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Sample records for reverse genetic applications

  1. [Reverse genetics system of rotaviruses: development and application for analysis of VP4 spike protein].

    PubMed

    Komoto, Satoshi

    2013-01-01

    The rotavirus genome is composed of 11 gene segments of double-stranded (ds)RNA. Reverse genetics is the powerful and ideal methodology for the molecular analysis of virus biology, which enables the virus genome to be artificially manipulated. Although reverse genetics systems exist for nearly all major groups of RNA viruses, development of such a system for rotaviruses is more challenging owing in part to the technical complexity of manipulation of their multi-segmented genome. A breakthrough in the field of rotavirus reverse genetics came in 2006, when we established the first reverse genetics system for rotaviruses, which is a partially plasmid-based system that permits replacement of a viral gene segment with the aid of a helper virus. Although this helper virus-driven system is technically limited and gives low levels of recombinant viruses, it allows alteration of the rotavirus genome, thus contributing to our understanding of these medically important viruses. In this review, I describe the development and application of our rotavirus reverse genetics system, and its future perspectives.

  2. 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

  3. [Progress in establishment and application of feline calicivirus reverse genetics operating system].

    PubMed

    Zhao, Yanli; Dong, Hongwei; Chen, Xiaoqing; Gao, Chao; Liu, Qiuyan; Yang, Songtao; Hu, Guixue

    2015-01-01

    Feline calicivirus (FCV) is an important and highly prevalent pathogen of cats that causes feline respiratory disease. The reverse genetic systems for FCV have been established in national and international laboratories since 1995. This technique has been used widely in FCV basic research and good progress has consequently been made to determine the relationship between viral genome structures and the function of their proteins, the expression of foreign proteins, virus-host interactions, and viral pathogenic mechanisms. In this article,we review the state of progress with regards to the establishment and application of the FCV reverse genetic operating system,which will provide a useful reference tool for future related research. PMID:25997334

  4. Reverse genetics of mononegavirales.

    PubMed

    Conzelmann, K K

    2004-01-01

    "Reverse genetics" or de novo synthesis of nonsegmented negative-sense RNA viruses (Mononegavirales) from cloned cDNA has become a reliable technique to study this group of medically important viruses. Since the first generation of a negative-sense RNA virus entirely from cDNA in 1994, reverse genetics systems have been established for members of most genera of the Rhabdo-, Paramyxo-, and Filoviridae families. These systems are based on intracellular transcription of viral full-length RNAs and simultaneous expression of viral proteins required to form the typical viral ribonucleoprotein complex (RNP). These systems are powerful tools to study all aspects of the virus life cycle as well as the roles of virus proteins in virus-host interplay and pathogenicity. In addition, recombinant viruses can be designed to have specific properties that make them attractive as biotechnological tools and live vaccines. PMID:15298166

  5. Marburg Virus Reverse Genetics Systems

    PubMed Central

    Schmidt, Kristina Maria; Mühlberger, Elke

    2016-01-01

    The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems. PMID:27338448

  6. Influenza reverse genetics: dissecting immunity and pathogenesis.

    PubMed

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

    2014-02-14

    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.

  7. Genetic engineering of rotaviruses by reverse genetics.

    PubMed

    Komoto, Satoshi; Taniguchi, Koki

    2013-07-01

    The rotavirus genome is composed of 11 gene segments of dsRNA. A recent breakthrough in the field of rotaviruses is the development of a reverse genetics system for generating recombinant rotaviruses possessing a gene segment derived from cloned cDNA. Although this approach is a helper virus-driven system that is technically limited and gives low levels of recombinant viruses, it allows alteration of the rotavirus genome, thus contributing to our understanding of these medically important viruses. So far, this approach has successfully been applied to three of the 11 viral segments in our laboratory and others, and the efficiency of recovery of recombinant viruses has been improved. However, we are still waiting for the development of a helper virus-free reverse genetics system for generating an infectious rotavirus entirely from cDNAs, as has been achieved for other members of the Reoviridae family.

  8. Reverse Genetics of Floral Scent: Application of Tobacco Rattle Virus-Based Gene Silencing in Petunia1[OA

    PubMed Central

    Spitzer, Ben; Zvi, Michal Moyal Ben; Ovadis, Marianna; Marhevka, Elena; Barkai, Oren; Edelbaum, Orit; Marton, Ira; Masci, Tania; Alon, Michal; Morin, Shai; Rogachev, Ilana; Aharoni, Asaph; Vainstein, Alexander

    2007-01-01

    Floral fragrance is responsible for attracting pollinators as well as repelling pathogens and pests. As such, it is of immense biological importance. Molecular dissection of the mechanisms underlying scent production would benefit from the use of model plant systems with big floral organs that generate an array of volatiles and that are amenable to methods of forward and reverse genetics. One candidate is petunia (Petunia hybrida), which has emerged as a convenient model system, and both RNAi and overexpression approaches using transgenes have been harnessed for the study of floral volatiles. Virus-induced gene silencing (VIGS) is characterized by a simple inoculation procedure and rapid results relative to transgenesis. Here, we demonstrate the applicability of the tobacco rattle virus-based VIGS system to studies of floral scent. Suppression of the anthocyanin pathway via chalcone synthase silencing was used as a reporter, allowing easy visual identification of anthocyaninless silenced flowers/tissues with no effect on the level of volatile emissions. Use of tobacco rattle virus constructs containing target genes involved in phenylpropanoid volatile production, fused to the chalcone synthase reporter, allowed simple identification of flowers with suppressed activity of the target genes. The applicability of VIGS was exemplified with genes encoding S-adenosyl-l-methionine:benzoic acid/salicylic acid carboxyl methyltransferase, phenylacetaldehyde synthase, and the myb transcription factor ODORANT1. Because this high-throughput reverse-genetics approach was applicable to both structural and regulatory genes responsible for volatile production, it is expected to be highly instrumental for large-scale scanning and functional characterization of novel scent genes. PMID:17720754

  9. [Reverse genetics and prenatal diagnosis].

    PubMed

    Plauchu, H

    1988-05-01

    "Reverse" genetics is a research process consisting in finding the gene of a disease, then in "descending" toward the final product that it codes. This reasoning is the reverse of the one normally used which "ascends from the protein to the gene" and can be applied to the discovery of the pathogenic mechanism of a disease. There are numerous spin-offs of this new type of approach for prenatal diagnosis (PND). Thus, the discovery of polymorphic tracers surrounding the gene enables an indirect PND in informative families. Reliability is great if we have many probes at our disposal. Then, discovery of the gene itself permits a direct PND with the use of intragenic probes and synthetic oligonucleotides.

  10. Reverse Genetics in Ecological Research

    PubMed Central

    Schwachtje, Jens; Kutschbach, Susan; Baldwin, Ian T.

