals, surrounded by ZnO-rich amorphous phases, were observed in annealed ZnO-doped Sb2Te3 composite films, and the segregated domains exhibited a relatively uniform distribution. The ZnO-doped Sb2Te3 composite films, especially with 5.2 at% ZnO concentration were found to have higher crystallization temperature, higher crystalline resistance, and faster crystallization speed in comparison with Ge2Sb2Te5. A reversible repetitive optical switching behavior can be observed in (ZnO)5.2(Sb2Te3)94.8, confirming that the ZnO doping is responsible for a fast switching and the compound is stable with cycling. Therefore, it is promising for the applications in phase change memory devices. PMID:24802948

  5. Programmable genetic algorithm IP core for sensing and surveillance applications

    NASA Astrophysics Data System (ADS)

    Katkoori, Srinivas; Fernando, Pradeep; Sankaran, Hariharan; Stoica, Adrian; Keymeulen, Didier; Zebulum, Ricardo

    2009-05-01

    Real-time evolvable systems are possible with a hardware implementation of Genetic Algorithms (GA). We report the design of an IP core that implements a general purpose GA engine which has been successfully synthesized and verified on a Xilinx Virtex II Pro FPGA Device (XC2VP30). The placed and routed IP core has an area utilization of only 13% and clock speed of 50MHz. The GA core can be customized in terms of the population size, number of generations, cross-over and mutation rates, and the random number generator seed. The GA engine can be tailored to a given application by interfacing with the application specific fitness evaluation module as well as the required storage memory (to store the current and new populations). The core is soft in nature i.e., a gate-level netlist is provided which can be readily integrated with the user's system. The GA IP core can be readily used in FPGA based platforms for space and military applications (for e.g., surveillance, target tracking). The main advantages of the IP core are its programmability, small footprint, and low power consumption. Examples of concept systems in sensing and surveillance domains will be presented.

  6. Innovative applications of genetic algorithms to problems in accelerator physics

    NASA Astrophysics Data System (ADS)

    Hofler, Alicia; Terzić, Balša; Kramer, Matthew; Zvezdin, Anton; Morozov, Vasiliy; Roblin, Yves; Lin, Fanglei; Jarvis, Colin

    2013-01-01

    The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion Collider at Jefferson Lab, and a radio frequency gun-based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, include a newly devised enhancement which leads to improved convergence to the optimum, and make recommendations for future GA developments and accelerator applications.

  7. Innovative Applications of Genetic Algorithms to Problems in Accelerator Physics

    SciTech Connect

    Hofler, Alicia; Terzic, Balsa; Kramer, Matthew; Zvezdin, Anton; Morozov, Vasiliy; Roblin, Yves; Lin, Fanglei; Jarvis, Colin

    2013-01-01

    The genetic algorithm (GA) is a relatively new technique that implements the principles nature uses in biological evolution in order to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing CEBAF facility, the proposed MEIC at Jefferson Lab, and a radio frequency (RF) gun based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, including a newly devised enhancement, which leads to improved convergence to the optimum and make recommendations for future GA developments and accelerator applications.

  8. Xanthan gum biosynthesis and application: a biochemical/genetic perspective.

    PubMed

    Becker, A; Katzen, F; Pühler, A; Ielpi, L

    1998-08-01

    Xanthan gum is a complex exopolysaccharide produced by the plant-pathogenic bacterium Xanthomonas campestris pv. campestris. It consists of D-glucosyl, D-mannosyl, and D-glucuronyl acid residues in a molar ratio of 2:2:1 and variable proportions of O-acetyl and pyruvyl residues. Because of its physical properties, it is widely used as a thickener or viscosifier in both food and non-food industries. Xanthan gum is also used as a stabilizer for a wide variety of suspensions, emulsions, and foams. This article outlines aspects of the biochemical assembly and genetic loci involved in its biosynthesis, including the synthesis of the sugar nucleotide substrates, the building and decoration of the pentasaccharide subunit, and the polymerization and secretion of the polymer. An overview of the applications and industrial production of xanthan is also covered. PMID:9763683

  9. Genetically engineered mesenchymal stem cells: applications in spine therapy.

    PubMed

    Aslan, Hadi; Sheyn, Dima; Gazit, Dan

    2009-01-01

    Spine disorders and intervertebral disc degeneration are considered the main causes for the clinical condition commonly known as back pain. Spinal fusion by implanting autologous bone to produce bony bridging between the two vertebrae flanking the degenerated-intervertebral disc is currently the most efficient treatment for relieving the symptoms of back pain. However, donor-site morbidity, complications and the long healing time limit the success of this approach. Novel developments undertaken by regenerative medicine might bring more efficient and available treatments. Here we discuss the pros and cons of utilizing genetically engineered mesenchymal stem cells for inducing spinal fusion. The combination of the stem cells, gene and carrier are crucial elements for achieving optimal spinal fusion in both small and large animal models, which hopefully will lead to the development of clinical applications. PMID:19105619

  10. Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis

    PubMed Central

    2014-01-01

    Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into ‘targetrons.’ Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and ‘cut-and-pastes’ (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology. PMID:24410776

  11. Genetics

    MedlinePLUS

    Homozygous; Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  12. Polarization Reversal Over Flooded Regions and Applications to Large-Scale Flood Mapping with Spaceborne Scatterometers

    NASA Technical Reports Server (NTRS)

    Nghiem, Son V.; Liu, W. Timothy; Xie, Xiao-Su

    1999-01-01

    We present the polarization reversal in backscatter over flooded land regions, and demonstrate for the first time the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. Scatterometer data were collected over the globe by the NASA Scatterometer (NSCAT) operated at 14 GHz on the Japanese ADEOS spacecraft from September 1996 to June 1997. During this time span, several severe floods occurred. Over most land surface, vertical polarization backscatter (Sigma(sub upsilon(upsilon)) is larger than horizontal polarization backscatter (sigma(sub hh)). Such polarization characteristics is reversed and sigma(sub upsilon(upsilon)) is smaller than sigma(sub hh) over flooded regions, except under a dense forest canopy. The total backscatter from the flooded landscape consists of direct backscatter and boundary-interaction backscatter. The direct term is contributed by direct backscattering from objects protruding above the water surface, and by backscattering from waves on the water surface. The boundary-interaction term is contributed by the forward scattering from the protruding objects and then reflected from the water surface, and also by the forward scattering from these objects after the water-surface reflection. Over flooded regions, the boundary-interaction term is dominant at large incidence angles and the strong water-surface reflection is much larger for horizontal polarization than the vertical one due to the Brewster effect in transverse-magnetic waves. These scattering mechanisms cause the polarization reversal over flooded regions. An example obtained with the Analytic Wave Theory is used to illustrate the scattering mechanisms leading to the polarization reversal. We then demonstrate the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. We process NSCAT data to obtain the polarization ratio sigma(sub hh)/sigma(sub upsilon(upsilon)) with colocated data at incidence angles larger than 40 deg. The results over Asian summer monsoon regions in September-October 1996 indicate flooded areas in many countries such as Bangladesh, India, Lao, Vietnam, Cambodia, and China. Reports documented by the United Nation Department of Humanitarian Affairs (now called UN Office for the Coordination of Humanitarian Affairs) show loss of many lives and severe flood related damages which affected many million people in the corresponding flooded areas. We also map the NSCAT polarization ratio over the same regions in the "dry season" in January 1997 as a reference to confirm our results. Furthermore, we obtain concurrent ocean wind fields also derived from NSCAT data, and Asia topographic data (USGS GTOPO30) to investigate the flooded area. The results show that winds during summer monsoon season blowing inland, which perplex flood problems. Overlaying the topographic map over NSCAT results reveals an excellent correspondence between the confinement of flooded area within the relevant topographic features, which very well illustrates the value of topographic wetness index. Finally, we discuss the applications of future spaceborne scatterometers, including QuikSCAT and Seawinds, for flood mapping over the globe.

  13. Investigations on the Suitability of Coated Steel Piping System for High Pressure Seawater Reverse Osmosis Application

    NASA Astrophysics Data System (ADS)

    Mobin, Mohammad

    2010-03-01

    This study deals with the investigations concerning with the suitability of coated steel piping system as an economically viable alternative to costly stainless steel piping for high pressure seawater reverse osmosis (SWRO) application. The piping system selected for investigation is a carbon steel piping coated internally and externally with thermoplastic coating (coating powder Plascoat PPA 571). The performance of thermoplastic coating was investigated by conducting SWRO pilot plant test, salt spray test, mechanical tests and testing of the coating under crevices (both in pilot plant and laboratory), and for leachable organics and inorganics (both in laboratory and pilot plant test). The testing of coating in the pilot plant resulted in the formation of some blisters on the internal surface of the pipes. The blisters were broken causing the corrosion of underneath steel. The coating showed a poor resistance to salt fog test. In general, the coating performed satisfactorily under the crevices but showed blistering on either side of the test panels. The adhesive strength of the coating was found to be poor; however, it showed good flexibility. The results of chemical analysis did not show the leaching of organic or inorganic pollutants from the coating.

  14. Contaminants of emerging concern in reverse osmosis brine concentrate from indirect/direct water reuse applications.

    PubMed

    Romeyn, Travis R; Harijanto, Wesley; Sandoval, Sofia; Delagah, Saied; Sharbatmaleki, Mohamadali

    2016-01-01

    Water shortage is becoming more common due to droughts and global population increases resulting in the increasing popularity of water reuse to create new water sources. Reverse osmosis (RO) membrane systems are popular in these applications since they can produce drinking water quality effluent. Unfortunately, RO systems have the drawback of generating concentrate streams that contain contaminants rejected by the membrane including chemicals of emerging concern (CECs). CECs are chemicals such as hormones, steroids, pesticides, pharmaceuticals, and personal care products that are used for their intended purpose and then released into wastewater. CECs are believed to be detrimental to aquatic wildlife health and pose an unknown human health risk. This research gathered the existing knowledge on CEC presence in concentrate, available proven concentrate treatment methods, their CEC removal abilities, and current CEC regulations. It was found that 127 CECs have been measured in RO concentrate with 100 being detected at least once. The most potent treatment process available is UV/H2O2 as it offers the highest removal rates for the widest range of chemicals. The less expensive process of ozone/biologically activated carbon offers slightly lower removal abilities. This comprehensive report will provide the groundwork for better understanding, regulating and treating concentrate stream CECs. PMID:26819378

  15. Second-law analysis and optimization of reverse brayton cycles of different configurations for cryogenic applications

    NASA Astrophysics Data System (ADS)

    Streit, James Ryder; Razani, Arsalan

    2012-06-01

    Second-law of thermodynamics (2nd law) and exergy analyses and optimization offour Reverse Brayton Refrigeration (RBR) cryogenic cycle configurations: Conventional 1-stage compression cycle; Conventional 2-stage compression cycle; 1-stage compressionModified cycle with intermediate cooling of the recuperator using an auxiliary cooler; andan Integrated 2-stage expansion RBR cycle are performed. The conventional RBR cyclesare analyzed for low and high pressure ratio applications using multistage compressorswith intercooling. Analytical solutions for the conventional cycles are developed includingthermal and fluid flow irreversibilities of the recuperators and all heat exchangers inaddition to the compression and expansion processes. Analytical solutions are used to findthe thermodynamic bounds for the performance of the cycles. Exergy irreversibilitydiagrams of the cycles are developed and the effects of important system parameters onRBR cycle performance are investigated. 2nd law/exergy analyses, and optimization of thecycles with intermediate cooling of the recuperator, considering the cooling temperatureand the recuperator effectiveness and pressure drop, are included. The effect of the 2ndlaw/exergy efficiency of the auxiliary cooler on the total system efficiencies is presented.

  16. Protein based tablets as reversible gelling systems for delayed release applications.

    PubMed

    Caillard, Romain; Subirade, Muriel

    2012-11-01

    Succinylated β-lactoglobulin (S-β-lg) was previously shown to be efficient as new excipient for the formation of enteric tablets, suitable for several applications including probiotics delivery. This work investigates the mechanisms leading to S-β-lg tablets delayed release. Release kinetics were evaluated in vitro. Fourier transformed infra red spectroscopy (FTIR) was used to visualize the effect of dissolution medium on matrix tablet surface. Results demonstrated that tablets release in simulated gastric fluids (SGF) might be due to water/drug diffusion through an in situ formed gel layer, as revealed by FTIR data. As SGF penetrated the tablet, regardless of protein succinylation rate (50% or 100%), molecular rearrangements occurred, allowing the development of an important band located in the 1621-1623 cm(-1) region. This band was characteristic of the formation of protein intermolecular β-sheets. The gel was showed to be reversible in intestinal conditions, allowing delayed release. While the molecular structure of the gel layer was not depending on protein succinylation rate, it appeared that 100% S-β-lg tablets showed slower release. This low release was probably related to 100% S-β-lg lower solubility, lower charge density, and their ability to form stronger intermolecular hydrogen bonds. This work highlights proteins potential for the conception of controlled drug delivery systems. PMID:22846408

  17. An experimental application of aeroacoustic time-reversal to the Aeolian tone.

    PubMed

    Mimani, A; Prime, Z; Moreau, D J; Doolan, C J

    2016-02-01

    This paper presents an experimental application of the aeroacoustic time-reversal (TR) source localization technique for studying flow-induced noise problems and compares the TR results with those obtained using conventional beamforming (CB). Experiments were conducted in an anechoic wind tunnel for the benchmark test-case of a full-span circular cylinder located in subsonic cross-flow wherein the far-field acoustic pressure was sampled using two line arrays (LAs) of microphones located above and below the cylinder. The source map obtained using the signals recorded at the two LAs without modeling the reflective surfaces of the contraction-outlet and cylinder during TR simulations revealed the lift-dipole nature of aeroacoustic source generated at the Aeolian tone; however, it indicates an error of 3/20 of Aeolian tone wavelength in the predicted location. Modeling the reflective contraction-outlet during TR was shown to improve the focal-resolution of the source and reduce side-lobe levels, especially in the low-frequency range. The experimental TR results were shown to be comparable to (a) the simulation results of an idealized dipole at the cylinder location in wind-tunnel flow and (b) that obtained by monopole and dipole CB, thereby demonstrating the suitability of TR method as a diagnostic tool to analyze flow-induced noise generation mechanism. PMID:26936557

  18. Hybrid Stirling / Reverse Brayton and Multi-stage Brayton Cryocoolers for Space Applications

    NASA Astrophysics Data System (ADS)

    Kirkconnell, C. S.; Zagarola, M. V.; Russo, J. T.

    2006-04-01

    Space infrared (IR) sensor applications place demanding requirements on the cryogenic cooling system. These systems must typically have 8+ year life and very high reliability, typically >0.95 at eight years. This has been achieved by several companies, including Raytheon with Stirling-class machines and by Creare with reverse turbo Brayton (RTB) devices. Other requirements virtually always present for space cryocoolers include low mass, high efficiency, and low vibration output. For typical space infrared sensor cryogenic cooling applications, existing Stirling-class cryocoolers (which includes pulse tubes) excel relative to the RTB with respect to mass and often efficiency, but the RTB exports much less vibration. An additional requirement sometimes present for a given payload is that the refrigeration must be provided remotely, perhaps several meters from the ambient environment where the cryocooler machinery typically resides and to which the waste heat must be rejected. A Stirling-class machine cannot meet this last requirement unless it is coupled with a single- or two-phase pumped loop, a cryogenic heat pipe, or a recirculating cooling system. One approach is to combine a Stirling-class machine with a Joule-Thomson (JT) cooling system. Another approach, one that embodies important reliability and integration benefits, is to combine a Stirling-class cryocooler with a RTB cryocooler. The case study results for a particular Stirling-Brayton hybrid system are presented, along with a discussion of its integration characteristics. Such a hybrid system, if properly designed, accentuates the advantages and mitigates the weaknesses of the individual technologies. Finally, the hybrid approach is compared to a straightforward multi-stage RTB cryocooler.

  19. Genetic mapping of the autosomal region involved in XX sex-reversal and horn development in goats.

    PubMed

    Vaiman, D; Koutita, O; Oustry, A; Elsen, J M; Manfredi, E; Fellous, M; Cribiu, E P

    1996-02-01

    Contrary to other genetic disorders, the genetic study of sex determination anomalies in humans stumbles over the difficulty in observing large pedigrees. In goats, abnormalities in sex determination are intimately linked to a dominant Mendelian gene coding for the "polled" (hornless) character, which could render this species an interesting animal model for the rare human cases of SRY-negative XX males. In this report, we describe genetic linkage between the polled/intersex synchome (PIS) and four microsatellite markers of the distal region of goat Chromosome 1 (CHI1), quite distinct from the bovine "polled" region. According to comparative mapping data, no sex-determining gene has been described so far in homologous regions in the human. This genetic localization constitutes a first step towards identifying a new autosomal sex-determining gene in mammals. PMID:8835530

  20. Thermally responsive polymer systems for self-healing, reversible adhesion and shape memory applications

    NASA Astrophysics Data System (ADS)

    Luo, Xiaofan

    Responsive polymers are "smart" materials that are capable of performing prescribed, dynamic functions under an applied stimulus. In this dissertation, we explore several novel design strategies to develop thermally responsive polymers and polymer composites for self-healing, reversible adhesion and shape memory applications. In the first case described in Chapters 2 and 3, a thermally triggered self-healing material was prepared by blending a high-temperature epoxy resin with a thermoplastic polymer, poly(epsilon-caprolactone) (PCL). The initially miscible system undergoes polymerization induced phase separation (PIPS) during the curing of epoxy and yields a variety of compositionally dependent morphologies. At a particular PCL loading, the cured blend displays a "bricks-and-mortar" morphology in which epoxy exists as interconnected spheres ("bricks") within a continuous PCL matrix ("mortar"). A heat induced "bleeding" phenomenon was observed in the form of spontaneous wetting of all free surfaces by the molten PCL, and is attributed to the volumetric thermal expansion of PCL above its melting point in excess of epoxy brick expansion, which we term differential expansive bleeding (DEB). This DEB is capable of healing damage such as cracks. In controlled self-healing experiments, heating of a cracked specimen led to PCL bleeding from the bulk that yields a liquid layer bridging the crack gap. Upon cooling, a "scar" composed of PCL crystals was formed at the site of the crack, restoring a significant portion of mechanical strength. We further utilized DEB to enable strong and thermally-reversible adhesion of the material to itself and to metallic substrates, without any requirement for macroscopic softening or flow. After that, Chapters 4--6 present a novel composite strategy for the design and fabrication of shape memory polymer composites. The basic approach involves physically combining two or more functional components into an interpenetrating fiber/matrix structure, allowing them to function in a synergistic fashion yet remain physically separated. This latter aspect is critical since it enables the control of overall composite properties and functions by separately tuning each component. Utilizing the intrinsic versatility of this approach, composites with novel properties and functions (in addition to "regular" shape memory) have been developed, including (1) shape memory elastomeric composites (SMECs; Chapter 4), (2) triple-shape polymeric composites (TSPCs; Chapter 5), and (3) electrically conductive nanocomposites (Chapter 6). Then in Chapter 7, by combining the success in both thermoplastic based self-healing and shape memory polymer composites, we demonstrate a thermally triggered self-healing coating. This coating features a unique "shape memory assisted self-healing" mechanism in which crack closure (via shape memory) and crack re-bonding (via melting and diffusion of the thermoplastic healing agent) are achieved simultaneously upon a single heating step, leading to both structural and functional (corrosion resistance) recovery. Finally, Chapter 8 presents for the first time the preparation of functionally graded shape memory polymers (SMPs) that, unlike conventional SMPs, have a range of glass transition temperatures that are spatially graded. This was achieved using a temperature gradient curing method that imposes different vitrification limits at different positions along the gradient. The resulting material is capable of responding to a wide range of thermal triggers and a good candidate for low-cost, material based temperature sensors. All the aforementioned materials and methods show great potential for practical applications due to their high performance, low cost and broad applicability. Some recommendations for future research and development are given in Chapter 9.

  1. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 ...

  2. Detection of genetically modified crops using multiplex asymmetric polymerase chain reaction and asymmetric hyperbranched rolling circle amplification coupled with reverse dot blot.

    PubMed

    Wang, Xiumin; Teng, Da; Guan, Qingfeng; Tian, Fang; Wang, Jianhua

    2015-04-15

    To meet the ever-increasing demand for detection of genetically modified crops (GMCs), low-cost, high-throughput and high-accuracy detection assays are needed. The new multiplex asymmetric polymerase chain reaction and asymmetric hyper-branched rolling circle amplification coupled with reverse dot blot (RDB) systems were developed to detect GMCs. Thirteen oligonucleotide probes were designed to identify endogenous targets (Lec1, Hmg and Sad1), event-specific targets (RRS-5C, RRS-3C, Bt176-3C and MON810-3C), screening targets (35S promoter and NOS terminator), and control targets (18S and PLX). Optimised conditions were as follows: tailed hybridization probes (1-2 pmol/l) were immobilized on a membrane by baking for 2h, and a 10:1 ratio of forward to reverse primers was used. The detection limits were 0.1 ?g/l of 2% RRS and 0.5 ng/l of DNA from genetically modified (GM) soybean. These results indicate that the RDB assay could be used to detect multiplex target genes of GMCs rapidly and inexpensively. PMID:25466120

  3. Interactions of biomacromolecules with reverse hexagonal liquid crystals: drug delivery and crystallization applications.

    PubMed

    Libster, Dima; Aserin, Abraham; Garti, Nissim

    2011-04-15

    Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications. The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products, and encapsulation and crystallization of proteins. Among the studied lyotropic mesophases, reverse hexagonal LLC (H(II)) of monoolein/water were not widely subjected to practical applications since these were stable only at elevated temperatures. Lately, we obtained stable H(II) mesophases at room temperature by incorporating triacylglycerol (TAG) molecules into the GMO/water mixtures and explored the physical properties of these structures. The present feature article summarizes recent systematic efforts in our laboratory to utilize the H(II) mesophases for solubilization, and potential release and crystallization of biomacromolecules. Such a concept was demonstrated in the case of two therapeutic peptides-cyclosporin A (CSA) and desmopressin, as well as RALA peptide, which is a model skin penetration enhancer, and eventually a larger macromolecule-lysozyme (LSZ). In the course of the study we tried to elucidate relationships between the different levels of organization of LLCs (from the microstructural level, through mesoscale, to macroscopic level) and find feasible correlations between them. Since the structural properties of the mesophase systems are a key factor in drug release applications, we investigated the effects of these guest molecules on their conformations and the way these molecules partition within the domains of the mesophases. The examined H(II) mesophases exhibited great potential as transdermal delivery vehicles for bioactive peptides, enabling tuning the release properties according to their chemical composition and physical properties. Furthermore, we showed a promising opportunity for crystallization of CSA and LSZ in single crystal form as model biomacromolecules for crystallographic structure determination. The main outcomes of our research demonstrated that control of the physical properties of hexagonal LLC on different length scales is key for rational design of these systems as delivery vehicles and crystallization medium for biomacromolecules. PMID:21315366

  4. Application of a hybrid model of neural networks and genetic algorithms to evaluate landslide susceptibility

    NASA Astrophysics Data System (ADS)

    Wang, H. B.; Li, J. W.; Zhou, B.; Yuan, Z. Q.; Chen, Y. P.

    2013-03-01

    In the last few decades, the development of Geographical Information Systems (GIS) technology has provided a method for the evaluation of landslide susceptibility and hazard. Slope units were found to be appropriate for the fundamental morphological elements in landslide susceptibility evaluation. Following the DEM construction in a loess area susceptible to landslides, the direct-reverse DEM technology was employed to generate 216 slope units in the studied area. After a detailed investigation, the landslide inventory was mapped in which 39 landslides, including paleo-landslides, old landslides and recent landslides, were present. Of the 216 slope units, 123 involved landslides. To analyze the mechanism of these landslides, six environmental factors were selected to evaluate landslide occurrence: slope angle, aspect, the height and shape of the slope, distance to river and human activities. These factors were extracted in terms of the slope unit within the ArcGIS software. The spatial analysis demonstrates that most of the landslides are located on convex slopes at an elevation of 100-150 m with slope angles from 135-225 and 40-60. Landslide occurrence was then checked according to these environmental factors using an artificial neural network with back propagation, optimized by genetic algorithms. A dataset of 120 slope units was chosen for training the neural network model, i.e., 80 units with landslide presence and 40 units without landslide presence. The parameters of genetic algorithms and neural networks were then set: population size of 100, crossover probability of 0.65, mutation probability of 0.01, momentum factor of 0.60, learning rate of 0.7, max learning number of 10 000, and target error of 0.000001. After training on the datasets, the susceptibility of landslides was mapped for the land-use plan and hazard mitigation. Comparing the susceptibility map with landslide inventory, it was noted that the prediction accuracy of landslide occurrence is 93.02%, whereas units without landslide occurrence are predicted with an accuracy of 81.13%. To sum up, the verification shows satisfactory agreement with an accuracy of 86.46% between the susceptibility map and the landslide locations. In the landslide susceptibility assessment, ten new slopes were predicted to show potential for failure, which can be confirmed by the engineering geological conditions of these slopes. It was also observed that some disadvantages could be overcome in the application of the neural networks with back propagation, for example, the low convergence rate and local minimum, after the network was optimized using genetic algorithms. To conclude, neural networks with back propagation that are optimized by genetic algorithms are an effective method to predict landslide susceptibility with high accuracy.

  5. DNA hybridization in reverse micelles and its application to mutation detection.

    PubMed

    Park, Lian-Chun; Maruyama, Tatsuo; Goto, Masahiro

    2003-02-01

    DNA hybridization was investigated in AOT (sodium di-2-ethylhexyl sulfosuccinate)/isooctane reverse micelles. The single-stranded DNA molecules were encapsulated in the nanoscale water pools formed in the reverse micelles, reducing the hybridization rate. The DNA hybridization can be monitored by simply measuring the UV absorbance of the reverse micellar solution at 260 nm. We found that the DNA hybridization occurred only at the restricted water content (Wo = [H2O]/[AOT] = 20) and below room temperature. We applied this DNA hybridization behavior in reverse micelles to mutation detection in a model gene p53 and successfully detected the single nucleotide mutations in 20-mer. 30-mer and 50-mer nucleotides without a DNA labeling. PMID:12625557

  6. The application of reverse tubular medial upper arm flap in the reconstruction of ripped facial defects

    PubMed Central

    Dong, Xianglin; Ma, Juan; Ma, Shaolin; Wen, Hao

    2014-01-01

    Reverse medial upper arm flap is usually utilized in the reconstruction of defects in soft tissues of head and facial skin and is with good clinical efficacy. However, it has not been used in the reconstruction of ripped defects. In this study, we used the reverse tubular medial upper arm flap to repair the ripped facial defects. The reverse tubular skin flap from the medial upper arm was longitudinally cut into two parts. One part was used for the reconstruction of ripped facial defects. The other part was used as inner lining to repair the defects of mucosa. Using this method, 3 patients with ripped facial defects were successfully repaired. Thus the reverse tubular medial upper arm flap was successfully used in the reconstruction of ripped facial defects with little surgical trauma, simple manipulation of the operation, increased success rate of the operation and reduced incidence of complications. PMID:25550953

  7. Reverse time migration: A seismic processing application on the connection machine

    NASA Technical Reports Server (NTRS)

    Fiebrich, Rolf-Dieter

    1987-01-01

    The implementation of a reverse time migration algorithm on the Connection Machine, a massively parallel computer is described. Essential architectural features of this machine as well as programming concepts are presented. The data structures and parallel operations for the implementation of the reverse time migration algorithm are described. The algorithm matches the Connection Machine architecture closely and executes almost at the peak performance of this machine.

  8. Designing a Multistage Supply Chain in Cross-Stage Reverse Logistics Environments: Application of Particle Swarm Optimization Algorithms

    PubMed Central

    Chiang, Tzu-An; Che, Z. H.

    2014-01-01

    This study designed a cross-stage reverse logistics course for defective products so that damaged products generated in downstream partners can be directly returned to upstream partners throughout the stages of a supply chain for rework and maintenance. To solve this reverse supply chain design problem, an optimal cross-stage reverse logistics mathematical model was developed. In addition, we developed a genetic algorithm (GA) and three particle swarm optimization (PSO) algorithms: the inertia weight method (PSOA_IWM), VMax method (PSOA_VMM), and constriction factor method (PSOA_CFM), which we employed to find solutions to support this mathematical model. Finally, a real case and five simulative cases with different scopes were used to compare the execution times, convergence times, and objective function values of the four algorithms used to validate the model proposed in this study. Regarding system execution time, the GA consumed more time than the other three PSOs did. Regarding objective function value, the GA, PSOA_IWM, and PSOA_CFM could obtain a lower convergence value than PSOA_VMM could. Finally, PSOA_IWM demonstrated a faster convergence speed than PSOA_VMM, PSOA_CFM, and the GA did. PMID:24772026

  9. Designing a multistage supply chain in cross-stage reverse logistics environments: application of particle swarm optimization algorithms.

    PubMed

    Chiang, Tzu-An; Che, Z H; Cui, Zhihua

    2014-01-01

    This study designed a cross-stage reverse logistics course for defective products so that damaged products generated in downstream partners can be directly returned to upstream partners throughout the stages of a supply chain for rework and maintenance. To solve this reverse supply chain design problem, an optimal cross-stage reverse logistics mathematical model was developed. In addition, we developed a genetic algorithm (GA) and three particle swarm optimization (PSO) algorithms: the inertia weight method (PSOA_IWM), V(Max) method (PSOA_VMM), and constriction factor method (PSOA_CFM), which we employed to find solutions to support this mathematical model. Finally, a real case and five simulative cases with different scopes were used to compare the execution times, convergence times, and objective function values of the four algorithms used to validate the model proposed in this study. Regarding system execution time, the GA consumed more time than the other three PSOs did. Regarding objective function value, the GA, PSOA_IWM, and PSOA_CFM could obtain a lower convergence value than PSOA_VMM could. Finally, PSOA_IWM demonstrated a faster convergence speed than PSOA_VMM, PSOA_CFM, and the GA did. PMID:24772026

  10. Cystic fibrosis genetics: from molecular understanding to clinical application

    PubMed Central

    Cutting, Garry R.

    2015-01-01

    The availability of the human genome sequence and tools for interrogating individual genomes provide an unprecedented opportunity to apply genetics to medicine. Mendelian conditions, which are caused by dysfunction of a single gene, offer powerful examples that illustrate how genetics can provide insights into disease. Cystic fibrosis, one of the more common lethalautosomal recessive Mendelian disorders, is presented here as an example. Recent progress in elucidating disease mechanism and causes of phenotypic variation, as well as in the development of treatments, demonstrates that genetics continues to play an important part in cystic fibrosis research 25 years after the d iscove1y of the disease-causing gene. PMID:25404111

  11. Application of reversed pattern transfer process for sub-90-nm technology

    NASA Astrophysics Data System (ADS)

    Sho, Koutaro; Shibata, Tsuyoshi; Kato, Hirokazu; Abe, Junko; Ohnishi, Yoshinobu; Urayama, Kazuhiko

    2003-06-01

    A reversed pattern transfer technique combined with ultra thin resist process is discussed. In the reversed pattern transfer technique, first a resist pattern is formed over an organic under layer, next a Water-Soluble Silicone (WSS) is coated on the pattern and recessed by RIE under oxide etching conditions until the top of the resist pattern appears (i.e. the silicone is filled between the resist patterns), and finally, the resist pattern and the under layer is etched by RIE under resist etching conditions, whereby the resist pattern is transferred to the under layer. For the middle imaging layer, cyclic olefin-maleic anhidride (COMA) - acrylate hybrid type ArF photo resist (1250 A thickness) and EB resist (700 A thickness) are used. 70 nm L/S patterns (for EB) and 110 nm L/S patterns (for ArF) were successfully transferred to the under layer using reversed pattern transfer technique.

  12. Noise of model target type thrust reversers for engine-over-the-wing applications

    NASA Technical Reports Server (NTRS)

    Stone, J. R.; Gutierrez, O. A.

    1974-01-01

    The results of experiments on the noise generated by V-gutter and semicylindrical target reversers with circular and short-aspect-ratio slot nozzles having diameters of about 5 cm are presented. The experiments were conducted with cold-flow jets at velocities from 190-290 m/sec. The reversers at subsonic jet velocities had a more uniform noise distribution and higher frequency than the nozzles alone. The reverser shape was shown to be more important than the nozzle shape in determining the noise characteristics. The maximum sideline pressure level varied with the sixth power of the jet velocity, and the data were correlated for angles along the sideline. An estimate of the noise level along the 152 m sideline for an engine-over-the-wing powered-lift airplane was made.

  13. Impact localization combined with haptic feedback for touch panel applications based on the time-reversal approach.

    PubMed

    Bai, Mingsian R; Tsai, Yao Kun

    2011-03-01

    In this paper, a combined impact localization and haptic feedback system based on time-reversal signal processing is presented for touch panel applications. Theoretical impulse responses are derived from a propagation model of bending waves in a thin elastic plate. On the basis of the impulse responses, the time-reversal technique is exploited to spot the impact location as well as to generate haptic feedback. The chief advantage of the time-reversal technique lies in its robustness of tackling broadband sources in a reverberant environment. Piezoelectric ceramic plates and voice-coil motors are used as sensors for localization, whereas only voice-coil motors are used as the actuator for haptic feedback. Experimental results demonstrated that the proposed system was effective in precise impact localization for a thin panel, while haptic feedback also implemented using time-reversal principle can generate an impulse at the previously touched position. The combined impact localization and haptic feedback system is capable of enhancing the sensation of man-machine interaction in real time fashion. PMID:21428493

  14. APPLICATION OF A SPRAY DEPOSITION METHOD FOR REVERSED PHASE LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY

    EPA Science Inventory

    Four coal gasification wastewater samples were analyzed for nonvolatile and polar organics by liquid chromatography-mass spectrometry (LC/MS). Samples were separated on a reverse phase liquid chromatographic column using an aqueous solvent as the eluant. A special spray depositio...

  15. Reversible assembly of magnetized particles: Application to water-borne pathogen enumeration

    NASA Astrophysics Data System (ADS)

    Ramadan, Qasem

    2009-12-01

    Reversible assembly of magnetized particles and cells has been proposed and implemented. The approach is based on magnetized particles or magnetically labeled cell immobilization in an array of individual particle/cell for optical counting. The device has been tested for few types of magnetic particles and one water-borne pathogen: Giardia Lamblia. An individual particle immobilization efficiency of 92% was achieved.

  16. Development of a Reverse Genetic System for Infectious Salmon Anemia Virus: Rescue of Recombinant Fluorescent Virus by Using Salmon Internal Transcribed Spacer Region 1 as a Novel Promoter

    PubMed Central

    Toro-Ascuy, Daniela; Tambley, Carolina; Beltran, Carolina; Mascayano, Carolina; Sandoval, Nicolas; Olivares, Eduardo; Medina, Rafael A.; Spencer, Eugenio

    2014-01-01

    Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report the development of a plasmid-based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). Salmon cells cotransfected with pSS-URG-based vectors expressing the eight viral RNA segments and four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, wild-type rISAV901_09 and rISAVrS6-NotI-HPR containing a NotI restriction site and rISAVS6/EGFP-HPR harboring the open reading frame of enhanced green fluorescent protein (EGFP), both within the highly polymorphic region (HPR) of segment 6. All rescued viruses showed replication activity and cytopathic effect in Atlantic salmon kidney-infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5 × 105 PFU/ml, similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and to develop a new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry. PMID:25480750

  17. Implementing reverse genetics in Rosaceae: analysis of T-DNA flanking sequences of insertional mutant lines in the diploid strawberry, Fragaria vesca.

    PubMed

    Oosumi, Teruko; Ruiz-Rojas, Juan Jairo; Veilleux, Richard E; Dickerman, Allan; Shulaev, Vladimir

    2010-09-01

    Reverse genetics is used for functional genomics research in model plants. To establish a model system for the systematic reverse genetics research in the Rosaceae family, we analyzed genomic DNA flanking the T-DNA insertions in 191 transgenic plants of the diploid strawberry, Fragaria vesca. One hundred and seventy-six T-DNA flanking sequences were amplified from the right border (RB) and 37 from the left border (LB) by thermal asymmetric interlaced PCR. Analysis of the T-DNA nick positions revealed that T-DNA was most frequently nicked at the cleavage sites. Analysis of 11 T-DNA integration sites indicated that T-DNA was integrated into the F. vesca genome by illegitimate recombination, as reported in other model plants: Arabidopsis, rice and tobacco. First, deletion of DNA was found at T-DNA integration target sites in all transgenic plants tested. Second, microsimilarities of a few base pairs between the left and/or right ends of the T-DNA and genomic sites were found in all transgenic plants tested. Finally, filler DNA was identified in four break-points. Out of 191 transgenic plants, T-DNA flanking sequences of 79 plants (41%) showed significant similarity to genes, elements or proteins of other plant species and 67 (35%) of the sequences are still unknown strawberry gene fragments. T-DNA flanking sequences of 126 plants (66%) showed homology to plant ESTs. This is the first report of T-DNA integration in a sizeable population of a rosaceous species. We have shown in this paper that T-DNA integration in strawberry is not random but directed by sequence microsimilarities in the host genome. PMID:20444194

  18. Genetics of Autism Spectrum Disorder: Current Status and Possible Clinical Applications.

    PubMed

    Yoo, Heejeong

    2015-12-01

    Autism spectrum disorder (ASD) is one of the most complex behavioral disorders with a strong genetic influence. The objectives of this article are to review the current status of genetic research in ASD, and to provide information regarding the potential candidate genes, mutations, and genetic loci possibly related to pathogenesis in ASD. Investigations on monogenic causes of ASD, candidate genes among common variants, rare de novo mutations, and copy number variations are reviewed. The current possible clinical applications of the genetic knowledge and their future possibilities are highlighted. PMID:26713075

  19. Genetics of Autism Spectrum Disorder: Current Status and Possible Clinical Applications

    PubMed Central

    2015-01-01

    Autism spectrum disorder (ASD) is one of the most complex behavioral disorders with a strong genetic influence. The objectives of this article are to review the current status of genetic research in ASD, and to provide information regarding the potential candidate genes, mutations, and genetic loci possibly related to pathogenesis in ASD. Investigations on monogenic causes of ASD, candidate genes among common variants, rare de novo mutations, and copy number variations are reviewed. The current possible clinical applications of the genetic knowledge and their future possibilities are highlighted. PMID:26713075

  20. Reverse Correlation in Neurophysiology

    ERIC Educational Resources Information Center

    Ringach, Dario; Shapley, Robert

    2004-01-01

    This article presents a review of reverse correlation in neurophysiology. We discuss the basis of reverse correlation in linear transducers and in spiking neurons. The application of reverse correlation to measure the receptive fields of visual neurons using white noise and m-sequences, and classical findings about spatial and color processing in

  1. Genetic admixture and obesity: recent perspectives and future applications

    PubMed Central

    Fernández, José R.; Pearson, Keith E.; Kell, Kenneth P.; Brown, Michelle M. Bohan

    2013-01-01

    The process of the colonization of the New World that occurred centuries ago served as a natural experiment, creating unique combinations of genetic material in newly formed admixed populations. The identification and genotyping of ancestry informative markers (AIMs) have allowed for the estimation of proportions of ancestral parental populations among individuals in a sample through the genetic admixture approach. These admixture estimates have been used in different ways to understand the genetic contributions to individual variation in obesity and body composition parameters, particularly among diverse admixed groups known to differ in obesity prevalence within the United States. Although progress has been made through the use of genetic admixture approaches, future investigations are needed in order to explore the interaction of environmental factors with the degree of genetic ancestry in individuals. A challenge to confront at this time would be to further stratify and define environments in progressively more granular terms, including nutrients, muscle biology, stress responses at the cellular level, and the social and built environments. PMID:24081225

  2. Quantitative Reverse Sample Genome Probing of Microbial Communities and Its Application to Oil Field Production Waters

    PubMed Central

    Voordouw, Gerrit; Shen, Yin; Harrington, Clare S.; Telang, Anita J.; Jack, Thomas R.; Westlake, Donald W. S.

    1993-01-01

    This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters. Images PMID:16349111

  3. Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters

    SciTech Connect

    Voordouw, G.; Shen, Y.; Harrington, C.S.; Teland, A.J. ); Jack, T.R. ); Westlake, W.S. )

    1993-12-01

    This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters.