    2008-01-01

    By precisely manipulating the expression of individual genetic elements thought to be important for ecological performance, reverse genetics has the potential to revolutionize plant ecology. However, untested concerns about possible side-effects of the transformation technique, caused by Agrobacterium infection and tissue culture, on plant performance have stymied research by requiring onerous sample sizes. We compare 5 independently transformed Nicotiana attenuata lines harboring empty vector control (EVC) T-DNA lacking silencing information with isogenic wild types (WT), and measured a battery of ecologically relevant traits, known to be important in plant-herbivore interactions: phytohormones, secondary metabolites, growth and fitness parameters under stringent competitive conditions, and transcriptional regulation with microarrays. As a positive control, we included a line silenced in trypsin proteinase inhibitor gene (TPI) expression, a potent anti-herbivore defense known to exact fitness costs in its expression, in the analysis. The experiment was conducted twice, with 10 and 20 biological replicates per genotype. For all parameters, we detected no difference between any EVC and WT lines, but could readily detect a fitness benefit of silencing TPI production. A statistical power analyses revealed that the minimum sample sizes required for detecting significant fitness differences between EVC and WT was 2–3 orders of magnitude larger than the 10 replicates required to detect a fitness effect of TPI silencing. We conclude that possible side-effects of transformation are far too low to obfuscate the study of ecologically relevant phenotypes. PMID:18253491

  11. RNA virus reverse genetics and vaccine design.

    PubMed

    Stobart, Christopher C; Moore, Martin L

    2014-06-25

    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.

  12. 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

  13. CRISPR: a versatile tool for both forward and reverse genetics research.

    PubMed

    Gurumurthy, Channabasavaiah B; Grati, M'hamed; Ohtsuka, Masato; Schilit, Samantha L P; Quadros, Rolen M; Liu, Xue Zhong

    2016-09-01

    Human genetics research employs the two opposing approaches of forward and reverse genetics. While forward genetics identifies and links a mutation to an observed disease etiology, reverse genetics induces mutations in model organisms to study their role in disease. In most cases, causality for mutations identified by forward genetics is confirmed by reverse genetics through the development of genetically engineered animal models and an assessment of whether the model can recapitulate the disease. While many technological advances have helped improve these approaches, some gaps still remain. CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated), which has emerged as a revolutionary genetic engineering tool, holds great promise for closing such gaps. By combining the benefits of forward and reverse genetics, it has dramatically expedited human genetics research. We provide a perspective on the power of CRISPR-based forward and reverse genetics tools in human genetics and discuss its applications using some disease examples. PMID:27384229

  14. CRISPR: a versatile tool for both forward and reverse genetics research.

    PubMed

    Gurumurthy, Channabasavaiah B; Grati, M'hamed; Ohtsuka, Masato; Schilit, Samantha L P; Quadros, Rolen M; Liu, Xue Zhong

    2016-09-01

    Human genetics research employs the two opposing approaches of forward and reverse genetics. While forward genetics identifies and links a mutation to an observed disease etiology, reverse genetics induces mutations in model organisms to study their role in disease. In most cases, causality for mutations identified by forward genetics is confirmed by reverse genetics through the development of genetically engineered animal models and an assessment of whether the model can recapitulate the disease. While many technological advances have helped improve these approaches, some gaps still remain. CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated), which has emerged as a revolutionary genetic engineering tool, holds great promise for closing such gaps. By combining the benefits of forward and reverse genetics, it has dramatically expedited human genetics research. We provide a perspective on the power of CRISPR-based forward and reverse genetics tools in human genetics and discuss its applications using some disease examples.

  15. Developments in Plant Negative-Strand RNA Virus Reverse Genetics.

    PubMed

    Jackson, Andrew O; Li, Zhenghe

    2016-08-01

    Twenty years ago, breakthroughs for reverse genetics analyses of negative-strand RNA (NSR) viruses were achieved by devising conditions for generation of infectious viruses in susceptible cells. Recombinant strategies have subsequently been engineered for members of all vertebrate NSR virus families, and research arising from these advances has profoundly increased understanding of infection cycles, pathogenesis, and complexities of host interactions of animal NSR viruses. These strategies also permitted development of many applications, including attenuated vaccines and delivery vehicles for therapeutic and biotechnology proteins. However, for a variety of reasons, it was difficult to devise procedures for reverse genetics analyses of plant NSR viruses. In this review, we discuss advances that have circumvented these problems and resulted in construction of a recombinant system for Sonchus yellow net nucleorhabdovirus. We also discuss possible extensions to other plant NSR viruses as well as the applications that may emanate from recombinant analyses of these pathogens. PMID:27359368

  16. 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.

  17. Reverse genetics tools in zebrafish: a forward dive into endocrinology.

    PubMed

    Sugano, Yuya; Neuhauss, Stephan C F

    2013-07-01

    The zebrafish is a powerful genetic model organism. In recent years, zebrafish has been increasingly used to model human diseases. Due to a number of recent technological advancements, the genetic tool box is now also stocked with sophisticated transgenic and reverse genetic tools. Here, we focus on both commonly used and recently established reverse genetic and transgenic tools available in zebrafish. These new developments make the zebrafish an even more attractive animal model in comparative endocrinology.

  18. 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.

  19. Reverse genetics in rice using Tos17.

    PubMed

    Mieulet, Delphine; Diévart, Anne; Droc, Gaëtan; Lanau, Nadège; Guiderdoni, Emmanuel

    2013-01-01

    Transposon of Oryza sativa 17 (Tos17), a Ty1-Copia Class I retroelement, is one of the few active retroelements identified in rice, the main cereal crop of human consumption and the model genome for cereals. Tos17 exists in two copies in the standard Nipponbare japonica genome (n = 12 and 379 Mb). Tos17 copies are inactive in the plant grown under normal conditions. However, the copy located on chromosome 7 can be activated upon tissue culture. Plants regenerated from 3- and 5-month-old tissue cultures harbor, respectively, an average of 3.5 and 8 newly transposed copies that are stably inserted at new positions in the genome. Due to its favorable features, Tos17 has been extensively used for insertion mutagenesis of the model genome and 31,403 sequence indexed inserts harbored by regenerants/T-DNA plants are available in the databases. The corresponding seed stocks can be ordered from the laboratories which generated them. Both forward genetics and reverse genetics approaches using these lines have allowed the deciphering of gene function in rice. We report here two protocols for ascertaining the presence of a Tos17 insertion in a gene of interest among R2/T2 seeds received from Tos17 mutant stock centers: The first protocol is PCR-based and allows the identification of azygous, heterozygous and homozygous plants among progenies segregating the insertion. The second protocol is based on DNA blot analysis and can be used to identify homozygous plants carrying the Tos17 copy responsible for gene disruption while cleaning the mutant background from other unwitting mutagen inserts. PMID:23918431

  20. Tackling feline infectious peritonitis via reverse genetics.

    PubMed

    Thiel, Volker; Thiel, Heinz-Jürgen; 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.

  1. Tackling feline infectious peritonitis via reverse genetics

    PubMed Central

    Thiel, Volker; Thiel, Heinz-Jürgen; 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

  2. Reverse Genetics System for Studying Human Rhinovirus Infections

    PubMed Central

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

    2015-01-01

    SUMMARY 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 the 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

  3. 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 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 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 cat’s internal genome. PMID:21147473

  4. 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.

  5. 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

  6. Reverse genetics and transient gene expression in fleshy fruits

    PubMed Central

    Orzaez, Diego

    2009-01-01

    Fast methods to validate relevant candidate genes associated to fruit ripening are needed specially to associate gene function to the overwhelming amount of leads provided by genomic projects. In tomato, the use of Fruit VIGS in a Del/Ros1 background as described in the Plant Physiology by Orzaez et al. 2009, overcomes the difficulties associated to low efficiency VIGS in tomato and increases the reliability and throughput of this fast reverse genetic assay. The advantages of this transient assay system are discussed here for the case of gene functions associated to fruit ripening and quality traits. The possibility of using other reporters or even the development of transient overexpression assays in the fruit is also discussed. PMID:19847114

  7. Integrating chemical mutagenesis and whole genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia

    PubMed Central

    Kokes, Marcela; Dunn, Joe Dan; Granek, Joshua A.; Nguyen, Bidong D.; Barker, Jeffrey R.; Valdivia, Raphael H.; Bastidas, Robert J.

    2015-01-01

    SUMMARY Gene inactivation by transposon insertion or allelic exchange is a powerful approach to probe gene function. Unfortunately, many microbes, including Chlamydia, are not amenable to routine molecular genetic manipulations. Here we describe an arrayed library of chemically-induced mutants of the genetically-intransigent pathogen Chlamydia trachomatis, in which all mutations have been identified by whole genome sequencing, providing a platform for reverse genetic applications. An analysis of possible loss-of-function mutations in the collection uncovered plasticity in the central metabolic properties of this obligate intracellular pathogen. We also describe the use of the library in a forward genetic screen that identified InaC as a bacterial factor that binds host ARF and 14-3-3 proteins to modulate F-actin assembly and Golgi redistribution around the pathogenic vacuole. This work provides a robust platform for reverse and forward genetic approaches in Chlamydia and should serve as a valuable resource to the community. PMID:25920978

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Genetic demographic networks: Mathematical model and applications.

    PubMed

    Kimmel, Marek; Wojdyła, Tomasz

    2016-10-01

    Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise

  13. 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.

  14. 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.

  15. [Advances in reverse genetics-based vaccines of foot and mouth disease].

    PubMed

    Yang, Bo; Yang, Fan; Wang, Song-Hao; Zhang, Yan; Cao, Wei-Jun; Yin, Hong; Zheng, Hai-Xue

    2014-03-01

    Reverse-genetic engineering of foot and mouth disease virus (FMDV) can improve the productivity, antigen matching, antigen stability, immune response ability, and biological safety of vaccines, so vaccine candidates with anticipated biological characteristics can be promptly achieved. Negative influence in taming of virulent strains can also be decreased or avoided. Reverse genetics not only make up for deficiencies like limitation of viral nature, low success rate, and time and energy consuming, but also realize more active designing of vaccines. Therefore, reverse genetics is significant in improving integral quality and efficiency of vaccines. In this review, we use FMDV vaccines as an example to summarize improvement in biological characteristics of virulent strains and provide a reference for related researches.

  16. Reverse genetics systems as tools for the development of novel therapies against filoviruses.

    PubMed

    Hoenen, Thomas; Feldmann, Heinz

    2014-10-01

    Filoviruses cause severe hemorrhagic fevers with case fatality rates of up to 90%, for which no antivirals are currently available. Their categorization as biosafety level 4 agents restricts work with infectious viruses to a few maximum containment laboratories worldwide, which constitutes a significant obstacle for the development of countermeasures. Reverse genetics facilitates the generation of recombinant filoviruses, including reporter-expressing viruses, which have been increasingly used for drug screening and development in recent years. Further, reverse-genetics based lifecycle modeling systems allow modeling of the filovirus lifecycle without the need for a maximum containment laboratory and have recently been optimized for use in high-throughput assays. The availability of these reverse genetics-based tools will significantly improve our ability to find novel antivirals against filoviruses. PMID:25169588

  17. 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 μm 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.

  18. 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

  19. 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.

  20. Genetic demographic networks: Mathematical model and applications.

    PubMed

    Kimmel, Marek; Wojdyła, Tomasz

    2016-10-01

    Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise

  1. Fly-TILL: reverse genetics using a living point mutation resource.

    PubMed

    Cooper, Jennifer L; Till, Bradley J; Henikoff, Steven

    2008-01-01

    Mutagenesis with ethylmethanesulfonate (EMS) has been the standard for traditional genetic screens, and in recent years has been applied to reverse genetics. However, reverse-genetic strategies require maintaining a viable germline library so that mutations that are discovered can subsequently be recovered. In applying our TILLING (Targeting Induced Local Lesions IN Genomes) method to establish a Drosophila reverse-genetic service (Fly-TILL), we chose to screen the Zuker lines, a large collection of EMS-mutagenized second- and third-chromosome balanced lines that had been established for forward-genetic screening. For the past four years, our Fly-TILL service has screened this collection to provide approximately 150 allelic series of point mutations for the fly community. Our analysis of >2000 point mutations and indels have provided a glimpse into the population dynamics of this valuable genetic resource. We found evidence for selection and differential recovery of mutations, depending on distance from balancer breakpoints. Although this process led to variable mutational densities, we have nevertheless been able to deliver potentially valuable mutations in genes selected by Fly-TILL users. We anticipate that our findings will help guide the future implementation of point-mutation resources for the Drosophila community.

  2. Wnt addiction of genetically defined cancers reversed by PORCN inhibition.

    PubMed

    Madan, B; Ke, Z; Harmston, N; Ho, S Y; Frois, A O; Alam, J; Jeyaraj, D A; Pendharkar, V; Ghosh, K; Virshup, I H; Manoharan, V; Ong, E H Q; Sangthongpitag, K; Hill, J; Petretto, E; Keller, T H; Lee, M A; Matter, A; Virshup, D M

    2016-04-28

    Enhanced sensitivity to Wnts is an emerging hallmark of a subset of cancers, defined in part by mutations regulating the abundance of their receptors. Whether these mutations identify a clinical opportunity is an important question. Inhibition of Wnt secretion by blocking an essential post-translational modification, palmitoleation, provides a useful therapeutic intervention. We developed a novel potent, orally available PORCN inhibitor, ETC-1922159 (henceforth called ETC-159) that blocks the secretion and activity of all Wnts. ETC-159 is remarkably effective in treating RSPO-translocation bearing colorectal cancer (CRC) patient-derived xenografts. This is the first example of effective targeted therapy for this subset of CRC. Consistent with a central role of Wnt signaling in regulation of gene expression, inhibition of PORCN in RSPO3-translocated cancers causes a marked remodeling of the transcriptome, with loss of cell cycle, stem cell and proliferation genes, and an increase in differentiation markers. Inhibition of Wnt signaling by PORCN inhibition holds promise as differentiation therapy in genetically defined human cancers.