  4. Reverse pharmacognosy: identifying biological properties for plants by means of their molecule constituents: application to meranzin.

    PubMed

    Do, Quoc-Tuan; Lamy, Ccile; Renimel, Isabelle; Sauvan, Nancy; Andr, Patrice; Himbert, Franck; Morin-Allory, Luc; Bernard, Philippe

    2007-10-01

    Reverse pharmacognosy aims at finding biological targets for natural compounds by virtual or real screening and identifying natural resources that contain the active molecules. We report herein a study focused on the identification of biological properties of meranzin, a major component isolated from Limnocitrus littoralis (Miq.) Swingle. Selnergy, an IN SILICO biological profiling software, was used to identify putative binding targets of meranzin. Among the 400 screened proteins, 3 targets were selected: COX1, COX2 and PPARgamma. Binding tests were realised for these 3 protein candidates, as well as two negative controls. The predictions made by Selnergy were consistent with the experimental results, meaning that these 3 targets can be modulated by an extract containing this compound in a suitable concentration. These results demonstrate that reverse pharmacognosy and its inverse docking component is a powerful tool to identify biological properties for natural molecules and hence for plants containing these compounds. PMID:17853346

  5. Applications of TEMCO to the spheromak and the reversed field pinch

    SciTech Connect

    Mirin, A.A.; Sgro, A.G.

    1986-02-01

    This paper deals with two subjects. One concerns the use of consistent boundary conditions when performing MHD simulations of the reversed field pinch. Of particular concern is the choice of constant current, which when combined with other commonly used boundary conditions, could lead to an inconsistency. The second subject area is that of MHD simulation of the CTX spheromak. A summary of results since the 1984 3-D MHD Workshop is presented.

  6. Asymmetry in family history implicates nonstandard genetic mechanisms: application to the genetics of breast cancer.

    PubMed

    Weinberg, Clarice R; Shi, Min; DeRoo, Lisa A; Taylor, Jack A; Sandler, Dale P; Umbach, David M

    2014-03-01

    Genome-wide association studies typically target inherited autosomal variants, but less studied genetic mechanisms can play a role in complex disease. Sex-linked variants aside, three genetic phenomena can induce differential risk in maternal versus paternal lineages of affected individuals: 1. maternal effects, reflecting the maternal genome's influence on prenatal development; 2. mitochondrial variants, which are inherited maternally; 3. autosomal genes, whose effects depend on parent of origin. We algebraically show that small asymmetries in family histories of affected individuals may reflect much larger genetic risks acting via those mechanisms. We apply these ideas to a study of sisters of women with breast cancer. Among 5,091 distinct families of women reporting that exactly one grandmother had breast cancer, risk was skewed toward maternal grandmothers (p<0.0001), especially if the granddaughter was diagnosed between age 45 and 54. Maternal genetic effects, mitochondrial variants, or variant genes with parent-of-origin effects may influence risk of perimenopausal breast cancer. PMID:24651610

  7. Detection by Reverse Transcription-PCR and Genetic Characterization of Field Isolates of Swine Hepatitis E Virus from Pigs in Different Geographic Regions of the United States

    PubMed Central

    Huang, F. F.; Haqshenas, G.; Guenette, D. K.; Halbur, P. G.; Schommer, S. K.; Pierson, F. W.; Toth, T.E.; Meng, X. J.

    2002-01-01

    Hepatitis E virus (HEV) is an important public health concern in many developing countries. HEV is also endemic in some industrialized counties, including the United States. With our recent discovery of swine HEV in pigs that is genetically closely related to human HEV, hepatitis E is now considered a zoonotic disease. Human strains of HEV are genetically heterogenic. So far in the United States, only one strain of swine HEV has been identified and characterized from a pig. To determine the extent of genetic variations and the nature of swine HEV infections in U.S. pigs, we developed a universal reverse transcription-PCR (RT-PCR) assay that is capable of detecting genetically divergent strains of HEV. By using this universal RT-PCR assay, we tested fecal and serum samples of pigs of 2 to 4 months of age from 37 different U.S. swine farms for the presence of swine HEV RNA. Thirty-four of the 96 pigs (35%) and 20 of the 37 swine herds (54%) tested were positive for swine HEV RNA. The sequences of a 348-bp region within the ORF2 gene of 27 swine HEV isolates from different geographic regions were determined. Sequence analyses revealed that the 27 U.S. swine HEV isolates shared 88 to 100% nucleotide sequence identities with each other and 89 to 98% identities with the prototype U.S. strain of swine HEV. These U.S. swine HEV isolates are only distantly related to the Taiwanese strains of swine HEV, with about 74 to 78% nucleotide sequence identities; to most known human strains of HEV worldwide, with <79% sequence identities; and to avian HEV, with 54 to 56% sequence identities. Phylogenetic analysis showed that all the U.S. swine HEV isolates identified in this study clustered in the same genotype with the prototype U.S. swine HEV and the two U.S. strains of human HEV. The data from this study indicated that swine HEV is widespread and enzoonotic in U.S. swine herds and that, as is with human HEV, swine HEV isolates from different geographic regions of the world are also genetically heterogenic. These data further raise potential concerns for zoonosis, xenozoonosis, and food safety. PMID:11923352

  8. Reverse engineering biological networks :applications in immune responses to bio-toxins.

    SciTech Connect

    Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-12-01

    Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

  9. Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization.

    PubMed

    Messer, William B; Yount, Boyd; Hacker, Kari E; Donaldson, Eric F; Huynh, Jeremy P; de Silva, Aravinda M; Baric, Ralph S

    2012-01-01

    Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ?19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis. PMID:22389731

  10. Application of Genetic/Genomic Approaches to Allergic Disorders

    PubMed Central

    Baye, Tesfaye M.; Martin, Lisa J.; Khurana Hershey, Gurjit K.

    2010-01-01

    Completion of the human genome project and rapid progress in genetics and bioinformatics have enabled the development of large public databases, which include genetic and genomic data linked to clinical health data. With the massive amount of information available, clinicians and researchers have the unique opportunity to complement and integrate their daily practice with the existing resources to clarify the underlying etiology of complex phenotypes such as allergic diseases. The genome itself is now often utilized as a starting point for many studies and multiple innovative approaches have emerged applying genetic/genomic strategies to key questions in the field of allergy and immunology. There have been several successes, which have uncovered new insights into the biologic underpinnings of allergic disorders. Herein, we will provide an in depth review of genomic approaches to identifying genes and biologic networks involved in allergic diseases. We will discuss genetic and phenotypic variation, statistical approaches for gene discovery, public databases, functional genomics, clinical implications, and the challenges that remain. PMID:20638111

  11. GENETIC MARKERS AND THEIR APPLICATION IN POULTRY BREEDING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current chicken genetic map contains at least 1,965 loci within 50 linkage groups and it covers about 4,000 cM. About 235 of these loci have homology with known human or mammalian genes. The remaining loci are anonymous molecular DNA markers, including microsatellites, AFLP, RAPD, CR1 and othe...

  12. [Craniofacial anthropometric patterns in genetic facial dysmorphism: methodology and applications].

    PubMed

    Guyot, L; Richard, O; Philip, N; Dutour, O

    2002-04-01

    Craniofacial anthropometric has become an important tool in medical genetics. The method is simple, non-invasive, reliable, and inexpensive. To provide reliable measurements, the method must be conducted with a precise procedure by a trained physician. Anthropometric determination of craniofacial morphology is helpful in identifying and describing syndromes associated with classical techniques. Additional studies may involve new approaches to facial morphogenesis. PMID:11997739

  13. QTL x Genetic Background Interaction: Application to Predicting Progeny Value

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Failures of the additive infinitesimal model continue to provide incentive to study other modes of gene action, in particular, epistasis. Epistasis can be modeled as a QTL by genetic background interaction. Association mapping models lend themselves to fitting such an interaction because they often ...

  14. Green's function estimation in speckle using the decomposition of the time reversal operator: application to aberration correction in medical imaging.

    PubMed

    Robert, Jean-Luc; Fink, Mathias

    2008-02-01

    The FDORT method (French acronym for decomposition of the time reversal operator using focused beams) is a time reversal based method that can detect point scatterers in a heterogeneous medium and extract their Green's function. It is particularly useful when focusing in a heterogeneous medium. This paper generalizes the theory of the FDORT method to random media (speckle), and shows that it is possible to extract Green's functions from the speckle signal using this method. Therefore it is possible to achieve a good focusing even if no point scatterers are present. Moreover, a link is made between FDORT and the Van Cittert-Zernike theorem. It is deduced from this interpretation that the normalized first eigenvalue of the focused time reversal operator is a well-known focusing criterion. The concept of an equivalent virtual object is introduced that allows the random problem to be replaced by an equivalent deterministic problem and leads to an intuitive understanding of FDORT in speckle. Applications to aberration correction are presented. The reduction of the variance of the Green's function estimate is discussed. Finally, it is shown that the method works well in the presence of strong interfering scatterers. PMID:18247890

  15. Local application of SCH 39166 reversibly and dose-dependently decreases acetylcholine release in the rat striatum.

    PubMed

    Acquas, E; Di Chiara, G

    1999-11-01

    The effect of local application by reverse dialysis of the dopamine D(1) receptor antagonist (-)-trans-6,7,7a,8,9, 13b-exahydro-3-chloro-2-hydroxy-N-methyl-5H-benzo-[d]-nap hto-[2, 1b]-azepine hydrochloride (SCH 39166) on acetylcholine release was studied in awake, freely moving rats implanted with concentric microdialysis probes in the dorsal striatum. In these experiments, the reversible acetylcholine esterase inhibitor, neostigmine, was added to the perfusion solution at two different concentrations, 0.01 and 0.1 microM. SCH 39166 (1, 5 and 10 microM), in the presence of 0.01 microM neostigmine, reversibly decreased striatal acetylcholine release (1 microM SCH 39166 by 8+/-4%; 5 microM SCH 39166 by 24+/-5%; 10 microM SCH 39166 by 27+/-7%, from basal). Similarly, SCH 39166, applied in the presence of a higher neostigmine concentration (0.1 microM), decreased striatal acetylcholine release by 14+/-4% at 1 microM, by 28+/-8% at 5 microM and by 30+/-5% at 10 microM, in a dose-dependent and time-dependent manner. These results are consistent with the existence of a facilitatory tone of dopamine on striatal acetylcholine transmission mediated by dopamine D(1) receptors located on striatal cholinergic interneurons. PMID:10594319

  16. Reverse pharmacognosy: application of selnergy, a new tool for lead discovery. The example of epsilon-viniferin.

    PubMed

    Do, Quoc-Tuan; Renimel, Isabelle; Andre, Patrice; Lugnier, Claire; Muller, Christian D; Bernard, Philippe

    2005-09-01

    The aim of reverse pharmacognosy is to find new biological targets for natural compounds by virtual or real screening and identify natural resources that contain the active molecules. To demonstrate the applicability of this concept, we report here a study on epsilon-viniferin, an active ingredient for cosmetic development. Nevertheless, this natural substance is weakly defined in terms of biological properties. SELNERGY, an inverse docking computer software, was used to identify putative binding biological targets for epsilon-viniferin. Among the 400 screened proteins two targets were retained. For cosmetic application, cyclic nucleotide phosphodiesterase 4 (PDE4) was the most interesting candidate. Moreover, other PDE subtypes (1, 2, 3, 5 and 6) were not retained, indicating a selectivity for PDE4. The experimental binding tests on the 6 subtypes of PDE revealed a significant selectivity of epsilon-viniferin for the PDE4 subtype. This selectivity was confirmed by evaluation of epsilon-viniferin on the secretion of TNF-alpha and Interleukin-8. Our data demonstrated that epsilon-viniferin possesses anti-inflammatory properties by inhibiting PDE4 subtype. In conclusion, reverse pharmacognosy and its inverse docking component cannot only be integrated into a program for new lead discovery but is also a useful approach to find new applications for identified compounds. PMID:16472225

  17. Applications of Genetic Algorithms to Solar Coronal Modeling

    NASA Astrophysics Data System (ADS)

    Gibson, S.; Charbonneau, P.

    1996-05-01

    Genetic algorithms are efficient and flexible means of attacking optimization problems that would otherwise be computationally prohibitive. Consider a model that represents an observable quantity in terms of a few parameters, with an associated chi (2) measuring goodness of fit with respect to data. If the modeled observable is non-linear in the parameters, there can exist a degeneracy of minimum chi (2) in parameter space. It is then essential to understand the location and extent of this degeneracy in order to find the global optimum and quantify the degeneracy error around it. Traditional methods of spanning parameter space such as a grid search or a Monte Carlo approach scale exponentially with the number of parameters, and waste a great deal of computational time looking at ``un-fit'' solutions. Genetic algorithms, on the other hand, converge rapidly onto regions of minimum chi (2) while continuously generate ``mutant solutions'', allowing an efficient and comprehensive exploration of parameter space. Our aim has been to develop an approach that simultaneously yields a best fit solution and global error estimates, by modifying and extending standard genetic algorithm-based techniques. We fit two magnetostatic models of the solar minimum corona to observations in white light. The first model allows horizontal bulk currents and the second also allows sheet currents enclosing and extending out from the equatorial helmet streamer. Using our genetic algorithm approach, we map out the degeneracy of model parameters that reproduce observations well. The flexibility of genetic algorithms facilitates incorporating the additional observational constraint of photospheric magnetic flux, reducing the degeneracy of solutions to a range represented by reasonable error bars on the model predictions. By using genetic algorithms we are able to identify and constrain the degeneracy inherent to the models, a task, which, particularly for the more complex second model, would be impractical using a traditional technique. The ultimate result is a greater understanding of the large scale structure of the solar corona, providing clues to the mechanisms heating the corona and accelerating the solar wind.

  18. Gyroviscous stability theory with application to the internal tilt mode of a field-reversed configuration

    SciTech Connect

    Steinhauer, L.C. ); Ishida, A. )

    1990-10-01

    The variational formulation for a gyroviscous fluid plasma is constructed. This theory offers a fluid-based description of perpendicular kinetic effects, generally called finite Larmor radius (FLR) effects. This approach avoids the complexity of a more complete kinetic treatment and avoids local singularities that can appear in the standard FLR expansion treatment. The method is applied to the internal tilt mode of a field-reversed configuration (FRC), an instance where standard FLR theory clearly breaks down. The relative simplicity of the variational gyroviscous fluid theory allows easy computation of stability properties, including the scaling of marginal stability conditions.

  19. Almost isometries of non-reversible metrics with applications to stationary spacetimes

    NASA Astrophysics Data System (ADS)

    Javaloyes, Miguel Angel; Lichtenfelz, Leandro; Piccione, Paolo

    2015-03-01

    We develop the basics of a theory of almost isometries for spaces endowed with a quasi-metric. The case of non-reversible Finsler (more specifically, Randers) metrics is of particular interest, and it is studied in more detail. The main motivation arises from General Relativity, and more specifically in spacetimes endowed with a timelike conformal field K, in which case conformal diffeomorphisms correspond to almost isometries of the Fermat metrics defined in the spatial part. A series of results on the topology and the Lie group structure of conformal maps are discussed.

  20. A General Reversible Hereditary Constitutive Model. Part 2; Application to a Titanium Alloy

    NASA Technical Reports Server (NTRS)

    Arnold, S. M.; Saleeb, A. F.; Castelli, M. G.

    1997-01-01

    Given the mathematical framework and specific viscoelastic model in Part 1 our primary goal in this second part is focused on model characterization and assessment for the specific titanium alloy, TIMETAL 21S. The model is motivated by experimental evidence suggesting the presence of significant rate/time effects in the so-called quasilinear, reversible, material response range. An explanation of the various experiments performed and their corresponding results are also included. Finally, model correlations and predictions are presented for a wide temperature range.

  1. Polygenic risk scores in imaging genetics: Usefulness and applications.

    PubMed

    Dima, Danai; Breen, Gerome

    2015-08-01

    Genetic factors account for up to 80% of the liability for schizophrenia and bipolar disorder. Genome-wide association studies (GWAS) have successfully identified several single nucleotide polymorphisms (SNPs) and genes associated with increased risk for both disorders. Single SNP analyses alone do not address the overall genomic or polygenic architecture of psychiatric disorders as the amount of phenotypic variation explained by each GWAS-supported SNP is small whereas the number of SNPs/regions underlying risk for illness is thought to be very large. The polygenic risk score models the aggregate effect of alleles associated with disease status present in each individual and allows us to utilise the power of large GWAS to be applied robustly in small samples. Here we make the case that risk prediction, intervention and personalised medicine can only benefit with the inclusion of polygenic risk scores in imaging genetics research. PMID:25944849

  2. Clinical application of exome sequencing in undiagnosed genetic conditions

    PubMed Central

    Need, Anna C; Shashi, Vandana; Hitomi, Yuki; Schoch, Kelly; Shianna, Kevin V; McDonald, Marie T; Meisler, Miriam H

    2012-01-01

    Background There is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that includes patients with a broad range of phenotypic presentations. Methods The authors present a pilot programme of whole-exome sequencing on 12 patients with unexplained and apparent genetic conditions, along with their unaffected parents. Unlike many previous studies, the authors did not seek patients with similar phenotypes, but rather enrolled any undiagnosed proband with an apparent genetic condition when predetermined criteria were met. Results This undertaking resulted in a likely genetic diagnosis in 6 of the 12 probands, including the identification of apparently causal mutations in four genes known to cause Mendelian disease (TCF4, EFTUD2, SCN2A and SMAD4) and one gene related to known Mendelian disease genes (NGLY1). Of particular interest is that at the time of this study, EFTUD2 was not yet known as a Mendelian disease gene but was nominated as a likely cause based on the observation of de novo mutations in two unrelated probands. In a seventh case with multiple disparate clinical features, the authors were able to identify homozygous mutations in EFEMP1 as a likely cause for macular degeneration (though likely not for other features). Conclusions This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised. PMID:22581936

  3. DNA marker applications to molecular genetics and genomics in tomato

    PubMed Central

    Shirasawa, Kenta; Hirakawa, Hideki

    2013-01-01

    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

  4. DNA marker applications to molecular genetics and genomics in tomato.

    PubMed

    Shirasawa, Kenta; Hirakawa, Hideki

    2013-03-01

    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

  5. On thermodynamic and microscopic reversibility

    SciTech Connect

    Crooks, Gavin E.

    2011-07-12

    The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.

  6. Time reversal of scattering wavefield with applications for imaging fault damaged zones close to bimaterial interfaces

    NASA Astrophysics Data System (ADS)

    Benites, R. A.; Ben-Zion, Y.

    2010-12-01

    We demonstrate that a time-reverse mirror (TRM) of data recorded by an array of broadband surface seismometers distributed across a bimaterial fault interface separating two quarter spaces, one of which includes a damaged zone with high crack density, can be used to image the spatial distribution of the damage. The generic cases presented in this study consider the damaged zone to be a region containing many thin, elliptical cracks randomly distributed laterally next to the fault and extending vertically down, in the medium with slower average S-wave velocity. The incident seismic wave is produced by a strike-slip line source corresponding to slip right on the fault plane at some prescribed depth. We first solve the forward problem, i.e. compute the full waveform synthetic seismogram at each element of the array using a boundary integral numerical scheme. Then we subtract the incident wave from each seismogram and time-reverse only the scattered wavefield, last phase first, back to their origin. The results show that the computed image can be obtained with high resolution for an array aperture size comparable to four times the largest length scale (width or depth) of the damage zone, and a seismometer interval distance comparable to one quarter of the smallest wavelength considered in the calculations. We present results of such images for several random realizations of crack distribution.

  7. Application of Statistical Thermodynamics To Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC.

    PubMed

    Tarasova, Irina A; Goloborodko, Anton A; Perlova, Tatyana Y; Pridatchenko, Marina L; Gorshkov, Alexander V; Evreinov, Victor V; Ivanov, Alexander R; Gorshkov, Mikhail V

    2015-07-01

    The theory of critical chromatography for biomacromolecules (BioLCCC) describes polypeptide retention in reversed-phase HPLC using the basic principles of statistical thermodynamics. However, whether this theory correctly depicts a variety of empirical observations and laws introduced for peptide chromatography over the last decades remains to be determined. In this study, by comparing theoretical results with experimental data, we demonstrate that the BioLCCC: (1) fits the empirical dependence of the polypeptide retention on the amino acid sequence length with R(2) > 0.99 and allows in silico determination of the linear regression coefficients of the log-length correction in the additive model for arbitrary sequences and lengths and (2) predicts the distribution coefficients of polypeptides with an accuracy from 0.98 to 0.99 R(2). The latter enables direct calculation of the retention factors for given solvent compositions and modeling of the migration dynamics of polypeptides separated under isocratic or gradient conditions. The obtained results demonstrate that the suggested theory correctly relates the main aspects of polypeptide separation in reversed-phase HPLC. PMID:26023813

  8. A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity

    USGS Publications Warehouse

    Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M.; Vakharia, Vikram N.

    2011-01-01

    Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-ΔNV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-ΔNV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-ΔNV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines.

  9. Clinical Application of Antenatal Genetic Diagnosis of Osteogenesis Imperfecta Type IV

    PubMed Central

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

    2015-01-01

    Background 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. Material/Methods 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. Results 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. Conclusions Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families. PMID:25835785

  10. Generation of Mutant Uukuniemi Viruses Lacking the Nonstructural Protein NSs by Reverse Genetics Indicates that NSs Is a Weak Interferon Antagonist

    PubMed Central

    Rezelj, Veronica V.; verby, Anna K.

    2015-01-01

    ABSTRACT Uukuniemi virus (UUKV) is a tick-borne member of the Phlebovirus genus (family Bunyaviridae) and has been widely used as a safe laboratory model to study aspects of bunyavirus replication. Recently, a number of new tick-borne phleboviruses have been discovered, some of which, like severe fever with thrombocytopenia syndrome virus and Heartland virus, are highly pathogenic in humans. UUKV could now serve as a useful comparator to understand the molecular basis for the different pathogenicities of these related viruses. We established a reverse-genetics system to recover UUKV entirely from cDNA clones. We generated two recombinant viruses, one in which the nonstructural protein NSs open reading frame was deleted from the S segment and one in which the NSs gene was replaced with green fluorescent protein (GFP), allowing convenient visualization of viral infection. We show that the UUKV NSs protein acts as a weak interferon antagonist in human cells but that it is unable to completely counteract the interferon response, which could serve as an explanation for its inability to cause disease in humans. IMPORTANCE Uukuniemi virus (UUKV) is a tick-borne phlebovirus that is apathogenic for humans and has been used as a convenient model to investigate aspects of phlebovirus replication. Recently, new tick-borne phleboviruses have emerged, such as severe fever with thrombocytopenia syndrome virus in China and Heartland virus in the United States, that are highly pathogenic, and UUKV will now serve as a comparator to aid in the understanding of the molecular basis for the virulence of these new viruses. To help such investigations, we have developed a reverse-genetics system for UUKV that permits manipulation of the viral genome. We generated viruses lacking the nonstructural protein NSs and show that UUKV NSs is a weak interferon antagonist. In addition, we created a virus that expresses GFP and thus allows convenient monitoring of virus replication. These new tools represent a significant advance in the study of tick-borne phleboviruses. PMID:25673721

  11. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    PubMed Central

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

  12. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    PubMed

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, Mara A; Van Damme, Patrick; Garcia, Willman; Tapia, Csar; Romero, Jos; Sigueas, Manuel; Hormaza, Jos I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

  13. Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus

    PubMed Central

    Scobey, Trevor; Yount, Boyd L.; Sims, Amy C.; Donaldson, Eric F.; Agnihothram, Sudhakar S.; Menachery, Vineet D.; Graham, Rachel L.; Swanstrom, Jesica; Bove, Peter F.; Kim, Jeeho D.; Grego, Sonia; Randell, Scott H.; Baric, Ralph S.

    2013-01-01

    Severe acute respiratory syndrome with high mortality rates (∼50%) is associated with a novel group 2c betacoronavirus designated Middle East respiratory syndrome coronavirus (MERS-CoV). We synthesized a panel of contiguous cDNAs that spanned the entire genome. Following contig assembly into genome-length cDNA, transfected full-length transcripts recovered several recombinant viruses (rMERS-CoV) that contained the expected marker mutations inserted into the component clones. Because the wild-type MERS-CoV contains a tissue culture-adapted T1015N mutation in the S glycoprotein, rMERS-CoV replicated ∼0.5 log less efficiently than wild-type virus. In addition, we ablated expression of the accessory protein ORF5 (rMERS•ORF5) and replaced it with tomato red fluorescent protein (rMERS-RFP) or deleted the entire ORF3, 4, and 5 accessory cluster (rMERS-ΔORF3–5). Recombinant rMERS-CoV, rMERS-CoV•ORF5, and MERS-CoV-RFP replicated to high titers, whereas MERS-ΔORF3–5 showed 1–1.5 logs reduced titer compared with rMERS-CoV. Northern blot analyses confirmed the associated molecular changes in the recombinant viruses, and sequence analysis demonstrated that RFP was expressed from the appropriate consensus sequence AACGAA. We further show dipeptidyl peptidase 4 expression, MERS-CoV replication, and RNA and protein synthesis in human airway epithelial cell cultures, primary lung fibroblasts, primary lung microvascular endothelial cells, and primary alveolar type II pneumocytes, demonstrating a much broader tissue tropism than severe acute respiratory syndrome coronavirus. The availability of a MERS-CoV molecular clone, as well as recombinant viruses expressing indicator proteins, will allow for high-throughput testing of therapeutic compounds and provide a genetic platform for studying gene function and the rational design of live virus vaccines. PMID:24043791

  14. Application of coevolutionary genetic algorithms for multiobjective optimization

    NASA Astrophysics Data System (ADS)

    Liu, Jian-guo; Li, Zu-shu; Wu, Wei-ping

    2007-12-01

    Multiobjective optimization is clearly one of the most important classes of problems in science and engineering. The solution of real problem involved in multiobjective optimization must satisfy all optimization objectives simultaneously, and in general the solution is a set of indeterminacy points. The task of multiobjective optimization is to estimate the distribution of this solution set, then to find the satisfying solution in it. Many methods solving multiobjective optimization using genetic algorithm have been proposed in recent twenty years. But these approaches tend to work negatively, causing that the population converges to small number of solutions due to the random genetic drift. To avoid this phenomenon, a multiobjective coevolutionary genetic algorithm (MoCGA) for multiobjective optimization is proposed. The primary design goal of the proposed approach is to produce a reasonably good approximation of the true Pareto front of a problem. In the algorithms, each objective corresponds to a population. At each generation, these populations compete among themselves. An ecological population density competition equation is used for reference to describe the relation between multiple objectives and to direct the adjustment over the relation at individual and population levels. The proposed approach store the Pareto optimal point obtained along the evolutionary process into external set. The proposed approach is validated using Schaffer's test function f II and it is compared with the Niched Pareto GA (nPGA). Simulation experiments prove that the algorithm has a better performance in finding the Pareto solutions, and the MoCGA can have advantages over the other algorithms under consideration in convergence to the Pareto-optimal front.

  15. [Application of population genetics in the field of medicine].

    PubMed

    Octavio-Aguilar, Pablo; Ramos-Frías, Josefina

    2014-01-01

    Human populations follow the same evolutionary principles as other organisms, although mixed with social and cultural elements, which can result in a high prevalence of certain diseases within specific ethnic groups. In this work, the Hardy-Weinberg principle is analyzed from a medical, social and biological viewpoint to understand the evolutionary processes of autosomal recessive diseases. It can be concluded that the incidence of these diseases is inversely related to the levels of genetic variability within populations, which depends on colonization, recolonization and migration events, as well as on social conventions such as racism, social stratification and segregation. PMID:24967923

  16. Identification of a new genetic variant of bovine beta-casein using reversed-phase high-performance liquid chromatography and mass spectrometric analysis.

    PubMed

    Visser, S; Slangen, C J; Lagerwerf, F M; Van Dongen, W D; Haverkamp, J

    1995-09-01

    Various components of the beta-casein fraction from bovine milk were separated by preparative reversed-phase high-performance liquid chromatography (RP-HPLC). They included the genetic variants beta A1, beta A2, beta A3, and an unknown component previously denoted beta X [S. Visser et al., J. Chromatogr. 548 (1991) 361-370]. Tryptic digests of these components were compared by RP-HPLC and most peaks were analysed by mass spectrometry (MS). The tryptic map of beta X was closest to that of beta A1, but with a few mutually different peak components. Electrospray ionisation MS revealed that in the beta X map these components had relative molecular masses of 16 higher than the corresponding ones in the beta A1 map. The main differential peaks represented the 114-169 fragments of beta A1 and beta X, respectively, which were both purified and then cleaved with cyanogen bromide. In the resulting mixtures, each of which contained three fragments, the corresponding peptides representing the 145-156 sequence showed the 16 relative molecular mass difference. In beta X this sequence contained a Leu residue at position 152 instead of the Pro-152 in beta A1, as established by fast-atom bombardment MS-MS. The Leu could be discriminated from an Ile residue by the presence of a side-chain-specific, D-type fragment ion in the MS-MS spectrum of the beta X CNBr peptide. The sequence of the two homologous 145-156 fragments was confirmed by regular amino acid sequence analysis. In accordance with internationally accepted guidelines for the nomenclature of milk proteins, the new genetic variant has been named beta-casein F-5P. PMID:7496485

  17. Preparation of a light-sensitive and reversible dissolution copolymer and its application in lysozyme purification.

    PubMed

    Wen, Wen; Wan, Junfen; Cao, Xuejun; Xia, Jinan

    2007-01-01

    A novel light-sensitive and cation-exchange copolymer (PNBCC) has been synthesized by random copolymerization of chlorophyllin sodium copper salt, crylic acid, n-butyl acrylate, and N-isopropylacrylamide. The PNBCC copolymer showed reversible dissolution and could be precipitated by 488 nm laser irradiation with the least light density of 1.70 x 10(5) W/m(2). By optimizing the ratio of monomers, pH, and ion concentration, over 95% copolymer was recovered by laser irradiation. The copolymer was used to purify lysozyme as light-sensitive cation exchanger, and its adsorption matched a Langmuir adsorption isotherm with maximum adsorption capacity of 98,900 U/g and dissociated constant of 852 U/mL. By applying the copolymer to the separation of lysozyme from egg white, the specific activity of lysozyme was improved from 399 to 6346 U/mg and the recovery of lysozyme achieved 81.3%. PMID:17880102

  18. Application of Adjoint Methodology to Supersonic Aircraft Design Using Reversed Equivalent Areas

    NASA Technical Reports Server (NTRS)

    Rallabhandi, Sriram K.

    2013-01-01

    This paper presents an approach to shape an aircraft to equivalent area based objectives using the discrete adjoint approach. Equivalent areas can be obtained either using reversed augmented Burgers equation or direct conversion of off-body pressures into equivalent area. Formal coupling with CFD allows computation of sensitivities of equivalent area objectives with respect to aircraft shape parameters. The exactness of the adjoint sensitivities is verified against derivatives obtained using the complex step approach. This methodology has the benefit of using designer-friendly equivalent areas in the shape design of low-boom aircraft. Shape optimization results with equivalent area cost functionals are discussed and further refined using ground loudness based objectives.

  19. Establishment of Reverse Direct ELISA and Its Application in Screening High-Affinity Monoclonal Antibodies

    PubMed Central

    Zhang, Chunmei; Li, Rende; Li, Yongming; Song, Chaojun; Liu, Zhijia; Zhang, Yun; Xu, Zhuwei; Zhuang, Ran; Yi, Jing; Yang, Angang; Yang, Kun

    2012-01-01

    Traditionally monoclonal antibody (MAb) titer is determined by indirect enzyme-linked immunosorbent assay (ELISA), which is primarily used to evaluate the quality of MAbs. In this study, the titer and affinity of a group of MAbs against ovalbumin (OVA) were tested by indirect ELISA and the ELISA method reported previously. Data showed that there may be great differences between the indirect ELISA antibody titer and affinity value of MAbs. For the first time, a simple and effective reverse direct ELISA (RD-ELISA) was established for the detection of high-affinity MAbs. Among the group of MAbs to OVA, a certain proportion of antibodies with high affinity but low indirect ELISA titer do exist and can be clearly and efficiently detected by RD-ELISA. This study demonstrates that RD-ELISA is an effective method for high-affinity MAb screening. PMID:22894783

  20. A low distorsion and reversible watermark: application to angiographic images of the retina.

    PubMed

    Coatrieux, G; Puentes, J; Roux, C; Lamard, M; Daccache, W

    2005-01-01

    Medical image security can be enhanced using watermarking, which allows embedding the protection information as a digital signature, by modifying the pixel gray levels of the image. In this paper we propose a reversible watermarking scheme which guarantees that once the embedded message is read, alterations introduced during the insertion process can be removed from the image. Thereafter, original pixel gray levels of the image are restored. The proposed approach relies on estimation of image signal that is invariant to the insertion process, and permits to introduce a very slight watermark within the image. In fact, the insertion process adds or subtracts at least one gray level to the pixels of the original image. Depending on the image to be watermarked, in our case angiographic images of the retina, it is expected that such image alteration will not have any impact on the diagnosis quality, and consequently that the watermark can be kept within the image while this one is interpreted. PMID:17282674

  1. Application of anti-listerial bacteriocins: monitoring enterocin expression by multiplex relative reverse transcription-PCR.

    PubMed

    Williams, D Ross; Chanos, Panagiotis

    2012-12-01

    Listeriosis is a deadly food-borne disease, and its incidence may be limited through the biotechnological exploitation of a number of anti-listerial biocontrol agents. The most widely used of these agents are bacteriocins and the Class II enterocins are characterized by their activity against Listeria. Enterocins are primarily produced by enterococci, particularly Enterococcus faecium and many strains have been described, often encoding multiple bacteriocins. The use of these strains in food will require that they are free of virulence functions and that they exhibit a high level expression of anti-listerial enterocins in fermentation conditions. Multiplex relative RT (reverse transcription)-PCR is a technique that is useful in the discovery of advantageous expression characteristics among enterocin-producing strains. It allows the levels of individual enterocin gene expression to be monitored and determination of how expression is altered under different growth conditions. PMID:23176514

  2. Next-generation sequencing technologies and applications for human genetic history and forensics

    PubMed Central

    2011-01-01

    Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics. PMID:22115430

  3. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  4. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  5. Application of Genetic Algorithm to Hexagon-Based Motion Estimation

    PubMed Central

    Cheng, Wan-Shu

    2014-01-01

    With the improvement of science and technology, the development of the network, and the exploitation of the HDTV, the demands of audio and video become more and more important. Depending on the video coding technology would be the solution for achieving these requirements. Motion estimation, which removes the redundancy in video frames, plays an important role in the video coding. Therefore, many experts devote themselves to the issues. The existing fast algorithms rely on the assumption that the matching error decreases monotonically as the searched point moves closer to the global optimum. However, genetic algorithm is not fundamentally limited to this restriction. The character would help the proposed scheme to search the mean square error closer to the algorithm of full search than those fast algorithms. The aim of this paper is to propose a new technique which focuses on combing the hexagon-based search algorithm, which is faster than diamond search, and genetic algorithm. Experiments are performed to demonstrate the encoding speed and accuracy of hexagon-based search pattern method and proposed method. PMID:24592178

  6. Water uptake in barley grain: Physiology; genetics and industrial applications.

    PubMed

    Cu, Suong; Collins, Helen M; Betts, Natalie S; March, Timothy J; Janusz, Agnieszka; Stewart, Doug C; Skadhauge, Birgitte; Eglinton, Jason; Kyriacou, Bianca; Little, Alan; Burton, Rachel A; Fincher, Geoffrey B

    2016-01-01

    Water uptake by mature barley grains initiates germination and is the first stage in the malting process. Here we have investigated the effects of starchy endosperm cell wall thickness on water uptake, together with the effects of varying amounts of the wall polysaccharide, (1,3;1,4)-?-glucan. In the latter case, we examined mutant barley lines from a mutant library and transgenic barley lines in which the (1,3;1,4)-?-glucan synthase gene, HvCslF6, was down-regulated by RNA interference. Neither cell wall thickness nor the levels of grain (1,3;1,4)-?-glucan were significantly correlated with water uptake but are likely to influence modification during malting. However, when a barley mapping population was phenotyped for rate of water uptake into grain, quantitative trait locus (QTL) analysis identified specific regions of chromosomes 4H, 5H and 7H that accounted for approximately 17%, 18% and 11%, respectively, of the phenotypic variation. These data indicate that variation in water uptake rates by elite malting cultivars of barley is genetically controlled and a number of candidate genes that might control the trait were identified under the QTL. The genomics data raise the possibility that the genetic variation in water uptake rates might be exploited by breeders for the benefit of the malting and brewing industries. PMID:26566843

  7. Feature generation using genetic programming with application to fault classification.

    PubMed

    Guo, Hong; Jack, Lindsay B; Nandi, Asoke K

    2005-02-01

    One of the major challenges in pattern recognition problems is the feature extraction process which derives new features from existing features, or directly from raw data in order to reduce the cost of computation during the classification process, while improving classifier efficiency. Most current feature extraction techniques transform the original pattern vector into a new vector with increased discrimination capability but lower dimensionality. This is conducted within a predefined feature space, and thus, has limited searching power. Genetic programming (GP) can generate new features from the original dataset without prior knowledge of the probabilistic distribution. In this paper, a GP-based approach is developed for feature extraction from raw vibration data recorded from a rotating machine with six different conditions. The created features are then used as the inputs to a neural classifier for the identification of six bearing conditions. Experimental results demonstrate the ability of GP to discover autimatically the different bearing conditions using features expressed in the form of nonlinear functions. Furthermore, four sets of results--using GP extracted features with artificial neural networks (ANN) and support vector machines (SVM), as well as traditional features with ANN and SVM--have been obtained. This GP-based approach is used for bearing fault classification for the first time and exhibits superior searching power over other techniques. Additionaly, it significantly reduces the time for computation compared with genetic algorithm (GA), therefore, makes a more practical realization of the solution. PMID:15719936

  8. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle.

    PubMed

    Li, Wanbo; Sartelet, Arnaud; Tamma, Nico; Coppieters, Wouter; Georges, Michel; Charlier, Carole

    2016-02-01

    In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed. PMID:26582259

  9. Molecular Identification and Genetic Analysis of Norovirus Genogroups I and II in Water Environments: Comparative Analysis of Different Reverse Transcription-PCR Assays?

    PubMed Central

    La Rosa, G.; Fontana, S.; Di Grazia, A.; Iaconelli, M.; Pourshaban, M.; Muscillo, M.

    2007-01-01

    Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses. PMID:17483265

  10. Overcoming statistical bias to estimate genetic mating systems in open populations: a comparison of Bateman's principles between the sexes in a sex-role-reversed pipefish.

    PubMed

    Mobley, Kenyon B; Jones, Adam G

    2013-03-01

    The genetic mating system is a key component of the sexual selection process, yet methods for the quantification of mating systems remain controversial. One approach involves metrics derived from Bateman's principles, which are based on variances in mating and reproductive success and the relationship between them. However, these measures are extremely difficult to measure for both sexes in open populations, because missing data can result in biased estimates. Here, we develop a novel approach for the estimation of mating system metrics based on Bateman's principles and apply it to a microsatellite-based parentage analysis of a natural population of the dusky pipefish, Syngnathus floridae. Our results show that both male and female dusky pipefish have significantly positive Bateman gradients. However, females exhibit larger values of the opportunity for sexual selection and the opportunity for selection compared to males. These differences translate into a maximum intensity of sexual selection (S'max) for females three times larger than that for males. Overall, this study identifies a critical source of bias that affects studies of mating systems in open populations, presents a novel method for overcoming this bias, and applies this method for the first time in a sex-role-reversed pipefish. PMID:23461316

  11. Molecular identification and genetic analysis of Norovirus genogroups I and II in water environments: comparative analysis of different reverse transcription-PCR assays.