  3. Wnt addiction of genetically defined cancers reversed by PORCN inhibition

    PubMed Central

    Madan, B; Ke, Z; Harmston, N; Ho, S Y; Frois, A O; Alam, J; Jeyaraj, D A; Pendharkar, V; Ghosh, K; Virshup, I H; Manoharan, V; Ong, E H Q; Sangthongpitag, K; Hill, J; Petretto, E; Keller, T H; Lee, M A; Matter, A; Virshup, D M

    2016-01-01

    Enhanced sensitivity to Wnts is an emerging hallmark of a subset of cancers, defined in part by mutations regulating the abundance of their receptors. Whether these mutations identify a clinical opportunity is an important question. Inhibition of Wnt secretion by blocking an essential post-translational modification, palmitoleation, provides a useful therapeutic intervention. We developed a novel potent, orally available PORCN inhibitor, ETC-1922159 (henceforth called ETC-159) that blocks the secretion and activity of all Wnts. ETC-159 is remarkably effective in treating RSPO-translocation bearing colorectal cancer (CRC) patient-derived xenografts. This is the first example of effective targeted therapy for this subset of CRC. Consistent with a central role of Wnt signaling in regulation of gene expression, inhibition of PORCN in RSPO3-translocated cancers causes a marked remodeling of the transcriptome, with loss of cell cycle, stem cell and proliferation genes, and an increase in differentiation markers. Inhibition of Wnt signaling by PORCN inhibition holds promise as differentiation therapy in genetically defined human cancers. PMID:26257057

  4. Pharmacological or Genetic Inactivation of the Serotonin Transporter Improves Reversal Learning in Mice

    PubMed Central

    Mathur, Poonam; Harvey-White, Judith; Izquierdo, Alicia; Saksida, Lisa M.; Bussey, Timothy J.; Fox, Stephanie; Deneris, Evan; Murphy, Dennis L.; Holmes, Andrew

    2010-01-01

    Growing evidence supports a major contribution of cortical serotonin (5-hydroxytryptamine, 5-HT) to the modulation of cognitive flexibility and the cognitive inflexibility evident in neuropsychiatric disorders. The precise role of 5-HT and the influence of 5-HT gene variation in mediating this process is not fully understood. Using a touch screen–based operant system, we assessed reversal of a pairwise visual discrimination as an assay for cognitive flexibility. Effects of constitutive genetic or pharmacological inactivation of the 5-HT transporter (5-HTT) on reversal were examined by testing 5-HTT null mice and chronic fluoxetine-treated C57BL/6J mice, respectively. Effects of constitutive genetic loss or acute pharmacological depletion of 5-HT were assessed by testing Pet-1 null mice and para-chlorophenylalanine (PCPA)–treated C57BL/6J mice, respectively. Fluoxetine-treated C57BL/6J mice made fewer errors than controls during the early phase of reversal when perseverative behavior is relatively high. 5-HTT null mice made fewer errors than controls in completing the reversal task. However, reversal in Pet-1 null and PCPA-treated C57BL/6J mice was not different from controls. These data further support an important role for 5-HT in modulating reversal learning and provide novel evidence that inactivating the 5-HTT improves this process. These findings could have important implications for understanding and treating cognitive inflexibility in neuropsychiatric disease. PMID:20032063

  5. 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.

  6. Time-reversal of nonlinear waves: Applicability and limitations

    NASA Astrophysics Data System (ADS)

    Ducrozet, G.; Fink, M.; Chabchoub, A.

    2016-09-01

    Time-reversal (TR) refocusing of waves is one of the fundamental principles in wave physics. Using the TR approach, time-reversal mirrors can physically create a time-reversed wave that exactly refocus back, in space and time, to its original source regardless of the complexity of the medium as if time were going backward. Laboratory experiments have proved that this approach can be applied not only in acoustics and electromagnetism, but also in the field of linear and nonlinear water waves. Studying the range of validity and limitations of the TR approach may determine and quantify its range of applicability in hydrodynamics. In this context, we report a numerical study of hydrodynamic time-reversal using a unidirectional numerical wave tank, implemented by the nonlinear high-order spectral method, known to accurately model the physical processes at play, beyond physical laboratory restrictions. The applicability of the TR approach is assessed over a variety of hydrodynamic localized and pulsating structures' configurations, pointing out the importance of high-order dispersive and particularly nonlinear effects in the refocusing of hydrodynamic stationary envelope solitons and breathers. We expect that the results may motivate similar experiments in other nonlinear dispersive media and encourage several applications with particular emphasis on the field of ocean engineering.

  7. ECOLOGICAL AND EVOLUTIONARY APPLICATIONS FOR ENVIRONMENTAL SEX REVERSAL OF FISH.

    PubMed

    Mcnair, Alistair; Lokman, P Mark; Closs, Gerard P; Nakagawa, Shinichi

    2015-03-01

    Environmental sex reversal (ESR), which results in a mismatch between genotypic and phenotypic sex, is well documented in numerous fish species and may be induced by chemical exposure. Historically, research involving piscine ESR has been carried out with a view to improving profitability in aquaculture or to elucidate the processes governing sex determination and sexual differentiation. However, recent studies in evolution and ecology suggest research on ESR now has much wider applications and ramifications. We begin with an overview of ESR in fish and a brief review of the traditional applications thereof. We then discuss ESR and its potential demographic consequences in wild populations. Theory even suggests sex-reversed fish may be purposefully released to manipulate population dynamics. We suggest new research directions that may prove fruitful in understanding how ESR at the individual level translates to population-level processes. In the latter portion of the review we focus on evolutionary applications of ESR. Sex-reversal studies from the aquaculture literature provide insight in to the evolvability of determinants of sexual phenotype. Additionally, induced sex reversal can provide information about the evolution of sex chromosomes and sex-linked traits. Recently, naturally occurring ESR has been implicated as a mechanism contributing to the evolution of sex chromosomes.

  8. 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

  9. 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.

  10. 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.

  11. Reveal, a general reverse engineering algorithm for inference of genetic network architectures.

    PubMed

    Liang, S; Fuhrman, S; Somogyi, R

    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(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.

  12. Prospects for fusion applications of reversed-field pinches

    NASA Astrophysics Data System (ADS)

    Bathke, C. G.; Krakowski, R. A.; Hagenson, R. L.

    1985-11-01

    The applicability of the Reversed-Field Pinch (RFP) as a source of fusion neutrons for use in developing key fusion nuclear technologies is examined. This Fusion Test Facility (FTF) would emphasize high neutron wall loading, small plasma volume, low fusion and driver powers, and steady-state operation. Both parametric tradeoffs based on present-day physics understanding and a conceptual design based on an approx. 1-MW/m (neutron) driven operation are reported.

  13. 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…

  14. 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

  15. Development of a PCR-Based Reverse Genetics System for an Attenuated Duck Tembusu Virus Strain.

    PubMed

    Wu, Xiaogang; Shi, Ying; Yan, Dawei; Li, Xuesong; Yan, Pixi; Gao, Xuyuan; Zhang, Yuee; Yu, Lei; Ren, Chaochao; Li, Guoxin; Yan, Liping; Teng, Qiaoyang; Li, Zejun

    2016-01-01

    The infectious disease caused by the duck Tembusu virus (DTMUV) has resulted in massive economic losses to the Chinese duck industry in China since 2010. Research on the molecular basis of DTMUV pathogenicity has been hampered by the lack of a reliable reverse genetics system for this virus. Here we developed a PCR-based reverse genetics system with high fidelity for the attenuated DTMUV strain FX2010-180P. The rescued virus was characterized by using both indirect immunofluorescence assays (IFA) and whole genome sequencing. The rescued virus (rFX2010-180P) grew to similar titers as compared with the wild-type virus in DF-1 cells, and had similar replication and immunogenicity properties in ducks. To determine whether exogenous proteins could be expressed from DTMUV, both an internal ribosomal entry site (IRES) and the enhanced green fluorescent protein (eGFP) gene were introduced between the NS5 gene and the 3' non-coding sequence of FX2010-180P. A recombinant DTMUV expressing eGFP was rescued, but eGFP expression was unstable after 4 passages in DF-1 cells due to a deletion of 1,294 nucleotides. The establishment of a reliable reverse genetics system for FX2010-180P provides a foundation for future studies of DTMUV. PMID:27248497

  16. Development of a PCR-Based Reverse Genetics System for an Attenuated Duck Tembusu Virus Strain

    PubMed Central

    Wu, Xiaogang; Shi, Ying; Yan, Dawei; Li, Xuesong; Yan, Pixi; Gao, Xuyuan; Zhang, Yuee; Yu, Lei; Ren, Chaochao; Li, Guoxin; Yan, Liping; Teng, Qiaoyang; Li, Zejun

    2016-01-01

    The infectious disease caused by the duck Tembusu virus (DTMUV) has resulted in massive economic losses to the Chinese duck industry in China since 2010. Research on the molecular basis of DTMUV pathogenicity has been hampered by the lack of a reliable reverse genetics system for this virus. Here we developed a PCR-based reverse genetics system with high fidelity for the attenuated DTMUV strain FX2010-180P. The rescued virus was characterized by using both indirect immunofluorescence assays (IFA) and whole genome sequencing. The rescued virus (rFX2010-180P) grew to similar titers as compared with the wild-type virus in DF-1 cells, and had similar replication and immunogenicity properties in ducks. To determine whether exogenous proteins could be expressed from DTMUV, both an internal ribosomal entry site (IRES) and the enhanced green fluorescent protein (eGFP) gene were introduced between the NS5 gene and the 3' non-coding sequence of FX2010-180P. A recombinant DTMUV expressing eGFP was rescued, but eGFP expression was unstable after 4 passages in DF-1 cells due to a deletion of 1,294 nucleotides. The establishment of a reliable reverse genetics system for FX2010-180P provides a foundation for future studies of DTMUV. PMID:27248497

  17. 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.

  18. 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

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

    SciTech Connect

    Albariño, César G. Wiggleton Guerrero, Lisa; Lo, Michael K.; Nichol, Stuart T.; Towner, Jonathan S.

    2015-10-15

    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. - Highlights: • Recombinant Ebola virus (EBOV) derived from Makona variant was rescued. • New protocol for viral rescue allows 100% efficiency. • Modified EBOV expresses a green fluorescent protein from a VP40-fused protein. • Modified EBOV was tested as tool to screen antiviral compounds and measure neutralizing antibodies.

  20. Evolved resistance to colistin and its loss due to genetic reversion in Pseudomonas aeruginosa

    PubMed Central

    Lee, Ji-Young; Park, Young Kyoung; Chung, Eun Seon; Na, In Young; Ko, Kwan Soo

    2016-01-01

    The increased reliance on colistin for treating multidrug-resistant Gram-negative bacterial infections has resulted in the emergence of colistin-resistant Pseudomonas aeruginosa. We attempted to identify genetic contributors to colistin resistance in vitro evolved isogenic colistin-resistant and -susceptible strains of two P. aeruginosa lineages (P5 and P155). Their evolutionary paths to acquisition and loss of colistin resistance were also tracked. Comparative genomic analysis revealed 13 and five colistin resistance determinants in the P5 and P155 lineages, respectively. Lipid A in colistin-resistant mutants was modified through the addition of 4-amino-L-arabinose; this modification was absent in colistin-susceptible revertant strains. Many amino acid substitutions that emerged during the acquisition of colistin resistance were reversed in colistin-susceptible revertants. We demonstrated that evolved colistin resistance in P. aeruginosa was mediated by a complicated regulatory network that likely emerges through diverse genetic alterations. Colistin-resistant P. aeruginosa became susceptible to the colistin upon its withdrawal because of genetic reversion. The mechanisms through which P. aeruginosa acquires and loses colistin resistance have implications on the treatment options that can be applied against P. aeruginosa infections, with respect to improving bactericidal efficacy and preventing further resistance to antibiotics. PMID:27150578

  1. 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

  2. Identification of host genes involved in geminivirus infection using a reverse genetics approach.

    PubMed

    Lozano-Durán, Rosa; Rosas-Díaz, Tábata; 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

  3. 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

  4. Reverse Aging of Composite Materials for Aeronautical Applications

    NASA Astrophysics Data System (ADS)

    lannone, Michele

    2008-08-01

    Hygro-thermal ageing of polymer matrix composite materials is a major issue for all the aeronautical structures. For carbon-epoxy composites generally used in aeronautical applications the major effect of ageing is the humidity absorption, which induces a plasticization effect, generally decreasing Tg and elastic moduli, and finally design allowables. A thermodynamical and kinetic study has been performed, aimed to establish a program of periodic heating of the composite part, able to reversing the ageing effect by inducing water desorption. The study was founded on a simple model based on Fick's law, coupled with a concept of "relative saturation coefficient" depending on the different temperature of the composite part and the environment. The behaviour of some structures exposed to humidity and "reverse aged" by heating has been virtually tested. The conclusion of the study allowed to issue a specific patent application for aeronautical structures to be designed on the basis of a "humidity free" concept which allows the use of higher design allowables; having as final results lighter composite structures with a simplified certification process.

  5. [Application of documentary in teaching genetics].

    PubMed

    Gao, Yong; Jian-Min, Chen

    2012-03-01

    This paper describes the advantages and the existing problems of the application of documentary in teaching genetics. Meanwhile, the corresponding improvement approaches were provided based on these problems. The advantages and function of documentary in teaching course will be fully developed and the teaching quality will be improved.

  6. Application of Time Reversed Acoustics for Seismic Source Characterization

    NASA Astrophysics Data System (ADS)

    Lu, R.; Toksöz, M.

    2005-05-01

    Traditionally an earthquake is located and the source mechanism is determined by using P and S phases. This uses only a limited portion of the information contained in a seismogram. A large part of the information carried by the waveform is not used. In this study we investigate the applicability of the Time Reversed Acoustics (TRA) technique, and thus the whole waveform of the recorded signal, for earthquake locations and source characterization. The basic concept involved in TRA is the fundamental symmetry of time reversal invariance. Injecting the recorded signal, with time running backwards, can focus the wave field to the source. TRA has emerged as an important technique in acoustics with applications to medicine, underwater sound, and many other disciplines. Numerical simulations show that the TRA technique can successfully locate a seismic source inside a layered earth model and can also recover the source time function. Finite difference modeling results show that TRA can determine the fault dip, rupture direction, and rupture length. The method is especially advantageous when data are available only from a sparse station network. Full seismograms contain source information from both waves radiated along the source-station ray path and from waves that radiated in all other directions but scattered toward the receivers. Application of the TRA technique to seismic source characterization requires the Green's function, which can be obtained in two ways. If the earth structure is known then the Green's function can be calculated numerically. To improve the efficiency, the method of constructing a medium response library is developed. This improves computation time significantly. The second approach uses small events (e.g., aftershocks) as an empirical Green's function. The performance of the TRA technique is demonstrated with data from real earthquakes.

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

    PubMed

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

    2010-04-01

    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.

  8. 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.