    PubMed

    La Rosa, G; Fontana, S; Di Grazia, A; Iaconelli, M; Pourshaban, M; Muscillo, M

    2007-07-01

    Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses. PMID:17483265

  12. Brainbow: new resources and emerging biological applications for multicolor genetic labeling and analysis.

    PubMed

    Weissman, Tamily A; Pan, Y Albert

    2015-02-01

    Brainbow is a genetic cell-labeling technique where hundreds of different hues can be generated by stochastic and combinatorial expression of a few spectrally distinct fluorescent proteins. Unique color profiles can be used as cellular identification tags for multiple applications such as tracing axons through the nervous system, following individual cells during development, or analyzing cell lineage. In recent years, Brainbow and other combinatorial expression strategies have expanded from the mouse nervous system to other model organisms and a wide variety of tissues. Particularly exciting is the application of Brainbow in lineage tracing, where this technique has been instrumental in parsing out complex cellular relationships during organogenesis. Here we review recent findings, new technical improvements, and exciting potential genetic and genomic applications for harnessing this colorful technique in anatomical, developmental, and genetic studies. PMID:25657347

  13. Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis

    PubMed Central

    Weissman, Tamily A.; Pan, Y. Albert

    2015-01-01

    Brainbow is a genetic cell-labeling technique where hundreds of different hues can be generated by stochastic and combinatorial expression of a few spectrally distinct fluorescent proteins. Unique color profiles can be used as cellular identification tags for multiple applications such as tracing axons through the nervous system, following individual cells during development, or analyzing cell lineage. In recent years, Brainbow and other combinatorial expression strategies have expanded from the mouse nervous system to other model organisms and a wide variety of tissues. Particularly exciting is the application of Brainbow in lineage tracing, where this technique has been instrumental in parsing out complex cellular relationships during organogenesis. Here we review recent findings, new technical improvements, and exciting potential genetic and genomic applications for harnessing this colorful technique in anatomical, developmental, and genetic studies. PMID:25657347

  14. Reversible loss of gravitropic sensitivity in maize roots after tip application of calcium chelators

    NASA Technical Reports Server (NTRS)

    Lee, J. S.; Mulkey, T. J.; Evans, M. L.

    1983-01-01

    The application of calcium chelating agents (EDTA or EGTA) to the tips of maize roots caused a loss of gravitropic sensitivity. When the chelator was replaced with calcium chloride, gravitropic sensitivity was restored. Asymmetric application of calcium chloride near the tip of a vertical root caused curvature toward the calcium source. When the calcium was applied to the upper surface of the tip of a root oriented horizontally, the root curved upward even though control roots exhibited strong downward curvature. Application of calcium chloride to the tips of decapped roots, which are known to be gravitropically insensitive, did not restore gravitropic sensitivity. However, asymmetric application of calcium chloride near the tips of decapped roots caused curvature toward the calcium source. Calcium may play a key role in linking gravity detection to gravitropic curvature in roots.

  15. Application of genetic programming for proton-proton interactions

    NASA Astrophysics Data System (ADS)

    El-Dahshan, EL-Sayed

    2011-06-01

    The aim of the present work is to use one of the machine learning techniques named the genetic programming (GP) to model the p-p interactions through discovering functions. In our study, GP is used to simulate and predict the multiplicity distribution of charged pions (P(n ch)), the average multiplicity () and the total cross section (? tot) at different values of high energies. We have obtained the multiplicity distribution as a function of the center of mass energy ( sqrt s ) and charged particles (n ch). Also, both the average multiplicity and the total cross section are obtained as a function of sqrt s . Our discovered functions produced by GP technique show a good match to the experimental data. The performance of the GP models was also tested at non-trained data and was found to be in good agreement with the experimental data.

  16. Application of genetic programming for proton-proton interactions

    NASA Astrophysics Data System (ADS)

    El-Dahshan, EL-Sayed A.

    2011-06-01

    The aim of the present work is to use one of the machine learning techniques named the genetic programming (GP) to model the p-p interactions through discovering functions. In our study, GP is used to simulate and predict the multiplicity distribution of charged pions ( P( n ch )), the average multiplicity (< n ch >) and the total cross section ( ? tot ) at different values of high energies. We have obtained the multiplicity distribution as a function of the center of mass energy ( sqrt s ) and charged particles ( n ch ). Also, both the average multiplicity and the total cross section are obtained as a function of sqrt s . Our discovered functions produced by GP technique show a good match to the experimental data. The performance of the GP models was also tested at non-trained data and was found to be in good agreement with the experimental data.

  17. The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry

    ERIC Educational Resources Information Center

    Gary, Ronald K.

    2004-01-01

    The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to…

  18. The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry

    ERIC Educational Resources Information Center

    Gary, Ronald K.

    2004-01-01

    The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to

  19. Application of modified reverse panoramic radiograph on lambdoid suture for age estimation

    PubMed Central

    Dwivedy, Shweta; Sah, Kunal; Sinha, Shruti

    2015-01-01

    Background Cranial suture closure has long been recognized as a character of human development related to aging. For this reason, it has been utilized for various forensic and archaeological studies to determine the age of an unidentified/or skeletonized individuals. Various cadaveric studies have established the role of lambdoid suture in age estimation, but not routinely practiced. The objective is to establish if any correlation exists between individuals age and lambdoid sutures closure status (ectocranially) in mortals through modified reverse panoramic radiograph (RPRg). Methods Total number of 85 subjects, 25 years and beyond were included in the study, and divided into four groups with an age interval of 10 years. Assessment of lambdoid suture closure was done according to Frederic Rating Scale on modified RPRg. Data obtained was subjected to statistical analysis using Spearmans correlation test. Results A significant difference was observed between the age group and suture closure. Correlation coefficient of 0.570 was obtained, and was interpreted as a good correlation between the age and suture closure status with a P value of <0.001. Conclusions Lambdoid suture can be very effective and practical tool for age assessment in mortals through modified RPRg (ectocranially). PMID:26435915

  20. Application of magneto-optical Kerr effect to first-order reversal curve measurements.

    PubMed

    Grfe, Joachim; Schmidt, Mathias; Audehm, Patrick; Schtz, Gisela; Goering, Eberhard

    2014-02-01

    First-order reversal curves (FORC) are a powerful method for magnetic sample characterization, separating all magnetic states of an investigated system according to their coercivity and internal magnetic interactions. A major drawback of using measurement techniques like VSM or SQUID, typically applied for FORC acquisition, is the long measurement time, limiting the resolution and the number of measurements due to time constraints. Faster techniques like MOKE result in problems regarding measurement stability over the curse of the acquisition of many minor loops, due to drift and non-absolute magnetization values. Here, we present an approach using a specialized field shape providing two anchor points for each minor loop for applying the magneto-optical Kerr effect (MOKE) technique to FORC measurements. This results in a high field resolution while keeping the total acquisition time to only a few minutes. MOKE FORC measurements are exemplarily applied to a simple permalloy film, an exchange-bias system, and a Gd/Fe multilayer system with perpendicular magnetic anisotropy, showcasing the versatility of the method. PMID:24593373

  1. The reversibility of ionic transport in PEDOT with application to a complementary electrochromic device

    NASA Astrophysics Data System (ADS)

    Chiang, Tun-Yuan; Huang, Ming-Chao; Tsai, Chien-Huang

    2014-07-01

    The electrochemistry and ion transport properties of PEDOT in different solvents have been investigated. Conductivity enhancement has been observed in dimethyl sulfoxide (DMSO) and ethylene glycol (EG). This is attributed to the transformation of polymer chains from compact to linear structure induced by such high dipole moment solvent treatment (DMSO or EG). The results of electrochemical quartz crystal microbalance (EQCM) indicate that the solvent plays an important role in redox process. The poly(3,4-ethylenedioxythiophene) (PEDOT) reveals a better reversibility of ionic transfer in DMSO compared with that measured in acetonitrile (ACN). A solution and thin film system electrochromic device (ECD) based on 4-phenothiazin-10-yl-anisole (APS) solution and a PEDOT thin film was assembled and studied. The device demonstrates the color change from colorless (0 V) to deep blue violet (1.6 V). A maximum transmittance window 65% was obtained at 520 nm with the operating potentials between 0 and 1.6 V in DMSO electrolytes. Coloration efficiency of the ECD has been found to be 410 cm2/C. No pre-darkening or pre-bleaching of the electrodes is required for assembly of such ECD.

  2. Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions

    NASA Astrophysics Data System (ADS)

    Schredder, J. M.; Fujita, T.

    1984-10-01

    The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

  3. Retention studies on uranium, thorium and lanthanides with amide modified reverse phase support and its applications.

    PubMed

    Raju, Ch Siva Kesava; Subramanian, M S; Sivaraman, N; Srinivasan, T G; Vasudeva Rao, P R

    2007-07-13

    The retention behaviour of uranium and thorium was investigated on modified reverse phase supports using 3-oxo-pentanedioicacid bis-[bis-(2-ethyl-hexyl)-amide (OPAEHA), 3-oxo-pentanedioicacid bis diisobutyl amide (OPAIBA) and bis-2-ethylhexyl succinamic acid (BEHSA). alpha-Hydroxy isobutyric acid (alpha-HIBA) was employed as the complexing reagent for elution. Elution profiles of uranium and thorium were studied as a function of the modifier concentration, mobile phase composition and its pH. Based on these investigations, a novel high performance liquid chromatography (HPLC) based separation technique was developed using BEHSA modified support for the isolation and quantitative determination of lanthanides as a group in uranium matrix. Hundreds of samples obtained from pyrochemical reprocessing of molten salts containing lanthanides in uranium matrix (e.g. 1:20,000) were separated and determined within 7 min using the coated support. The advantage of the present HPLC technique lies in the simultaneous separation and assay of total lanthanides and uranium whereas other analytical methods necessitate the separation of uranium matrix prior to lanthanide assay. PMID:17240383

  4. Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions

    NASA Technical Reports Server (NTRS)

    Schredder, J. M.; Fujita, T.

    1984-01-01

    The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

  5. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    PubMed

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana. PMID:24099390

  6. Application of reverse dot blot hybridization to simultaneous detection and identification of harmful algae.

    PubMed

    Chen, Guo Fu; Zhang, Chun Yun; Wang, Yuan Yuan; Chen, Wen

    2015-07-01

    Warning and monitoring projects of harmful algal blooms require simple and rapid methods for simultaneous and accurate detection and identification of causative algae present in the environmental samples. Here, reverse dot blot hybridization (RDBH) was employed to simultaneously detect several harmful algae by using five representative bloom-forming microalgae along the Chinese coast. A set of specific probes for RDBH were developed by PCR, cloning, and sequencing of the internal transcribed spacer (ITS), alignment analysis, and probe design. Each probe was oligo (dT)-tailed and spotted onto positively charged nylon membrane to make up a low-density oligonucleotide array. Universal primers designed within the conserved regions were used to amplify the ITS sequences by using genomic DNA of target as templates. The digoxigenin (Dig)-labeled PCR products were denatured and then hybridized to the oligonucleotide array. The array produced a unique hybridization pattern for each target species differentiating them from each other. The preparations of oligonucleotide array and hybridization conditions were optimized. The developed RDBH demonstrated a detection limit up to 10 cells. The detection performance of RDBH was relatively stable and not affected by non-target species and the fixation time of target species over at least 30 days. The RDBH could recover all the target species from the simulated field samples and target species confirmed by the subsequent microscopy examination in the environmental samples. These results indicate that RDBH can be a new technical platform for parallel discrimination of harmful algae and is promising for environmental monitoring of these microorganisms. PMID:25731086

  7. Non-Genetic Engineering Approaches for Isolating and Generating Novel Yeasts for Industrial Applications

    NASA Astrophysics Data System (ADS)

    Chambers, P. J.; Bellon, J. R.; Schmidt, S. A.; Varela, C.; Pretorius, I. S.

    Generating novel yeast strains for industrial applications should be quite straightforward; after all, research into the genetics, biochemistry and physiology of Baker's Yeast, Saccharomyces cerevisiae, has paved the way for many advances in the modern biological sciences. We probably know more about this humble eukaryote than any other, and it is the most tractable of organisms for manipulation using modern genetic engineering approaches. In many countries, however, there are restrictions on the use of genetically-modified organisms (GMOs), particularly in foods and beverages, and the level of consumer acceptance of GMOs is, at best, variable. Thus, many researchers working with industrial yeasts use genetic engineering techniques primarily as research tools, and strain development continues to rely on non-GM technologies. This chapter explores the non-GM tools and strategies available to such researchers.

  8. [Application of genetic data to clinical practice of MPN].

    PubMed

    Edahiro, Yoko

    2015-08-01

    After the discovery of the JAK2V617F mutation in 2005, followed by the discovery of the MPL and JAK2 exon 12 mutations, and the CALR mutation in 2013, the majority of patients with Philadelphia negative myeloproliferative neoplasms (MPN) have been shown to display one of these somatic mutations. In regards to the pathogenesis of MPN, the CALR mutation has been shown to activate the JAK2 downstream cascade. However, the mechanism has yet to be elucidated. Nevertheless, these investigations have changed our understanding of MPN, especially in terms of diagnosis and treatment. Reports on the clinical effects of the different somatic mutations have revealed that MPN patients with CALR-mutated ET are less likely to have thrombosis, and that PMF patients with the CALR mutation have better overall survival. Hereafter, evaluations of the status of these gene mutations are necessary for the diagnosis of MPN, and it is important to consider how to put these genetic data to the best possible practical use. PMID:26345552

  9. An Advanced Reverse Osmosis Technology For Application in Nuclear Desalination Facilities

    SciTech Connect

    Humphries, J.R.; Davies, K.; Ackert, J.A.

    2002-07-01

    The lack of adequate supplies of clean, safe water is a growing global problem that has reached crisis proportions in many parts of the world. It is estimated that 1.5 billion people do not have access to adequate supplies of safe water, and that as a result nearly 10,000 people die every day and thousands more suffer from a range of debilitating illnesses due to water related diseases. Included in this total is an estimated 2.2 million child deaths annually. As the world's need for additional sources of fresh water continues to grow, seawater and brackish water desalination are providing an increasingly important contribution to the solution of this problem. Because desalination is an energy intensive process, nuclear desalination provides an economically attractive and environmentally sound alternative to the burning of fossil fuels for desalination. Nevertheless, the enormity of the problem dictates that additional steps must be taken to improve the efficiency of energy utilization and reduce the cost of water production in order to reduce the financial and environmental burden to communities in need. An advanced reverse osmosis (RO) desalination technology has been developed that emphasizes a nontraditional approach to system design and operation, and makes use of a sophisticated design optimization process that can lead to highly optimized design configurations and operating regimes. The technology can be coupled with a nuclear generating station (NGS) to provide an integrated facility for the co-generation of both water and electricity. Waste heat from the NGS allows the use of 'preheated' feedwater into the RO system, improving the efficiency of the RO process and reducing the cost of water production. Because waste heat, rather than process heat, is used the desalination system can be readily coupled to any existing or advanced reactor technology with little or no impact on reactor design and operation and without introducing additional reactor safety considerations. Analyses of nuclear desalination systems employing this advanced RO technology under a variety of seawater feed conditions have consistently shown that the cost of potable water production can be reduced by as much as 15-20% relative to systems designed in a more traditional manner. Demonstration testing has been carried out using a trailer mounted system producing up to 150 m{sup 3}/d of potable water. Experimental results from the demonstration testing are behaving as expected based on the analytical performance models, validating the advanced design concept and confirming that the performance improvements indicated by the analyses can be achieved in operating systems. Further demonstration testing is planned using a 1000 m{sup 3}/d containerized system, currently under design, coupled to an existing nuclear power reactor. (authors)

  10. Parallelized genetic optimization of spatial light modulator addressing for diffractive applications.

    PubMed

    Haist, Tobias; Lingel, Christian; Adler, Rodolfo; Osten, Wolfgang

    2014-03-01

    We describe a new technique for optimizing the addressing of spatial light modulators in dynamic holographic applications. The method utilizes 200 times parallelization using imaging of subholograms in combination with genetic optimization. Compared to a fixed linear addressing curve for all different gratings, the diffraction efficiency can be improved by up to 25% for a Holoeye Pluto LCoS modulator. PMID:24663371

  11. Optimization of meander line antennas for RFID applications by using genetic algorithm

    NASA Astrophysics Data System (ADS)

    Bucuci, Stefania C.; Anchidin, Liliana; Dumitrascu, Ana; Danisor, Alin; Berescu, Serban; Tamas, Razvan D.

    2015-02-01

    In this paper, we propose an approach of optimization of meander line antennas by using genetic algorithm. Such antennas are used in RFID applications. As opposed to other approaches for meander antennas, we propose the use of only two optimization objectives, i.e. gain and size. As an example, we have optimized a single meander dipole antenna, resonating at 869 MHz.

  12. Credit card fraud detection: An application of the gene expression messy genetic algorithm

    SciTech Connect

    Kargupta, H.; Gattiker, J.R.; Buescher, K.

    1996-05-01

    This paper describes an application of the recently introduced gene expression messy genetic algorithm (GEMGA) (Kargupta, 1996) for detecting fraudulent transactions of credit cards. It also explains the fundamental concepts underlying the GEMGA in the light of the SEARCH (Search Envisioned As Relation and Class Hierarchizing) (Kargupta, 1995) framework.

  13. The application and performance of single nucleotide polymorphism markers for population genetic analyses of Lepidoptera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single nucleotide polymorphisms (SNPs) are nucleotide substitution mutations that tend to be at high densities within eukaryotic genomes. The development of assays that detect allelic variation at SNP loci is attractive for genome mapping, population genetics, and phylogeographic applications. A p...

  14. Genetic programme of cardiogenesis: implications for therapeutic application

    PubMed Central

    van Tuyn, J.; de Vries, A.A.F.; van der Laarse, A.; Schalij, M.J.; van der Wall, E.E.; Atsma, D.E.

    2004-01-01

    It has become accepted that new cardiomyocytes can be derived from stem cells. Although the potential for therapeutic application is evident, the reported efficiency of differentiation varies greatly from 0.02 to 54%. To obtain clinically relevant numbers of newly differentiated cardiac cells, stem cell differentiation should be as efficient as possible. A plausible way to increase the efficiency of differentiation of stem cells into cardiomyocytes is through the introduction of cardiac specific regulatory genes in the stem cells. This review summarises the role of several key transcription factors in cardiogenesis. PMID:25696254

  15. Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine.

    PubMed

    Jimenez-Guardeo, Jose M; Regla-Nava, Jose A; Nieto-Torres, Jose L; DeDiego, Marta L; Castao-Rodriguez, Carlos; Fernandez-Delgado, Raul; Perlman, Stanley; Enjuanes, Luis

    2015-10-01

    A SARS-CoV lacking the full-length E gene (SARS-CoV-?E) was attenuated and an effective vaccine. Here, we show that this mutant virus regained fitness after serial passages in cell culture or in vivo, resulting in the partial duplication of the membrane gene or in the insertion of a new sequence in gene 8a, respectively. The chimeric proteins generated in cell culture increased virus fitness in vitro but remained attenuated in mice. In contrast, during SARS-CoV-?E passage in mice, the virus incorporated a mutated variant of 8a protein, resulting in reversion to a virulent phenotype. When the full-length E protein was deleted or its PDZ-binding motif (PBM) was mutated, the revertant viruses either incorporated a novel chimeric protein with a PBM or restored the sequence of the PBM on the E protein, respectively. Similarly, after passage in mice, SARS-CoV-?E protein 8a mutated, to now encode a PBM, and also regained virulence. These data indicated that the virus requires a PBM on a transmembrane protein to compensate for removal of this motif from the E protein. To increase the genetic stability of the vaccine candidate, we introduced small attenuating deletions in E gene that did not affect the endogenous PBM, preventing the incorporation of novel chimeric proteins in the virus genome. In addition, to increase vaccine biosafety, we introduced additional attenuating mutations into the nsp1 protein. Deletions in the carboxy-terminal region of nsp1 protein led to higher host interferon responses and virus attenuation. Recombinant viruses including attenuating mutations in E and nsp1 genes maintained their attenuation after passage in vitro and in vivo. Further, these viruses fully protected mice against challenge with the lethal parental virus, and are therefore safe and stable vaccine candidates for protection against SARS-CoV. PMID:26513244

  16. Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice.

    PubMed

    Toyomasu, Tomonobu; Usui, Masami; Sugawara, Chizu; Otomo, Kazuko; Hirose, Yuko; Miyao, Akio; Hirochika, Hirohiko; Okada, Kazunori; Shimizu, Takafumi; Koga, Jinichiro; Hasegawa, Morifumi; Chuba, Masaru; Kawana, Yoshiaki; Kuroda, Masaharu; Minami, Eiichi; Mitsuhashi, Wataru; Yamane, Hisakazu

    2014-01-01

    A variety of labdane-related diterpenoids, including phytocassanes, oryzalexins and momilactones, were identified as phytoalexins in rice (Oryza sativa L.). Momilactone B was also isolated as an allelochemical exuded from rice roots. The biosynthetic genes of these phytoalexins have been identified, including six labdane-related diterpene cyclase genes such as OsCPS2, OsCPS4, OsKSL4, OsKSL7, OsKSL8 and OsKSL10. Here we identified an OsCPS4 knockdown mutant, cps4-tos, by screening Tos17 mutant lines using polymerase chain reaction. OsCPS4 encodes a syn-copalyl diphosphate synthase responsible for momilactones and oryzalexin S biosynthesis. Because Tos17 was inserted into the third intron of OsCPS4, the mature OsCPS4 mRNA was detected in the cps4-tos mutant as well as the wild type. Nevertheless, mature OsCPS4 transcript levels in the cps4-tos mutant were about one sixth those in the wild type. The cps4-tos mutant was more susceptible to rice blast fungus than the wild type, possibly due to lower levels of momilactones and oryzalexin S in the mutant. Moreover, co-cultivation experiments suggested that the allelopathic effect of cps4-tos against some kinds of lowland weeds was significantly lower than that of the wild type, probably because of lower momilactone content exuded from cps4-tos roots. A reverse-genetic strategy using the cps4-tos mutant showed the possible roles of momilactones not only as phytoalexins but also as allelopathic substances. PMID:23621683

  17. Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine

    PubMed Central

    Nieto-Torres, Jose L.; DeDiego, Marta L.; Castaño-Rodriguez, Carlos; Fernandez-Delgado, Raul; Perlman, Stanley; Enjuanes, Luis

    2015-01-01

    A SARS-CoV lacking the full-length E gene (SARS-CoV-∆E) was attenuated and an effective vaccine. Here, we show that this mutant virus regained fitness after serial passages in cell culture or in vivo, resulting in the partial duplication of the membrane gene or in the insertion of a new sequence in gene 8a, respectively. The chimeric proteins generated in cell culture increased virus fitness in vitro but remained attenuated in mice. In contrast, during SARS-CoV-∆E passage in mice, the virus incorporated a mutated variant of 8a protein, resulting in reversion to a virulent phenotype. When the full-length E protein was deleted or its PDZ-binding motif (PBM) was mutated, the revertant viruses either incorporated a novel chimeric protein with a PBM or restored the sequence of the PBM on the E protein, respectively. Similarly, after passage in mice, SARS-CoV-∆E protein 8a mutated, to now encode a PBM, and also regained virulence. These data indicated that the virus requires a PBM on a transmembrane protein to compensate for removal of this motif from the E protein. To increase the genetic stability of the vaccine candidate, we introduced small attenuating deletions in E gene that did not affect the endogenous PBM, preventing the incorporation of novel chimeric proteins in the virus genome. In addition, to increase vaccine biosafety, we introduced additional attenuating mutations into the nsp1 protein. Deletions in the carboxy-terminal region of nsp1 protein led to higher host interferon responses and virus attenuation. Recombinant viruses including attenuating mutations in E and nsp1 genes maintained their attenuation after passage in vitro and in vivo. Further, these viruses fully protected mice against challenge with the lethal parental virus, and are therefore safe and stable vaccine candidates for protection against SARS-CoV. PMID:26513244

  18. Experimental Pathways towards Developing a Rotavirus Reverse Genetics System: Synthetic Full Length Rotavirus ssRNAs Are Neither Infectious nor Translated in Permissive Cells

    PubMed Central

    Richards, James E.; Desselberger, Ulrich; Lever, Andrew M.

    2013-01-01

    At present the ability to create rationally engineered mutant rotaviruses is limited because of the lack of a tractable helper virus-free reverse genetics system. Using the cell culture adapted bovine RV RF strain (G6P6 [1]), we have attempted to recover infectious RV by co-transfecting in vitro transcribed ssRNAs which are identical in sequence to the positive sense strand of each of the 11 dsRNA genomic segments of the RF strain. The RNAs were produced either from cDNAs cloned by a target sequence-independent procedure, or from purified double layered RV particles (DLPs). We have validated their translational function by in vitro synthesis of 35S-labelled proteins in rabbit reticulocyte lysates; all 11 proteins encoded by the RV genome were expressed. Transfection experiments with DLP- or cDNA-derived ssRNAs suggested that the RNAs do not act independently as mRNAs for protein synthesis, once delivered into various mammalian cell lines, and exhibit cytotoxicity. Transfected RNAs were not infectious since a viral cytopathic effect was not observed after infection of MA104 cells with lysates from transfected cells. By contrast, an engineered mRNA encoding eGFP was expressed when transfected under identical conditions into the same cell lines. Co-expression of plasmids encoding NSP2 and NSP5 using a fowlpox T7 polymerase recombinant virus revealed viroplasm-like structure formation, but this did not enable the translation of transfected RV ssRNAs. Attempts to recover RV from ssRNAs transcribed intracellularly from transfected cDNAs were also unsuccessful and suggested that these RNAs were also not translated, in contrast to successful translation from a transfected cDNA encoding an eGFP mRNA. PMID:24019962

  19. N348I in Reverse Transcriptase Provides a Genetic Pathway for HIV-1 to Select TAMs and Mutations Antagonistic to TAMs

    PubMed Central

    Radzio, Jessica; Yap, Soo-Huey; Tachedjian, Gilda; Sluis-Cremer, Nicolas

    2010-01-01

    Objective Several nonnucleoside (e.g. Y181C) and nucleoside (e.g. L74V, M184V) resistance mutations in HIV-1 reverse transcriptase (RT) are antagonistic toward thymidine analog mutations (TAMs) that confer zidovudine (AZT) resistance. The N348I mutation in the connection domain of RT also confers AZT resistance however the mechanisms involved are different from TAMs. In this study, we examined whether N348I compensates for the antagonism of the TAM K70R by Y181C, L74V and M184V. Design and Methods The AZT-monophosphate (AZT-MP) and ribonuclease H (RNase H) activities of recombinant purified HIV-1 RT containing combinations of K70R, N348I and Y181C, L74V or M184V were assessed using standard biochemical and antiviral assays. Results As expected, the introduction of the Y181C, L74V or M184V mutations into K70R HIV-1 RT significantly diminished the ATP-mediated AZT-MP excision activity of the enzyme. However, the N348I mutation compensated for this antagonism on RNA/DNA template/primers by significantly decreasing the frequency of secondary RNase H cleavages that reduce the overall efficiency of the excision reaction. Conclusion The acquisition of N348I in HIV-1 RT - which can occur early in therapy, oftentimes before TAMs - may provide a simple genetic pathway that allows the virus to select both TAMs and mutations that are antagonistic toward TAMs. PMID:20160634

  20. Efficient Reverse Genetics Reveals Genetic Determinants of Budding and Fusogenic Differences between Nipah and Hendra Viruses and Enables Real-Time Monitoring of Viral Spread in Small Animal Models of Henipavirus Infection

    PubMed Central

    Yun, Tatyana; Park, Arnold; Hill, Terence E.; Pernet, Olivier; Beaty, Shannon M.; Juelich, Terry L.; Smith, Jennifer K.; Zhang, Lihong; Wang, Yao E.; Vigant, Frederic; Gao, Junling; Wu, Ping

    2014-01-01

    ABSTRACT Nipah virus (NiV) and Hendra virus (HeV) are closely related henipaviruses of the Paramyxovirinae. Spillover from their fruit bat reservoirs can cause severe disease in humans and livestock. Despite their high sequence similarity, NiV and HeV exhibit apparent differences in receptor and tissue tropism, envelope-mediated fusogenicity, replicative fitness, and other pathophysiologic manifestations. To investigate the molecular basis for these differences, we first established a highly efficient reverse genetics system that increased rescue titers by ≥3 log units, which offset the difficulty of generating multiple recombinants under constraining biosafety level 4 (BSL-4) conditions. We then replaced, singly and in combination, the matrix (M), fusion (F), and attachment glycoprotein (G) genes in mCherry-expressing recombinant NiV (rNiV) with their HeV counterparts. These chimeric but isogenic rNiVs replicated well in primary human endothelial and neuronal cells, indicating efficient heterotypic complementation. The determinants of budding efficiency, fusogenicity, and replicative fitness were dissociable: HeV-M budded more efficiently than NiV-M, accounting for the higher replicative titers of HeV-M-bearing chimeras at early times, while the enhanced fusogenicity of NiV-G-bearing chimeras did not correlate with increased replicative fitness. Furthermore, to facilitate spatiotemporal studies on henipavirus pathogenesis, we generated a firefly luciferase-expressing NiV and monitored virus replication and spread in infected interferon alpha/beta receptor knockout mice via bioluminescence imaging. While intraperitoneal inoculation resulted in neuroinvasion following systemic spread and replication in the respiratory tract, intranasal inoculation resulted in confined spread to regions corresponding to olfactory bulbs and salivary glands before subsequent neuroinvasion. This optimized henipavirus reverse genetics system will facilitate future investigations into the growing numbers of novel henipavirus-like viruses. IMPORTANCE Nipah virus (NiV) and Hendra virus (HeV) are recently emergent zoonotic and highly lethal pathogens with pandemic potential. Although differences have been observed between NiV and HeV replication and pathogenesis, the molecular basis for these differences has not been examined. In this study, we established a highly efficient system to reverse engineer changes into replication-competent NiV and HeV, which facilitated the generation of reporter-expressing viruses and recombinant NiV-HeV chimeras with substitutions in the genes responsible for viral exit (the M gene, critical for assembly and budding) and viral entry (the G [attachment] and F [fusion] genes). These chimeras revealed differences in the budding and fusogenic properties of the M and G proteins, respectively, which help explain previously observed differences between NiV and HeV. Finally, to facilitate future in vivo studies, we monitored the replication and spread of a bioluminescent reporter-expressing NiV in susceptible mice; this is the first time such in vivo imaging has been performed under BSL-4 conditions. PMID:25392218

  1. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  2. Reverse Genetics for Fusogenic Bat-Borne Orthoreovirus Associated with Acute Respiratory Tract Infections in Humans: Role of Outer Capsid Protein σC in Viral Replication and Pathogenesis

    PubMed Central

    Kawagishi, Takahiro; Kanai, Yuta; Tani, Hideki; Shimojima, Masayuki; Saijo, Masayuki; Matsuura, Yoshiharu; Kobayashi, Takeshi

    2016-01-01

    Nelson Bay orthoreoviruses (NBVs) are members of the fusogenic orthoreoviruses and possess 10-segmented double-stranded RNA genomes. NBV was first isolated from a fruit bat in Australia more than 40 years ago, but it was not associated with any disease. However, several NBV strains have been recently identified as causative agents for respiratory tract infections in humans. Isolation of these pathogenic bat reoviruses from patients suggests that NBVs have evolved to propagate in humans in the form of zoonosis. To date, no strategy has been developed to rescue infectious viruses from cloned cDNA for any member of the fusogenic orthoreoviruses. In this study, we report the development of a plasmid-based reverse genetics system free of helper viruses and independent of any selection for NBV isolated from humans with acute respiratory infection. cDNAs corresponding to each of the 10 full-length RNA gene segments of NBV were cotransfected into culture cells expressing T7 RNA polymerase, and viable NBV was isolated using a plaque assay. The growth kinetics and cell-to-cell fusion activity of recombinant strains, rescued using the reverse genetics system, were indistinguishable from those of native strains. We used the reverse genetics system to generate viruses deficient in the cell attachment protein σC to define the biological function of this protein in the viral life cycle. Our results with σC-deficient viruses demonstrated that σC is dispensable for cell attachment in several cell lines, including murine fibroblast L929 cells but not in human lung epithelial A549 cells, and plays a critical role in viral pathogenesis. We also used the system to rescue a virus that expresses a yellow fluorescent protein. The reverse genetics system developed in this study can be applied to study the propagation and pathogenesis of pathogenic NBVs and in the generation of recombinant NBVs for future vaccines and therapeutics. PMID:26901882

  3. Biomedical applications of polymers derived by reversible addition - fragmentation chain-transfer (RAFT).

    PubMed

    Fairbanks, Benjamin D; Gunatillake, Pathiraja A; Meagher, Laurence

    2015-08-30

    RAFT- mediated polymerization, providing control over polymer length and architecture as well as facilitating post polymerization modification of end groups, has been applied to virtually every facet of biomedical materials research. RAFT polymers have seen particularly extensive use in drug delivery research. Facile generation of functional and telechelic polymers permits straightforward conjugation to many therapeutic compounds while synthesis of amphiphilic block copolymers via RAFT allows for the generation of self-assembled structures capable of carrying therapeutic payloads. With the large and growing body of literature employing RAFT polymers as drug delivery aids and vehicles, concern over the potential toxicity of RAFT derived polymers has been raised. While literature exploring this complication is relatively limited, the emerging consensus may be summed up in three parts: toxicity of polymers generated with dithiobenzoate RAFT agents is observed at high concentrations but not with polymers generated with trithiocarbonate RAFT agents; even for polymers generated with dithiobenzoate RAFT agents, most reported applications call for concentrations well below the toxicity threshold; and RAFT end-groups may be easily removed via any of a variety of techniques that leave the polymer with no intrinsic toxicity attributable to the mechanism of polymerization. The low toxicity of RAFT-derived polymers and the ability to remove end groups via straightforward and scalable processes make RAFT technology a valuable tool for practically any application in which a polymer of defined molecular weight and architecture is desired. PMID:26050529

  4. Genetic algorithms and genetic programming for multiscale modeling: Applications in materials science and chemistry and advances in scalability

    NASA Astrophysics Data System (ADS)

    Sastry, Kumara Narasimha

    2007-03-01

    Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common building blocks in organic chemistry---indicate that MOGAs produce High-quality semiempirical methods that (1) are stable to small perturbations, (2) yield accurate configuration energies on untested and critical excited states, and (3) yield ab initio quality excited-state dynamics. The proposed method enables simulations of more complex systems to realistic, multi-picosecond timescales, well beyond previous attempts or expectation of human experts, and 2--3 orders-of-magnitude reduction in computational cost. While the two applications use simple evolutionary operators, in order to tackle more complex systems, their scalability and limitations have to be investigated. The second part of the thesis addresses some of the challenges involved with a successful design of genetic algorithms and genetic programming for multiscale modeling. The first issue addressed is the scalability of genetic programming, where facetwise models are built to assess the population size required by GP to ensure adequate supply of raw building blocks and also to ensure accurate decision-making between competing building blocks. This study also presents a design of competent genetic programming, where traditional fixed recombination operators are replaced by building and sampling probabilistic models of promising candidate programs. The proposed scalable GP, called extended compact GP (eCGP), combines the ideas from extended compact genetic algorithm (eCGA) and probabilistic incremental program evolution (PIPE) and adaptively identifies, propagates and exchanges important subsolutions of a search problem. Results show that eCGP scales cubically with problem size on both GP-easy and GP-hard problems. Finally, facetwise models are developed to explore limitations of scalability of MOGAs, where the scalability of multiobjective algorithms in reliably maintaining Pareto-optimal solutions is addressed. The results show that even when the building blocks are accurately identified, massive multimodality of the search problems can easily overwhelm the nicher (diversity preserving operator) and lead to exponential scale-up. Facetwise models are developed, which incorporate the combined effects of model accuracy, decision making, and sub-structure supply, as well as the effect of niching on the population sizing, to predict a limit on the growth rate of a maximum number of sub-structures that can compete in the two objectives to circumvent the failure of the niching method. The results show that if the number of competing building blocks between multiple objectives is less than the proposed limit, multiobjective GAs scale-up polynomially with the problem size on boundedly-difficult problems.

  5. Application of a reversible chemical reaction system to solar thermal power plants

    NASA Technical Reports Server (NTRS)

    Hanseth, E. J.; Won, Y. S.; Seibowitz, L. P.

    1980-01-01

    Three distributed dish solar thermal power systems using various applications of SO2/SO3 chemical energy storage and transport technology were comparatively assessed. Each system features various roles for the chemical system: (1) energy storage only, (2) energy transport, or (3) energy transport and storage. These three systems were also compared with the dish-Stirling, using electrical transport and battery storage, and the central receiver Rankine system, with thermal storage, to determine the relative merit of plants employing a thermochemical system. As an assessment criterion, the busbar energy costs were compared. Separate but comparable solar energy cost computer codes were used for distributed receiver and central receiver systems. Calculations were performed for capacity factors ranging from 0.4 to 0.8. The results indicate that SO2/SO3 technology has the potential to be more cost effective in transporting the collected energy than in storing the energy for the storage capacity range studied (2-15 hours)

  6. Nested Quantization Index Modulation for Reversible Watermarking and Its Application to Healthcare Information Management Systems

    PubMed Central

    Ko, Lu-Ting; Chen, Jwu-E.; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

    2012-01-01

    Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented. PMID:22194776

  7. Nested quantization index modulation for reversible watermarking and its application to healthcare information management systems.

    PubMed

    Ko, Lu-Ting; Chen, Jwu-E; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

    2012-01-01

    Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented. PMID:22194776

  8. Development and application of reverse transcriptase nested polymerase chain reaction test for the detection of exogenous avian leukosis virus.

    PubMed

    Garca, Maricarmen; El-Attrache, John; Riblet, Sylva M; Lunge, Vagner R; Fonseca, Andr S K; Villegas, Pedro; Ikuta, Nilo

    2003-01-01

    A polymerase chain reaction (PCR) assay that utilizes nested primers to amplify a fragment of the long terminal repeat of exogenous avian leukosis virus (ALV) was developed and evaluated for detection of ALV subgroup J directly from clinical samples. Compilation of sequence data from different endogenous and exogenous ALVs allowed the selection of a conserved set of nested primers specific for the amplification of exogenous ALV subgroups A, B, C, D, and J and excluded amplification of endogenous viruses or endogenous viral sequences within the chicken genome. The nested primers were successfully used in both PCR and reverse transcriptase (RT)-PCR assays to detect genetically diverse ALV-J field isolates. Detection limits of ALV-J isolate ADOL-Hc1 DNA by nested PCR and RNA by RT-nested PCR were superior to detection of group-specific antigen by enzyme-linked immunosorbent assay (ELISA) in cell culture. Detection of ALV-J in cloacal swabs by RT-nested PCR was compared with direct detection by antigen-capture (ac)-ELISA; RT-nested PCR detected fewer positive samples than ac-ELISA, suggesting that RT-nested PCR excluded detection of endogenous virus in clinical samples. Detection of ALV-J in plasma samples by RT-nested PCR was compared with virus isolation in C/E chicken embryo fibroblasts; the level of agreement between both assays as applied to plasma samples ranged from low to moderate. The main disagreement between both assays was observed for a group of plasma samples found positive by RT-nested PCR and negative by virus isolation, suggesting that RT-nested PCR detected ALV-J genome in plasma samples of transiently or intermittently infected birds. ALV-J transient and intermittent infection profiles are characterized by inconsistent virus isolation responses throughout the life of a naturally infected flock. PMID:12713157

  9. Genetic and epigenetic variations in iPSCs: potential causes and implications for application

    PubMed Central

    Liang, Gaoyang; Zhang, Yi

    2013-01-01

    The ability to reprogram somatic cells to induced pluripotent stem cells (iPSCs) has revolutionized the field of regenerative medicine. However, recent studies on the genetic and epigenetic variations in iPSCs have raised concerns that these variations may compromise the utility of iPSCs. In this Perspective, we review the current understanding of genetic and epigenetic variations in iPSCs, trace their causes, discuss the implications of these variations for iPSC applications, and propose approaches to cope with these variations. PMID:23910082

  10. The Design and Application of Genetically Encodable Biosensors Based on Fluorescent Proteins

    PubMed Central

    Newman, Robert H.; Zhang, Jin

    2014-01-01

    To track the activity of cellular signaling molecules within the endogenous cellular environment, researchers have developed a diverse set of genetically encodable fluorescent biosensors. These sensors, which can be targeted to specific subcellular regions to monitor specific pools of a given signaling molecule in real time, rely upon conformational changes in a sensor domain to alter the photophysical properties of green fluorescent protein (GFP) family members. In this introductory chapter, we first discuss the properties of GFP family members before turning our attention to the design and application of genetically encodable fluorescent biosensors to live cell imaging. PMID:24052376

  11. Application of computational methods in genetic study of inflammatory bowel disease

    PubMed Central

    Li, Jin; Wei, Zhi; Hakonarson, Hakon

    2016-01-01

    Genetic factors play an important role in the etiology of inflammatory bowel disease (IBD). The launch of genome-wide association study (GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods. PMID:26811639

  12. Application of computational methods in genetic study of inflammatory bowel disease.

    PubMed

    Li, Jin; Wei, Zhi; Hakonarson, Hakon

    2016-01-21

    Genetic factors play an important role in the etiology of inflammatory bowel disease (IBD). The launch of genome-wide association study (GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods. PMID:26811639

  13. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology.

    PubMed

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P; Guerra, Miguel P

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ?130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field. PMID:26284102

  14. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

    PubMed Central

    Rogalski, Marcelo; do Nascimento Vieira, Leila; Fraga, Hugo P.; Guerra, Miguel P.

    2015-01-01

    During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100–220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field. PMID:26284102

  15. Preparation and application of reversed phase Chromatorotor for the isolation of natural products by centrifugal preparative chromatography.

    PubMed

    Muhammad, Ilias; Samoylenko, Volodymyr; Machumi, Francis; Zakia, Mohamed Ahmed; Mohammed, Rabab; Hetta, Mona H; Gillum, Van

    2013-03-01

    A method of preparation of rotors with a reversed phase (RP) solid silica gel sorbent layer has been developed for centrifugal preparative chromatography (CPC), also known as rotational planar chromatography (RPC). The rotors consist of binder free RP solid SiO2 layers of different thicknesses packed between two supported circular glass discs and can be used in any appropriate device for centrifugal chromatography, like Chromatotron and CycloGraph. Polar and /or semi-polar compounds with close R(f) values, as well as extracts and column fractions were separated and/or purified in a preparative and/or semi-preparative scale using the RP rotors, eluted with mixtures of aqueous-based solvents. We herein report three examples of its application, using RP Chromatorotors, for the isolation of the diastereoisomeric alkaloids banistenosides I and II from Banisteriopsis caapi, saponins III and IV from Fagonia cretica, and the sesquiterpenes artemisinin (V) and artemisinic acid (VI) from Artemisia annua. PMID:23678798

  16. Synthesis, characterization, and application of reversible PDLLA-PEG-PDLLA copolymer thermogels in vitro and in vivo.

    PubMed

    Shi, Kun; Wang, Ya-Li; Qu, Ying; Liao, Jin-Feng; Chu, Bing-Yang; Zhang, Hua-Ping; Luo, Feng; Qian, Zhi-Yong

    2016-01-01

    In this study, a series of injectable thermoreversible and thermogelling PDLLA-PEG-PDLLA copolymers were developed and a systematic evaluation of the thermogelling system both in vitro and in vivo was performed. The aqueous PDLLA-PEG-PDLLA solutions above a critical gel concentration could transform into hydrogel spontaneously within 2?minutes around the body temperature in vitro or in vivo. Modulating the molecular weight, block length and polymer concentration could adjust the sol-gel transition behavior and the mechanical properties of the hydrogels. The gelation was thermally reversible due to the physical interaction of copolymer micelles and no crystallization formed during the gelation. Little cytotoxicity and hemolysis of this polymer was found, and the inflammatory response after injecting the hydrogel to small-animal was acceptable. In vitro and in vivo degradation experiments illustrated that the physical hydrogel could retain its integrity as long as several weeks and eventually be degraded by hydrolysis. A rat model of sidewall defect-bowel abrasion was employed, and a significant reduction of post-operative adhesion has been found in the group of PDLLA-PEG-PDLLA hydrogel-treated, compared with untreated control group and commercial hyaluronic acid (HA) anti-adhesion hydrogel group. As such, this PDLLA-PEG-PDLLA hydrogel might be a promising candidate of injectable biomaterial for medical applications. PMID:26752008

  17. Synthesis, characterization, and application of reversible PDLLA-PEG-PDLLA copolymer thermogels in vitro and in vivo

    PubMed Central

    Shi, Kun; Wang, Ya-Li; Qu, Ying; Liao, Jin-Feng; Chu, Bing-Yang; Zhang, Hua-Ping; Luo, Feng; Qian, Zhi-Yong

    2016-01-01

    In this study, a series of injectable thermoreversible and thermogelling PDLLA-PEG-PDLLA copolymers were developed and a systematic evaluation of the thermogelling system both in vitro and in vivo was performed. The aqueous PDLLA-PEG-PDLLA solutions above a critical gel concentration could transform into hydrogel spontaneously within 2 minutes around the body temperature in vitro or in vivo. Modulating the molecular weight, block length and polymer concentration could adjust the sol-gel transition behavior and the mechanical properties of the hydrogels. The gelation was thermally reversible due to the physical interaction of copolymer micelles and no crystallization formed during the gelation. Little cytotoxicity and hemolysis of this polymer was found, and the inflammatory response after injecting the hydrogel to small-animal was acceptable. In vitro and in vivo degradation experiments illustrated that the physical hydrogel could retain its integrity as long as several weeks and eventually be degraded by hydrolysis. A rat model of sidewall defect-bowel abrasion was employed, and a significant reduction of post-operative adhesion has been found in the group of PDLLA-PEG-PDLLA hydrogel-treated, compared with untreated control group and commercial hyaluronic acid (HA) anti-adhesion hydrogel group. As such, this PDLLA-PEG-PDLLA hydrogel might be a promising candidate of injectable biomaterial for medical applications. PMID:26752008

  18. Reversible redox activity of ferrocene functionalized hydroxypropyl cellulose and its application to detect H2O2.

    PubMed

    Li, Pingping; Kang, Hongliang; Zhang, Chao; Li, Weiwei; Huang, Yong; Liu, Ruigang

    2016-04-20

    Novel ferrocene functionalized hydroxypropyl cellulose (HPC-Fc) were prepared by azide-alkyne cycloaddition and characterized. HPC-Fc exhibits an excellent reversible redox activity and could establish amazing electron transfer ability between enzyme and electrode. HPC-Fc and horseradish peroxidase (HRP) were coated on a platinized carbon electrode to prepare an amperometric biosensor for hydrogen peroxide (H2O2) detection. The amperometric response was measured as a function of H2O2 concentration at a fixed potential of 0.35V in 100mM phosphate buffer solution (pH 7.0). The novel biosensor exhibits a fast linear response toward H2O2 in the range of 0.1-8μM with sensitivity of 4.21nA/μM. Moreover, the enzyme assays measured by the spectrophotometer method confirm that abundant hydroxyl groups of HPC backbones are conductive for HRP to maintaining or even enhancing their activity. The redox active HPC-Fc with the unique properties of both ferrocene and cellulose is a good candidate for biosensor applications. PMID:26876825

  19. Reversal of acute complex regional pain syndrome using the practical application of neurodiagnostic evaluation process: a case study.

    PubMed

    Anderson, Karen E

    2013-01-01

    In 2005, a patient in my practice developed complex regional pain syndrome type 1 (CRPS 1) after bunion surgery. The condition was properly diagnosed within 4 weeks with a diagnostic technique that I routinely use to diagnose chronic musculoskeletal pain, and it was successfully treated. The tests, which are based on primitive and postural reflexes in infants, were adapted to reflect normal and abnormal motor behaviors in adults after provocation of reflexes of the autonomic nervous system (afferent C fibers in peripheral nerves). Approximately 60 days after my patient's operation, the tests indicated a positive reflex at the posterior tibial nerve in the operated foot. Surgery to remove an accessory ossicle from the talus adjacent to this nerve resolved the CRPS 1 within 2 weeks. Since CRPS 1 is a dysfunctional state of the autonomic regulatory control of pain, it was postulated that a test based on autonomic nerve function could isolate the source of CRPS 1. The Practical Application of Neurodiagnostic Evaluation process was shown to be diagnostic for the cause of acute CRPS 1 and to allow its reversal. Further evaluation of the test for diagnosis and treatment of CRPS is needed. PMID:24355904

  20. Application of genetically engineered microbial whole-cell biosensors for combined chemosensing.

    PubMed

    He, Wei; Yuan, Sheng; Zhong, Wen-Hui; Siddikee, Md Ashaduzzaman; Dai, Chuan-Chao

    2016-02-01

    The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way. PMID:26615397

  1. Pulse-Reverse Electrodeposition and Micromachining of Graphene-Nickel Composite: An Efficient Strategy toward High-Performance Microsystem Application.

    PubMed

    Li, Jinhua; An, Zhonglie; Wang, Zhuqing; Toda, Masaya; Ono, Takahito

    2016-02-17

    Graphene reinforced nickel (Ni) is an intriguing nanocomposite with tremendous potential for microelectromechanical system (MEMS) applications by remedying mechanical drawbacks of the metal matrix for device optimization, though very few related works have been reported. In this paper, we developed a pulse-reverse electrodeposition method for synthesizing graphene-Ni (G-Ni) composite microcomponents with high content and homogeneously dispersed graphene filler. While the Vickers hardness is largely enhanced by 2.7-fold after adding graphene, the Young's modulus of composite under dynamic condition shows ∼1.4-fold increase based on the raised resonant frequency of a composite microcantilever array. For the first time, we also demonstrate the application of G-Ni composite in microsystems by fabricating a Si micromirror with the composite supporting beams as well as investigate the long-term stability of the mirror at resonant vibration. Compared with the pure Ni counterpart, the composite mirror shows an apparently lessened fluctuations of resonant frequency and scanning angle due to a suppressed plastic deformation even under the sustaining periodic loading. This can be ascribed to the reduced grain size of Ni matrix and dislocation hindering in the presence of graphene by taking into account the crystalline refinement strengthen mechanism. The rational discussions also imply that the strong interface and efficient load transfer between graphene layers and metal matrix play an important role for improving stiffness in composite. It is believed that a proper design of graphene-metal composite makes it a promising structural material candidate for advanced micromechanical devices. PMID:26812267

  2. BB Seminar: Methods application to genetic variants for smoking & lung cancer

    Cancer.gov

    Methods developed for causal mediation analysis with a dichotomous outcome, applicable to case-control studies via prevalence weighting will be presented. These methods generalize traditional approaches to mediation in the social sciences by allowing for interactions and non-linear models. Methods for sensitivity analysis for unmeasured confounding and measurement error in the context of mediated effects will be described. The methodology is used to resolve a question concerning direct and indirect effects in genetic epidemiology.

  3. Applications in genetic risk estimation of data on the induction of dominant skeletal mutations in mice

    SciTech Connect

    Selby, P.B.

    1982-01-01

    Studies on the induction of dominant skeleton mutations and of dominant cataract mutations provide means of estimating genetic hazard to humans from radiation. The breeding-test method of studying the induction of dominant skeletal mutations is slow and cumbersome. In an attempt to devise a more rapid method, three non-breeding-test methods have been developed which are likely to have wider application in mutagenicity testing. (ACR)

  4. Extracting directed information flow networks: An application to genetics and semantics

    NASA Astrophysics Data System (ADS)

    Masucci, A. P.; Kalampokis, A.; Eguluz, V. M.; Hernndez-Garca, E.

    2011-02-01

    We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge.

  5. Simulating Population Genetics of Pathogen Vectors in Changing Landscapes: Guidelines and Application with Triatoma brasiliensis

    PubMed Central

    Rebaudo, Francois; Costa, Jane; Almeida, Carlos E.; Silvain, Jean-Francois; Harry, Myriam; Dangles, Olivier

    2014-01-01

    Background Understanding the mechanisms that influence the population dynamics and spatial genetic structure of the vectors of pathogens infecting humans is a central issue in tropical epidemiology. In view of the rapid changes in the features of landscape pathogen vectors live in, this issue requires new methods that consider both natural and human systems and their interactions. In this context, individual-based model (IBM) simulations represent powerful yet poorly developed approaches to explore the response of pathogen vectors in heterogeneous social-ecological systems, especially when field experiments cannot be performed. Methodology/Principal Findings We first present guidelines for the use of a spatially explicit IBM, to simulate population genetics of pathogen vectors in changing landscapes. We then applied our model with Triatoma brasiliensis, originally restricted to sylvatic habitats and now found in peridomestic and domestic habitats, posing as the most important Trypanosoma cruzi vector in Northeastern Brazil. We focused on the effects of vector migration rate, maximum dispersal distance and attraction by domestic habitat on T. brasiliensis population dynamics and spatial genetic structure. Optimized for T. brasiliensis using field data pairwise fixation index (FST) from microsatellite loci, our simulations confirmed the importance of these three variables to understand vector genetic structure at the landscape level. We then ran prospective scenarios accounting for land-use change (deforestation and urbanization), which revealed that human-induced land-use change favored higher genetic diversity among sampling points. Conclusions/Significance Our work shows that mechanistic models may be useful tools to link observed patterns with processes involved in the population genetics of tropical pathogen vectors in heterogeneous social-ecological landscapes. Our hope is that our study may provide a testable and applicable modeling framework to a broad community of epidemiologists for formulating scenarios of landscape change consequences on vector dynamics, with potential implications for their surveillance and control. PMID:25102068

  6. Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

    SciTech Connect

    Sankaran, Ramanan; Angel, Jordan; Brown, W. Michael

    2015-04-08

    The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on the performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.

  7. Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

    DOE PAGESBeta

    Sankaran, Ramanan; Angel, Jordan; Brown, W. Michael

    2015-04-08

    The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on themore » performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.« less

  8. Cytogenetic map for Anopheles nili: application for population genetics and comparative physical mapping

    PubMed Central

    Sharakhova, Maria V.; Antonio-Nkondjio, Christophe; Xia, Ai; Ndo, Cyrille; Awono-Ambene, Parfait; Simard, Frederic; Sharakhov, Igor V.

    2010-01-01

    Anopheles nili is one of the major malaria vectors in Africa with a wide geographic distribution. However, the taxonomic and population genetic studies on this species are scarce. New research tools are urgently needed to genetically characterize this important malaria vector. In this study, a high-resolution cytogenetic map was developed for An. nili polytene chromosomes. Chromosomes were straightened and subdivided into 46 numbered divisions according to the banding pattern. Population analysis of An. nili females collected in Burkina Faso revealed the presence of two highly polymorphic inversions on the 2R chromosomal arm. A statistically significant departure from Hardy-Weinberg equilibrium due to a deficit in heterozygotes was detected for inversion 2Rb. To determine chromosome homologies and gene order conservation between An. nili and other major malaria vectors, PCR probes based on the An. gambiae coding sequences were mapped to An. nili chromosomes. Comparative mapping demonstrated that An. nili chromosomes have an An.stephensi-like arm association and that whole arm translocations and paracentric inversions were the major types of rearrangement in evolution of these mosquitoes. The minimum number of fixed inversions among An. nili, An. gambiae, and An. stephensi was calculated using the Multiple Genome Rearrangements (MGR), Genome Rearrangements In Man and Mouse (GRIMM), and Sorting Permutation by Reversals and block-INterchanGes (SPRING) programs. The data suggest that the An. nili is, at least, as diverged from An. gambiae as An. stephensi. We provide evidence that 2La/a arrangement of An. gambiae is present in outgroup species An. nili and An. stephensi confirming the ancestral status of the 2La inversion in the An. gambiae complex. Availability of the new polytene chromosome map, polymorphic inversions, and physically mapped DNA markers for An. nili will further stimulate population genetic, taxonomic, and genomic studies of this neglected malaria vector. PMID:20603229

  9. The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events

    PubMed Central

    2014-01-01

    Background Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to disease, we developed an Ontology of Genetic Susceptibility Factors (OGSF), a biomedical ontology in the domain of genetic susceptibility and genetic susceptibility factors. The OGSF framework was then applied in the area of vaccine adverse events (VAEs). Results OGSF aligns with the Basic Formal Ontology (BFO). OGSF defines ‘genetic susceptibility’ as a subclass of BFO:disposition and has a material basis ‘genetic susceptibility factor’. The ‘genetic susceptibility to pathological bodily process’ is a subclasses of ‘genetic susceptibility’. A VAE is a type of pathological bodily process. OGSF represents different types of genetic susceptibility factors including various susceptibility alleles (e.g., SNP and gene). A general OGSF design pattern was developed to represent genetic susceptibility to VAE and associated genetic susceptibility factors using experimental results in genetic association studies. To test and validate the design pattern, two case studies were populated in OGSF. In the first case study, human gene allele DBR*15:01 is susceptible to influenza vaccine Pandemrix-induced Multiple Sclerosis. The second case study reports genetic susceptibility polymorphisms associated with systemic smallpox VAEs. After the data of the Case Study 2 were represented using OGSF-based axioms, SPARQL was successfully developed to retrieve the susceptibility factors stored in the populated OGSF. A network of data from the Case Study 2 was constructed by using ontology terms and individuals as nodes and ontology relations as edges. Different social network analys is (SNA) methods were then applied to verify core OGSF terms. Interestingly, a SNA hub analysis verified all susceptibility alleles of SNPs and a SNA closeness analysis verified the susceptibility genes in Case Study 2. These results validated the proper OGSF structure identified different ontology aspects with SNA methods. Conclusions OGSF provides a verified and robust framework for representing various genetic susceptibility types and genetic susceptibility factors annotated from experimental VAE genetic association studies. The RDF/OWL formulated ontology data can be queried using SPARQL and analyzed using centrality-based network analysis methods. PMID:24963371

  10. Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction

    PubMed Central

    Hill, William G.

    2014-01-01

    Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas. PMID:24395822

  11. Molecular characterization with RAPD-PCR: Application of genetic diagnostics to biological control of the sweetpotato whitefly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The application of genetic diagnostics under the umbrella of classical taxonomy was imperative for successful development and delivery of the biological control program against the sweet potato whitefly, Bemisia tabaci Gennadius biotype B (= silverleaf whitefly, B. argentifolii Bellows and Perring)....

  12. Defect Band Luminescence Intensity Reversal as Related to Application of Anti-Reflection Coating on mc-Si PV Cells: Preprint

    SciTech Connect

    Guthrey, H.; Johnston, S.; Yan, F.; Gorman, B.; Al-Jassim, M.

    2012-06-01

    Photoluminescence (PL) imaging is widely used to identify defective regions within mc-Si PV cells. Recent PL imaging investigations of defect band luminescence (DBL) in mc-Si have revealed a perplexing phenomenon. Namely, the reversal of the DBL intensity in various regions of mc-Si PV material upon the application of a SiNx:H anti-reflective coating (ARC). Regions with low DBL intensity before ARC application often exhibit high DBL intensity afterwards, and the converse is also true. PL imaging alone cannot explain this effect. We have used high resolution cathodoluminescence (CL) spectroscopy and electron beam induced current (EBIC) techniques to elucidate the origin of the DBL intensity reversal. Multiple sub-bandgap energy levels were identified that change in peak position and intensity upon the application of the ARC. Using this data, in addition to EBIC contrast information, we provide an explanation for the DBL intensity reversal based on the interaction of the detected energy levels with the SiNx:H ARC application. Multiple investigations have suggested that this is a global problem for mc-Si PV cells. Our results have the potential to provide mc-Si PV producers a pathway to increased efficiencies through defect mitigation strategies.

  13. Fibrous proteins: At the crossroads of genetic engineering and biotechnological applications.

    PubMed

    Yigit, Sezin; Dinjaski, Nina; Kaplan, David L

    2016-05-01

    Fibrous proteins, such as silk, elastin and collagen are finding broad impact in biomaterial systems for a range of biomedical and industrial applications. Some of the key advantages of biosynthetic fibrous proteins compared to synthetic polymers include the tailorability of sequence, protein size, degradation pattern, and mechanical properties. Recombinant DNA production and precise control over genetic sequence of these proteins allows expansion and fine tuning of material properties to meet the needs for specific applications. We review current approaches in the design, cloning, and expression of fibrous proteins, with a focus on strategies utilized to meet the challenges of repetitive fibrous protein production. We discuss recent advances in understanding the fundamental basis of structure-function relationships and the designs that foster fibrous protein self-assembly towards predictable architectures and properties for a range of applications. We highlight the potential of functionalization through genetic engineering to design fibrous protein systems for biotechnological and biomedical applications. Biotechnol. Bioeng. 2016;113: 913-929. © 2015 Wiley Periodicals, Inc. PMID:26332660

  14. Applications of Genetically Modified Tools to Safety Assessment in Drug Development

    PubMed Central

    Kay, Hee Yeon; Wu, Hongmin; Lee, Seo In

    2010-01-01

    The process of new drug development consists of several stages; after identifying potential candidate compounds, preclinical studies using animal models link the laboratory and human clinical trials. Among many steps in preclinical studies, toxicology and safety assessments contribute to identify potential adverse events and provide rationale for setting the initial doses in clinical trials. Gene modulation is one of the important tools of modern biology, and is commonly employed to examine the function of genes of interest. Advances in new drug development have been achieved by exploding information on target selection and validation using genetically modified animal models as well as those of cells. In this review, a recent trend of genetically modified methods is discussed with reference to safety assessments, and the exemplary applications of gene-modulating tools to the tests in new drug development were summarized. PMID:24278499

  15. Application of quantitative metabolomics in systems genetics in rodent models of complex phenotypes.

    PubMed

    Gauguier, Dominique

    2016-01-01

    Genome-wide association studies (GWAS) have provided remarkable advances in our understanding of the etiology of complex diseases in humans and have underlined the need to improve patients' phenotype characterization with intermediate molecular phenotypes. High resolution metabolomics is becoming an increasingly popular and robust strategy for metabolic phenotyping large cohorts of patients and controls in genetic studies, in order to map the genetic control of metabotypes in various biological matrices (organ extracts and biofluids) through Quantitative Trait Locus (mQTL) analysis. This article reviews results from ongoing research in mQTL mapping in rodent models of human complex traits, with a specific focus on the cardiometabolic syndrome, and prospects of applications of untargeted metabolomics to improve knowledge of multilevel genome expression control in health and disease and to detect potential novel biomarkers for complex phenotypes in experimental systems in mice and rats. PMID:26391925

  16. Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture.

    PubMed

    Martnez, Paulino; Vias, Ana M; Snchez, Laura; Daz, Noelia; Ribas, Laia; Piferrer, Francesc

    2014-01-01

    Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs. PMID:25324858

  17. Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture

    PubMed Central

    Martínez, Paulino; Viñas, Ana M.; Sánchez, Laura; Díaz, Noelia; Ribas, Laia; Piferrer, Francesc

    2014-01-01

    Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs. PMID:25324858

  18. Reversible dementias

    PubMed Central

    Tripathi, Manjari; Vibha, Deepti

    2009-01-01

    In recent years, more attention has been given to the early diagnostic evaluation of patients with dementia which is essential to identify patients with cognitive symptoms who may have treatable conditions. Guidelines suggest that all patients presenting with dementia or cognitive symptoms should be evaluated with a range of laboratory tests, and with structural brain imaging with computed tomography (CT) or magnetic resonance imaging (MRI). While many of the disorders reported as ‘reversible dementias’ are conditions that may well be associated with cognitive or behavioral symptoms, these symptoms are not always sufficiently severe to fulfill the clinical criteria for dementia. Thus, while the etiology of a condition may be treatable it should not be assumed that the associated dementia is fully reversible. Potentially reversible dementias should be identified and treatment considered, even if the symptoms are not sufficiently severe to meet the clinical criteria for dementia, and even if partial or full reversal of the cognitive symptoms cannot be guaranteed. In the literature, the most frequently observed potentially reversible conditions identified in patients with cognitive impairment or dementia are depression, adverse effects of drugs, drug or alcohol abuse, space-occupying lesions, normal pressure hydrocephalus, and metabolic conditions land endocrinal conditions like hypothyroidism and nutritional conditions like vitamin B-12 deficiency. Depression is by far the most common of the potentially reversible conditions. The review, hence addresses the common causes of reversible dementia and the studies published so far. PMID:21416018

  19. Genetic analysis of the roles of phytochromes A and B1 in the reversed gravitropic response of the lz-2 tomato mutant

    NASA Technical Reports Server (NTRS)

    Behringer, F. J.; Lomax, T. L.

    1999-01-01

    The lz-2 mutation in tomato (Lycopersicon esculentum) causes conditional reversal of shoot gravitropism by light. This response is mediated by phytochrome. To further elicit the mechanism by which phytochrome regulates the lz-2 phenotype, phytochrome-deficient lz-2 plants were generated. Introduction of au alleles, which severely block chromophore biosynthesis, eliminated the reversal of hypocotyl gravitropism in continuous red and far-red light. The fri1 and tri1 alleles were introduced to specifically deplete phytochromes A and B1, respectively. In dark-grown seedlings, phytochrome A was necessary for response to high-irradiance far-red light, a complete response to low fluence red light, and also mediated the effects of blue light in a far-red reversible manner. Loss of phytochrome B1 alone did not significantly affect the behaviour of lz-2 plants under any light treatment tested. However, dark-grown lz-2 plants lacking both phytochrome A and B1 exhibited reduced responses to continuous red and were less responsive to low fluence red light and high fluence blue light than plants that were deficient for phytochrome A alone. In high light, full spectrum greenhouse conditions, lz-2 plants grew downward regardless of the phytochrome deficiency. These results indicate that phytochromes A and B1 play significant roles in mediating the lz-2 phenotype and that at least one additional phytochrome is involved in reversing shoot gravitropism in this mutant.

  20. Protective efficacy of reverse genetics based on inactivated American and Asian neuraminidase DIVA marker vaccines against highly pathogenic H5N1 avian influenza viruses in chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian H5N1 highly pathogenic avian influenza has become endemic in several countries, and vaccination is commonly being used. Vaccination can affect surveillance, and therefore there is considerable interest in DIVA (differentiate infected from vaccinated animals) vaccine strategies. Using reverse...

  1. Reversible Sterilization

    ERIC Educational Resources Information Center

    Largey, Gale

    1977-01-01

    Notes that difficult questions arise concerning the use of sterilization for alleged eugenic and euthenic purposes. Thus, how reversible sterilization will be used with relation to the poor, mentally ill, mentally retarded, criminals, and minors, is questioned. (Author/AM)

  2. Reversible Cardiomyopathies

    PubMed Central

    Patel, Harsh; Madanieh, Raef; Kosmas, Constantine E; Vatti, Satya K; Vittorio, Timothy J

    2015-01-01

    Cardiomyopathies (CMs) have many etiological factors that can result in severe structural and functional dysregulation. Fortunately, there are several potentially reversible CMs that are known to improve when the root etiological factor is addressed. In this article, we discuss several of these reversible CMs, including tachycardia-induced, peripartum, inflammatory, hyperthyroidism, Takotsubo, and chronic illness–induced CMs. Our discussion also includes a review on their respective pathophysiology, as well as possible management solutions. PMID:26052233

  3. Genetic background comparison using distance-based regression, with applications in population stratification evaluation and adjustment.

    PubMed

    Li, Qizhai; Wacholder, Sholom; Hunter, David J; Hoover, Robert N; Chanock, Stephen; Thomas, Gilles; Yu, Kai

    2009-07-01

    Population stratification (PS) can lead to an inflated rate of false-positive findings in genome-wide association studies (GWAS). The commonly used approach of adjustment for a fixed number of principal components (PCs) could have a deleterious impact on power when selected PCs are equally distributed in cases and controls, or the adjustment of certain covariates, such as self-identified ethnicity or recruitment center, already included in the association analyses, correctly maps to major axes of genetic heterogeneity. We propose a computationally efficient procedure, PC-Finder, to identify a minimal set of PCs while permitting an effective correction for PS. A general pseudo F statistic, derived from a non-parametric multivariate regression model, can be used to assess whether PS exists or has been adequately corrected by a set of selected PCs. Empirical data from two GWAS conducted as part of the Cancer Genetic Markers of Susceptibility (CGEMS) project demonstrate the application of the procedure. Furthermore, simulation studies show the power advantage of the proposed procedure in GWAS over currently used PS correction strategies, particularly when the PCs with substantial genetic variation are distributed similarly in cases and controls and therefore do not induce PS. PMID:19140130

  4. Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications.

    PubMed

    Wong, A; Forbes, M R; Smith, M L

    2001-08-01

    Amplified fragment length polymorphism (AFLP) analysis is becoming increasingly popular as a method for generating molecular markers for population genetic applications. For practical considerations, it is generally assumed in population studies that AFLPs segregate as dominant markers, i.e., that present and absent are the only possible states of a given locus. We tested the assumption of dominance in natural populations of the damselfly Nehalennia irene (Hagen) (Odonata: Coenagrionidae). Electro-blotted AFLP products from 21 samples were probed with individual markers. Eleven markers were analyzed, of which two were monomorphic and nine were polymorphic. Only two of the polymorphic markers behaved in a strictly dominant manner. The remaining seven polymorphic markers displayed various degrees of codominance, with 2-10 visible alleles in the sample. Of the three markers displaying the highest degree of variability, two contained microsatellite repeat tracts. Our results suggest that the assumption of dominance is unfounded. As a result, AFLP analysis may be unsuitable for estimating several important population genetic parameters, including genetic diversity. PMID:11550904

  5. Regularization Methods for High-Dimensional Instrumental Variables Regression With an Application to Genetical Genomics

    PubMed Central

    Lin, Wei; Feng, Rui; Li, Hongzhe

    2014-01-01

    In genetical genomics studies, it is important to jointly analyze gene expression data and genetic variants in exploring their associations with complex traits, where the dimensionality of gene expressions and genetic variants can both be much larger than the sample size. Motivated by such modern applications, we consider the problem of variable selection and estimation in high-dimensional sparse instrumental variables models. To overcome the difficulty of high dimensionality and unknown optimal instruments, we propose a two-stage regularization framework for identifying and estimating important covariate effects while selecting and estimating optimal instruments. The methodology extends the classical two-stage least squares estimator to high dimensions by exploiting sparsity using sparsity-inducing penalty functions in both stages. The resulting procedure is efficiently implemented by coordinate descent optimization. For the representative L1 regularization and a class of concave regularization methods, we establish estimation, prediction, and model selection properties of the two-stage regularized estimators in the high-dimensional setting where the dimensionality of co-variates and instruments are both allowed to grow exponentially with the sample size. The practical performance of the proposed method is evaluated by simulation studies and its usefulness is illustrated by an analysis of mouse obesity data. Supplementary materials for this article are available online. PMID:26392642

  6. Field application of a genetically engineered microorganism for polycyclic aromatic hydrocarbon bioremediation process monitoring and control

    SciTech Connect

    Sayler, G.S.; Cox, C.D.; Ripp, S.; Nivens, D.E.; Werner, C.; Ahn, Y.; Matrubutham, U.; Burlage, R.

    1998-11-01

    On October 30, 1996, the US Environmental Protection Agency (EPA) commenced the first test release of genetically engineered microorganisms (GEMs) for use in bioremediation. The specific objectives of the investigation were multifaceted and include (1) testing the hypothesis that a GEM can be successfully introduced and maintained in a bioremediation process, (2) testing the concept of using, at the field scale, reporter organisms for direct bioremediation process monitoring and control, and (3) acquiring data that can be used in risk assessment decision making and protocol development for future field release applications of GEMs. The genetically engineered strain under investigation is Pseudomonas fluorescens strain HK44 (King et al., 1990). The original P. fluorescens parent strain was isolated from polycyclic aromatic hydrocarbon (PAH) contaminated manufactured gas plant soil. Thus, this bacterium is able to biodegrade naphthalene (as well as other substituted naphthalenes and other PAHs) and is able to function as a living bioluminescent reporter for the presence of naphthalene contamination, its bioavailability, and the functional process of biodegradation. A unique component of this field investigation was the availability of an array of large subsurface soil lysimeters. This article describes the experience associated with the release of a genetically modified microorganism, the lysimeter facility and its associated instrumentation, as well as representative data collected during the first eighteen months of operation.

  7. Dissociable effects of 5-HT2C receptor antagonism and genetic inactivation on perseverance and learned non-reward in an egocentric spatial reversal task.

    PubMed

    Nilsson, Simon R O; Somerville, Elizabeth M; Clifton, Peter G

    2013-01-01

    Cognitive flexibility can be assessed in reversal learning tests, which are sensitive to modulation of 5-HT2C receptor (5-HT2CR) function. Successful performance in these tests depends on at least two dissociable cognitive mechanisms which may separately dissipate associations of previous positive and negative valence. The first is opposed by perseverance and the second by learned non-reward. The current experiments explored the effect of reducing function of the 5-HT2CR on the cognitive mechanisms underlying egocentric reversal learning in the mouse. Experiment 1 used the 5-HT2CR antagonist SB242084 (0.5 mg/kg) in a between-groups serial design and Experiment 2 used 5-HT2CR KO mice in a repeated measures design. Animals initially learned to discriminate between two egocentric turning directions, only one of which was food rewarded (denoted CS+, CS-), in a T- or Y-maze configuration. This was followed by three conditions; (1) Full reversal, where contingencies reversed; (2) Perseverance, where the previous CS+ became CS- and the previous CS- was replaced by a novel CS+; (3) Learned non-reward, where the previous CS- became CS+ and the previous CS+ was replaced by a novel CS-. SB242084 reduced perseverance, observed as a decrease in trials and incorrect responses to criterion, but increased learned non-reward, observed as an increase in trials to criterion. In contrast, 5-HT2CR KO mice showed increased perseverance. 5-HT2CR KO mice also showed retarded egocentric discrimination learning. Neither manipulation of 5-HT2CR function affected performance in the full reversal test. These results are unlikely to be accounted for by increased novelty attraction, as SB242084 failed to affect performance in an unrewarded novelty task. In conclusion, acute 5-HT2CR antagonism and constitutive loss of the 5-HT2CR have opposing effects on perseverance in egocentric reversal learning in mice. It is likely that this difference reflects the broader impact of 5HT2CR loss on the development and maintenance of cognitive function. PMID:24204954

  8. Reversible shape memory

    NASA Astrophysics Data System (ADS)

    Sheiko, Sergei; Zhou, Jing; White, Sarah; Ashby, Valerie

    2012-02-01

    An ``Achilles' heel'' of shape memory materials is that shape transformations triggered by an external stimulus are usually irreversible. Here we present a new concept of reversible transitions between two well-defined shapes by controlling hierarchic crystallization of a dual-network elastomer. The reversibility was demonstrated for different types of shape transformations including rod bending, winding of a helical coil, and widening an aperture. The distinct feature of the reversible shape alterations is that both counter-shapes are infinitely stable at a temperature of exploitation. Shape reversibility is highly desirable property in many practical applications such as non-surgical removal of a previously inserted catheter and handfree wrapping up of an earlier unraveled solar sail on a space shuttle.

  9. Development and application of a hexaplex reverse transcription polymerase chain reaction for screening global Citrus tristeza virus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The discovery of the diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures. To simplify the identification and differentiation of CTV genotypes, an efficient multiplex reverse transcription polymerase chain reaction (M-RT-PCR) technique for the screenin...

  10. A School-Based Application of Modified Habit Reversal for Tourette Syndrome via a Translator: A Case Study

    ERIC Educational Resources Information Center

    Gilman, Rich; Connor, Nancy; Haney, Michelle

    2005-01-01

    A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline

  11. Preparation and application of reversed phase chromatorotor for the isolation of natural products by centrifugal preparative chromatography

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method of preparation of Chromatorotor or plates with a reversed phase (RP) solid silica gel sorbent layer has been developed for preparative centrifugal chromatography. The RP-rotor plates consist of binder free RP solid SiO2 sorbent layers of different thicknesses paked between two supported cir...

  12. Development and application of a hexaplex reverse transcription polymerase chain reaction for screening global citrus tristeza virus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The discovery of the diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures. To simplify the identification and differentiation of CTV genotypes, an efficient multiplex reverse transcription polymerase chain reaction (M-RT-PCR) technique for the screenin...

  13. A School-Based Application of Modified Habit Reversal for Tourette Syndrome via a Translator: A Case Study

    ERIC Educational Resources Information Center

    Gilman, Rich; Connor, Nancy; Haney, Michelle

    2005-01-01

    A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline…

  14. An Application of Reverse Engineering to Automatic Item Generation: A Proof of Concept Using Automatically Generated Figures

    ERIC Educational Resources Information Center

    Lorié, William A.

    2013-01-01

    A reverse engineering approach to automatic item generation (AIG) was applied to a figure-based publicly released test item from the Organisation for Economic Cooperation and Development (OECD) Programme for International Student Assessment (PISA) mathematical literacy cognitive instrument as part of a proof of concept. The author created an item…

  15. Genetic algorithm for the design of high frequency diffraction gratings for high power laser applications

    NASA Astrophysics Data System (ADS)

    Thomson, Martin J.; Waddie, Andrew J.; Taghizadeh, Mohammad R.

    2006-04-01

    We present a genetic algorithm with small population sizes for the design of diffraction gratings in the rigorous domain. A general crossover and mutation scheme is defined, forming fifteen offspring from 3 parents, which enables the algorithm to be used for designing gratings with diverse optical properties by careful definition of the merit function. The initial parents are randomly selected and the parents of the subsequent generations are selected by survival of the fittest. The performance of the algorithm is demonstrated by designing diffraction gratings with specific application to high power laser beam lines. Gratings are designed that act as beam deflectors, polarisers, polarising beam splitters, harmonic separation gratings and pulse compression gratings. By imposing fabrication constraints within the design process, we determine which of these elements have true potential for application within high power laser beam lines.

  16. Biochemistry, genetics, and applications of exopolysaccharide production in Streptococcus thermophilus: a review.

    PubMed

    Broadbent, J R; McMahon, D J; Welker, D L; Oberg, C J; Moineau, S

    2003-02-01

    Many strains of Streptococcus thermophilus synthesize extracellular polysaccharides. These molecules may be produced as capsules that are tightly associated with the cell, or they may be liberated into the medium as a loose slime (i.e., "ropy" polysaccharide). Although the presence of exopolysaccharide does not confer any obvious advantage to growth or survival of S. thermophilus in milk, in situ production by this species or other dairy lactic acid bacteria typically imparts a desirable "ropy" or viscous texture to fermented milk products. Recent work has also shown that exopolysaccharide-producing S. thermophilus can enhance the functional properties of Mozzarella cheese, but they are not phage-proof. As our understanding of the genetics, physiology, and functionality of bacterial exopolysaccharides continues to improve, novel applications for polysaccharides and polysaccharide-producing cultures are likely to emerge inside and outside the dairy industry. This article provides an overview of biochemistry, genetics, and applications of exopolysaccharide production in S. thermophilus. PMID:12647947

  17. Genetics and Evolution: An iOS Application to Supplement Introductory Courses in Transmission and Evolutionary Genetics

    PubMed Central

    Myers, Russell B.; Millman, Brandon; Noor, Mohamed A. F.

    2014-01-01

    Students in college courses struggle to understand many concepts fundamental to transmission and evolutionary genetics, including multilocus inheritance, recombination, Hardy-Weinberg, and genetic drift. These students consistently ask for more demonstrations and more practice problems. With this demand in mind, the Genetics and Evolution app was designed to help students (and their instructors) by providing a suite of tools granting them the ability to: (1) simulate genetic crosses with varying numbers of genes and patterns of inheritance, (2) simulate allele frequency changes under natural selection and/ or genetic drift, (3) quiz themselves to reinforce terminology (customizable by any instructor for their whole classroom), *4) solve various problems (recombination fractions, Hardy-Weinberg, heritability, population growth), and (5) generate literally an infinite number of practice problems in all of these areas to try on their own. Although some of these functions are available elsewhere, the alternatives do not have the ability to instantly generate new practice problems or achieve these diverse functions in devices that students carry in their pockets every day. PMID:24727286

  18. MONITORING MYCOTOXIN PRODUCTION AT THE GENETIC LEVEL ON VARIOUS GROWTH SUBSTRATES USING QUANTITATIVE REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION?EXPERIMENT DESIGN

    EPA Science Inventory

    The paper describes a method of analyzing the production of mycotoxins at the genetic level by monitoring the intracellular levels of messenger RNA (mRNA). Initial work will focus on threshing out the mycotoxin gene clusters in Stachybotrys chartarum followed by analysis of toxin...

  19. A Reverse Genetic System Provides a Powerful Tool in the Design of Foot-and-Mouth Disease Viruses with Enhanced Properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fact that the foot-and-mouth disease viral (FMDV) RNA can be made infectious in the absence of other components of the virion allows the recovery of genetically engineered new viruses from in vitro-generated RNA molecules. We utilize infectious cDNA technology to produce recombinant FMDV, retain...