  9. Efficient reverse genetics generation of infectious junin viruses differing in glycoprotein processing.

    PubMed

    Albariño, César G; Bergeron, Eric; Erickson, Bobbie Rae; Khristova, Marina L; Rollin, Pierre E; Nichol, Stuart T

    2009-06-01

    The New World arenaviruses, Junin, Machupo, Guanarito, Sabia, and Chapare, are associated with rapidly progressing severe hemorrhagic fever with a high rate of case fatality in various regions of South America. The threat of natural or deliberate outbreaks associated with these viruses makes the development of preventive or therapeutic measures important. Here we describe a Junin virus functional minigenome system and a reverse genetics system for production of infectious Junin virus. This robust, highly efficient system involves transfection of cells with only two plasmids which transcribe the virus S and L antigenomic RNAs. The utility of the system is demonstrated by generating Junin viruses which encode a glycoprotein precursor (GPC) containing the following: (i) the wild-type (SKI-1/S1P peptidase) cleavage site, (ii) no cleavage site, or (iii) a cleavage site where the SKI-1/S1P motif (RSLK) is replaced by a furin cleavage site (RRKR). In contrast to the wild-type virus, Junin virus lacking a GPC cleavage site replicated within successfully transfected cells but failed to yield infectious virus particles. This confirms observations with other arenaviruses suggesting that GPC cleavage is essential for arenavirus infectivity. In contrast, infectious Junin virus which encoded GPC cleaved by furin-like proteases was easily generated. The two-plasmid, high efficiency aspects of this Junin virus reverse genetics system show great promise for addressing important questions regarding arenavirus hemorrhagic fever disease and for development of precisely attenuated live arenavirus vaccines.

  10. 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

  11. A Multi-Stage Reverse Logistics Network Problem by Using Hybrid Priority-Based Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Lee, Jeong-Eun; Gen, Mitsuo; Rhee, Kyong-Gu

    Today remanufacturing problem is one of the most important problems regarding to the environmental aspects of the recovery of used products and materials. Therefore, the reverse logistics is gaining become power and great potential for winning consumers in a more competitive context in the future. This paper considers the multi-stage reverse Logistics Network Problem (m-rLNP) while minimizing the total cost, which involves reverse logistics shipping cost and fixed cost of opening the disassembly centers and processing centers. In this study, we first formulate the m-rLNP model as a three-stage logistics network model. Following for solving this problem, we propose a Genetic Algorithm pri (GA) with priority-based encoding method consisting of two stages, and introduce a new crossover operator called Weight Mapping Crossover (WMX). Additionally also a heuristic approach is applied in the 3rd stage to ship of materials from processing center to manufacturer. Finally numerical experiments with various scales of the m-rLNP models demonstrate the effectiveness and efficiency of our approach by comparing with the recent researches.

  12. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components.

    PubMed

    Leal, Nicole A; Kim, Hyo-Joong; Hoshika, Shuichi; Kim, Myong-Jung; Carrigan, Matthew A; Benner, Steven A

    2015-04-17

    Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA.

  13. 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. PMID:27034780

  14. 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.

  15. Improved dual promotor-driven reverse genetics system for influenza viruses.

    PubMed

    Mostafa, Ahmed; Kanrai, Pumaree; Ziebuhr, John; Pleschka, Stephan

    2013-11-01

    Reverse genetic systems for influenza A virus (IAV) allow the generation of genetically manipulated infectious virus from a set of transfected plasmid DNAs encoding the eight genomic viral RNA segments (vRNA). For this purpose, cDNAs representing these eight vRNA segments are cloned into specific plasmid vectors that allow the generation of vRNA-like transcripts using polymerase I (Pol I). In addition, these plasmids support the transcription of viral mRNA by polymerase II (Pol II), leading to the expression of viral protein(s) encoded by the respective transcripts. In an effort to develop this system further, we constructed the bi-directional vector pMPccdB. It is based on pHW2000 (Hoffmann et al., 2000b) but contains additionally (i) the ccdB gene whose expression is lethal for most Escherichia coli strains and therefore used as a negative selection marker and (ii) more efficient AarI cloning sites that flank the ccdB gene on either side. Furthermore, we used a modified one-step restriction/ligation protocol to insert the desired cDNA into the respective pMPccdB vector DNA. Both the use of a negative selection marker and an improved cloning protocol were shown to facilitate the generation of genetically engineered IAV as illustrated in this study by the cloning and rescue of the 2009 pandemic isolate A/Giessen/6/2009 (Gi-H1N1). PMID:23886561

  16. The Applications of Genetic Algorithms in Medicine.

    PubMed

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

    2015-11-01

    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

  17. 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

  18. Development of a reverse genetics system to generate recombinant Marburg virus derived from a bat isolate.

    PubMed

    Albariño, César G; Uebelhoer, Luke S; Vincent, Joel P; Khristova, Marina L; Chakrabarti, Ayan K; McElroy, Anita; Nichol, Stuart T; Towner, Jonathan S

    2013-11-01

    Recent investigations have shown the Egyptian fruit bat (Rousettus aegyptiacus) to be a natural reservoir for marburgviruses. To better understand the life cycle of these viruses in the natural host, a new reverse genetics system was developed for the reliable rescue of a Marburg virus (MARV) originally isolated directly from a R. aegyptiacus bat (371Bat). To develop this system, the exact terminal sequences were first determined by 5' and 3' RACE, followed by the cloning of viral proteins NP, VP35, VP30 and L into expression plasmids. Novel conditions were then developed to efficiently replicate virus mini-genomes followed by the construction of full-length genomic clones from which recombinant wild type and GFP-containing MARVs were rescued. Surprisingly, when these recombinant MARVs were propagated in primary human macrophages, a dramatic difference was found in their ability to grow and to elicit anti-viral cytokine responses.

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

    PubMed

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

    2015-05-01

    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.

  20. Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome

    NASA Astrophysics Data System (ADS)

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.

    2016-03-01

    Optical imaging of genetically encoded probes has revolutionized biomedical studies by providing valuable information about targeted biological processes. Here, we report a novel imaging technique, termed reversibly switchable photoacoustic tomography (RS-PAT), which exhibits large penetration depth, high detection sensitivity, and super-resolution. RS-PAT combines advanced photoacoustic imaging techniques with, for the first time, a nonfluorescent photoswitchable bacterial phytochrome. This bacterial phytochrome is the most near-infrared shifted genetically encoded probe reported so far. Moreover, this bacterial phytochrome is reversibly photoconvertible between its far-red and near-infrared light absorption states. Taking maximum advantage of the powerful imaging capability of PAT and the unique photochemical properties of the phytochrome, RS-PAT has broken through both the optical diffusion limit for deep-tissue imaging and the optical diffraction limit for super-resolution photoacoustic microscopy. Specifically, with RS-PAT we have achieved an unprecedented detection sensitivity of ~2 μM, or as few as ~20 tumor cells, at a centimeter depth. Such high sensitivity is fully demonstrated in our study by monitoring tumor growth and metastasis at whole-body level with ~100 μm resolution. Moreover, our microscopic implementation of RS-PAT is capable of imaging mammalian cells with a sub-diffraction lateral resolution of ~140 nm and axial resolution of ~400 nm, which are respectively ~2-fold and ~75-fold finer than those of our conventional photoacoustic microscopy. Overall, RS-PAT is a new and promising imaging technology for studying biological processes at different length scales.