  20. Contribution of genetics to ecological restoration.

    PubMed

    Mijangos, Jose Luis; Pacioni, Carlo; Spencer, Peter B S; Craig, Michael D

    2015-01-01

    Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration. PMID:25377524

  1. The partially reversible formation of Li-metal particles on a solid Li electrolyte: applications toward nanobatteries

    SciTech Connect

    Arruda, Thomas M; Kumar, Amit; Kalinin, Sergei V; Jesse, Stephen

    2012-01-01

    The feasibility of large-scale implementation of Li-air batteries (LABs) hinges on understanding the thermodynamic and kinetic factors that control charge-discharge rates, efficiency and life times. Here, the kinetics of bias-induced reactions is explored locally on the surface of Li-ion conductive glass ceramics, a preferred electrolyte for LABs, using direct current-voltage and strain spectroscopies. Above a critical bias, particle growth kinetics were found to be linear in both the bias and time domains. Partial reversibility was observed for Li particles as evidenced by the presence of anodic peaks following the Li{sup +} reduction, as well an associated reduction in particle height. The degree of reversibility was highest for the smallest particles formed. These observations thus suggest the possibility of producing nanobatteries with an active anode volume of the order of 0.1 al.

  2. PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics

    PubMed Central

    2013-01-01

    Background Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. Results A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. Conclusions We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax. PMID:24128060

  3. Update: Biochemistry of Genetic Manipulation.

    ERIC Educational Resources Information Center

    Barker, G. R.

    1983-01-01

    Various topics on the biochemistry of genetic manipulation are discussed. These include genetic transformation and DNA; genetic expression; DNA replication, repair, and mutation; technology of genetic manipulation; and applications of genetic manipulation. Other techniques employed are also considered. (JN)

  4. The Genetic Algorithm and Its Application to Calibrating Conceptual Rainfall-Runoff Models

    NASA Astrophysics Data System (ADS)

    Wang, Q. J.

    1991-09-01

    The genetic algorithm is a search procedure based on the mechanics of natural selection and natural genetics, which combines an artificial survival of the fittest with genetic operators abstracted from nature. In this paper, a genetic algorithm for function optimization is introduced and applied to calibration of a conceptual rainfall-runoff model for data from a particular catchment. All seven parameters of the model are optimized. The results show that the genetic algorithm can be efficient and robust.

  5. Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design

    PubMed Central

    Che, Z. H.; Chiang, Tzu-An; Kuo, Y. C.

    2014-01-01

    In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

  6. Hybrid algorithms for fuzzy reverse supply chain network design.

    PubMed

    Che, Z H; Chiang, Tzu-An; Kuo, Y C; Cui, Zhihua

    2014-01-01

    In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

  7. The application of genetic markers for EBLV surveillance in European bat species.

    PubMed

    Harris, S L; Johnson, N; Brookes, S M; Hutson, A M; Fooks, A R; Jones, G

    2008-01-01

    The United Kingdom has performed passive surveillance for European bat lyssaviruses (EBLVs) since 1987, and species-targeted surveillance since 2003. One critical component of these studies is the accurate identification of bats either submitted for testing or sampled in the field. Identification is dependent on numerous morphological characteristics. Whilst this is an effective means of bat identification, a number of problems remain with this approach. It relies on the experience of bat specialists and can lead to problems in differentiating members of the Myotis genus, particularly between Myotis mystacinus (whiskered bat) and Myotis brandtii (Brandt's bat), and between the most common species of the genus Pipistrellus. Furthermore, degradation of bats submitted for testing can also lead to problems in making an accurate species identification. Comparison of genetic sequence data could offer an alternative approach to differentiating bat species when morphological characterisation is not possible. Using tissue samples from UK resident bat species, sequence analysis of the mitochondrial DNA cytochrome b gene, and the beta-actin gene allowed for identification of many of the most common bat species in the UK, and genetic separation of two morphologically cryptic species. Application of this approach identified the species of a bat infected with EBLV-2 in Surrey as Myotis daubentoni (Daubenton's bat). PMID:18634497

  8. Diagnostic application of an extensive gene panel for Leber congenital amaurosis with severe genetic heterogeneity.

    PubMed

    Seong, Moon-Woo; Seo, Soo Hyun; Yu, Young Suk; Hwang, Jeong-Min; Cho, Sung Im; Ra, Eun Kyung; Park, Hyunwoong; Lee, Seung Jun; Kim, Ji Yeon; Park, Sung Sup

    2015-01-01

    Leber congenital amaurosis (LCA) is a genetically heterogeneous disorder and the most severe form of inherited retinal dystrophy. We report results of a diagnostic application of an extensive gene panel composed of 204 retinal dystrophy-related genes and discuss its feasibility as a diagnostic tool. Nineteen unrelated LCA patients were included in the study: two patients for validation purposes of our gene panel, 15 previously analyzed patients with no identified mutations, and two previously unanalyzed patients. Genetic diagnosis for each patient was conducted according to whether the variants were consistent with the known inheritance pattern of each gene. We identified two heterozygous or homozygous pathogenic variants in seven of 19 patients. On the basis of mutation information, clinical features were re-reviewed, and clinical diagnoses for two patients were revised from LCA to LCA-related disorders. In addition, a coverage simulation was performed to determine the optimal depth of coverage of the gene panel. Using our gene panel, we diagnosed LCA and LCA-related disorders in 36.8% of patients and one or more deleterious variants or variants of unknown significance in 89.5% of patients. Molecular diagnosis using this extensive gene panel is expected to facilitate diagnosis of retinal dystrophy and help provide proper treatment to patients, although further analyses is needed for a complete clinical validation. PMID:25445212

  9. The evolution of colorectal cancer geneticsPart 2: clinical implications and applications

    PubMed Central

    Schlussel, Andrew T.; Gagliano, Ronald A.; Eggerding, Faye; Donlon, Timothy; Berenberg, Jeffrey; Lynch, Henry T.

    2014-01-01

    The genetic understanding of colorectal cancer (CRC) continues to grow, and it is now estimated that 10% of the population has a known hereditary CRC syndrome. This article will examine the evolving surgical and medical management of hereditary CRC syndromes, and the impact of tumor genetics on therapy. This review will focus on the most common hereditary CRC-prone diseases seen in clinical practice, which include Lynch syndrome (LS), familial adenomatous polyposis (FAP) & attenuated FAP (AFAP), MutYH-associated polyposis (MAP), and serrated polyposis syndrome (SPS). Each section will review the current recommendations in the evaluation and treatment of these syndromes, as well as review surgical management and operative planning. A highly detailed multigeneration cancer family history with verified genealogy and pathology documentation whenever possible, coupled with germline mutation testing when indicated, is critically important to management decisions. Although caring for patients with these syndromes remains complex, the application of this knowledge facilitates better treatment of both individuals and their affected family members for generations to come. PMID:25276406

  10. The evolution of colorectal cancer genetics-Part 2: clinical implications and applications.

    PubMed

    Schlussel, Andrew T; Gagliano, Ronald A; Seto-Donlon, Susan; Eggerding, Faye; Donlon, Timothy; Berenberg, Jeffrey; Lynch, Henry T

    2014-10-01

    The genetic understanding of colorectal cancer (CRC) continues to grow, and it is now estimated that 10% of the population has a known hereditary CRC syndrome. This article will examine the evolving surgical and medical management of hereditary CRC syndromes, and the impact of tumor genetics on therapy. This review will focus on the most common hereditary CRC-prone diseases seen in clinical practice, which include Lynch syndrome (LS), familial adenomatous polyposis (FAP) & attenuated FAP (AFAP), MutYH-associated polyposis (MAP), and serrated polyposis syndrome (SPS). Each section will review the current recommendations in the evaluation and treatment of these syndromes, as well as review surgical management and operative planning. A highly detailed multigeneration cancer family history with verified genealogy and pathology documentation whenever possible, coupled with germline mutation testing when indicated, is critically important to management decisions. Although caring for patients with these syndromes remains complex, the application of this knowledge facilitates better treatment of both individuals and their affected family members for generations to come. PMID:25276406

  11. Analysis and Application of European Genetic Substructure Using 300 K SNP Information

    PubMed Central

    Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F

    2008-01-01

    European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans. PMID:18208329

  12. Analysis and application of European genetic substructure using 300 K SNP information.

    PubMed

    Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F

    2008-01-01

    European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans. PMID:18208329

  13. Route to genetically targeted optical electrophysiology: development and applications of voltage-sensitive fluorescent proteins

    PubMed Central

    Akemann, Walther; Song, Chenchen; Mutoh, Hiroki; Knöpfel, Thomas

    2015-01-01

    Abstract. The invention of membrane voltage protein indicators widens the reach of optical voltage imaging in cell physiology, most notably neurophysiology, by enabling membrane voltage recordings from genetically defined cell types in chronic and life-long preparations. While the last years have seen a dramatic improvement in the technical performance of these indicators, concomitant innovations in optogenetics, optical axon tracing, and high-speed digital microscopy are beginning to fulfill the age-old vision of an all-optical analysis of neuronal circuits, reaching beyond the limits of traditional electrode-based recordings. We will present our personal account of the development of protein voltage indicators from the pioneering days to the present state, including their applications in neurophysiology that has inspired our own work for more than a decade. PMID:26082930

  14. Application of artificial neural network and genetic algorithm in flow and transport simulations

    NASA Astrophysics Data System (ADS)

    Morshed, Jahangir; Kaluarachchi, Jagath J.

    Artificial neural network (ANN) is considered to be a powerful tool for solving groundwater problems which require a large number of flow and contaminant transport (GFCT) simulations. Often, GFCT models are nonlinear, and they are difficult to solve using traditional numerical methods to simulate specific input-output responses. In order to avoid these difficulties, ANN may be used to simulate the GFCT responses explicitly. In this manuscript, recent research related to the application of ANN in simulating GFCT responses is critically reviewed, and six research areas are identified. In order to study these areas, a one-dimensional unsaturated flow and transport scenario was developed, and ANN was used to simulate the effects of specific GFCT parameters on overall results. Using these results, ANN concepts related to architecture, sampling, training, and multiple function approximations are studied, and ANN training using back-propagation algorithm (BPA) and genetic algorithm (GA) are compared. These results are summarized, and appropriate conclusions are made.

  15. Optimisation of halogenase enzyme activity by application of a genetic algorithm.

    PubMed

    Muffler, Kai; Retzlaff, Marco; van Pe, Karl-Heinz; Ulber, Roland

    2007-01-10

    A genetic algorithm (GA) was applied for the optimisation of an enzyme assay composition respectively the enzyme activity of a recombinantly produced FADH(2)-dependent halogenating enzyme. The examined enzyme belongs to the class of halogenases and is capable to halogenate tryptophan regioselective in position 5. Therefore, the expressed trp-5-halogenase can be an interesting tool in the manufacturing of serotonin precursors. The application of stochastic search strategies (e.g. GAs) is well suited for fast determination of the global optimum in multidimensional search spaces, where statistical approaches or even the popular classical one-factor-at-a-time method often failures by misleading to local optima. The concentrations of six different medium components were optimised and the maximum yield of the halogenated tryptophan could be increased from 3.5 up to 65%. PMID:16919347

  16. Application of genetic algorithms to the optimization design of electron optical system

    NASA Astrophysics Data System (ADS)

    Gu, Changxin; Wu, M. Q.; Shan, Liying; Lin, G.

    2001-12-01

    The application of Genetic Algorithms (GAs) to the optimization design method, such as Simplex method and Powell method etc, can determine the final optimum structure and electric parameters of an electron optical system from given electron optical properties, but it may be landed in the localization of optimum search process. The GAs is a novel direct search optimization method based on principles of natural selection and survival of the fittest from natural evolution. Through the reproduction, crossover, and mutation iterative process, GAs can search the global optimum result. We applied the GAs to optimize an electron emission system and an extended field lens (EFL) respectively. The optimal structure and corresponding electrical parameters with a criterion of minimum objective function value, crossover radius for electron emission system and spherical aberration coefficient for EFL, have been searched and presented in this paper. The GAs, as a direct search method and an adaptive search technique, has significant advantage in the optimization design of electron optical systems.

  17. A Genetic-Based Scheduling Algorithm to Minimize the Makespan of the Grid Applications

    NASA Astrophysics Data System (ADS)

    Entezari-Maleki, Reza; Movaghar, Ali

    Task scheduling algorithms in grid environments strive to maximize the overall throughput of the grid. In order to maximize the throughput of the grid environments, the makespan of the grid tasks should be minimized. In this paper, a new task scheduling algorithm is proposed to assign tasks to the grid resources with goal of minimizing the total makespan of the tasks. The algorithm uses the genetic approach to find the suitable assignment within grid resources. The experimental results obtained from applying the proposed algorithm to schedule independent tasks within grid environments demonstrate the applicability of the algorithm in achieving schedules with comparatively lower makespan in comparison with other well-known scheduling algorithms such as, Min-min, Max-min, RASA and Sufferage algorithms.

  18. Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays

    PubMed Central

    Kim, Do Hyun; Kim, Moon Il; Park, Hyun Gyu

    2015-01-01

    Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes. PMID:26436087

  19. Automatic design of fuzzy systems using genetic algorithms and its application to lateral vehicle guidance

    NASA Astrophysics Data System (ADS)

    Hessburg, Thomas; Lee, Michael; Takagi, Hideyuki; Tomizuka, Masayoshi

    1993-12-01

    A method of tuning a fuzzy logic controller (FLC) by a genetic algorithm (GA) is proposed for lane following maneuvers in an automated highway system. The GA simultaneously determines the shape of membership functions, number of rules, and consequent parameters of the FLC. The GA approach operates on binary representations of FLCs and uses an expression for a fitness score to be maximized, which takes into account the tracking error, yaw rate error, lateral acceleration error, rate of lateral acceleration, front wheel steering angle, and rate of front wheel steering angle, to find an optimal controller. Apriori knowledge about both the physical application and FLCs is incorporated into the design method to increase the performance of the design method and the resulting controller. The controllers designed by this method are compared in simulation to a conventional PID controller, a frequency shaped linear quadratic controller, and previously designed FLCs tuned manually.

  20. Application of Genetic Algorithm to the Design Optimization of Complex Energy Saving Glass Coating Structure

    NASA Astrophysics Data System (ADS)

    Johar, F. M.; Azmin, F. A.; Shibghatullah, A. S.; Suaidi, M. K.; Ahmad, B. H.; Abd Aziz, M. Z. A.; Salleh, S. N.; Shukor, M. Md

    2014-04-01

    Attenuation of GSM, GPS and personal communication signal leads to poor communication inside the building using regular shapes of energy saving glass coating. Thus, the transmission is very low. A brand new type of band pass frequency selective surface (FSS) for energy saving glass application is presented in this paper for one unit cell. Numerical Periodic Method of Moment approach according to a previous study has been applied to determine the new optimum design of one unit cell energy saving glass coating structure. Optimization technique based on the Genetic Algorithm (GA) is used to obtain an improved in return loss and transmission signal. The unit cell of FSS is designed and simulated using the CST Microwave Studio software at based on industrial, scientific and medical bands (ISM). A unique and irregular shape of an energy saving glass coating structure is obtained with lower return loss and improved transmission coefficient.

  1. Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport.

    PubMed

    Terai, Takuya; Kohno, Moe; Boncompain, Gaelle; Sugiyama, Shigeru; Saito, Nae; Fujikake, Ryo; Ueno, Tasuku; Komatsu, Toru; Hanaoka, Kenjiro; Okabe, Takayoshi; Urano, Yasuteru; Perez, Franck; Nagano, Tetsuo

    2015-08-26

    Artificial ligands of streptavidin (ALiS) with association constants of ?10(6) M(-1) were discovered by high-throughput screening of our chemical library, and their binding characteristics, including X-ray crystal structure of the streptavidin complex, were determined. Unlike biotin and its derivatives, ALiS exhibits fast dissociation kinetics and excellent cell permeability. The streptavidin-ALiS system provides a novel, practical compound-dependent methodology for repeated reversible cycling of protein localization between intracellular organella. PMID:26261872

  2. Vasectomy reversal.

    PubMed

    Belker, A M

    1987-02-01

    A vasovasostomy may be performed on an outpatient basis with local anesthesia, but also may be performed on an outpatient basis with epidural or general anesthesia. Local anesthesia is preferred by most of my patients, the majority of whom choose this technique. With proper preoperative and intraoperative sedation, patients sleep lightly through most of the procedure. Because of the length of time often required for bilateral microsurgical vasoepididymostomy, epidural or general anesthesia and overnight hospitalization are usually necessary. Factors influencing the preoperative choice for vasovasostomy or vasoepididymostomy in patients undergoing vasectomy reversal are considered. The preoperative planned choice of vasovasostomy or vasoepididymostomy for patients having vasectomy reversal described herein does not have the support of all urologists who regularly perform these procedures. My present approach has evolved as the data reported in Tables 1 and 2 have become available, but it may change as new information is evaluated. However, it offers a logical method for planning choices of anesthesia and inpatient or outpatient status for patients undergoing vasectomy reversal procedures. PMID:3811050

  3. Development of a low-level setup for gamma spectroscopy: Application for nuclear astrophysics using reverse kinematics

    NASA Astrophysics Data System (ADS)

    Genard, G.; Nuttens, V. E.; Bouchat, V.; Terwagne, G.

    2010-05-01

    It is more and more necessary to improve the sensitivity of gamma-ray spectroscopy systems, especially in nuclear astrophysics. In the case of radiative proton capture reactions, one means is to avoid the reactions on the target impurities by using reverse kinematics. This technique is possible with the LARN accelerator and can provide very clean cross-section measurements. For that purpose, a hydrogen standard has been carried out by means of ion implantation in silicon. In addition, a low-level setup has been put in place on a new beam line of the accelerator. A high efficiency and high resolution germanium detector is used conjointly with a double shielding. A passive lead castle shielding system is used to reduce the natural radioactivity and an active shielding consisting of an anti-cosmic veto is provided by an anticoincidence between the plastic scintillator and the gamma-ray detector. The setup allows a reduction of 70% of the background interference and provides an approximately 200 fold sensitivity gain of between 600 and 3000 keV. Some other developments have also been carried out to optimize the setup. The entire setup and the reverse kinematics have been validated by measuring the cross-section of the 13C(p,?)14N and 15N(p,?)16O reactions that present some astrophysical interest.

  4. Model for the reversible magnetization of high-κ type-II superconductors: Application to high-Tc superconductors

    NASA Astrophysics Data System (ADS)

    Hao, Zhidong; Clem, John R.; McElfresh, M. W.; Civale, L.; Malozemoff, A. P.; Holtzberg, F.

    1991-02-01

    A simple theoretical model is proposed for the reversible magnetization of type-II superconductors as a function of the applied field H for the entire field region between Hc1 and Hc2. For H~=Hc1, the theory reduces to a variational model, from which Hc1 can be accurately computed in the Ginzburg-Landau regime. In calculating the free energy, we include, in addition to the supercurrent kinetic energy and the magnetic-field energy, the kinetic-energy and the condensation-energy terms arising from suppression of the order parameter in the vortex core. The model is further extended to include anisotropy by introducing an effective-mass tensor for the case when H is parallel to one of the principal axes. The theory is compared to reversible-magnetization data on a YBa2Cu3O7 single crystal. The method permits an accurate determination of Hc2 versus temperature from measurements of the magnetization versus temperature at fixed magnetic field and explains why the measurements have different slopes in different fields, contrary to what might have been expected from the linear Abrikosov formula near Hc2. The deduced dHc2/dT is (-1.65+/-0.23) T/K for H parallel to the c axis near Tc, implying ξab(0)=(17+/-1) Å.

  5. Determination of platelet-activating factor by reverse phase high-performance liquid chromatography and its application in viral hepatitis

    PubMed Central

    Cao, Hong-Cui; Chen, Xiao-Ming; Xu, Wei

    2005-01-01

    AIM: To detect the platelet-activating factor (PAF) and the plasma or serum levels of tumor necrosis factor-? (TNF-?) malondialdehyde (MDA), endotoxin (ET) and to discuss their significance in various types of viral hepatitis. METHODS: PAF, TNF-?, MDA, and ET levels in 60 controls, 16 cases of acute viral hepatitis, 71 cases of chronic viral hepatitis, 19 cases of severe viral hepatitis were detected by reverse phase high-performance liquid chromatography (rHPLC), bio-assay, ELISA, thiobarbituric acid (TBA), and limulus lysate test (LLT), respectively. RESULTS: The rHPLC was more sensitive and specific than bio-assay (r = 0.912, P<0.01). The plasma levels of PAF, TNF-?, MDA, and ET in patients with viral hepatitis were higher than those in controls (P<0.01). CONCLUSION: rHPLC is more reliable and accurate for the detection of PAF. PMID:16437644

  6. Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development

    PubMed Central

    He, Yongqun; Xiang, Zuoshuang; Mobley, Harry L. T.

    2010-01-01

    Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for >70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program. PMID:20671958

  7. GENETIC ACTIVITY PROFILES--APPLICATION IN ASSESSING POTENTIAL CARCINOGENICITY OF COMPLEX ENVIRONMENTAL MIXTURES

    EPA Science Inventory

    Some knowledge of the potential genetic activity of a complex environmental mixture may be gained from an assessment of the genetic activity of its component chemicals. he expanded Genetic Activity Profile (GAP) data base provides a computer generated graphic representation of ge...

  8. Reverse osmosis reverses conventional wisdom with Superfund cleanup success

    SciTech Connect

    Collins, M. ); Miller, K. )

    1994-09-01

    Although widely recognized as the most efficient means of water purification, reverse osmosis has not been considered effective for remediating hazardous wastewater. Scaling and fouling, which can cause overruns and downtime, and require membrane replacement, have inhibited success in high-volume wastewater applications. Despite this background, a reverse osmosis technology developed in Europe recently was used successfully to treat large volumes of contaminated water at a major Superfund site in Texas. The technology's success there may increase the chances for reverse osmosis to find wider use in future cleanups and other waste treatment applications.

  9. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    PubMed Central

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  10. A kernel machine method for detecting effects of interaction between multidimensional variable sets: an imaging genetics application.

    PubMed

    Ge, Tian; Nichols, Thomas E; Ghosh, Debashis; Mormino, Elizabeth C; Smoller, Jordan W; Sabuncu, Mert R

    2015-04-01

    Measurements derived from neuroimaging data can serve as markers of disease and/or healthy development, are largely heritable, and have been increasingly utilized as (intermediate) phenotypes in genetic association studies. To date, imaging genetic studies have mostly focused on discovering isolated genetic effects, typically ignoring potential interactions with non-genetic variables such as disease risk factors, environmental exposures, and epigenetic markers. However, identifying significant interaction effects is critical for revealing the true relationship between genetic and phenotypic variables, and shedding light on disease mechanisms. In this paper, we present a general kernel machine based method for detecting effects of the interaction between multidimensional variable sets. This method can model the joint and epistatic effect of a collection of single nucleotide polymorphisms (SNPs), accommodate multiple factors that potentially moderate genetic influences, and test for nonlinear interactions between sets of variables in a flexible framework. As a demonstration of application, we applied the method to the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to detect the effects of the interactions between candidate Alzheimer's disease (AD) risk genes and a collection of cardiovascular disease (CVD) risk factors, on hippocampal volume measurements derived from structural brain magnetic resonance imaging (MRI) scans. Our method identified that two genes, CR1 and EPHA1, demonstrate significant interactions with CVD risk factors on hippocampal volume, suggesting that CR1 and EPHA1 may play a role in influencing AD-related neurodegeneration in the presence of CVD risks. PMID:25600633

  11. Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development

    SciTech Connect

    Jin, Huanan; Song, Zhihong; Nikolau, Basil J.

    2012-03-31

    Acetoacetyl CoA thiolase (AACT, EC 2.3.1.9) catalyzes the condensation of two acetyl?CoA molecules to form acetoacetyl?CoA. Two AACT?encoding genes, At5g47720 (AACT1) and At5g48230 (AACT2), were functionally identified in the Arabidopsis genome by direct enzymological assays and functional expression in yeast. Promoter::GUS fusion experiments indicated that AACT1 is primarily expressed in the vascular system and AACT2 is highly expressed in root tips, young leaves, top stems and anthers. Characterization of T?DNA insertion mutant alleles at each AACT locus established that AACT2 function is required for embryogenesis and for normal male gamete transmission. In contrast, plants lacking AACT1 function are completely viable and show no apparent growth phenotypes, indicating that AACT1 is functionally redundant with respect to AACT2 function. RNAi lines that express reduced levels of AACT2 show pleiotropic phenotypes, including reduced apical dominance, elongated life span and flowering duration, sterility, dwarfing, reduced seed yield and shorter root length. Microscopic analysis reveals that the reduced stature is caused by a reduction in cell size and fewer cells, and male sterility is caused by loss of the pollen coat and premature degeneration of the tapetal cells. Biochemical analyses established that the roots of AACT2 RNAi plants show quantitative and qualitative alterations in phytosterol profiles. These phenotypes and biochemical alterations are reversed when AACT2 RNAi plants are grown in the presence of mevalonate, which is consistent with the role of AACT2 in generating the bulk of the acetoacetyl?CoA precursor required for the cytosol?localized, mevalonate?derived isoprenoid biosynthetic pathway.

  12. Tomato TILLING Technology: Development of a Reverse Genetics Tool for the Efficient Isolation of Mutants from Micro-Tom Mutant Libraries

    PubMed Central

    Okabe, Yoshihiro; Asamizu, Erika; Saito, Takeshi; Matsukura, Chiaki; Ariizumi, Tohru; Brs, Ccile; Rothan, Christophe; Mizoguchi, Tsuyoshi; Ezura, Hiroshi

    2011-01-01

    To accelerate functional genomic research in tomato, we developed a Micro-Tom TILLING (Targeting Induced Local Lesions In Genomes) platform. DNA pools were constructed from 3,052 ethyl methanesulfonate (EMS) mutant lines treated with 0.5 or 1.0% EMS. The mutation frequency was calculated by screening 10 genes. The 0.5% EMS population had a mild mutation frequency of one mutation per 1,710 kb, whereas the 1.0% EMS population had a frequency of one mutation per 737 kb, a frequency suitable for producing an allelic series of mutations in the target genes. The overall mutation frequency was one mutation per 1,237 kb, which affected an average of three alleles per kilobase screened. To assess whether a Micro-Tom TILLING platform could be used for efficient mutant isolation, six ethylene receptor genes in tomato (SlETR1SlETR6) were screened. Two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) that resulted in reduced ethylene responses were identified, indicating that our Micro-Tom TILLING platform provides a powerful tool for the rapid detection of mutations in an EMS mutant library. This work provides a practical and publicly accessible tool for the study of fruit biology and for obtaining novel genetic material that can be used to improve important agronomic traits in tomato. PMID:21965606

  13. Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries.

    PubMed

    Okabe, Yoshihiro; Asamizu, Erika; Saito, Takeshi; Matsukura, Chiaki; Ariizumi, Tohru; Brs, Ccile; Rothan, Christophe; Mizoguchi, Tsuyoshi; Ezura, Hiroshi

    2011-11-01

    To accelerate functional genomic research in tomato, we developed a Micro-Tom TILLING (Targeting Induced Local Lesions In Genomes) platform. DNA pools were constructed from 3,052 ethyl methanesulfonate (EMS) mutant lines treated with 0.5 or 1.0% EMS. The mutation frequency was calculated by screening 10 genes. The 0.5% EMS population had a mild mutation frequency of one mutation per 1,710 kb, whereas the 1.0% EMS population had a frequency of one mutation per 737 kb, a frequency suitable for producing an allelic series of mutations in the target genes. The overall mutation frequency was one mutation per 1,237 kb, which affected an average of three alleles per kilobase screened. To assess whether a Micro-Tom TILLING platform could be used for efficient mutant isolation, six ethylene receptor genes in tomato (SlETR1-SlETR6) were screened. Two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) that resulted in reduced ethylene responses were identified, indicating that our Micro-Tom TILLING platform provides a powerful tool for the rapid detection of mutations in an EMS mutant library. This work provides a practical and publicly accessible tool for the study of fruit biology and for obtaining novel genetic material that can be used to improve important agronomic traits in tomato. PMID:21965606

  14. The dawn of active genetics.

    PubMed

    Gantz, Valentino M; Bier, Ethan

    2016-01-01

    On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild-type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of "active genetics," its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. Also watch the Video Abstract. PMID:26660392

  15. Reversible Semiconducting-to-Metallic Phase Transition in Chemical Vapor Deposition Grown Monolayer WSe2 and Applications for Devices.

    PubMed

    Ma, Yuqiang; Liu, Bilu; Zhang, Anyi; Chen, Liang; Fathi, Mohammad; Shen, Chenfei; Abbas, Ahmad N; Ge, Mingyuan; Mecklenburg, Matthew; Zhou, Chongwu

    2015-07-28

    Two-dimensional (2D) semiconducting monolayer transition metal dichalcogenides (TMDCs) have stimulated lots of interest because they are direct bandgap materials that have reasonably good mobility values. However, contact between most metals and semiconducting TMDCs like 2H phase WSe2 are highly resistive, thus degrading the performance of field effect transistors (FETs) fabricated with WSe2 as active channel materials. Recently, a phase engineering concept of 2D MoS2 materials was developed, with improved device performance. Here, we applied this method to chemical vapor deposition (CVD) grown monolayer 2H-WSe2 and demonstrated semiconducting-to-metallic phase transition in atomically thin WSe2. We have also shown that metallic phase WSe2 can be converted back to semiconducting phase, demonstrating the reversibility of this phase transition. In addition, we fabricated FETs based on these CVD-grown WSe2 flakes with phase-engineered metallic 1T-WSe2 as contact regions and intact semiconducting 2H-WSe2 as active channel materials. The device performance is substantially improved with metallic phase source/drain electrodes, showing on/off current ratios of 10(7) and mobilities up to 66 cm(2)/Vs for monolayer WSe2. These results further suggest that phase engineering can be a generic strategy to improve device performance for many kinds of 2D TMDC materials. PMID:26125321

  16. A reversed-phase/hydrophilic interaction mixed-mode C18-Diol stationary phase for multiple applications.

    PubMed

    Wang, Qing; Ye, Mao; Xu, Li; Shi, Zhi-guo

    2015-08-12

    A mixed-mode chromatographic packing material, C18 and diol groups modified silica (C18-Diol), was prepared with controllable hydrophobicity and hydrophilicity. It demonstrated excellent aqueous compatibility and stability in aqueous mobile phase; compared to the traditional C18 column, improved peak shape of basic analytes was also obtained. Additionally, it exhibited both reversed-phase liquid chromatographic (RPLC) and hydrophilic interaction chromatographic (HILIC) performance; the analyte separation scope was thus enlarged, demonstrated by simultaneous separation of twenty acids, bases and neutrals. More interestingly, a novel on-line two-dimensional liquid chromatography on the single column (2D-LC-1C) was established by modifying the high performance liquid chromatographic instrument only with the addition of an extra six-port two-position valve. The early co-eluted components of the extract of Lonicera japonica on the 1st-dimension (RPLC) were collected for the online re-injection to the 2nd-dimension (HILIC) by conveniently varying the mobile phase components. Six more peaks were obtained. The established system was simple, easy operation and low cost, which had advantages in analyzing complicated samples. PMID:26320974

  17. Reversible hypogammaglobulinaemia.

    PubMed

    Desar, I M E; Weemaes, C M R; van Deuren, M; van der Meer, J W M

    2007-11-01

    In this report we present four patients with reversible hypogammaglobulinaemia who required immunoglobulin substitution for several years. One patient had documented systemic lupus erythematosus (SLE), the other three patients had primary hypogammaglobulinaemia without known cause. Whereas the cessation of azathioprine therapy may have contributed to the recovery in the patient with SLE, the restoration of the immunoglobulin production in the other three patients occurred spontaneously. All four patients were IgA deficient when the hypogammaglobulinaemia was first detected and remained so after IgM and IgG production had recovered. Two of the three patients who also had anti-IgA antibodies started to produce anti-IgA again after stopping the immunoglobulin substitution. We conclude that recovery of hypogammaglobulinaemia is possible but rare. When recovery is suspected, we recommend that immunoglobulin substitution is stopped and the antibody response to vaccination is tested. PMID:18057460

  18. Genetically engineered Pseudomonas: a factory of new bioplastics with broad applications.

    PubMed

    Olivera, E R; Carnicero, D; Jodra, R; Miñambres, B; García, B; Abraham, G A; Gallardo, A; Román, J S; García, J L; Naharro, G; Luengo, J M

    2001-10-01

    New bioplastics containing aromatic or mixtures of aliphatic and aromatic monomers have been obtained using genetically engineered strains of Pseudomonas putida. The mutation (-) or deletion (Delta) of some of the genes involved in the beta-oxidation pathway (fadA(-), fadB(-) Delta fadA or Delta fad BA mutants) elicits a strong intracellular accumulation of unusual homo- or co-polymers that dramatically alter the morphology of these bacteria, as more than 90% of the cytoplasm is occupied by these macromolecules. The introduction of a blockade in the beta-oxidation pathway, or in other related catabolic routes, has allowed the synthesis of polymers other than those accumulated in the wild type (with regard to both monomer size and relative percentage), the accumulation of certain intermediates that are rapidly catabolized in the wild type and the accumulation in the culture broths of end catabolites that, as in the case of phenylacetic acid, phenylbutyric acid, trans-cinnamic acid or their derivatives, have important medical or pharmaceutical applications (antitumoral, analgesic, radiopotentiators, chemopreventive or antihelmintic). Furthermore, using one of these polyesters (poly 3-hydroxy-6-phenylhexanoate), we obtained polymeric microspheres that could be used as drug vehicles. PMID:11722541

  19. Targeted Application of Human Genetic Variation Can Improve Red Blood Cell Production from Stem Cells.

    PubMed

    Giani, Felix C; Fiorini, Claudia; Wakabayashi, Aoi; Ludwig, Leif S; Salem, Rany M; Jobaliya, Chintan D; Regan, Stephanie N; Ulirsch, Jacob C; Liang, Ge; Steinberg-Shemer, Orna; Guo, Michael H; Esko, Tnu; Tong, Wei; Brugnara, Carlo; Hirschhorn, Joel N; Weiss, Mitchell J; Zon, Leonard I; Chou, Stella T; French, Deborah L; Musunuru, Kiran; Sankaran, Vijay G

    2016-01-01

    Multipotent and pluripotent stem cells are potential sources for cell and tissue replacement therapies. For example, stem cell-derived red blood cells (RBCs) are a potential alternative to donated blood, but yield and quality remain a challenge. Here, we show that application of insight from human population genetic studies can enhance RBC production from stem cells. The SH2B3 gene encodes a negative regulator of cytokine signaling and naturally occurring loss-of-function variants in this gene increase RBC counts invivo. Targeted suppression of SH2B3 in primary human hematopoietic stem and progenitor cells enhanced the maturation and overall yield of in-vitro-derived RBCs. Moreover, inactivation of SH2B3 by CRISPR/Cas9 genome editing in human pluripotent stem cells allowed enhanced erythroid cell expansion with preserved differentiation. Our findings therefore highlight the potential for combining human genome variation studies with genome editing approaches to improve cell and tissue production for regenerative medicine. PMID:26607381

  20. Genetic characterization of caffeine degradation by bacteria and its potential applications

    PubMed Central

    Summers, Ryan M; Mohanty, Sujit K; Gopishetty, Sridhar; Subramanian, Mani

    2015-01-01

    The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida?CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated. PMID:25678373

  1. Linear genetic programming application for successive-station monthly streamflow prediction

    NASA Astrophysics Data System (ADS)

    Danandeh Mehr, Ali; Kahya, Ercan; Yerdelen, Cahit

    2014-09-01

    In recent decades, artificial intelligence (AI) techniques have been pronounced as a branch of computer science to model wide range of hydrological phenomena. A number of researches have been still comparing these techniques in order to find more effective approaches in terms of accuracy and applicability. In this study, we examined the ability of linear genetic programming (LGP) technique to model successive-station monthly streamflow process, as an applied alternative for streamflow prediction. A comparative efficiency study between LGP and three different artificial neural network algorithms, namely feed forward back propagation (FFBP), generalized regression neural networks (GRNN), and radial basis function (RBF), has also been presented in this study. For this aim, firstly, we put forward six different successive-station monthly streamflow prediction scenarios subjected to training by LGP and FFBP using the field data recorded at two gauging stations on Çoruh River, Turkey. Based on Nash-Sutcliffe and root mean squared error measures, we then compared the efficiency of these techniques and selected the best prediction scenario. Eventually, GRNN and RBF algorithms were utilized to restructure the selected scenario and to compare with corresponding FFBP and LGP. Our results indicated the promising role of LGP for successive-station monthly streamflow prediction providing more accurate results than those of all the ANN algorithms. We found an explicit LGP-based expression evolved by only the basic arithmetic functions as the best prediction model for the river, which uses the records of the both target and upstream stations.

  2. Genetic characterization of caffeine degradation by bacteria and its potential applications.

    PubMed

    Summers, Ryan M; Mohanty, Sujit K; Gopishetty, Sridhar; Subramanian, Mani

    2015-05-01

    The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida?CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated. PMID:25678373

  3. Passive vibration control via unusual geometries: the application of genetic algorithm optimization to structural design

    NASA Astrophysics Data System (ADS)

    Keane, A. J.

    1995-08-01

    In the majority of aerospace structures, vibration transmission problems are dealt with by the application of heavy, viscoelastic damping materials. More recently, interest has focussed on using active vibration control methods to reduce noise transmission. This paper examines a third, and potentially much cheaper method: that of redesigning the load bearing structure so that it has intrinsic, passive noise filtration characteristics. It shows that very significant, broadband noise isolation characteristics (of around 60 dB over a 100 Hz band) can be achieved without compromising other aspects of the design. Here, the genetic algorithm (GA), which is one of a number of recently developed evolutionary computing methods, is employed to produce the desired designs. The problem is set up as one in multi-dimensional optimization where the geometric parameters of the design are the free variables and the band averaged noise transmission the objective function. The problem is then constrained by the need to maintain structural integrity. Set out in this way, even a simple structural problem has many tens of variables; a real structure would have many hundreds. Consequently, the optimization domain is very time consuming for traditional methods to deal with. This is where modern evolutionary techniques become so useful: their convergence rates are typically less rapidly worsened by increases in the number of variables than those of more traditional methods. Even so, they must be used with some care to gain the best results.

  4. CRISPR-Cas9 for medical genetic screens: applications and future perspectives.

    PubMed

    Xue, Hui-Ying; Ji, Li-Juan; Gao, Ai-Mei; Liu, Ping; He, Jing-Dong; Lu, Xiao-Jie

    2016-02-01

    CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) systems have emerged as versatile and convenient (epi)genome editing tools and have become an important player in medical genetic research. CRISPR-Cas9 and its variants such as catalytically inactivated Cas9 (dead Cas9, dCas9) and scaffold-incorporating single guide sgRNA (scRNA) have been applied in various genomic screen studies. CRISPR screens enable high-throughput interrogation of gene functions in health and diseases. Compared with conventional RNAi screens, CRISPR screens incur less off-target effects and are more versatile in that they can be used in multiple formats such as knockout, knockdown and activation screens, and can target coding and non-coding regions throughout the genome. This powerful screen platform holds the potential of revolutionising functional genomic studies in the near future. Herein, we introduce the mechanisms of (epi)genome editing mediated by CRISPR-Cas9 and its variants, introduce the procedures and applications of CRISPR screen in functional genomics, compare it with conventional screen tools and at last discuss current challenges and opportunities and propose future directions. PMID:26673779

  5. Application of pre-stack reverse time migration based on FWI velocity estimation to ground penetrating radar data

    NASA Astrophysics Data System (ADS)

    Liu, Sixin; Lei, Linlin; Fu, Lei; Wu, Junjun

    2014-08-01

    Reverse-time migration (RTM) is used for subsurface imaging to handle complex velocity models including steeply dipping interfaces and dramatic lateral variations and promises better imaging results compared to traditional migration method such as Kirchhoff migration algorithm. RTM has been increasingly used in seismic surveys for hydrocarbon resource explorations. Based on the similarity of kinematics and dynamics between electromagnetic wave and elastic wave, we develop pre-stack RTM method and apply it to process ground penetrating radar (GPR) data. Finite-difference time domain (FDTD) numerical method is used to simulate the electromagnetic wave propagation including forward and backward extrapolations, the cross-correlation imaging condition is used to obtain the final image. In order to provide a velocity model with relatively higher accuracy as the initial velocity model for RTM, we apply a full waveform inversion (FWI) in time domain to estimate the subsurface velocity structure based on reflection radar data. For testing the effectiveness of the algorithm, we have constructed a complex geological model, common-offset radar data and common-shot profile (CSP) radar reflection data are synthesized. All data are migrated with traditional Kirchhoff migration method and pre-stack RTM method separately, the migration results from pre-stack RTM show better coincidence with the true model. Furthermore, we have performed a physical experiment in a sandbox where a polyvinyl chloride (PVC) box is buried in the sand, the obtained common-offset radar data and common-shot radar data are migrated by using Kirchhoff migration method and pre-stack RTM algorithm separately, the pre-stack RTM result shows that RTM algorithm could get better imaging results.

  6. High capacity, reversible alloying reactions in SnSb/C nanocomposites for Na-ion battery applications

    SciTech Connect

    Xiao, Lifen; Cao, Yuliang; Xiao, Jie; Wang, Wei; Kovarik, Libor; Nie, Zimin; Liu, Jun

    2012-04-04

    A new SnSb/C nanocomposite based on Na alloying reactions is demonstrated as anode for Na-ion battery applications. The electrode can achieve an exceptionally high capacity (544 mA h g?1, almost double that of intercalation carbon materials), good rate capacity and cyclability (80% capacity retention over 50 cycles) for Na-ion storage.

  7. Ternary Cu2SnS3 cabbage-like nanostructures: large-scale synthesis and their application in Li-ion batteries with superior reversible capacity

    NASA Astrophysics Data System (ADS)

    Qu, Baihua; Li, Hongxing; Zhang, Ming; Mei, Lin; Chen, Libao; Wang, Yanguo; Li, Qiuhong; Wang, Taihong

    2011-10-01

    In this paper, novel ternary Cu2SnS3 cabbage-like nanostructures are synthesized on a large scale via a facile solvothermal route. The individual Cu2SnS3 cabbage-like hierarchitecture is constructed from 2D nanosheets with thickness of about 15.6 nm. The Cu2SnS3 electrodes exhibit an initial reversible capacity of 842 mAh g-1 and still reach 621 mAh g-1 after 50 cycles. Such an admirable performance could be related to their 3D porous structural features as well as the high electrical conductivity induced by Cu. The electrochemical properties of the 3D hierarchical nanostructures imply its potential application in high energy density Li-ion batteries.

  8. Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map

    PubMed Central

    Wang, Wei; Chen, Bingzhi; Zhang, Lei; Yan, Junjie; Lu, Yuanping; Zhang, Xiaoyin; Jiang, Yuji; Wu, Taju; van Peer, Arend Frans; Li, Shaojie; Xie, Baogui

    2015-01-01

    Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi. PMID:26204838

  9. Genetic algorithm based input selection for a neural network function approximator with applications to SSME health monitoring

    NASA Technical Reports Server (NTRS)

    Peck, Charles C.; Dhawan, Atam P.; Meyer, Claudia M.

    1991-01-01

    A genetic algorithm is used to select the inputs to a neural network function approximator. In the application considered, modeling critical parameters of the space shuttle main engine (SSME), the functional relationship between measured parameters is unknown and complex. Furthermore, the number of possible input parameters is quite large. Many approaches have been used for input selection, but they are either subjective or do not consider the complex multivariate relationships between parameters. Due to the optimization and space searching capabilities of genetic algorithms they were employed to systematize the input selection process. The results suggest that the genetic algorithm can generate parameter lists of high quality without the explicit use of problem domain knowledge. Suggestions for improving the performance of the input selection process are also provided.

  10. Application of Long-Range and Binding Reverse Transcription-Quantitative PCR To Indicate the Viral Integrities of Noroviruses

    PubMed Central

    De Keuckelaere, Ann; Uyttendaele, Mieke

    2014-01-01

    This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm2, no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles. PMID:25107982

  11. Genetic analysis without replications: Model evaluation and application in spring wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic data collected from plant breeding and genetic studies may not be replicated in field designs even though field variation is present. In this study, we addressed this problem using spring wheat (Triticum eastivum L.) trial data collected from two locations. There were no intra-location repl...

  12. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    ERIC Educational Resources Information Center

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  13. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    ERIC Educational Resources Information Center

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques

  14. Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications

    NASA Astrophysics Data System (ADS)

    Aria, Adrianus Indrat

    In this thesis, dry chemical modification methods involving UV/ozone, oxygen plasma, and vacuum annealing treatments are explored to precisely control the wettability of CNT arrays. The effect of oxidation using UV/ozone and oxygen plasma treatments is highly reversible as long as the O/C ratio of the CNT arrays is kept below 18%. At O/C ratios higher than 18%, the effect of oxidation is no longer reversible. This irreversible oxidation is caused by irreversible changes to the CNT atomic structure during the oxidation process. During the oxidation process, CNT arrays undergo three different processes. For CNT arrays with O/C ratios lower than 40%, the oxidation process results in the functionalization of CNT outer walls by oxygenated groups. Although this functionalization process introduces defects, vacancies and micropores opening, the graphitic structure of the CNT is still largely intact. For CNT arrays with O/C ratios between 40% and 45%, the oxidation process results in the etching of CNT outer walls. This etching process introduces large scale defects and holes that can be obviously seen under TEM at high magnification. Most of these holes are found to be several layers deep and, in some cases, a large portion of the CNT side walls are cut open. For CNT arrays with O/C ratios higher than 45%, the oxidation process results in the exfoliation of the CNT walls and amorphization of the remaining CNT structure. This amorphization process can be implied from the disappearance of C-C sp2 peak in the XPS spectra associated with the pi-bond network. The impact behavior of water droplet impinging on superhydrophobic CNT arrays in a low viscosity regime is investigated for the first time. Here, the experimental data are presented in the form of several important impact behavior characteristics including critical Weber number, volume ratio, restitution coefficient, and maximum spreading diameter. As observed experimentally, three different impact regimes are identified while another impact regime is proposed. These regimes are partitioned by three critical Weber numbers, two of which are experimentally observed. The volume ratio between the primary and the secondary droplets is found to decrease with the increase of Weber number in all impact regimes other than the first one. In the first impact regime, this is found to be independent of Weber number since the droplet remains intact during and subsequent to the impingement. Experimental data show that the coefficient of restitution decreases with the increase of Weber number in all impact regimes. The rate of decrease of the coefficient of restitution in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Experimental data also show that the maximum spreading factor increases with the increase of Weber number in all impact regimes. The rate of increase of the maximum spreading factor in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Phenomenological approximations and interpretations of the experimental data, as well as brief comparisons to the previously proposed scaling laws, are shown here. Dry oxidation methods are used for the first time to characterize the influence of oxidation on the capacitive behavior of CNT array EDLCs. The capacitive behavior of CNT array EDLCs can be tailored by varying their oxygen content, represented by their O/C ratio. The specific capacitance of these CNT arrays increases with the increase of their oxygen content in both KOH and Et4NBF4/PC electrolytes. As a result, their gravimetric energy density increases with the increase of their oxygen content. However, their gravimetric power density decreases with the increase of their oxygen content. The optimally oxidized CNT arrays are able to withstand more than 35,000 charge/discharge cycles in Et4NBF4/PC at a current density of 5 A/g while only losing 10% of their original capacitance. (Abstract shortened by UMI.)

  15. Genetic Aberrations in Childhood Acute Lymphoblastic Leukaemia: Application of High-Density Single Nucleotide Polymorphism Array

    PubMed Central

    Sulong, Sarina

    2010-01-01

    Screening of the entire human genome using high-density single nucleotide polymorphism array (SNPA) has become a powerful technique used in cancer genetics and population genetics studies. The GeneChip Mapping Array, introduced by Affymetrix, is one SNPA platform utilised for genotyping studies. This GeneChip system allows researchers to gain a comprehensive view of cancer biology on a single platform for the quantification of chromosomal amplifications, deletions, and loss of heterozygosity or for allelic imbalance studies. Importantly, this array analysis has the potential to reveal novel genetic findings involved in the multistep development of cancer. Given the importance of genetic factors in leukaemogenesis and the usefulness of screening the whole genome, SNPA analysis has been utilised in many studies to characterise genetic aberrations in childhood acute lymphoblastic leukaemia. PMID:22135543

  16. K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

    PubMed Central

    Wen, Jia; Chan, Raymond H.; Yau, Shek-Chung; He, Rong L.; Yau, Stephen S. T.

    2014-01-01

    Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency. PMID:24858075

  17. Reversible simulation of irreversible computation

    NASA Astrophysics Data System (ADS)

    Li, Ming; Tromp, John; Vitnyi, Paul

    1998-09-01

    Computer computations are generally irreversible while the laws of physics are reversible. This mismatch is penalized by among other things generating excess thermic entropy in the computation. Computing performance has improved to the extent that efficiency degrades unless all algorithms are executed reversibly, for example by a universal reversible simulation of irreversible computations. All known reversible simulations are either space hungry or time hungry. The leanest method was proposed by Bennett and can be analyzed using a simple reversible pebble game. The reachable reversible simulation instantaneous descriptions (pebble configurations) of such pebble games are characterized completely. As a corollary we obtain the reversible simulation by Bennett and, moreover, show that it is a space-optimal pebble game. We also introduce irreversible steps and give a theorem on the tradeoff between the number of allowed irreversible steps and the memory gain in the pebble game. In this resource-bounded setting the limited erasing needs to be performed at precise instants during the simulation. The reversible simulation can be modified so that it is applicable also when the simulated computation time is unknown.

  18. An application of LOH analysis for detecting the genetic influences of space environmental radiation

    NASA Astrophysics Data System (ADS)

    Yatagai, F.; Umebayashi, Y.; Honma, M.; Abe, T.; Suzuki, H.; Shimazu, T.; Ishioka, N.; Iwaki, M.

    To detect the genetic influence of space environmental radiation at the chromosome level we proposed an application of loss of heterozygosity LOH analysis system for the mutations induced in human lymphoblastoid TK6 cells Surprisingly we succeeded the mutation detection in the frozen dells which were exposed to a low-dose 10 cGy of carbon-ion beam irradiation Mutation assays were performed within a few days or after about one month preservation at --80 r C following irradiation The results showed an increase in mutation frequency at the thymidine kinase TK gene locus 1 6-fold 2 5 X 10 -6 to 3 9 X 10 -6 and 2 1-fold 2 5 X 10 -6 to 5 3 X 10 -6 respectively Although the relative distributions of mutation classes were not changed by the radiation exposure in either assay an interesting characteristic was detected using this LOH analysis system two TK locus markers and eleven microsatellite loci spanning chromosome 17 The radiation-specific patterns of interstitial deletions were observed in the hemizygous LOH mutants which were considered as a result of end-joining repair of carbon ion-induced DNA double-strand breaks These results clearly demonstrate that this analysis can be used for the detection of low-dose ionizing radiation effects in the frozen cells In addition we performed so called adaptive response experiments in which TK6 cells were pre-irradiated with low-dose 2 5 sim 10 cGy of X-ray and then exposed to challenging dose 2Gy of X-rays Interestingly the

  19. Integrative Bayesian analysis of neuroimaging-genetic data with application to cocaine dependence.

    PubMed

    Azadeh, Shabnam; Hobbs, Brian P; Ma, Liangsuo; Nielsen, David A; Moeller, F Gerard; Baladandayuthapani, Veerabhadran

    2016-01-15

    Neuroimaging and genetic studies provide distinct and complementary information about the structural and biological aspects of a disease. Integrating the two sources of data facilitates the investigation of the links between genetic variability and brain mechanisms among different individuals for various medical disorders. This article presents a general statistical framework for integrative Bayesian analysis of neuroimaging-genetic (iBANG) data, which is motivated by a neuroimaging-genetic study in cocaine dependence. Statistical inference necessitated the integration of spatially dependent voxel-level measurements with various patient-level genetic and demographic characteristics under an appropriate probability model to account for the multiple inherent sources of variation. Our framework uses Bayesian model averaging to integrate genetic information into the analysis of voxel-wise neuroimaging data, accounting for spatial correlations in the voxels. Using multiplicity controls based on the false discovery rate, we delineate voxels associated with genetic and demographic features that may impact diffusion as measured by fractional anisotropy (FA) obtained from DTI images. We demonstrate the benefits of accounting for model uncertainties in both model fit and prediction. Our results suggest that cocaine consumption is associated with FA reduction in most white matter regions of interest in the brain. Additionally, gene polymorphisms associated with GABAergic, serotonergic and dopaminergic neurotransmitters and receptors were associated with FA. PMID:26484829

  20. Fast and sensitive method to determine parabens by capillary electrophoresis using automatic reverse electrode polarity stacking mode: application to hair samples.

    PubMed

    Sako, Alysson V F; Dolzan, Maressa D; Micke, Gustavo Amadeu

    2015-09-01

    This paper describes a fast and sensitive method for the determination of methyl, ethyl, propyl, and butylparaben in hair samples by capillary electrophoresis using automatic reverse electrode polarity stacking mode. In the proposed method, solutions are injected using the flush command of the analysis software (940mbar) and the polarity switching is carried out automatically immediately after the sample injection. The advantages compared with conventional stacking methods are the increased analytical frequency, repeatability, and inter-day precision. All analyses were performed in a fused silica capillary (50cm, 41.5cm in effective length, 50?m i.d.), and the background electrolyte was composed of 20mmolL(-1) sodium tetraborate in 10% of methanol, pH 9.3. For the reverse polarity, -25kV/35s was applied followed by application of +30kV for the electrophoretic run. Temperature was set at 20C, and all analytes were monitored at 297nm. The method showed acceptable linearity (r (2)?>?0.997) in the studied range of 0.1-5.0mgL(-1), limits of detection below 0.017mgL(-1), and inter-day, intra-day, and instrumental precision better than 6.2, 3.6, and 4.6%, respectively. Considering parabens is widely used as a preservative in many products and the reported possibility of damage to the hair and also to human health caused by these compounds, the proposed method was applied to evaluate the adsorption of parabens in hair samples. The results indicate that there is a greater adsorption of methylparaben compared to the other parabens tested and also dyed hairs had a greater adsorption capacity for parabens than natural hairs. PMID:26168974

  1. Isolobal analogies in intermetallics: the reversed approximation MO approach and applications to CrGa4- and Ir3Ge7-type phases.

    PubMed

    Yannello, Vincent J; Kilduff, Brandon J; Fredrickson, Daniel C

    2014-03-01

    Intermetallic phases offer a wealth of unique and unexplained structural features, which pose exciting challenges for the development of new bonding concepts. In this article, we present a straightforward approach to rapidly building bonding descriptions of such compounds: the reversed approximation Molecular Orbital (raMO) method. In this approach, we reverse the usual technique of using linear combinations of simple functions to approximate true wave functions and employ the fully occupied crystal orbitals of a compound as a basis set for the determination of the eigenfunctions of a simple, chemically transparent model Hamiltonian. The solutions fall into two sets: (1) a series of functions representing the best-possible approximations to the model system's eigenstates constructible from the occupied crystal orbitals and (2) a second series of functions that are orthogonal to the bonding picture represented by the model Hamiltonian. The electronic structure of a compound is thus quickly resolved into a series of orthogonal bonding subsystems. We first demonstrate the raMO analysis on a familiar molecule, 1,3-butadiene, and then move to illustrating its use in discovering new bonding phenomena through applications to three intermetallic phases: the PtHg4-type CrGa4 and the Ir3Ge7-type compounds Os3Sn7 and Ir3Sn7. For CrGa4, a density of states (DOS) minimum coinciding with its Fermi energy is traced to 18-electron configurations on the Cr atoms. For Os3Sn7 and Ir3Sn7, 18-electron configurations also underlie DOS pseudogaps. This time, however, the 18-electron counts involve multicenter interactions isolobal with classical Ir-Ir or Os-Os covalent bonds, as well as Sn-Sn single bonds serving as electron reservoirs. Our results are based on DFT-calibrated Hckel calculations, but in principle the raMO analysis can be implemented in any method employing one-electron wave functions. PMID:24555770

  2. Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis).

    PubMed

    Ong, P W; Maizura, I; Abdullah, N A P; Rafii, M Y; Ooi, L C L; Low, E T L; Singh, R

    2015-01-01

    The genetic evaluation of oil palm germplasm collections is required for insight into the variability among populations. The information obtained is also useful for incorporating new genetic materials into current breeding programs. Single nucleotide polymorphisms (SNPs) have been widely used in many plant genetic studies due to the availability of large numbers of genomic sequences and expressed sequence tags. The present study examined 219 oil palms collected from two natural Angolan populations, a few hundred kilometers apart. A total of 62 SNPs were designed from oil palm genomic sequences and converted to cleaved amplified polymorphic sequence (CAPS). Of these, nine were found to be informative across the two populations. The nine informative SNPs revealed mean major allele frequency of 0.693. The average expected and observed heterozygosities were 0.398 and 0.400, respectively. The mean polymorphism information content was 0.315 (ranging between 0.223 and 0.375). None of the loci deviated from Hardy-Weinberg equilibrium and no rare alleles were detected. In cluster analysis using unweighted pair group method with arithmetic, the 219 oil palms fell into two clusters. This was further supported by the population structure analysis result (K = 2), suggesting that the samples were divided into two main genetic groups. However, the two groups did not coincide with the geographic populations. Analysis of molecular variance indicated that within-population variation contributed 93% of the total genetic variation. This study showed that SNP-based CAPS markers are useful for studying the genetic diversity of oil palm and have potential application for marker-trait association studies. PMID:26505369

  3. An Application of Computer Simulation to the Teaching of Genetics in the Upper Secondary School

    ERIC Educational Resources Information Center

    Dean, P. G.; Murphy, P. J.

    1973-01-01

    Describes an exercise in which senior high school biology students used a computer to simulate genetic mapping. The exercise was designed to enhance the students' grasp of the concepts of linkage and crossing-over. (JR)

  4. Application of a multiple-trait, multiple-country genetic evaluation model for female fertility traits.

    PubMed

    Nilforooshan, M A; Jakobsen, J H; Fikse, W F; Berglund, B; Jorjani, H

    2010-12-01

    The need to implement a method that can handle multiple traits per country in international genetic evaluations is evident. Today, many countries have implemented multiple-trait national genetic evaluations and they may expect to have their traits simultaneously analyzed in international genetic evaluations. Traits from the same country are residually correlated and the method currently in use, single-trait multiple across-country evaluation (ST-MACE), cannot handle nonzero residual correlations. Therefore, multiple-trait, multiple across-country evaluation (MT-MACE) was proposed to handle several traits from the same country simultaneously. To test the robustness of MT-MACE on real data, female fertility was chosen as a complex trait with low heritability. Data from 7 Holstein populations, 3 with 2 traits and 4 with 1 trait, were used. The differences in the estimated genetic correlations by MT-MACE and the single ST-MACE analysis (average absolute deviation of 0.064) were due to the bias of considering several traits from the same country in the ST-MACE analysis. However, the differences between the estimated genetic correlations by MT-MACE and multiple ST-MACE analyses avoiding more than one trait per country in each analysis (average absolute deviation of 0.066) were due to the lack of analysis of the correlated traits from the same country together and using the reported within-country genetic correlations. Applying MT-MACE resulted in reliability gain in international genetic evaluations, which was different from trait to trait and from bull to bull. The average reliability gain by MT-MACE over ST-MACE was 3.0 points for domestic bulls and 6.3 points for foreign bulls. Even countries with 1 trait benefited from the joint analysis of traits from the 2-trait countries. Another superiority of MT-MACE over ST-MACE is that the bulls that do not have national genetic evaluation for some traits from multiple trait countries will receive international genetic evaluations for those traits. Rank correlations were high between ST-MACE and MT-MACE when considering all bulls. However, the situation was different for the top 100 bulls. Simultaneous analysis of traits from the same country affected bull ranks, especially for top 100 bulls. Multi-trait MACE is a recommendable and robust method for international genetic evaluations and is appropriate for handling multiple traits per country, which can increase the reliability of international genetic evaluations. PMID:21094772

  5. New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications.

    PubMed

    Fekete, Szabolcs; Veuthey, Jean-Luc; Guillarme, Davy

    2012-10-01

    In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 ?m particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources. PMID:22475515

  6. Reverse engineering molecular hypergraphs.

    PubMed

    Rahman, Ahsanur; Poirel, Christopher L; Badger, David J; Estep, Craig; Murali, T M

    2013-01-01

    Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multiway interactions among molecules, which occur very often within cells. Hypergraphs may be better representations for networks having such interactions, since hyperedges can naturally represent relationships among multiple molecules. Here, we propose using hypergraphs to capture the uncertainty inherent in reverse engineering gene-gene networks. Some subsets of nodes may induce highly varying subgraphs across an ensemble of networks inferred by a reverse engineering algorithm. We provide a novel formulation of hyperedges to capture this uncertainty in network topology. We propose a clustering-based approach to discover hyperedges. We show that our approach can recover hyperedges planted in synthetic data sets with high precision and recall, even for moderate amount of noise. We apply our techniques to a data set of pathways inferred from genetic interaction data in S. cerevisiae related to the unfolded protein response. Our approach discovers several hyperedges that capture the uncertain connectivity of genes in relevant protein complexes, suggesting that further experiments may be required to precisely discern their interaction patterns. We also show that these complexes are not discovered by an algorithm that computes frequent and dense subgraphs. PMID:24384702

  7. Reverse Engineering Molecular Hypergraphs

    PubMed Central

    Rahman, Ahsanur; Poirel, Christopher L.; Badger, David J.; Estep, Craig; Murali, T.M.

    2014-01-01

    Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multiway interactions among molecules, which occur very often within cells. Hypergraphs may be better representations for networks having such interactions, since hyperedges can naturally represent relationships among multiple molecules. Here, we propose using hypergraphs to capture the uncertainty inherent in reverse engineering gene-gene networks. Some subsets of nodes may induce highly varying subgraphs across an ensemble of networks inferred by a reverse engineering algorithm. We provide a novel formulation of hyperedges to capture this uncertainty in network topology. We propose a clustering-based approach to discover hyperedges. We show that our approach can recover hyperedges planted in synthetic data sets with high precision and recall, even for moderate amount of noise. We apply our techniques to a data set of pathways inferred from genetic interaction data in S. cerevisiae related to the unfolded protein response. Our approach discovers several hyperedges that capture the uncertain connectivity of genes in relevant protein complexes, suggesting that further experiments may be required to precisely discern their interaction patterns. We also show that these complexes are not discovered by an algorithm that computes frequent and dense subgraphs. PMID:24384702

  8. Analysis of Genetic Variation and Potential Applications in Genome-Scale Metabolic Modeling

    PubMed Central

    Cardoso, João G. R.; Andersen, Mikael Rørdam; Herrgård, Markus J.; Sonnenschein, Nikolaus

    2015-01-01

    Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic variation during a long term production process may lead to significant economic losses and it is important to understand how to control this type of variation. With the emergence of next-generation sequencing technologies, genetic variation in microbial strains can now be determined on an unprecedented scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular phenotypes. PMID:25763369

  9. [Novel methods and their applicability in the evaluation of the genetic background of endocrine system tumours].

    PubMed

    Patcs, Attila; Lik, Istvn; Butz, Henriett; Baghy, Kornlia; Rcz, Kroly

    2015-12-20

    The technical developments leading to revolution in clinical genetic testing offer new approaches for patients with cancer. From one mutation or one gene approach the scale of genetic testing moved to whole exome or whole genome scale. It is well known that many tumours are genetically determined and they are part of familial tumour syndromes. In addition, some mutations indicate specific molecular targeted therapies. Although sampling and sample preparation are different for testing germline and somatic mutations, the technical background of the analysis is the same. The aim of clinical genetic testing is to identify patients who are carriers of disease-causing mutations or to test tumour tissue for the presence of genetic alterations which may be targets for therapeutic approaches. In this review the authors summarize novel possibilities offered by next-generation sequencing in clinical genetic testing of patients with endocrine tumours. In addition, the authors review recent guidelines on technical and ethical issues related to these novel methods. PMID:26654542

  10. Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)

    PubMed Central

    Holtgrwe, Daniela; Srensen, Thomas Rosleff; Viehver, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

    2014-01-01

    Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

  11. Novel Design for Reversible Arithmetic Logic Unit

    NASA Astrophysics Data System (ADS)

    Zhou, Rigui; Li, Yancheng; Zhang, Manqun; Hu, BenQiong

    2015-02-01

    Reversible logic circuits are of high interests to calculate with minimum energy consumption having applications in low-power CMOS design, optical computing and nanotechnology, especially in quantum computer. Quantum computer requires quantum arithmetic. A new design of a reversible arithmetic logic unit (reversible ALU) for quantum arithmetic has been proposed in this article. As we known, ALU is an important part of central processing unit (CPU) as the execution unit. So this article provides explicit construction of reversible ALU effecting basic arithmetic operations. By provided the corresponding control unit, the proposed reversible ALU can combine the classical arithmetic and logic operation in a reversible integrated system. This article provides a new more powerful ALU which contains more functions and it will make contribute to the realization of reversible Programmable Logic Device (RPLD) in future using reversible ALU.

  12. Application of integrated genetic monitoring: the optimal approach for detecting environmental carcinogens.

    PubMed Central

    Legator, M S; Au, W W

    1994-01-01

    Short-term in vitro genetic toxicity assays have not fulfilled their anticipated role in predicting the carcinogenicity of environmental agents reliably and economically. A reduction in emphasis from nonanimal systems to relevant animal assays and population monitoring will help to reestablish the credibility of this field. An analysis of the various steps in the carcinogenic process indicates the biological responses occurring during these stages can be utilized for early detection of environmental carcinogens. Emphasis should be placed on using the earliest significant response that indicates genetic damage (e.g., gene mutations and chromosome alterations). Assays that detect pregenomic damage (e.g., adduct formation), without evidence of subsequent heritable genetic alterations, may produce misleading results for risk assessment and should not be considered as stand-alone monitoring procedures. Late biological responses may occur in tissues or organs where genetic damage may be difficult to measure, and the opportunity for intervention diminishes as we approach the clinical outcome. For example, analyzing localized cells that contain activated protooncogenes and inactivated tumor suppressor genes, although they further document adverse response from exposure to carcinogens, may be of greater value for indicating clinical outcome than for genetic monitoring. With few notable exceptions, the window of opportunity for genetic monitoring is the period after exposure where genetic damage is evident and where circulating lymphocytes can faithfully record this damage. An ongoing study of butadiene-exposed workers illustrates an optimum protocol, where multiple assays can be carried out and correlated with both external and internal measurements of exposure.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7698074

  13. Reversible DNA compaction.

    PubMed

    Gonzlez-Prez, Alfredo

    2014-01-01

    In this review we summarize and discuss the different methods we can use to achieve reversible DNA compaction in vitro. Reversible DNA compaction is a natural process that occurs in living cells and viruses. As a result these process long sequences of DNA can be concentrated in a small volume (compacted) to be decompacted only when the information carried by the DNA is needed. In the current work we review the main artificial compacting agents looking at their suitability for decompaction. The different approaches used for decompaction are strongly influenced by the nature of the compacting agent that determines the mechanism of compaction. We focus our discussion on two main artificial compacting agents: multivalent cations and cationic surfactants that are the best known compacting agents. The reversibility of the process can be achieved by adding chemicals like divalent cations, alcohols, anionic surfactants, cyclodextrins or by changing the chemical nature of the compacting agents via pH modifications, light induced conformation changes or by redox-reactions. We stress the relevance of electrostatic interactions and self-assembly as a main approach in order to tune up the DNA conformation in order to create an on-off switch allowing a transition between coil and compact states. The recent advances to control DNA conformation in vitro, by means of molecular self-assembly, result in a better understanding of the fundamental aspects involved in the DNA behavior in vivo and serve of invaluable inspiration for the development of potential biomedical applications. PMID:24444152

  14. Quantitative determination of casein genetic variants in goat milk: Application in Girgentana dairy goat breed.

    PubMed

    Montalbano, Maria; Segreto, Roberta; Di Gerlando, Rosalia; Mastrangelo, Salvatore; Sardina, Maria Teresa

    2016-02-01

    The study was conducted to develop a high-performance liquid chromatographic (HPLC) method to quantify casein genetic variants (?s2-, ?-, and ?-casein) in milk of homozygous individuals of Girgentana goat breed. For calibration experiments, pure genetic variants were extracted from individual milk samples of animals with known genotypes. The described HPLC approach was precise, accurate and highly suitable for quantification of goat casein genetic variants of homozygous individuals. The amount of each casein per allele was: ?s2-casein A = 2.9 0.8 g/L and F = 1.8 0.4 g/L; ?-casein C = 3.0 0.8 g/L and C1 = 2.0 0.7 g/L and ?-casein A = 1.6 0.3 g/L and B = 1.1 0.2 g/L. A good correlation was found between the quantities of ?s2-casein genetic variants A and F, and ?-casein C and C1 with other previously described method. The main important result was obtained for ?-casein because, till now, no data were available on quantification of single genetic variants for this protein. PMID:26304408

  15. Applications

    NASA Astrophysics Data System (ADS)

    Stern, Arthur M.

    1986-07-01

    Economic incentives have spurred numerous applications of genetically engineered organisms in manufacture of pharmaceuticals and industrial chemicals. These successes, involving a variety of methods of genetic manipulation, have dispelled early fears that genetic engineering could not be handled safely, even in the laboratory. Consequently, the potential for applications in the wider environment without physical containment is being considered for agriculture, mining, pollution control, and pest control. These proposed applications range from modest extensions of current plant breeding techniques for new disease-resistant species to radical combinations of organisms (for example, nitrogen-fixing corn plants). These applications raise concerns about potential ecological impacts (see chapter 5), largely because of adverse experiences with both deliberate and inadvertent introductions of nonindigenous species.

  16. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora

    PubMed Central

    Chen, Yongmei; Hou, Yansong; Guo, Zixiao; Wang, Wenqing; Zhong, Cairong; Zhou, Renchao; Shi, Suhua

    2015-01-01

    The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I) reconstruct the phylogeny, (II) examine the genetic structure and (III) identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP) region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches. PMID:26674070

  17. Characterization of Reverse Genetics-Derived Cold-Adapted Master Donor Virus A/Leningrad/134/17/57 (H2N2) and Reassortants with H5N1 Surface Genes in a Mouse Model

    PubMed Central

    Isakova-Sivak, Irina; Chen, Li-Mei; Bourgeois, Melissa; Matsuoka, Yumiko; Voeten, J. Theo M.; Heldens, Jacco G. M.; van den Bosch, Han; Klimov, Alexander; Rudenko, Larisa; Cox, Nancy J.

    2014-01-01

    Live attenuated influenza vaccines (LAIV) offer significant advantages over subunit or split inactivated vaccines to mitigate an eventual influenza pandemic, including simpler manufacturing processes and more cross-protective immune responses. Using an established reverse genetics (rg) system for wild-type (wt) A/Leningrad/134/1957 and cold-adapted (ca) A/Leningrad/134/17/1957 (Len17) master donor virus (MDV), we produced and characterized three rg H5N1 reassortant viruses carrying modified HA and intact NA genes from either A/Vietnam/1203/2004 (H5N1, VN1203, clade 1) or A/Egypt/321/2007 (H5N1, EG321, clade 2) virus. A mouse model of infection was used to determine the infectivity and tissue tropism of the parental wt viruses compared to the ca master donor viruses as well as the H5N1 reassortants. All ca viruses showed reduced replication in lungs and enhanced replication in nasal epithelium. In addition, the H5N1 HA and NA enhanced replication in lungs unless it was restricted by the internal genes of the ca MDV. Mice inoculated twice 4 weeks apart with the H5N1 reassortant LAIV candidate viruses developed serum hemagglutination inhibition HI and IgA antibody titers to the homologous and heterologous viruses consistent with protective immunity. These animals remained healthy after challenge inoculation with a lethal dose with homologous or heterologous wt H5N1 highly pathogenic avian influenza (HPAI) viruses. The profiles of viral replication in respiratory tissues and the immunogenicity and protective efficacy characteristics of the two ca H5N1 candidate LAIV viruses warrant further development into a vaccine for human use. PMID:24648485

  18. Genetic Engineering of Mesenchymal Stem Cells and Its Application in Human Disease Therapy

    PubMed Central

    Hodgkinson, Conrad P.; Gomez, José A.; Mirotsou, Maria

    2010-01-01

    Abstract The use of stem cells for tissue regeneration and repair is advancing both at the bench and bedside. Stem cells isolated from bone marrow are currently being tested for their therapeutic potential in a variety of clinical conditions including cardiovascular injury, kidney failure, cancer, and neurological and bone disorders. Despite the advantages, stem cell therapy is still limited by low survival, engraftment, and homing to damage area as well as inefficiencies in differentiating into fully functional tissues. Genetic engineering of mesenchymal stem cells is being explored as a means to circumvent some of these problems. This review presents the current understanding of the use of genetically engineered mesenchymal stem cells in human disease therapy with emphasis on genetic modifications aimed to improve survival, homing, angiogenesis, and heart function after myocardial infarction. Advancements in other disease areas are also discussed. PMID:20825283

  19. Ant Colony Optimization with Genetic Operation and Its Application to Traveling Salesman Problem

    NASA Astrophysics Data System (ADS)

    Wang, Rong-Long; Zhou, Xiao-Fan; Okazaki, Kozo

    Ant colony optimization (ACO) algorithms are a recently developed, population-based approach which has been successfully applied to optimization problems. However, in the ACO algorithms it is difficult to adjust the balance between intensification and diversification and thus the performance is not always very well. In this work, we propose an improved ACO algorithm in which some of ants can evolve by performing genetic operation, and the balance between intensification and diversification can be adjusted by numbers of ants which perform genetic operation. The proposed algorithm is tested by simulating the Traveling Salesman Problem (TSP). Experimental studies show that the proposed ACO algorithm with genetic operation has superior performance when compared to other existing ACO algorithms.

  20. Clinical genetic testing for male factor infertility: current applications and future directions.

    PubMed

    Hotaling, J; Carrell, D T

    2014-05-01

    Spermatogenesis involves the aggregated action of up to 2300 genes, any of which, could, potentially, provide targets for diagnostic tests of male factor infertility. Contrary to the previously proposed common variant hypothesis for common diseases such as male infertility, genome-wide association studies and targeted gene sequencing in cohorts of infertile men have identified only a few gene polymorphisms that are associated with male infertility. Unfortunately, the search for genetic variants associated with male infertility is further hampered by the lack of viable animal models of human spermatogenesis, difficulty in robustly phenotyping infertile men and the complexity of pedigree studies in male factor infertility. In this review, we describe basic genetic principles involved in understanding the genetic basis of male infertility and examine the utility and proper clinical use of the proven genetic assays of male factor infertility, specifically Y chromosome microdeletions, chromosomal translocations, karyotype, cystic fibrosis transmembrane conductance regulator mutation analysis and sperm genetic tests. Unfortunately, these tests are only able to diagnose the cause of about 20% of male factor infertility. The remainder of the review will be devoted to examining novel tests and diagnostic tools that have the potential to explain the other 80% of male factor infertility that is currently classified as idiopathic. Those tests include epigenetic analysis of the spermatozoa and the evaluation of rare genetic variants and copy number variations in patients. Success in advancing to the implementation of such areas is not only dependent on technological advances in the laboratory, but also improved phenotyping in the clinic. PMID:24711280

  1. Reversible ion exchange and structural stability of garnet-type Nb-doped Li7La3Zr2O12 in water for applications in lithium batteries

    NASA Astrophysics Data System (ADS)

    Liu, Cai; Rui, Kun; Shen, Chen; Badding, Michael E.; Zhang, Gaoxiao; Wen, Zhaoyin

    2015-05-01

    H+/Li+ ion exchange and structural stability of the high ionic conductivity Nb-doped Zr-garnet Li6.75La3Nb0.25Zr1.75O12 (LLNZO) are investigated in this study. Relationships between ion exchange and Li-population per unit cell, which are necessary to establish the practical framework of garnet electrolytes, are deduced for garnet oxides within ion-exchange process. H+/Li+ ion exchange of cubic LLNZO powder is performed continuously in distilled water and products with various exchange levels are obtained via this simple method. FTIR spectra show the evolution of H-O bonding through the ion-exchange process. A maximum of 74.8% exchange of Li+ by H+ was found, consistent with a preferential replacement of octahedrally coordinated Li. The cubic garnet phase is maintained throughout all levels of proton exchange observed. The formation of garnet-type solid solution of Li6.75-xHxLa3Nb0.25Zr1.75O12 is indicated by well-resolved lattice fringes as well as the linear evolution of crystal lattice parameters with the ion exchange level. The reverse ion exchange of H+ by Li+ is successfully achieved in Li+ containing aqueous solutions, demonstrating its high structural stability and good compatibility for promising applications in lithium batteries.

  2. Preparation, characterization and application of a reversed phase liquid chromatography/hydrophilic interaction chromatography mixed-mode C18-DTT stationary phase.

    PubMed

    Wang, Qing; Long, Yao; Yao, Lin; Xu, Li; Shi, Zhi-Guo; Xu, Lanying

    2016-01-01

    A mixed-mode chromatographic stationary phase, C18-DTT (dithiothreitol) silica (SiO2) was prepared through "thiol-ene" click chemistry. The obtained material was characterized by fourier transform infrared spectroscope, nitrogen adsorption analysis and contact angle analysis. Chromatographic performance of the C18-DTT was systemically evaluated by studying the effect of acetonitrile content, pH, buffer concentration of the mobile phase and column temperature. It was demonstrated that the novel stationary phase possessed reversed phase liquid chromatography (RPLC)/hydrophilic interaction liquid chromatography (HILIC) mixed-mode property. The stop-flow test revealed that C18-DTT exhibited excellent compatibility with 100% aqueous mobile phase. Additionally, the stability and column-to-column reproducibility of the C18-DTT material were satisfactory, with relative standard deviations of retention factor of the tested analytes (verapamil, fenbufen, guanine, tetrandrine and nicotinic acid) in the range of 1.82-3.72% and 0.85-1.93%, respectively. Finally, the application of C18-DTT column was demonstrated in the separation of non-steroidal anti-inflammatory drugs, aromatic carboxylic acids, alkaloids, nucleo-analytes and polycyclic aromatic hydrocarbons. It had great resolving power in the analysis of various compounds in HILIC and RPLC chromatographic conditions and was a promising RPLC/HILIC mixed-mode stationary phase. PMID:26695288

  3. Surfactant-Free Vanadium Oxides from Reverse Micelles and Organic Oxidants: Solution Processable Nanoribbons with Potential Applicability as Battery Insertion Electrodes Assembled in Different Configurations.

    PubMed

    Tartaj, Pedro; Amarilla, Jose M; Vazquez-Santos, Maria B

    2015-11-17

    Vanadium oxides similar to other metal transition oxides are prototypes of multifunctionality. Implementing new synthesis routes that lead to dry vanadium oxide nanomaterials with good functional and structural properties as well as good processing capabilities is thus of general interest. Here we report a facile method based on reverse micelles for the growth at room temperature and atmospheric pressure of surfactant-free vanadium oxide nanoribbons that retain after drying excellent solution-processable capabilities. Essential for the success of the method is the use of a soluble organic oxidant that acts as oxidant and cosurfactant during the synthesis, and facilitates surfactant removal with a simple washing protocol. Interestingly, this simple surfactant removal protocol could be of general applicability. As a proof-of-concept of the functional, structural, and processing capabilities of the dry vanadium oxide nanoribbons here prepared, we have checked their lithium insertion capabilities as battery cathodes built upon different configurations. Specifically, we show efficient insertion both in dry nanoribbons processed as films using doctor blade and organic solvents and in dry nanoribbons infiltrated in three-dimensional metal collectors from aqueous suspensions. PMID:26513340

  4. Synthesis of magnetic molecularly imprinted polymers by reversible addition fragmentation chain transfer strategy and its application in the Sudan dyes residue analysis.