  1. Enterovirus A71 DNA-Launched Infectious Clone as a Robust Reverse Genetic Tool

    PubMed Central

    Tan, Chee Wah; Tee, Han Kang; Lee, Michelle Hui Pheng; Sam, I-Ching; Chan, Yoke Fun

    2016-01-01

    Enterovirus A71 (EV-A71) causes major outbreaks of hand, foot and mouth disease, and is occasionally associated with neurological complications and death in children. Reverse genetics is widely used in the field of virology for functional study of viral genes. For EV-A71, such tools are limited to clones that are transcriptionally controlled by T7/SP6 bacteriophage promoter. This is often time-consuming and expensive. Here, we describe the development of infectious plasmid DNA-based EV-A71 clones, for which EV-A71 genome expression is under transcriptional control by the CMV-intermediate early promoter and SV40 transcriptional-termination signal. Transfection of this EV-A71 infectious DNA produces good virus yield similar to in vitro-transcribed EV-A71 infectious RNA, 6.4 and 5.8 log10PFU/ml, respectively. Infectious plasmid with enhanced green fluorescence protein and Nano luciferase reporter genes also produced good virus titers, with 4.3 and 5.0 log10 PFU/ml, respectively. Another infectious plasmid with both CMV and T7 promoters was also developed for easy manipulation of in vitro transcription or direct plasmid transfection. Transfection with either dual-promoter infectious plasmid DNA or infectious RNA derived from this dual-promoter clone produced infectious viral particles. Incorporation of hepatitis delta virus ribozyme, which yields precise 3’ ends of the DNA-launched EV-A71 genomic transcripts, increased infectious viral production. In contrast, the incorporation of hammerhead ribozyme in the DNA-launched EV-A71 resulted in lower virus yield, but improved the virus titers for T7 promoter-derived infectious RNA. This study describes rapid and robust reverse genetic tools for EV-A71. PMID:27617744

  2. 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

  3. Enterovirus A71 DNA-Launched Infectious Clone as a Robust Reverse Genetic Tool.

    PubMed

    Tan, Chee Wah; Tee, Han Kang; Lee, Michelle Hui Pheng; Sam, I-Ching; Chan, Yoke Fun

    2016-01-01

    Enterovirus A71 (EV-A71) causes major outbreaks of hand, foot and mouth disease, and is occasionally associated with neurological complications and death in children. Reverse genetics is widely used in the field of virology for functional study of viral genes. For EV-A71, such tools are limited to clones that are transcriptionally controlled by T7/SP6 bacteriophage promoter. This is often time-consuming and expensive. Here, we describe the development of infectious plasmid DNA-based EV-A71 clones, for which EV-A71 genome expression is under transcriptional control by the CMV-intermediate early promoter and SV40 transcriptional-termination signal. Transfection of this EV-A71 infectious DNA produces good virus yield similar to in vitro-transcribed EV-A71 infectious RNA, 6.4 and 5.8 log10PFU/ml, respectively. Infectious plasmid with enhanced green fluorescence protein and Nano luciferase reporter genes also produced good virus titers, with 4.3 and 5.0 log10 PFU/ml, respectively. Another infectious plasmid with both CMV and T7 promoters was also developed for easy manipulation of in vitro transcription or direct plasmid transfection. Transfection with either dual-promoter infectious plasmid DNA or infectious RNA derived from this dual-promoter clone produced infectious viral particles. Incorporation of hepatitis delta virus ribozyme, which yields precise 3' ends of the DNA-launched EV-A71 genomic transcripts, increased infectious viral production. In contrast, the incorporation of hammerhead ribozyme in the DNA-launched EV-A71 resulted in lower virus yield, but improved the virus titers for T7 promoter-derived infectious RNA. This study describes rapid and robust reverse genetic tools for EV-A71. PMID:27617744

  4. Development of a novel single-step reverse genetics system for the generation of classical swine fever virus.

    PubMed

    Li, Ling; Pang, Huining; Wu, Rui; Zhang, Yanwen; Tan, Yiluo; Pan, Zishu

    2016-07-01

    We describe an alternative reverse genetics system for generating classical swine fever virus (CSFV) based on swine RNA polymerase I promoter (pSPI)-mediated vRNA transcription. The recombinant plasmid pSPTI/SM harboring a full-length CSFV Shimen strain cDNA, flanked by a swine RNA polymerase I (pol I) promoter sequence at the 5' end and a murine pol I terminator sequence at the 3' end, was constructed. When the plasmid pSPTI/SM was introduced into PK-15 cells by transfection, an infectious CSFV with termini identical to those of the parental virus was generated directly. CSFV rescued from this reverse genetics system exhibited similar growth kinetics and plaque formation compared with the parental CSFV. When the novel reverse genetics system was used to generate the CSFV vaccine C-strain, infectious virus was detected in the supernatant of PK-15 cells transfected with the recombinant plasmid pSPTI/C. This novel reverse genetics system is a simple and efficient tool for the investigation of the structure and function of the viral genome, for molecular pathogenicity studies, and for the development of genetically engineered vaccines for CSFV. PMID:27068166

  5. 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

  6. 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

  7. 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 μm(2)/s; however, above their phase transition temperature, the proteins form distinct microdomains (0.1-2 μm) with a reduced diffusion coefficient of 1.1 μm(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

  8. Application of time reversal acoustics focusing for nonlinear imaging ms

    NASA Astrophysics Data System (ADS)

    Sarvazyan, Armen; Sutin, Alexander

    2001-05-01

    Time reversal acoustic (TRA) focusing of ultrasound appears to be an effective tool for nonlinear imaging in industrial and medical applications because of its ability to efficiently concentrate ultrasonic energy (close to diffraction limit) in heterogeneous media. In this study, we used two TRA systems to focus ultrasonic beams with different frequencies in coinciding focal points, thus causing the generation of ultrasonic waves with combination frequencies. Measurements of the intensity of these combination frequency waves provide information on the nonlinear parameter of medium in the focal region. Synchronized stirring of two TRA focused beams enables obtaining 3-D acoustic nonlinearity images of the object. Each of the TRA systems employed an aluminum resonator with piezotransducers glued to its facet. One of the free facets of each resonator was submerged into a water tank and served as a virtual phased array capable of ultrasound focusing and beam steering. To mimic a medium with spatially varying acoustical nonlinearity a simplest model such as a microbubble column in water was used. Microbubbles were generated by electrolysis of water using a needle electrode. An order of magnitude increase of the sum frequency component was observed when the ultrasound beams were focused in the area with bubbles.

  9. Advantages of time reversal acoustic focusing system in biomedical applications

    NASA Astrophysics Data System (ADS)

    Sutin, Alexander; Sarvazyan, Armen

    2005-09-01

    The development and biomedical applications of time reversal acoustics (TRA) systems for focusing and manipulating ultrasound beams are reviewed. The TRA focusing system (TRA FS) is capable to deliver ultrasound energy to the chosen region in highly inhomogeneous medium (including soft tissues and bones) with focusing efficacy hardly achievable using conventional phased array transmitters. TRA FS is able to focus and stir ultrasound beams in a 3-D volume using just a few piezoceramic transducers glued to the facets an aluminum block. Another advantage of TRA FS is its ability to produce pulses with arbitrary waveforms in a wide frequency band. A custom-designed compact multichannel TRA system operating in a wide frequency range from 0.01 to 10 MHz has been developed. Measurements of TRA field structure were conducted in a large variety of inhomogeneous tissue phantoms and ex vivo bones and soft tissues. Principles of TRA focusing optimization based on acoustical properties of the resonator material, parameters of the sonicated medium, and the coupling of the TRA resonator with the medium were developed and applied in the tested TRA systems. [Work was supported by NIH.

  10. 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

  11. 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.

  12. Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis.