    PubMed

    Xie, Xiaoyu; Chen, Liang; Pan, Xiaoyan; Wang, Sicen

    2015-07-31

    Magnetic molecularly imprinted polymers (MMIPs) have become a hotspot owing to the dual functions of target recognition and magnetic separation. In this study, the MMIPs were obtained by the surface-initiated reversible addition fragmentation chain transfer (RAFT) polymerization using Sudan I as the template. The resultant MMIPs were characterized by transmission electron microscope, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometer, and X-ray diffraction. Benefiting from the controlled/living property of the RAFT strategy, the uniform MIP layer was successfully grafted on the surface of RAFT agent-modified Fe3O4@SiO2 nanoparticles, favoring the fast mass transfer and rapid binding kinetics. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four Sudan dyes (Sudan I, II, III, and IV) from chili powder samples. The recoveries of the spiked samples in chili powder samples ranged from 74.1 to 93.3% with RSD lower than 6.4% and the relative standard uncertainty lower than 0.029. This work provided a good platform for the extraction and removal of Sudan dyes in complicated matrixes and demonstrated a bright future for the application of the well-constructed MMIPs in the field of solid-phase extraction. PMID:26077971

  5. Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications

    PubMed Central

    Tassa, Carlos; Liong, Monty; Hilderbrand, Scott; Sandler, Jason E.; Reiner, Thomas; Keliher, Edmund J.; Weissleder, Ralph; Shaw, Stanley Y.

    2013-01-01

    Methods for rapid surface immobilization of bioactive small molecules with control over orientation and immobilization density are highly desirable for biosensor and microarray applications. In this Study, we use a highly efficient covalent bioorthogonal [4+2] cycloaddition reaction between trans-cyclooctene (TCO) and 1,2,4,5-tetrazine (Tz) to enable the microfluidic immobilization of TCO/Tz-derivatized molecules. We monitor the process in real-time under continuous flow conditions using surface plasmon resonance (SPR). To enable reversible immobilization and extend the experimental range of the sensor surface, we combine a non-covalent antigen-antibody capture component with the cycloaddition reaction. By alternately presenting TCO or Tz moieties to the sensor surface, multiple capture-cycloaddition processes are now possible on one sensor surface for on-chip assembly and interaction studies of a variety of multi-component structures. We illustrate this method with two different immobilization experiments on a biosensor chip; a small molecule, AP1497 that binds FK506-binding protein 12 (FKBP12); and the same small molecule as part of an immobilized and in situ-functionalized nanoparticle. PMID:24084440

  6. Low electric field, easily reversible electrical set and reset processes in a Ge15Te83Si2 glass for phase change memory applications

    NASA Astrophysics Data System (ADS)

    Anbarasu, M.; Asokan, S.

    2011-04-01

    We report here an easily reversible set-reset process in a new Ge15Te83Si2 glass that could be a promising candidate for phase change random access memory applications. The I-V characteristics of the studied sample show a comparatively low threshold electric field (Eth) of 7.3 kV/cm. Distinct differences in the type of switching behavior are achieved by means of controlling the on state current. It enables the observation of a threshold type for less than 0.7 mA beyond memory type (set) switching. The set and reset processes have been achieved with a similar magnitude of 1 mA, and with a triangular current pulse for the set process and a short duration rectangular pulse of 10 msec width for the reset operation. Further, a self-resetting effect is seen in this material upon excitation with a saw-tooth/square pulse, and their response of leading and trailing edges are discussed. About 6.5 104 set-reset cycles have been undertaken without any damage to the device.

  7. Genetics of Primary Inherited Disorders of the Optic Nerve: Clinical Applications.

    PubMed

    Allen, Keri F; Gaier, Eric D; Wiggs, Janey L

    2015-07-01

    Inherited disorders of the optic nerve significantly impact vision in children and adults. The optic nerve disorders most commonly encountered clinically are glaucoma and primary optic neuropathy including Leber's hereditary optic neuropathy (LHON) and autosomal dominant or Kjer's optic atrophy. Current knowledge of the genetics of optic neuropathy and glaucoma makes it possible to test for mutations in disease-causing genes allowing for presymptomatic testing and risk assessment, and recent advances have revealed important disease mechanisms that may suggest potential therapeutic targets. In this perspective, we describe the current approaches and limitations to genetic testing for these disorders and provide an update on the development of gene-based therapies. PMID:26134840

  8. The Cre/loxP system in Giardia lamblia: genetic manipulations in a binucleate tetraploid protozoan.

    PubMed

    Wampfler, Petra B; Faso, Carmen; Hehl, Adrian B

    2014-07-01

    The bacteriophage-derived Cre/loxP system is a valuable tool that has revolutionised genetic and cell biological research in many organisms. We implemented this system in the intestinal parasite Giardia lamblia, an evolutionarily diverged protozoan whose binucleate and tetraploid genome organisation severely limits the application of reverse genetic approaches. We show that Cre-recombinase is functionally expressed in G. lamblia and demonstrate "recycling" of selectable markers. Providing the means for more complex and versatile genetic modifications, this technique massively increases the scope of functional investigations in G. lamblia and other protozoa with similar limitations with respect to genetic manipulation. PMID:24747534

  9. Application of a single-objective, hybrid genetic algorithm approach to pharmacokinetic model building.

    PubMed

    Sherer, Eric A; Sale, Mark E; Pollock, Bruce G; Belani, Chandra P; Egorin, Merrill J; Ivy, Percy S; Lieberman, Jeffrey A; Manuck, Stephen B; Marder, Stephen R; Muldoon, Matthew F; Scher, Howard I; Solit, David B; Bies, Robert R

    2012-08-01

    A limitation in traditional stepwise population pharmacokinetic model building is the difficulty in handling interactions between model components. To address this issue, a method was previously introduced which couples NONMEM parameter estimation and model fitness evaluation to a single-objective, hybrid genetic algorithm for global optimization of the model structure. In this study, the generalizability of this approach for pharmacokinetic model building is evaluated by comparing (1) correct and spurious covariate relationships in a simulated dataset resulting from automated stepwise covariate modeling, Lasso methods, and single-objective hybrid genetic algorithm approaches to covariate identification and (2) information criteria values, model structures, convergence, and model parameter values resulting from manual stepwise versus single-objective, hybrid genetic algorithm approaches to model building for seven compounds. Both manual stepwise and single-objective, hybrid genetic algorithm approaches to model building were applied, blinded to the results of the other approach, for selection of the compartment structure as well as inclusion and model form of inter-individual and inter-occasion variability, residual error, and covariates from a common set of model options. For the simulated dataset, stepwise covariate modeling identified three of four true covariates and two spurious covariates; Lasso identified two of four true and 0 spurious covariates; and the single-objective, hybrid genetic algorithm identified three of four true covariates and one spurious covariate. For the clinical datasets, the Akaike information criterion was a median of 22.3 points lower (range of 470.5 point decrease to 0.1 point decrease) for the best single-objective hybrid genetic-algorithm candidate model versus the final manual stepwise model: the Akaike information criterion was lower by greater than 10 points for four compounds and differed by less than 10 points for three compounds. The root mean squared error and absolute mean prediction error of the best single-objective hybrid genetic algorithm candidates were a median of 0.2 points higher (range of 38.9 point decrease to 27.3 point increase) and 0.02 points lower (range of 0.98 point decrease to 0.74 point increase), respectively, than that of the final stepwise models. In addition, the best single-objective, hybrid genetic algorithm candidate models had successful convergence and covariance steps for each compound, used the same compartment structure as the manual stepwise approach for 6 of 7 (86 %) compounds, and identified 54 % (7 of 13) of covariates included by the manual stepwise approach and 16 covariate relationships not included by manual stepwise models. The model parameter values between the final manual stepwise and best single-objective, hybrid genetic algorithm models differed by a median of 26.7 % (q? = 4.9 % and q? = 57.1 %). Finally, the single-objective, hybrid genetic algorithm approach was able to identify models capable of estimating absorption rate parameters for four compounds that the manual stepwise approach did not identify. The single-objective, hybrid genetic algorithm represents a general pharmacokinetic model building methodology whose ability to rapidly search the feasible solution space leads to nearly equivalent or superior model fits to pharmacokinetic data. PMID:22767341

  10. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  11. Applicability of Mamdani and Sugeno fuzzy genetic approaches for modeling reference evapotranspiration

    NASA Astrophysics Data System (ADS)

    Kisi, Ozgur

    2013-11-01

    Two different fuzzy genetic (FG) models are compared in modeling evapotranspiration.Sugeno FG (SGF) model is found to be better than the Mamdani FG (MFG) model.MFG models have much more computational times for training than the SFG models.The optimal FG models are also compared with commonly used empirical equations.SFG models perform better than the corresponding empirical equations.

  12. Genetic Vectors as a Tool in Association Studies: Definitions and Application for Study of Rheumatoid Arthritis

    PubMed Central

    Sandalov, Igor; Padyukov, Leonid

    2015-01-01

    To identify putative relations between different genetic factors in the human genome in the development of common complex disease, we mapped the genetic data to an ensemble of spin chains and analysed the data as a quantum system. Each SNP is considered as a spin with three states corresponding to possible genotypes. The combined genotype represents a multispin state, described by the product of individual-spin states. Each person is characterized by a single genetic vector (GV) and individuals with identical GVs comprise the GV group. This consolidation of genotypes into GVs provides integration of multiple genetic variants for a single statistical test and excludes ambiguity of biological interpretation known for allele and haplotype associations. We analyzed two independent cohorts, with 2633 rheumatoid arthritis cases and 2108 healthy controls, and data for 6 SNPs from the HTR2A locus plus shared epitope allele. We found that GVs based on selected markers are highly informative and overlap for 98.3% of the healthy population between two cohorts. Interestingly, some of the GV groups contain either only controls or only cases, thus demonstrating extreme susceptibility or protection features. By using this new approach we confirmed previously detected univariate associations and demonstrated the most efficient selection of SNPs for combined analyses for functional studies. PMID:25834811

  13. Novel polymorphic microsatellite markers for Bellamya and their application in population genetics of three species.

    PubMed

    Gu, Q H; Cheng, Q Q; Li, X J; Zhou, C J

    2015-01-01

    Bellamya is a widely distributed freshwater snail genus in China; however, its genetic diversity is completely unknown. Sixty-five novel microsatellite loci were isolated and characterized from a microsatellite-enriched library of Bellamya aeruginosa genomic DNA. Most of the 65 loci were successfully amplified. We found high polymorphic information content values for these loci, ranging from 0.235 to 0.892. There were 3 to 12 alleles per locus, and the HE and HO varied from 0.425 to 0.953 and 0.026 to 1.000, respectively. Fifteen loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction. All 65 SSR markers were tested in an additional five Bellamya species, and 96.9% of the 325 locus/taxon combinations tested resulted in cross-species amplification. Seven polymorphic microsatellite markers were randomly selected for comparison among nine populations of three species. All populations had moderate to high genetic diversity. In genetic distance-based cluster analysis, the populations of B. aeruginosa and B. dispiralis formed species-based clusters, whereas populations of B. angularia did not. The three examined Bellamya species could be differentiated using SSR markers. These microsatellite loci should be useful for genetic diversity analysis, analysis of phylogenetic relationship, and species delimitation of Bellamya. PMID:26634483

  14. Application of exome sequencing in the search for genetic causes of rare disorders of copper metabolism.

    PubMed

    Fuchs, Sabine A; Harakalova, Magdalena; van Haaften, Gijs; van Hasselt, Peter M; Cuppen, Edwin; Houwen, Roderick H J

    2012-07-01

    The genetic defect in a number of rare disorders of metal metabolism remains elusive. The limited number of patients with these disorders impedes the identification of the causative gene through positional cloning, which requires numerous families with multiple affected individuals. However, with next-generation sequencing all coding DNA (exomes) or whole genomes of patients can be sequenced to identify genes that are consistently mutated in patients. With this strategy only a limited number of patients and/or pedigrees is needed, bringing the elucidation of the genetic cause of even very rare diseases within reach. The main challenge associated with whole exome sequencing is the identification of the disease-causing mutation(s) among abundant genetic candidate variants. We describe several strategies to manage this data wealth, including comparison with control databases, increasing the number of patients and controls, and reducing the genomic region under investigation through homozygosity mapping. In this review we introduce a number of rare disorders of copper metabolism, with a suspected but yet unknown monogenetic cause, as an attractive target for this strategy. We anticipate that use of these novel techniques will identify the basic defect in the disorders described in this review, as well as in other genetic disorders of metal metabolism, in the next few years. PMID:22555275

  15. Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions.

    PubMed

    Schuldiner, M; Collins, S R; Weissman, J S; Krogan, N J

    2006-12-01

    The use of the budding yeast Saccharomyces cerevisiae as a simple eukaryotic model system for the study of chromatin assembly and regulation has allowed rapid discovery of genes that influence this complex process. The functions of many of the proteins encoded by these genes have not yet been fully characterized. Here, we describe a high-throughput methodology that can be used to illuminate gene function and discuss its application to a set of genes involved in the creation, maintenance and remodeling of chromatin structure. Our technique, termed E-MAPs, involves the generation of quantitative genetic interaction maps that reveal the function and organization of cellular proteins and networks. PMID:17101447

  16. Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components

    PubMed Central

    Tichoniuk, Mariusz; Ligaj, Marta; Filipiak, Marian

    2008-01-01

    An electrochemical biosensor for the detection of genetically modified food components is presented. The biosensor was based on 21-mer single-stranded oligonucleotide (ssDNA probe) specific to either 35S promoter or nos terminator, which are frequently present in transgenic DNA cassettes. ssDNA probe was covalently attached by 5′-phosphate end to amino group of cysteamine self-assembled monolayer (SAM) on gold electrode surface with the use of activating reagents – water soluble 1-ethyl-3(3′-dimethylaminopropyl)-carbodiimide (EDC) and N-hydroxy-sulfosuccinimide (NHS). The hybridization reaction on the electrode surface was detected via methylene blue (MB) presenting higher affinity to ssDNA probe than to DNA duplex. The electrode modification procedure was optimized using 19-mer oligoG and oligoC nucleotides. The biosensor enabled distinction between DNA samples isolated from soybean RoundupReady® (RR soybean) and non-genetically modified soybean. The frequent introduction of investigated DNA sequences in other genetically modified organisms (GMOs) give a broad perspectives for analytical application of the biosensor.

  17. 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 . PMID:19072282

  18. Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication.

    PubMed

    Wang, Biao; Wang, Ren-Rui; Cui, Zhen-Hua; Bi, Wen-Lu; Li, Jing-Wei; Li, Bai-Quan; Ozudogru, Elif Aylin; Volk, Gayle M; Wang, Qiao-Chun

    2014-01-01

    Rapid increases in human populations provide a great challenge to ensure that adequate quantities of food are available. Sustainable development of agricultural production by breeding more productive cultivars and by increasing the productive potential of existing cultivars can help meet this demand. The present paper provides information on the potential uses of cryogenic techniques in ensuring food security, including: (1) long-term conservation of a diverse germplasm and successful establishment of cryo-banks; (2) maintenance of the regenerative ability of embryogenic tissues that are frequently the target for genetic transformation; (3) enhancement of genetic transformation and plant regeneration of transformed cells, and safe, long-term conservation for transgenic materials; (4) production and maintenance of viable protoplasts for transformation and somatic hybridization; and (5) efficient production of pathogen-free plants. These roles demonstrate that cryogenic technologies offer opportunities to ensure food security. PMID:24681087

  19. Cleft lip and palate genetics and application in early embryological development

    PubMed Central

    Yu, Wenli; Serrano, Maria; Miguel, Symone San; Ruest, L. Bruno; Svoboda, Kathy K.H.

    2009-01-01

    The development of the head involves the interaction of several cell populations and coordination of cell signalling pathways, which when disrupted can cause defects such as facial clefts. This review concentrates on genetic contributions to facial clefts with and without cleft palate (CP). An overview of early palatal development with emphasis on muscle and bone development is blended with the effects of environmental insults and known genetic mutations that impact human palatal development. An extensive table of known genes in syndromic and non-syndromic CP, with or without cleft lip (CL), is provided. We have also included some genes that have been identified in environmental risk factors for CP/L. We include primary and review references on this topic. PMID:19884679

  20. Telegenetics: application of a tele-education program in genetic syndromes for Brazilian students.

    PubMed

    Maximino, Luciana Paula; Picolini-Pereira, Mirela Machado; Carvalho, Jos Luiz Brito

    2014-01-01

    With the high occurrence of genetic anomalies in Brazil and the manifestations of communication disorders associated with these conditions, the development of educative actions that comprise these illnesses can bring unique benefits in the identification and appropriate treatment of these clinical pictures. Objective The aim of this study was to develop and analyze an educational program in genetic syndromes for elementary students applied in two Brazilian states, using an Interactive Tele-education model. Material and Methods The study was carried out in 4 schools: two in the state of So Paulo, Southeast Region, Brazil, and two in the state of Amazonas, North Region, Brazil. Forty-five students, both genders, aged between 13 and 14 years, of the 9th grade of the basic education of both public and private system, were divided into two groups: 21 of So Paulo Group (SPG) and 24 of Amazonas Group (AMG). The educational program lasted about 3 months and was divided into two stages including both classroom and distance activities on genetic syndromes. The classroom activity was carried out separately in each school, with expository lessons, graphs and audiovisual contents. In the activity at a distance the educational content was presented to students by means of the Interactive Tele-education model. In this stage, the students had access a Cybertutor, using the Young Doctor Project methodology. In order to measure the effectiveness of the educational program, the Problem Situation Questionnaire (PSQ) and the Web Site Motivational Analysis Checklist adapted (FPM) were used. Results The program developed was effective for knowledge acquisition in 80% of the groups. FPM showed a high satisfaction index from the participants in relation to the Interactive Tele-education, evaluating the program as "awesome course". No statistically significant differences between the groups regarding type of school or state were observed. Conclusion Thus, the Tele-Education Program can be used as a tool for educational purposes in genetic syndromes of other populations, in several regions of Brazil. PMID:25591016

  1. Genetic screening for the next decade: application of present and new technologies.

    PubMed

    McCabe, E R

    1991-01-01

    Molecular genetic technology is diffusing from the research laboratory to the clinical laboratory, where it has already begun to influence prenatal diagnosis and counseling. In the very near future, this technology will be applied more generally, using population-based screening strategies. Pilot programs are beginning to evaluate the technical feasibility and efficacy of recombinant DNA techniques for newborn screening follow-up. DNA-based population screening is being considered for heterozygous carriers of an autosomal recessive disorder such as cystic fibrosis in order to identify carrier couples at risk of having an affected child. We will review the current DNA methodologies in the context of three genetic disorders: sickle-cell disease, Duchenne muscular dystrophy, and cystic fibrosis. We will then consider the requirements for implementation of these new technologies. We will conclude that implementation will require two key factors: machines and people. Machines are required to automate molecular genetic procedures, which are currently personnel-intensive, so that the expense can be reduced and the procedures made more cost-effective. The people who are required are health professionals knowledgeable in the clinical aspects of the target disorders, as well as in the DNA laboratory testing. These professionals will be able to facilitate sample acquisition and information exchange among the laboratory, the primary health care provider, and the families requesting consultation. PMID:1680260

  2. Optimization of fuels from waste composition with application of genetic algorithm.

    PubMed

    Małgorzata, Wzorek

    2014-05-01

    The objective of this article is to elaborate a method to optimize the composition of the fuels from sewage sludge (PBS fuel - fuel based on sewage sludge and coal slime, PBM fuel - fuel based on sewage sludge and meat and bone meal, PBT fuel - fuel based on sewage sludge and sawdust). As a tool for an optimization procedure, the use of a genetic algorithm is proposed. The optimization task involves the maximization of mass fraction of sewage sludge in a fuel developed on the basis of quality-based criteria for the use as an alternative fuel used by the cement industry. The selection criteria of fuels composition concerned such parameters as: calorific value, content of chlorine, sulphur and heavy metals. Mathematical descriptions of fuel compositions and general forms of the genetic algorithm, as well as the obtained optimization results are presented. The results of this study indicate that the proposed genetic algorithm offers an optimization tool, which could be useful in the determination of the composition of fuels that are produced from waste. PMID:24718361

  3. The application of PCR and reverse line blot hybridization to detect arthropod-borne hemopathogens of dogs and cats in Trinidad.

    PubMed

    Georges, Karla; Ezeokoli, Chukwudozi D; Newaj-Fyzul, Aweeda; Campbell, Mervyn; Mootoo, Natasha; Mutani, Alexander; Sparagano, Olivier A E

    2008-12-01

    Arthropod-borne diseases are important causes of morbidity and mortality of companion animals in Trinidad. As clinical signs are vague, more sensitive methods to diagnose these diseases based on the polymerase chain reaction (PCR) followed by reverse line blot hybridization (RLB) of amplified products are being developed. An RLB of 14 oligonucleotide probes coupled with polymerase chain-amplified regions of 16S rRNA or 18S rRNA genes of hemoparasites from cats and dogs detected Ehrlichia canis, Anaplasma platys, Babesia canis vogeli, feline mycoplasmas ("Candidatus Mycoplasma haemominutum,"Mycoplasma haemofelis), and some unknown species within the Babesia/Theileria group and the Anaplasma/Ehrlichia tribe. Amplified products were obtained from blood samples collected from 348 dogs and 15 cats. Overall, hemopathogen DNA was detected in 92 (26.4%) dogs and six (40.0%) cats. E. canis (49, 14.1%) and feline mycoplasma (5, 33.3%) DNA were most frequently identified in dogs and cats, respectively. B. canis vogeli (1, 6.7%) and E. canis (1, 6.7%) were also detected in cats. Mixed infections of Anaplasma/Ehrlichia sp. and Babesia sp. were present in five (1.4%) dogs, while mixed infections of the feline mycoplasmas were present in two (13.3%) cats, one of which was also positive for E. canis. Pyrexia was significantly associated with a positive RLB result in dogs (P= 0.00, chi(2), 1 df). This is the first reported application of macro-arraying techniques to detect arthropod-borne hemopathogens of companion animals in the Americas and the first detection of DNA of B. canis vogeli and E. canis in cats in Trinidad. PMID:19120209

  4. Preparation, telomerization, immobilization and application of N-alkyl L-phenylalanine-derived polymerizable organogelator for reversed-phase high-performance liquid chromatography.

    PubMed

    Rahman, M Mizanur; Takafuji, Makoto; Ihara, Hirotaka

    2008-08-29

    Silica-polymer hybrid materials (Sil-T1) have been successfully synthesized from a self-assembling polymerizable organogelator; N'-octadecyl-N(alpha)-(4-vinyl)-benzoyl-L-phenylalanineamide (C(18)-L-Phe-St or 1). Telomerization of compound 1 has been done with commonly used silane coupling agent; 3-mercaptopropyltrimethoxysilane (MPS), and the telomer (T1) was grafted onto porous silica surface to prepare a stationary phase (Sil-T1) for reversed-phase high-performance liquid chromatography. The composition of the new hybrid material (Sil-T1) was determined by elemental analysis, DRIFT-IR, TGA and by (13)C and (29)Si (CP/MAS) NMR spectroscopic measurements. The elemental analysis measurements revealed that the surface coverage by organic phase in Sil-T1 is significantly (about 135%) lower than commercial polymeric octadecylsilyalted silica (ODS-p). In addition, the results of (13)C CP/MAS NMR demonstrated that the N-alkyl moieties of the grafted polymers chain in Sil-T1 remained disordered, amorphous, and mobile represented by gauche conformational form. Furthermore, from the characterization data, the successful grafting process and unagglomerated state of the grafted particles (as observed by scanning electron microscopic, SEM measurements) prove the material to be suitable for HPLC application. The evaluation of chromatographic performance has been done from the retention studies of different size and shape PAHs and aromatic positional isomers. Significantly higher selectivity for PAHs was attributed by Sil-T1 than ODS-p regardless it has low surface coverage and lower order of alkyl chain. The enhancement of selectivity obtained by Sil-T1 can be explained by the contribution of multiple pi-pi interactions between the guest PAHs and the pi-electrons sources (carbonyls and aromatic moieties) of the organic phase of Sil-T1. PMID:18656202

  5. Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease.

    PubMed

    Chu, Tianjiao; Bunce, Kimberly; Hogge, W Allen; Peters, David G

    2009-05-15

    There is currently great interest in the development of methods for the minimally invasive diagnosis of fetal genetic disease using cell-free DNA from maternal plasma samples obtained in the first trimester of pregnancy. With the rapid development of high-throughput sequencing technology, the possibility of detecting the presence of trisomy fetal genomes in the maternal plasma DNA sample has recently been explored. The major concern of this whole genome sequencing approach is that, while detecting the karyotype of the fetal genome from the maternal plasma requires extremely high accuracy of copy number estimation, the majority of the available high-throughput sequencing technologies require polymerase chain reaction (PCR) and are subject to the substantial bias that is inherent to the PCR process. We introduce a novel and sophisticated statistical model for the whole genome sequencing data, and based on this model, develop a highly sensitive method of Minimally Invasive Karyotyping (MINK) for the diagnosis of the fetal genetic disease. Specifically we demonstrate, by applying our statistical method to ultra high-throughput whole sequencing data, that trisomy 21 can be detected in a minor ('fetal') genome when it is mixed into a major ('maternal') background genome at frequencies as low as 5%. This observation provides additional proof of concept and justification for the further development of this method towards its eventual clinical application. Here, we describe the statistical and experimental methods that illustrate this approach and discuss future directions for technical development and potential clinical applications. PMID:19307238

  6. Genetics Home Reference: Recombinant 8 syndrome

    MedlinePLUS

    ... are related to the loss and addition of genetic material on these regions of chromosome 8. Researchers are ... DNA is reversed and reinserted into the chromosome. Genetic material is typically not lost as a result of ...

  7. Forward and reverse mutagenesis in C. elegans

    PubMed Central

    Kutscher, Lena M.; Shaham, Shai

    2014-01-01

    Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal. PMID:24449699

  8. Reverse-Genetic Analysis of the Two Biotin-Containing Subunit Genes of the Heteromeric Acetyl-Coenzyme A Carboxylase in Arabidopsis Indicates a Unidirectional Functional Redundancy1[C][W][OA

    PubMed Central

    Li, Xu; Ilarslan, Hilal; Brachova, Libuse; Qian, Hui-Rong; Li, Ling; Che, Ping; Wurtele, Eve Syrkin; Nikolau, Basil J.

    2011-01-01

    The heteromeric acetyl-coenzyme A carboxylase catalyzes the first and committed reaction of de novo fatty acid biosynthesis in plastids. This enzyme is composed of four subunits: biotin carboxyl-carrier protein (BCCP), biotin carboxylase, α-carboxyltransferase, and β-carboxyltransferase. With the exception of BCCP, single-copy genes encode these subunits in Arabidopsis (Arabidopsis thaliana). Reverse-genetic approaches were used to individually investigate the physiological significance of the two paralogous BCCP-coding genes, CAC1A (At5g16390, codes for BCCP1) and CAC1B (At5g15530, codes for BCCP2). Transfer DNA insertional alleles that completely eliminate the accumulation of BCCP2 have no perceptible effect on plant growth, development, and fatty acid accumulation. In contrast, transfer DNA insertional null allele of the CAC1A gene is embryo lethal and deleteriously affects pollen development and germination. During seed development the effect of the cac1a null allele first becomes apparent at 3-d after flowering, when the synchronous development of the endosperm and embryo is disrupted. Characterization of CAC1A antisense plants showed that reducing BCCP1 accumulation to 35% of wild-type levels, decreases fatty acid accumulation and severely affects normal vegetative plant growth. Detailed expression analysis by a suite of approaches including in situ RNA hybridization, promoter:reporter transgene expression, and quantitative western blotting reveal that the expression of CAC1B is limited to a subset of the CAC1A-expressing tissues, and CAC1B expression levels are only about one-fifth of CAC1A expression levels. Therefore, a likely explanation for the observed unidirectional redundancy between these two paralogous genes is that whereas the BCCP1 protein can compensate for the lack of BCCP2, the absence of BCCP1 cannot be tolerated as BCCP2 levels are not sufficient to support heteromeric acetyl-coenzyme A carboxylase activity at a level that is required for normal growth and development. PMID:21030508

  9. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test.

    PubMed

    Rouet, Franois; Chaix, Marie-Laure; Nerrienet, Eric; Ngo-Giang-Huong, Nicole; Plantier, Jean-Christophe; Burgard, Marianne; Peeters, Martine; Damond, Florence; Ekouevi, Didier Koumavi; Msellati, Philippe; Ferradini, Laurent; Rukobo, Sandra; Marchal, Valrie; Schvachsa, Nilda; Wakrim, Lahcen; Rafalimanana, Christian; Rakotoambinina, Benjamin; Viard, Jean-Paul; Seigneurin, Jean-Marie; Rouzioux, Christine

    2007-08-01

    The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays. PMID:17468666

  10. Probing Yeast Polarity with Acute, Reversible, Optogenetic Inhibition of Protein Function.

    PubMed

    Jost, Anna Payne-Tobin; Weiner, Orion D

    2015-10-16

    We recently developed a technique for rapidly and reversibly inhibiting protein function through light-inducible sequestration of proteins away from their normal sites of action. Here, we adapt this method for inducible inactivation of Bem1, a scaffold protein involved in budding yeast polarity. We find that acute inhibition of Bem1 produces profound defects in cell polarization and cell viability that are not observed in bem1?. By disrupting Bem1 activity at specific points in the cell cycle, we demonstrate that Bem1 is essential for the establishment of polarity and bud emergence but is dispensable for the growth of an emerged bud. By taking advantage of the reversibility of Bem1 inactivation, we show that pole size scales with cell size, and that this scaling is dependent on the actin cytoskeleton. Our experiments reveal how rapid reversible inactivation of protein function complements traditional genetic approaches. This strategy should be widely applicable to other biological contexts. PMID:26035630

  11. An application of kernel methods to variety identification based on SSR markers genetic fingerprinting

    PubMed Central

    2011-01-01

    Background In crop production systems, genetic markers are increasingly used to distinguish individuals within a larger population based on their genetic make-up. Supervised approaches cannot be applied directly to genotyping data due to the specific nature of those data which are neither continuous, nor nominal, nor ordinal but only partially ordered. Therefore, a strategy is needed to encode the polymorphism between samples such that known supervised approaches can be applied. Moreover, finding a minimal set of molecular markers that have optimal ability to discriminate, for example, between given groups of varieties, is important as the genotyping process can be costly in terms of laboratory consumables, labor, and time. This feature selection problem also needs special care due to the specific nature of the data used. Results An approach encoding SSR polymorphisms in a positive definite kernel is presented, which then allows the usage of any kernel supervised method. The polymorphism between the samples is encoded through the Nei-Li genetic distance, which is shown to define a positive definite kernel between the genotyped samples. Additionally, a greedy feature selection algorithm for selecting SSR marker kits is presented to build economical and efficient prediction models for discrimination. The algorithm is a filter method and outperforms other filter methods adapted to this setting. When combined with kernel linear discriminant analysis or kernel principal component analysis followed by linear discriminant analysis, the approach leads to very satisfactory prediction models. Conclusions The main advantage of the approach is to benefit from a flexible way to encode polymorphisms in a kernel and when combined with a feature selection algorithm resulting in a few specific markers, it leads to accurate and economical identification models based on SSR genotyping. PMID:21595989

  12. Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.

    PubMed

    Davis, Nicholas A; Lareau, Caleb A; White, Bill C; Pandey, Ahwan; Wiley, Graham; Montgomery, Courtney G; Gaffney, Patrick M; McKinney, B A

    2013-09-01

    Open source tools are needed to facilitate the construction, analysis, and visualization of gene-gene interaction networks for sequencing data. To address this need, we present Encore, an open source network analysis pipeline for genome-wide association studies and rare variant data. Encore constructs Genetic Association Interaction Networks or epistasis networks using two optional approaches: our previous information-theory method or a generalized linear model approach. Additionally, Encore includes multiple data filtering options, including Random Forest/Random Jungle for main effect enrichment and Evaporative Cooling and Relief-F filters for enrichment of interaction effects. Encore implements SNPrank network centrality for identifying susceptibility hubs (nodes containing a large amount of disease susceptibility information through the combination of multivariate main effects and multiple gene-gene interactions in the network), and it provides appropriate files for interactive visualization of a network using tools from our online Galaxy instance. We implemented these algorithms in C++ using OpenMP for shared-memory parallel analysis on a server or desktop. To demonstrate Encore's utility in analysis of genetic sequencing data, we present an analysis of exome resequencing data from healthy individuals and those with Systemic Lupus Erythematous (SLE). Our results verify the importance of the previously associated SLE genes HLA-DRB and NCF2, and these two genes had the highest gene-gene interaction degrees among the susceptibility hubs. An additional 14 genes previously associated with SLE emerged in our epistasis network model of the exome data, and three novel candidate genes, ST8SIA4, CMTM4, and C2CD4B, were implicated in the model. In summary, we present a comprehensive tool for epistasis network analysis and the first such analysis of exome data from a genetic study of SLE. PMID:23740754

  13. Application of Genetic Algorithms in the New Air Ttraffic Management Simulation System

    NASA Astrophysics Data System (ADS)

    Guo, Hang

    The air traffic control systems are facing more and more serious congestions because of the increasing of air traffic flow in China. To solve the problem we have developed a New Air Traffic Management Simulation System that is according to the ideology of the New Air Traffic Management and the concept of Free Flight. First this paper analyses the mass design idea and the module functions, and then use the genetic algorithms to give the detail methods to solve the airline conflicts on airlines and aircraft sequence takeoff-landfall sorting schedule in the terminal airport area at last we has achieved anticipative effect by use stimulant data compute in the system

  14. Telegenetics: application of a tele-education program in genetic syndromes for Brazilian students

    PubMed Central

    MAXIMINO, Luciana Paula; PICOLINI-PEREIRA, Mirela Machado; CARVALHO, José Luiz Brito

    2014-01-01

    With the high occurrence of genetic anomalies in Brazil and the manifestations of communication disorders associated with these conditions, the development of educative actions that comprise these illnesses can bring unique benefits in the identification and appropriate treatment of these clinical pictures. Objective The aim of this study was to develop and analyze an educational program in genetic syndromes for elementary students applied in two Brazilian states, using an Interactive Tele-education model. Material and Methods The study was carried out in 4 schools: two in the state of São Paulo, Southeast Region, Brazil, and two in the state of Amazonas, North Region, Brazil. Forty-five students, both genders, aged between 13 and 14 years, of the 9th grade of the basic education of both public and private system, were divided into two groups: 21 of São Paulo Group (SPG) and 24 of Amazonas Group (AMG). The educational program lasted about 3 months and was divided into two stages including both classroom and distance activities on genetic syndromes. The classroom activity was carried out separately in each school, with expository lessons, graphs and audiovisual contents. In the activity at a distance the educational content was presented to students by means of the Interactive Tele-education model. In this stage, the students had access a Cybertutor, using the Young Doctor Project methodology. In order to measure the effectiveness of the educational program, the Problem Situation Questionnaire (PSQ) and the Web Site Motivational Analysis Checklist adapted (FPM) were used. Results The program developed was effective for knowledge acquisition in 80% of the groups. FPM showed a high satisfaction index from the participants in relation to the Interactive Tele-education, evaluating the program as "awesome course". No statistically significant differences between the groups regarding type of school or state were observed. Conclusion Thus, the Tele-Education Program can be used as a tool for educational purposes in genetic syndromes of other populations, in several regions of Brazil. PMID:25591016

  15. Application of BP Neural Network Based on Genetic Algorithm in Quantitative Analysis of Mixed GAS

    NASA Astrophysics Data System (ADS)

    Chen, Hongyan; Liu, Wenzhen; Qu, Jian; Zhang, Bing; Li, Zhibin

    Aiming at the problem of mixed gas detection in neural network and analysis on the principle of gas detection. Combining BP algorithm of genetic algorithm with hybrid gas sensors, a kind of quantitative analysis system of mixed gas is designed. The local minimum of network learning is the main reason which affects the precision of gas analysis. On the basis of the network study to improve the learning algorithms, the analyses and tests for CO, CO2 and HC compounds were tested. The results showed that the above measures effectively improve and enhance the accuracy of the neural network for gas analysis.

  16. Genetic algorithm based adaptive neural network ensemble and its application in predicting carbon flux

    USGS Publications Warehouse

    Xue, Y.; Liu, S.; Hu, Y.; Yang, J.; Chen, Q.

    2007-01-01

    To improve the accuracy in prediction, Genetic Algorithm based Adaptive Neural Network Ensemble (GA-ANNE) is presented. Intersections are allowed between different training sets based on the fuzzy clustering analysis, which ensures the diversity as well as the accuracy of individual Neural Networks (NNs). Moreover, to improve the accuracy of the adaptive weights of individual NNs, GA is used to optimize the cluster centers. Empirical results in predicting carbon flux of Duke Forest reveal that GA-ANNE can predict the carbon flux more accurately than Radial Basis Function Neural Network (RBFNN), Bagging NN ensemble, and ANNE. ?? 2007 IEEE.

  17. Application of support vector machine and quantum genetic algorithm in infrared target recognition

    NASA Astrophysics Data System (ADS)

    Wang, Hongliang; Huang, Yangwen; Ding, Haifei

    2010-08-01

    In this paper, a kind of classifier based on support vector machine (SVM) is designed for infrared target recognition. In allusion to the problem how to choose kernel parameter and error penalty factor, quantum genetic algorithm (QGA) is used to optimize the parameters of SVM model, it overcomes the shortcoming of determining its parameters after trial and error in the past. Classification experiments of infrared target features extracted by this method show that the convergence speed is fast and the rate of accurate recognition is high.

  18. Reversible Thermoset Adhesives

    NASA Technical Reports Server (NTRS)

    Mac Murray, Benjamin C. (Inventor); Tong, Tat H. (Inventor); Hreha, Richard D. (Inventor)

    2016-01-01

    Embodiments of a reversible thermoset adhesive formed by incorporating thermally-reversible cross-linking units and a method for making the reversible thermoset adhesive are provided. One approach to formulating reversible thermoset adhesives includes incorporating dienes, such as furans, and dienophiles, such as maleimides, into a polymer network as reversible covalent cross-links using Diels Alder cross-link formation between the diene and dienophile. The chemical components may be selected based on their compatibility with adhesive chemistry as well as their ability to undergo controlled, reversible cross-linking chemistry.

  19. Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns

    PubMed Central

    2010-01-01

    Background The analysis of Inter-Alu PCR patterns obtained from human genomic DNA samples is a promising technique for a simultaneous analysis of many genomic loci flanked by Alu repetitive sequences in order to detect the presence of genetic polymorphisms. Inter-Alu PCR products may be separated and analyzed by capillary electrophoresis using an automatic sequencer that generates a complex pattern of peaks. We propose an algorithmic method based on the Haar-Walsh Wavelet Packet Transformation (WPT) for an efficient detection of fingerprint-type patterns generated by PCR-based methodologies. We have tested our algorithmic approach on inter-Alu patterns obtained from the genomic DNA of three couples of monozygotic twins, expecting that the inter-Alu patterns of each twins couple will show differences due to unavoidable experimental variability. On the contrary the differences among samples of different twins are supposed to originate from genetic variability. Our goal is to automatically detect regions in the inter-Alu pattern likely associated to the presence of genetic polymorphisms. Results We show that the WPT algorithm provides a reliable tool to identify sample to sample differences in complex peak patterns, reducing the possible errors and limits associated to a subjective evaluation. The redundant decomposition of the WPT algorithm allows for a procedure of best basis selection which maximizes the pattern differences at the lowest possible scale. Our analysis points out few classifying signal regions that could indicate the presence of possible genetic polymorphisms. Conclusions The WPT algorithm based on the Haar-Walsh wavelet is an efficient tool for a non-supervised pattern classification of inter-ALU signals provided by a genetic analyzer, even if it was not possible to estimate the power and false positive rate due to the lacking of a suitable data base. The identification of non-reproducible peaks is usually accomplished comparing different experimental replicates of each sample. Moreover, we remark that, albeit we developed and optimized an algorithm able to analyze patterns obtained through inter-Alu PCR, the method is theoretically applicable to whatever fingerprint-type pattern obtained analyzing anonymous DNA fragments through capillary electrophoresis, and it could be usefully applied on a wide range of fingerprint-type methodologies. PMID:21143911

  20. WASTEWATER DEMINERALIZATION BY TUBULAR REVERSE OSMOSIS PROCESS

    EPA Science Inventory

    A 16 1pm (4.2 gpm) tubular reverse osmosis pilot plant was operated at Pomona Advanced Wastewater Treatment Research Facility for over one year. The purpose of the study was to investigate the applicability of the tubular reverse osmosis process to wastewater demineralization. Th...

  1. Genetic variation and its maintenance

    SciTech Connect

    Roberts, D.F.; De Stefano, G.F.

    1986-01-01

    This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

  2. Curve-based multivariate distance matrix regression analysis: application to genetic association analyses involving repeated measures

    PubMed Central

    Salem, Rany M.; O'Connor, Daniel T.

    2010-01-01

    Most, if not all, human phenotypes exhibit a temporal, dosage-dependent, or age effect. Despite this fact, it is rare that data are collected over time or in sequence in relevant studies of the determinants of these phenotypes. The costs and organizational sophistication necessary to collect repeated measurements or longitudinal data for a given phenotype are clearly impediments to this, but greater efforts in this area are needed if insights into human phenotypic expression are to be obtained. Appropriate data analysis methods for genetic association studies involving repeated or longitudinal measures are also needed. We consider the use of longitudinal profiles obtained from fitted functions on repeated data collections from a set of individuals whose similarities are contrasted between sets of individuals with different genotypes to test hypotheses about genetic influences on time-dependent phenotype expression. The proposed approach can accommodate uncertainty of the fitted functions, as well as weighting factors across the time points, and is easily extended to a wide variety of complex analysis settings. We showcase the proposed approach with data from a clinical study investigating human blood vessel response to tyramine. We also compare the proposed approach with standard analytic procedures and investigate its robustness and power via simulation studies. The proposed approach is found to be quite flexible and performs either as well or better than traditional statistical methods. PMID:20423962

  3. Study on the application of parent-of-origin specific DNA methylation markers to forensic genetics.

    PubMed

    Zhao, Guisen; Yang, Qingen; Huang, Daixin; Yu, Chunying; Yang, Rongzhi; Chen, Hui; Mei, Kun

    2005-11-25

    In paternity test, especially in motherless cases, the allele inherited from father (obligatory gene, OG) often cannot be determined. The paternity exclusion probability (PE) of a genetic marker is reduced considerably. Therefore, it is necessary to develop a new technique, by which the parental origin of alleles can be determined without genealogical analysis. In this paper, we explored the possibility of using parent-of-origin specific DNA methylation markers to determine the parental origin of alleles, choosing the imprinted single nucleotide polymorphism (SNP) locus rs220028 (A/G) as a model system. We typed the SNP by mutagenically separated PCR (MS-PCR). The frequencies of alleles were A = 0.5085, G = 0.4915; the unbiased heterozygosity was 0.5020. In order to discriminate between the maternal allele and paternal allele, post-digestion MS-PCR, a novel PCR based methylation analysis and SNP typing technique was developed and performed on 18 heterozygous children, and the methylated maternal allele was detected specifically. As a pilot study on the use of epigenetic markers in forensic genetics, our results demonstrated the feasibility of using parent-of-origin specific DNA methylation markers to determine the parental origin of alleles. PMID:16182958

  4. Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases

    PubMed Central

    Tassy, Olivier; Pourqui, Olivier

    2014-01-01

    The function of genes is often evolutionarily conserved, and comparing the annotation of ortholog genes in different model organisms has proved to be a powerful predictive tool to identify the function of human genes. Here, we describe Manteia, a resource available online at http://manteia.igbmc.fr. Manteia allows the comparison of embryological, expression, molecular and etiological data from human, mouse, chicken and zebrafish simultaneously to identify new functional and structural correlations and gene-disease associations. Manteia is particularly useful for the analysis of gene lists produced by high-throughput techniques such as microarrays or proteomics. Data can be easily analyzed statistically to characterize the function of groups of genes and to correlate the different aspects of their annotation. Sophisticated querying tools provide unlimited ways to merge the information contained in Manteia along with the possibility of introducing custom user-designed biological questions into the system. This allows for example to connect all the animal experimental results and annotations to the human genome, and take advantage of data not available for human to look for candidate genes responsible for genetic disorders. Here, we demonstrate the predictive and analytical power of the system to predict candidate genes responsible for human genetic diseases. PMID:24038354

  5. The application of molecular genetics to the study of familial arterial hypertension.

    PubMed

    Corvol, P; Jeunematre, X; Plouin, P F; Cambien, F; Soubrier, F

    1989-01-01

    The hereditary nature of familial hypertension has been clearly established by a number of clinical studies. Most of the present work has been concentrated on the correlation between various phenotypic traits and the level of blood pressure. The development of molecular genetics allow now to establish a link between high blood pressure and specific phenotypes. As analyzed in this paper, several strategies can be used for the genetic study of arterial hypertension: linkage studies in informative families, population association studies, analysis of subjects with contrasted predisposition to high blood pressure, affected sib-pair method. The identification of the loci implicated in blood pressure regulation and which contribute to the development of arterial hypertension can then be performed in this clinical material by two main approaches. One is based on the study of candidate genes, genes whose products are known to participate in blood pressure regulation, such as those of the renin-angiotensin system which are examplified. The other involves testing a series of markers distributed randomly throughout the genome in order to establish a link between increased blood pressure and a particular region of the genome. PMID:2676250

  6. Properly apply reverse osmosis

    SciTech Connect

    Kucera, J.

    1997-02-01

    Reverse osmosis (RO) is a water purification technique used to reduce the loading of dissolved solids in solution. The popularity of RO for treating boiler feedwater is growing because of the rising cost of ion-exchange-based demineralization as well as safety concerns associated with handling acid and caustic. A properly designed and operated RO-based boiler-feedwater-treatment system can reduce the load to, and costs associated with, ion exchange demineralization. This article discusses RO feedwater quality recommendations, pretreatment techniques, and system monitoring necessary to achieve optimum RO system performance in the most cost-effective manner. Regardless of the application--whether it is the treatment of boiler feedwater, industrial wastewater, or process water--the approach to pretreatment and the other design and operating guidance offered here remains the same.

  7. Tubal ligation reversal

    MedlinePLUS

    Tubal ligation reversal is surgery done to allow a woman who has had her tubes tied (tubal ligation) to become pregnant again. The fallopian tubes are reconnected in this reversal surgery. A tubal ligation can't always be ...

  8. Dynamics of the Genetic Diversity of Subsurface Microbial Communities and Their Applications to Contaminated Site Cleanups

    EPA Science Inventory

    When compared to traditional approaches, the utilization of molecular and genomic techniques to soil and groundwater cleanup investigations can reduce inherent parameter variability when conducting bench and pilot-scale investigations or carrying out full-scale field applications...

  9. Application of reversal electron attachment for ultrasensitive detection of thermal electron-attaching molecules - CCl4 and C6H5O2

    NASA Technical Reports Server (NTRS)

    Bernius, Mark T.; Chutjian, Ara

    1990-01-01

    A standard gas-dilution method was used to determine the selective response of the reversal electron attachment detector to carbon tetrachloride concentrations in nitrogen. Data are provided that determine the lowest concentration of sample detectable with the present instrumental configuration as being below 1.0 part per trillion by volume. The incorporation of a 90-deg electrostatic deflector with the quadrupole mass spectrometer is shown to be vital, and with it, negative-ion quadrupole mass spectrometry is used to characterize the ionization process. Observations are also made of the reversal electron attachment response to nitrobenzene. The analytical potential of reversal electron capture negative-ion mass spectrometry is examined, and areas for future development are discussed.

  10. Hair analysis of histamine after fluorescence labeling by column-switching reversed-phase liquid chromatography with electrospray ionization mass spectrometry and application to human hair.

    PubMed

    Toyo'oka, Toshimasa; Suzuki, Ayako; Fukushima, Takeshi; Kato, Masaru

    2004-10-15

    Sensitive determination of histamine (HA) in hair was carried out by column-switching reversed-phase high-performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-ESI-MS). HA was labeled with excess amounts of 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F) at 60 degrees C for 30 min in a mixture of 0.1 M borax (pH 9.3) and acetonitrile (CH(3)CN). The resulting DBD-HA derivative was roughly separated by a Mightysil RP-18 GP (100 x 2mm i.d., 3 microm) with an acidic mobile phase containing 0.1% trifluoroacetic acid. DBD-HA in the fraction flowing due to a position change in the six-port column-switching valve was then completely separated by a Wakopak Navi C30 (150 x 2mm i.d., 5 microm) with 20 mM AcONH(4)-CH(3)CN (8:2). The mass spectrometer was operated in the selected reaction monitoring (SRM) mode for the product ion (m/z 292) obtained from MS-MS measurement using the protonated molecular ion [M+H](+) (m/z 337) as the precursor ion. Good linearity was achieved from the calibration curve obtained by plotting peak area ratios of the internal standard (HA-d(4)) against the injected amounts of HA (1.66-16.6 pmol, r(2)=0.999). The coefficients of variation, at 1.66- and 16.6-pmol injections, were 5.6 and 3.7%, respectively (n=6). Furthermore, the detection limit was 0.167 pmol. The efficiency of the recommended procedure was identified from the determination in the rat hair root after intraperitoneal administration of HA. The proposed method was applied to HA determination in the hair shaft of Dark Agouti rats and healthy volunteers. The variations in the concentrations in 1mg of hair shaft were 0.80-1.84 pmol (mean+/-SD=1.33+/-0.33, n=12) in rats and 0.94-72.3 pmol (17.2+/-21.5, n=16) in humans. The determination of HA in the plasma of rats and humans was also performed successfully by this method. Because the proposed method provides good precision and trace detection of HA in hair, the analytical technique seems to be applicable for the determination of various biogenic amines in hair. PMID:15450798

  11. Application of cryopreservation to genetic analyses of a photosynthetic picoeukaryote community.

    PubMed

    Kawachi, Masanobu; Kataoka, Takafumi; Sato, Mayumi; Nol, Mary-Hlne; Kuwata, Akira; Demura, Mikihide; Yamaguchi, Haruyo

    2016-02-01

    Cryopreservation is useful for long-term maintenance of living strains in microbial culture collections. We applied this technique to environmental specimens from two monitoring sites at Sendai Bay, Japan and compared the microbial diversity of photosynthetic picoeukaryotes in samples before and after cryopreservation. Flow cytometry (FCM) showed no considerable differences between specimens. We used 2500 cells sorted with FCM for next-generation sequencing of 18S rRNA gene amplicons and after removing low-quality sequences obtained 10,088-37,454 reads. Cluster analysis and comparative correlation analysis of observed high-level operational taxonomic units indicated similarity between specimens before and after cryopreservation. The effects of cryopreservation on cells were assessed with representative culture strains, including fragile cryptophyte cells. We confirmed the usefulness of cryopreservation for genetic studies on environmental specimens, and found that small changes in FCM cytograms after cryopreservation may affect biodiversity estimation. PMID:26506442

  12. Application of carrier testing to genetic counseling for X-linked agammaglobulinemia

    SciTech Connect

    Allen, R.C.; Nachtman, R.G.; Belmont, J.W.; Rosenblatt, H.M.

    1994-01-01

    Bruton X-linked agammaglobulinemia (XLA) is a phenotypically recessive genetic disorder of B lymphocyte development. Female carriers of XLA, although asymptomatic, have a characteristic B cell lineage-specific skewing of the pattern of X inactivation. Skewing apparently results from defective growth and maturation of B cell precursors bearing a mutant active X chromosome. In this study, carrier status was tested in 58 women from 22 families referred with a history of agammaglobulinemia. Primary carrier analysis to examine patterns of X inactivation in CD19[sup +] peripheral blood cells (B lymphocytes) was conducted using quantitative PCR at the androgen-receptor locus. Obligate carriers of XLA demonstrated >95% skewing of X inactivation in peripheral blood CD19[sup +] cells but not in CD19[sup [minus

  13. Containment of genetically engineered organisms after application to subsurface environments. Technical completion report

    SciTech Connect

    Crawford, D.; Crawford, R.; Kellogg, S.; Orser, C.; Ralston, D.

    1993-06-01

    The feasibility of containing genetically engineered bacteria with enhanced dehalogenating properties for in situ bioremediation was investigated. (1) An agarose matrix microbead protocol and a detection system for contained microorganisms or DNA were developed. Multiplex Polymerase Chain Reaction (PCR) allowed tracking of a consortium of encapsulated organisms or several gene targets from a single species. Gene sequences encoding the enzymes responsible for initiating the biodegradation of toluene, octane, and 2,4-D were detected by multiplex PCR and nucleic acid probes from similar to 1-10 biodegradative cells/g soil. Improved DNA extraction methods resulted in PCR reactions detecting similar to 6 cells/g soil. (2) The pcpB gene (for the broad-spectrum detoxicant pentachlorophenol (PCP) hydroxylase) isolated from Flavobacterium sp. strain ATCC 39723 was used in attempts to develop an improved dehalogenating recombinant microorganism for containment experiments.

  14. Calibration of neural networks using genetic algorithms, with application to optimal path planning

    NASA Technical Reports Server (NTRS)

    Smith, Terence R.; Pitney, Gilbert A.; Greenwood, Daniel

    1987-01-01

    Genetic algorithms (GA) are used to search the synaptic weight space of artificial neural systems (ANS) for weight vectors that optimize some network performance function. GAs do not suffer from some of the architectural constraints involved with other techniques and it is straightforward to incorporate terms into the performance function concerning the metastructure of the ANS. Hence GAs offer a remarkably general approach to calibrating ANS. GAs are applied to the problem of calibrating an ANS that finds optimal paths over a given surface. This problem involves training an ANS on a relatively small set of paths and then examining whether the calibrated ANS is able to find good paths between arbitrary start and end points on the surface.

  15. Molecular biology as a tool for genetic research in hypertension: application to the renin gene.

    PubMed

    Soubrier, F; Houot, A M; Jeunemaitre, X; Plouin, P F; Corvol, P

    1988-01-01

    Hypertension is a multifactorial and heterogeneous disease caused by the addition of environmental and genetic factors. Heritability of systolic and diastolic blood pressure has been well established. Among 6,594 hypertensive patients studied in our clinic, 42% had a history of hypertension in one of their parents and in this group, 13% also had a hypertensive sibling. Anamnestic but not clinical features of patients with familial hypertension slightly differ from patients without familial hypertension. A general strategy is proposed to test the hypothesis that genes known to regulate blood pressure are also responsible for liability to hypertension. In a preliminary report, a study of the TaqI polymorphism of the human renin gene did not reveal a significant difference between hypertensive patients with a family history of hypertension and normotensive controls. A linkage study with DNA markers in informative families is also proposed as an alternative. PMID:2467101

  16. Reverse Sample Genome Probing, a New Technique for Identification of Bacteria in Environmental Samples by DNA Hybridization, and Its Application to the Identification of Sulfate-Reducing Bacteria in Oil Field Samples

    PubMed Central

    Voordouw, Gerrit; Voordouw, Johanna K.; Karkhoff-Schweizer, Roxann R.; Fedorak, Phillip M.; Westlake, Donald W. S.

    1991-01-01

    A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a standard) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples. Images PMID:16348574

  17. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

    PubMed Central

    Powell, W; Morgante, M; McDevitt, R; Vendramin, G G; Rafalski, J A

    1995-01-01

    Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations. Images Fig. 2 PMID:7644491

  18. Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding

    PubMed Central

    Brown, James K.M.; Chartrain, Latitia; Lasserre-Zuber, Pauline; Saintenac, Cyrille

    2015-01-01

    This paper reviews current knowledge about genes for resistance to Septoria tritici blotch (STB) of wheat, caused by Zymoseptoria tritici (formerly Mycosphaerella graminicola). These genes can be placed into two classes, although a few may have characteristics of both classes. Qualitative resistance is controlled by genes which control large fractions of genetic variation, 21 of which have been discovered and mapped so far. Most of them have been shown to be genotype-specific, being effective against the minority of Z. tritici isolates which are avirulent, and Stb6 has been shown to control a gene-for-gene relationship. Most qualitative resistances are unlikely to be durable and some formerly effective genes have been overcome by the evolution of pathogen virulence. Quantitative resistance is generally controlled by genes with small-to-moderate effects on STB. They have generally weaker specificity than qualitative genes and have provided more durable resistance. 89 genome regions carrying quantitative trait loci (QTL) or meta-QTL have been identified to date. Some QTL have been mapped at or near loci of qualitative genes, especially Stb6, which is present in several sources of resistance. Another gene of particular interest is Stb16q, which has been effective against all Z. tritici isolates tested so far. In addition to resistance, the susceptibility of wheat cultivars to STB can also be reduced by disease escape traits, some of which may be undesirable in breeding. The fundamental requirements for breeding for STB-resistance are genetic diversity for resistance in wheat germplasm and a field trial site at which STB epidemics occur regularly and effective selection can be conducted for resistance combined with other desirable traits. If these are in place, knowledge of resistance genes can be applied to improving control of STB. PMID:26092788

  19. Application of Genetic Algorithm to Predict Optimal Sowing Region and Timing for Kentucky Bluegrass in China

    PubMed Central

    Peng, Tingting; Jiang, Bo; Guo, Jiangfeng; Lu, Hongfei; Du, Liqun

    2015-01-01

    Temperature is a predominant environmental factor affecting grass germination and distribution. Various thermal-germination models for prediction of grass seed germination have been reported, in which the relationship between temperature and germination were defined with kernel functions, such as quadratic or quintic function. However, their prediction accuracies warrant further improvements. The purpose of this study is to evaluate the relative prediction accuracies of genetic algorithm (GA) models, which are automatically parameterized with observed germination data. The seeds of five P. pratensis (Kentucky bluegrass, KB) cultivars were germinated under 36 day/night temperature regimes ranging from 5/5 to 40/40°C with 5°C increments. Results showed that optimal germination percentages of all five tested KB cultivars were observed under a fluctuating temperature regime of 20/25°C. Meanwhile, the constant temperature regimes (e.g., 5/5, 10/10, 15/15°C, etc.) suppressed the germination of all five cultivars. Furthermore, the back propagation artificial neural network (BP-ANN) algorithm was integrated to optimize temperature-germination response models from these observed germination data. It was found that integrations of GA-BP-ANN (back propagation aided genetic algorithm artificial neural network) significantly reduced the Root Mean Square Error (RMSE) values from 0.21~0.23 to 0.02~0.09. In an effort to provide a more reliable prediction of optimum sowing time for the tested KB cultivars in various regions in the country, the optimized GA-BP-ANN models were applied to map spatial and temporal germination percentages of blue grass cultivars in China. Our results demonstrate that the GA-BP-ANN model is a convenient and reliable option for constructing thermal-germination response models since it automates model parameterization and has excellent prediction accuracy. PMID:26154163

  20. Application of Genetic Algorithm to Predict Optimal Sowing Region and Timing for Kentucky Bluegrass in China.

    PubMed

    Pi, Erxu; Qu, Liqun; Tang, Xi; Peng, Tingting; Jiang, Bo; Guo, Jiangfeng; Lu, Hongfei; Du, Liqun

    2015-01-01

    Temperature is a predominant environmental factor affecting grass germination and distribution. Various thermal-germination models for prediction of grass seed germination have been reported, in which the relationship between temperature and germination were defined with kernel functions, such as quadratic or quintic function. However, their prediction accuracies warrant further improvements. The purpose of this study is to evaluate the relative prediction accuracies of genetic algorithm (GA) models, which are automatically parameterized with observed germination data. The seeds of five P. pratensis (Kentucky bluegrass, KB) cultivars were germinated under 36 day/night temperature regimes ranging from 5/5 to 40/40 C with 5 C increments. Results showed that optimal germination percentages of all five tested KB cultivars were observed under a fluctuating temperature regime of 20/25 C. Meanwhile, the constant temperature regimes (e.g., 5/5, 10/10, 15/15 C, etc.) suppressed the germination of all five cultivars. Furthermore, the back propagation artificial neural network (BP-ANN) algorithm was integrated to optimize temperature-germination response models from these observed germination data. It was found that integrations of GA-BP-ANN (back propagation aided genetic algorithm artificial neural network) significantly reduced the Root Mean Square Error (RMSE) values from 0.21~0.23 to 0.02~0.09. In an effort to provide a more reliable prediction of optimum sowing time for the tested KB cultivars in various regions in the country, the optimized GA-BP-ANN models were applied to map spatial and temporal germination percentages of blue grass cultivars in China. Our results demonstrate that the GA-BP-ANN model is a convenient and reliable option for constructing thermal-germination response models since it automates model parameterization and has excellent prediction accuracy. PMID:26154163

  1. Reverse Engineering Adverse Outcome Pathways in Ecotoxicology

    EPA Science Inventory

    The toxicological effects of many stressors are mediated through unknown, or incompletely characterized, mechanisms of action. We describe the application of reverse engineering complex interaction networks from high dimensional omics data (gene, protein, meabolic, signaling) t...

  2. DNA genetic artificial fish swarm constant modulus blind equalization algorithm and its application in medical image processing.

    PubMed

    Guo, Y C; Wang, H; Zhang, B L

    2015-01-01

    This study proposes use of the DNA genetic artificial fish swarm constant modulus blind equalization algorithm (DNA-G-AFS-CMBEA) to overcome the local convergence of the CMBEA. In this proposed algorithm, after the fusion of the fast convergence of the AFS algorithm and the global search capability of the DNA-G algorithm to drastically optimize the position vector of the artificial fish, the global optimal position vector is obtained and used as the initial optimal weight vector of the CMBEA. The result of application of this improved method in medical image processing demonstrates that the proposed algorithm outperforms the CMBEA and the AFS-CMBEA in removing the noise in a medical image and improving the peak signal to noise ratio. PMID:26436505

  3. Binary Classification using Decision Tree based Genetic Programming and Its Application to Analysis of Bio-mass Data

    NASA Astrophysics Data System (ADS)

    To, Cuong; Pham, Tuan D.

    2010-01-01

    In machine learning, pattern recognition may be the most popular task. "Similar" patterns identification is also very important in biology because first, it is useful for prediction of patterns associated with disease, for example cancer tissue (normal or tumor); second, similarity or dissimilarity of the kinetic patterns is used to identify coordinately controlled genes or proteins involved in the same regulatory process. Third, similar genes (proteins) share similar functions. In this paper, we present an algorithm which uses genetic programming to create decision tree for binary classification problem. The application of the algorithm was implemented on five real biological databases. Base on the results of comparisons with well-known methods, we see that the algorithm is outstanding in most of cases.

  4. A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

    2003-01-01

    In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

  5. Estimation of Genetic Relationships Between Individuals Across Cohorts and Platforms: Application to Childhood Height.

    PubMed

    Fedko, Iryna O; Hottenga, Jouke-Jan; Medina-Gomez, Carolina; Pappa, Irene; van Beijsterveldt, Catharina E M; Ehli, Erik A; Davies, Gareth E; Rivadeneira, Fernando; Tiemeier, Henning; Swertz, Morris A; Middeldorp, Christel M; Bartels, Meike; Boomsma, Dorret I

    2015-09-01

    Combining genotype data across cohorts increases power to estimate the heritability due to common single nucleotide polymorphisms (SNPs), based on analyzing a Genetic Relationship Matrix (GRM). However, the combination of SNP data across multiple cohorts may lead to stratification, when for example, different genotyping platforms are used. In the current study, we address issues of combining SNP data from different cohorts, the Netherlands Twin Register (NTR) and the Generation R (GENR) study. Both cohorts include children of Northern European Dutch background (N = 3102 + 2826, respectively) who were genotyped on different platforms. We explore imputation and phasing as a tool and compare three GRM-building strategies, when data from two cohorts are (1) just combined, (2) pre-combined and cross-platform imputed and (3) cross-platform imputed and post-combined. We test these three strategies with data on childhood height for unrelated individuals (N = 3124, average age 6.7 years) to explore their effect on SNP-heritability estimates and compare results to those obtained from the independent studies. All combination strategies result in SNP-heritability estimates with a standard error smaller than those of the independent studies. We did not observe significant difference in estimates of SNP-heritability based on various cross-platform imputed GRMs. SNP-heritability of childhood height was on average estimated as 0.50 (SE = 0.10). Introducing cohort as a covariate resulted in ≈2 % drop. Principal components (PCs) adjustment resulted in SNP-heritability estimates of about 0.39 (SE = 0.11). Strikingly, we did not find significant difference between cross-platform imputed and combined GRMs. All estimates were significant regardless the use of PCs adjustment. Based on these analyses we conclude that imputation with a reference set helps to increase power to estimate SNP-heritability by combining cohorts of the same ethnicity genotyped on different platforms. However, important factors should be taken into account such as remaining cohort stratification after imputation and/or phenotypic heterogeneity between and within cohorts. Whether one should use imputation, or just combine the genotype data, depends on the number of overlapping SNPs in relation to the total number of genotyped SNPs for both cohorts, and their ability to tag all the genetic variance related to the specific trait of interest. PMID:26036992

  6. Morphological evolution of protective works by Genetic Algorithms: An application to Mt Etna

    NASA Astrophysics Data System (ADS)

    Marocco, Davide; Spataro, William; D'Ambrosio, Donato; Filippone, Giuseppe; Rongo, Rocco; Iovine, Giulio; Neri, Marco

    2013-04-01

    The hazard induced by dangerous flow-type phenomena - e.g. lava flows, earth flows, debris flows, and debris avalanches - has increased in recent years due to continuous urbanization. In many cases, the numerical simulation of hypothetical events can help to forecast the flow path in advance and therefore give indications about the areas that can be considered for the construction of protective works - e.g. earth barriers or channels. In this way, urbanized areas, as well as cultural heritage sites or even important infrastructures, can be protected by diverting the flow towards lower interest regions. Here, we have considered the numerical Cellular Automata model Sciara-fv2 for simulating lava flows at Mt Etna and Genetic Algorithms for optimizing the position, orientation and extension of an earth barrier built to protect the Rifugio Sapienza, a well-known touristic facility located near the summit of the volcano. The Rifugio Sapienza area was in fact interested by a lava flow in 2003, which destroyed a Service Center, a parking area and a Cafeteria. In this study, a perimeter was devised around the Rifugio (i.e., security perimeter), which delimitates the area that has to be protected by the flow. Furthermore, another perimeter was devised (i.e., work perimeter), specifying the area in which the earth barrier can be located. The barrier is specified by three parameters, namely the two geographic coordinates of the vertex and the height. In fact, in this preliminary analysis the barrier was modeled as a segment (in plant) having a constant height. Though preliminary, the study has produced extremely positive results. Among different alternatives generated by the genetic algorithm, an interesting scenario consists of a 35 meters barrier high solution, which completely deviates the flow avoiding that the lava reaches the inhabited area. The relative elevated height of the barrier is high due to the fact that the crater is located close to the area to be protected and, consequently, the lava rate is very high.

  7. Reversal of Oral Anticoagulation

    PubMed Central

    Limdi, Nita A.

    2013-01-01

    Although the use of dabigatran and rivaroxaban are increasing, data on reversal of their effects are limited. The lack of reliable monitoring methods and specific reversal agents renders treatment strategies empirical and as a result, , treatment consists mainly of supportive measures. Therefore, we performed a systematic search of the PubMed database to find studies and reviews pertaining to oral anticoagulation reversal strategies. This review discusses current anticoagulation reversal recommendations for the oral anticoagulants warfarin, dabigatran, and rivaroxaban for patients at a heightened risk of bleeding, actively bleeding or those in need for pre-procedural anticoagulation reversal. We highlight the literature that shaped these recommendations and provide directions for future research to address knowledge gaps. While reliable recommendations are available for anticoagulation reversal in patients treated with warfarin, guidance on reversal of dabigatran and rivaroxaban is varied and equivocal. Given the increasing use of the newer agents, focused research is needed to identify effective reversal strategies and develop and implement an accurate method (assay) to guide reversal of the newer agents. Determining patient-specific factors that influence the effectiveness of reversal treatments and comparing the effectiveness of various treatment strategies are pertinent areas for future anticoagulation reversal research. PMID:23606318

  8. Applications of High-Performance Computing (HPC) in Plant Breeding, Conservation, and Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasingly powerful and informative DNA sequencing and genotyping techniques, instruments, and software are being developed and used for a wide variety of applications in agriculture. However, the increasing flux and accumulation of data will also require more HPC facilities and expertise. In co...

  9. The use of yeast genetic diversity for agricultural and biotechnological applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many yeasts have been shown to be effective for biocontrol of field, greenhouse, and storage diseases of agricultural crops. Yeasts are generally regarded as safe for a wide variety of applications and some species establish large populations on leaf and fruit surfaces, resulting in disease control ...

  10. A case study of crop model applications in an increasing diversity of genetically modified traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted to develop variety files for six GM cultivars. Several experiments were conducted between 2001 and 2006 by varying cultivars, nitrogen, irrigation, and PIX applications on two different soils in two different growing seasons. In each experiment, plant height and numbers of main...

  11. The use of yeast genetic diversity for agricultural and biotechnological applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many types of yeast have been shown to be effective for biocontrol of field, greenhouse, and storage diseases of agricultural crops. Yeasts are generally regarded as safe for a wide variety of applications and some species establish large populations on leaf and fruit surfaces, resulting in disease ...

  12. Genetic editing of HLA expression in hematopoietic stem cells to broaden their human application

    PubMed Central

    Torikai, Hiroki; Mi, Tiejuan; Gragert, Loren; Maiers, Martin; Najjar, Amer; Ang, Sonny; Maiti, Sourindra; Dai, Jianliang; Switzer, Kirsten C.; Huls, Helen; Dulay, Gladys P.; Reik, Andreas; Rebar, Edward J.; Holmes, Michael C.; Gregory, Philip D.; Champlin, Richard E.; Shpall, Elizabeth J.; Cooper, Laurence J. N.

    2016-01-01

    Mismatch of human leukocyte antigens (HLA) adversely impacts the outcome of patients after allogeneic hematopoietic stem-cell transplantation (alloHSCT). This translates into the clinical requirement to timely identify suitable HLA-matched donors which in turn curtails the chances of recipients, especially those from a racial minority, to successfully undergo alloHSCT. We thus sought to broaden the existing pool of registered unrelated donors based on analysis that eliminating the expression of the HLA-A increases the chance for finding a donor matched at HLA-B, -C, and -DRB1 regardless of a patient’s race. Elimination of HLA-A expression in HSC was achieved using artificial zinc finger nucleases designed to target HLA-A alleles. Significantly, these engineered HSCs maintain their ability to engraft and reconstitute hematopoiesis in immunocompromised mice. This introduced loss of HLA-A expression decreases the need to recruit large number of donors to match with potential recipients and has particular importance for patients whose HLA repertoire is under-represented in the current donor pool. Furthermore, the genetic engineering of stem cells provides a translational approach to HLA-match a limited number of third-party donors with a wide number of recipients. PMID:26902653

  13. Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution

    PubMed Central

    Crawford, Forrest W.; Suchard, Marc A.

    2011-01-01

    A birth-death process is a continuous-time Markov chain that counts the number of particles in a system over time. In the general process with n current particles, a new particle is born with instantaneous rate ?n and a particle dies with instantaneous rate ?n. Currently no robust and efficient method exists to evaluate the finite-time transition probabilities in a general birth-death process with arbitrary birth and death rates. In this paper, we first revisit the theory of continued fractions to obtain expressions for the Laplace transforms of these transition probabilities and make explicit an important derivation connecting transition probabilities and continued fractions. We then develop an efficient algorithm for computing these probabilities that analyzes the error associated with approximations in the method. We demonstrate that this error-controlled method agrees with known solutions and outperforms previous approaches to computing these probabilities. Finally, we apply our novel method to several important problems in ecology, evolution, and genetics. PMID:21984359

  14. Genetic manipulation of acidophilic bacteria which are potentially applicable in coal beneficiation

    SciTech Connect

    Roberto, F.F.; Glenn, A.W.; Bulmer, D.; Bruhn, D.F.; Ward, T.E.

    1991-01-01

    The economic and practical aspects of a biological coal desulfurization process are the subject of increasing study. Depyritization of coal by the bacterium Thiobacillus ferrooxidans has been known for some time and pilot scale experiments are underway. A number of limitations have already been recognized for this process, foremost of which is the speed with which the microorganisms grow and attack the pyritic sulfur. Metal toxicity and mass transfer dynamics also present formidable hurdles. Removal of organic sulfur substituents poses even more difficult problems at this time, not least of which is the leak of efficient candidate organisms. Potential candidates at this time resemble members of the Psedomonadaceae, common environmental bacteria. The various limitations in the microorganisms being examined for a viable desulfurization process have led us to initiate studies on the extension of molecular genetic techniques to acidophilic bacteria, with an ultimate goal of introducing desirable characteristics for desulfurization (enhanced growth rate, metal resistance, biochemical capacity to degrade organic sulfur) either directly into T. ferrooxidans, or, alternatively, into a heterotrophic acidophile which can coexist in the same environment as T. ferrooxidans. We are focusing on members of the genus Acidiphilium, one such acidophilic heterotroph. 22 refs., 1 fig., 2 tabs.

  15. Application of the genetic optimizaton method to the design of ultrasonic motors

    NASA Astrophysics Data System (ADS)

    Bouchilloux, Philippe; Uchino, Kenji

    2002-07-01

    Ultrasonic motors often use a combination of structural modes to generate the desired elliptical vibration field that ultimately results in the linear or rotary motion of an object. Designing an ultrasonic device that combines structural modes of vibration represents a non-trivial exercise, especially when it is desired to maximize the electromechanical coupling coefficient of the piezoelectric elements, the amplitude of vibration, and the force factor of the device. Other parameters may also be combined and render the exercise even more difficult: targeting a specific frequency, constraining dimensions, electrical constraints, etc. To help designing such ultrasonic structures, we propose to use the genetic optimization method in combination to the finite element method. Although evolutionary methods are not new and have been successfully applied to a variety of problems (including smart devices), they have never been applied, to the best of our knowledge, to the design of ultrasonic motors. In this paper, we review the general aspects of the method utilized, and provide several examples, including experimental verification.

  16. The beneficial effects of preimplantation genetic diagnosis for aneuploidy support extensive clinical application.

    PubMed

    Gianaroli, Luca; Magli, M Cristina; Ferraretti, Anna P; Tabanelli, Carla; Trengia, Vincenzo; Farfalli, Valeria; Cavallini, Giorgio

    2005-05-01

    The aim of this study was to evaluate the clinical impact of preimplantation genetic diagnosis (PGD) for aneuploidy on 193 patients who subsequently achieved 208 clinical pregnancies, in relation to their reproductive history. The 208 clinical pregnancies included in the study resulted from 1029 assisted conception cycles in combination with PGD for aneuploidy in 740 couples with a history of poor reproductive performance. According to the reproductive history of the 193 patients, 61 had previously experienced 112 pregnancies with 105 abortions and seven deliveries, corresponding to 3.6% take-home baby rate and 10.9% implantation rate. During the PGD cycle, preimplantation embryos were analysed for 5-9 chromosomes. The transfer of euploid embryos was performed in 699 cycles (68% of oocyte retrievals), generating 171 term pregnancies with 210 infants born, whereas 34 aborted spontaneously and three were ectopic, giving a take-home baby rate per pregnant patient of 88.6% and an ongoing implantation rate per pregnant patient of 53.2%. According to these data, selection made in preimplantation embryos against chromosomal abnormalities is associated with a significantly higher (P < 0.001) take-home baby rate when compared with the previous reproductive history of the parents. PMID:15949222

  17. Application of genetic algorithms to a detailed chemical reaction system for secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Xia, A.; Stroud, C.; Makar, P.

    2009-12-01

    An explicit chemical mechanism is instrumental to modeling secondary organic aerosol (SOA) formation. It is, however, difficult to implement an explicit mechanism in a 3-dimensional air quality model because of the high computational cost caused by a large number of reactions and organic species involved. To address this issue, a new simplified chemical reaction system is first proposed for ?-pinene SOA formation, which uses the volatility-basis set speciation for condensable products. The simple reaction system reflects the evolution of chemical species from a near-explicit master chemical mechanism (MCM) and it also unifies reactions between SOA precursors with different oxidants under different conditions. A total of 440 unknown parameters (product yields of parameterized products, reaction rates, etc.) from the new reaction system are estimated by using multi-objective genetic algorithms operating on the detailed mechanism. The number of species was reduced from 300 in the detailed mechanism to 30 in the simplified mechanism. Output species profiles, obtained from original subset of MCM reactions for ?-pinene oxidation, are reproduced for scenarios under a wide range of HC/NOx conditions. Ultimately, the same unified simple reaction system with updated parameters could be used to describe the SOA formation from different precursors.

  18. Genetic algorithm based approach to investigate doped metal oxide materials: Application to lanthanide-doped ceria

    NASA Astrophysics Data System (ADS)

    Hooper, James; Ismail, Arif; Giorgi, Javier B.; Woo, Tom K.

    2010-06-01

    A genetic algorithm (GA)-inspired method to effectively map out low-energy configurations of doped metal oxide materials is presented. Specialized mating and mutation operations that do not alter the identity of the parent metal oxide have been incorporated to efficiently sample the metal dopant and oxygen vacancy sites. The search algorithms have been tested on lanthanide-doped ceria (L=Sm,Gd,Lu) with various dopant concentrations. Using both classical and first-principles density-functional-theory (DFT) potentials, we have shown the methodology reproduces the results of recent systematic searches of doped ceria at low concentrations (3.2% L2O3 ) and identifies low-energy structures of concentrated samarium-doped ceria (3.8% and 6.6% L2O3 ) which relate to the experimental and theoretical findings published thus far. We introduce a tandem classical/DFT GA algorithm in which an inexpensive classical potential is first used to generate a fit gene pool of structures to enhance the overall efficiency of the computationally demanding DFT-based GA search.

  19. Application of genetic programming and Landsat multi-date imagery for urban growth monitoring

    NASA Astrophysics Data System (ADS)

    Djerriri, Khelifa; Malki, Mimoun

    2013-10-01

    Monitoring of earth surface changes from space by using multi-date satellite imagery was always a main concern to researchers in the field of remotely sensed image processing. Thus, several techniques have been proposed to saving technicians from interpreting and digitizing hundreds of areas by hand. The exploiting of simple, easy to memorize and often comprehensible mathematical models such band-ratios and indices are one of the widely used techniques in remote sensing for the extraction of particular land-cover/land-use like urban and vegetation areas. The results of these models generally only need the definition of adequate threshold or using simple unsupervised classification algorithms to discriminate between the class of interest and the background. In our work a genetic programming based approach has been adopted to evolve simple mathematical expression to extract urban areas from image series. The model is built from a single image by using a basic set of operators between spectral bands and maximizing a fitness function, which is based on the using of the M-statistic criterion. The model was constructed from the Landsat 5 TM image acquired in 2006 by using training samples extracted with the help of a Quick-bird high spatial resolution satellite image acquired the same day as the Landsat image over the city of Oran, Algeria. The model has been tested to extract urban areas from multi-date series of Landsat TM imagery

  20. Genetic editing of HLA expression in hematopoietic stem cells to broaden their human application.

    PubMed

    Torikai, Hiroki; Mi, Tiejuan; Gragert, Loren; Maiers, Martin; Najjar, Amer; Ang, Sonny; Maiti, Sourindra; Dai, Jianliang; Switzer, Kirsten C; Huls, Helen; Dulay, Gladys P; Reik, Andreas; Rebar, Edward J; Holmes, Michael C; Gregory, Philip D; Champlin, Richard E; Shpall, Elizabeth J; Cooper, Laurence J N

    2016-01-01

    Mismatch of human leukocyte antigens (HLA) adversely impacts the outcome of patients after allogeneic hematopoietic stem-cell transplantation (alloHSCT). This translates into the clinical requirement to timely identify suitable HLA-matched donors which in turn curtails the chances of recipients, especially those from a racial minority, to successfully undergo alloHSCT. We thus sought to broaden the existing pool of registered unrelated donors based on analysis that eliminating the expression of the HLA-A increases the chance for finding a donor matched at HLA-B, -C, and -DRB1 regardless of a patient's race. Elimination of HLA-A expression in HSC was achieved using artificial zinc finger nucleases designed to target HLA-A alleles. Significantly, these engineered HSCs maintain their ability to engraft and reconstitute hematopoiesis in immunocompromised mice. This introduced loss of HLA-A expression decreases the need to recruit large number of donors to match with potential recipients and has particular importance for patients whose HLA repertoire is under-represented in the current donor pool. Furthermore, the genetic engineering of stem cells provides a translational approach to HLA-match a limited number of third-party donors with a wide number of recipients. PMID:26902653