    PubMed

    Verslues, Paul E; Lasky, Jesse R; Juenger, Thomas E; Liu, Tzu-Wen; Kumar, M Nagaraj

    2014-01-01

    Arabidopsis (Arabidopsis thaliana) exhibits natural genetic variation in drought response, including varying levels of proline (Pro) accumulation under low water potential. As Pro accumulation is potentially important for stress tolerance and cellular redox control, we conducted a genome-wide association (GWAS) study of low water potential-induced Pro accumulation using a panel of natural accessions and publicly available single-nucleotide polymorphism (SNP) data sets. Candidate genomic regions were prioritized for subsequent study using metrics considering both the strength and spatial clustering of the association signal. These analyses found many candidate regions likely containing gene(s) influencing Pro accumulation. Reverse genetic analysis of several candidates identified new Pro effector genes, including thioredoxins and several genes encoding Universal Stress Protein A domain proteins. These new Pro effector genes further link Pro accumulation to cellular redox and energy status. Additional new Pro effector genes found include the mitochondrial protease LON1, ribosomal protein RPL24A, protein phosphatase 2A subunit A3, a MADS box protein, and a nucleoside triphosphate hydrolase. Several of these new Pro effector genes were from regions with multiple SNPs, each having moderate association with Pro accumulation. This pattern supports the use of summary approaches that incorporate clusters of SNP associations in addition to consideration of individual SNP probability values. Further GWAS-guided reverse genetics promises to find additional effectors of Pro accumulation. The combination of GWAS and reverse genetics to efficiently identify new effector genes may be especially applicable for traits difficult to analyze by other genetic screening methods.

  13. 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.

  14. 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.

  15. 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

  16. Establishment of a Reverse Genetics System for Studying Human Bocavirus in Human Airway Epithelia

    PubMed Central

    Cheng, Fang; Luo, Yong; Shen, Weiran; Lei-Butters, Diana C. M.; Chen, Aaron Yun; Li, Yi; Tang, Liang; Söderlund-Venermo, Maria; Engelhardt, John F.; Qiu, Jianming

    2012-01-01

    Human bocavirus 1 (HBoV1) has been identified as one of the etiological agents of wheezing in young children with acute respiratory-tract infections. In this study, we have obtained the sequence of a full-length HBoV1 genome (including both termini) using viral DNA extracted from a nasopharyngeal aspirate of an infected patient, cloned the full-length HBoV1 genome, and demonstrated DNA replication, encapsidation of the ssDNA genome, and release of the HBoV1 virions from human embryonic kidney 293 cells. The HBoV1 virions generated from this cell line-based production system exhibits a typical icosahedral structure of approximately 26 nm in diameter, and is capable of productively infecting polarized primary human airway epithelia (HAE) from the apical surface. Infected HAE showed hallmarks of lung airway-tract injury, including disruption of the tight junction barrier, loss of cilia and epithelial cell hypertrophy. Notably, polarized HAE cultured from an immortalized airway epithelial cell line, CuFi-8 (originally derived from a cystic fibrosis patient), also supported productive infection of HBoV1. Thus, we have established a reverse genetics system and generated the first cell line-based culture system for the study of HBoV1 infection, which will significantly advance the study of HBoV1 replication and pathogenesis. PMID:22956907

  17. 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

  18. Reverse genetics for peste-des-petits-ruminants virus (PPRV): promoter and protein specificities.

    PubMed

    Bailey, Dalan; Chard, Louisa S; Dash, Pradyot; Barrett, Tom; Banyard, Ashley C

    2007-06-01

    Peste-des-petits-ruminants virus (PPRV) (family Paramyxoviridae, genus Morbillivirus) causes an acute febrile illness in sheep and goats resulting in significant morbidity and mortality in infected herds. The paramyxoviruses all have negative sense, non-segmented RNA genomes and their host range and pathogenic determinants have been extensively studied using reverse genetics. This technology also enables a more rational approach to be taken with respect to vaccine design. In order to initiate this type of work for PPRV we constructed a PPRV minigenome and studied its expression in transfected cells. As for other morbilliviruses, the minimum requirements for minigenome rescue were shown to be the cis-acting elements of the genome (GP) and antigenome (AGP) promoters as well as the three trans-acting helper proteins N (nucleocapsid), P (phosphoprotein) and L (large polymerase). Homologous PPRV helper proteins were compared to their heterologous analogues from the closely related rinderpest virus (RPV) and heterologous minigenome rescue was found to be a much less efficient process. By engineering two GP/AGP chimeric minigenomes we also identified differences between the two viruses in the specific interactions between the promoters and the transcriptase/replicase complexes. The PPRV minigenome was also shown not to strictly comply with the "rule of six"in vitro. PMID:17350130

  19. 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.

  20. 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.

  1. 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.

  2. [Application status of rapid prototyping technology in artificial bone based on reverse engineering].

    PubMed

    Fang, Ao; Zheng, Min; Fan, Ding

    2015-02-01

    Artificial bone replacement has made an important contribution to safeguard human health and improve the quality of life. The application requirements of rapid prototyping technology based on reverse engineering in individualized artificial bone with individual differences are particularly urgent. This paper reviewed the current research and applications of rapid prototyping and reverse engineering in artificial bone. The research developments and the outlook of bone kinematics and dynamics simulation are also introduced.

  3. 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

  4. 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.

  5. 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

  6. Tetrahymena thermophila genetics: concepts and applications.

    PubMed

    Orias, Eduardo

    2012-01-01

    The differentiation of germline and somatic genomes in Tetrahymena thermophila results in two independent systems of genetic transmission. One is the conserved, sexual Mendelian genetics system of the germline genome. The other is a random genetic assortment mechanism, which operates in the somatic genome during asexual propagation. This chapter describes both systems, their interplay, and how they are exploited to construct useful biological reagents and powerful tools, which can be used to answer a variety of experimental questions.

  7. Molecular genetics and clinical applications for RH

    PubMed Central

    Flegel, Willy A.

    2011-01-01

    Rhesus is the clinically most important protein-based blood group system. It represents the largest number of antigens and the most complex genetics of the 30 known blood group systems. The RHD and RHCE genes are strongly homologous. Some genetic complexity is explained by their close chromosomal proximity and unusual orientation, with their tail ends facing each other. The antigens are expressed by the RhD and the RhCE proteins. Rhesus exemplifies the correlation of genotype and phenotype, facilitating the understanding of general genetic mechanisms. For clinical purposes, genetic diagnostics of Rhesus antigens will improve the cost-effective development of transfusion medicine. PMID:21277262

  8. 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…

  9. MINIGENOMES, TRANSCRIPTION AND REPLICATION COMPETENT VIRUS-LIKE PARTICLES AND BEYOND: REVERSE GENETICS SYSTEMS FOR FILOVIRUSES AND OTHER NEGATIVE STRANDED HEMORRHAGIC FEVER VIRUSES

    PubMed Central

    Hoenen, Thomas; Groseth, Allison; de Kok-Mercado, Fabian; Kuhn, Jens H.; Wahl-Jensen, Victoria

    2012-01-01

    Reverse-genetics systems are powerful tools enabling researchers to study the replication cycle of RNA viruses, including filoviruses and other hemorrhagic fever viruses, as well as to discover new antivirals. They include full-length clone systems as well as a number of life cycle modeling systems. Full-length clone systems allow for the generation of infectious, recombinant viruses, and thus are an important tool for studying the virus replication cycle in its entirety. In contrast, life cycle modeling systems such as minigenome and transcription and replication competent virus-like particle systems can be used to simulate and dissect parts of the virus life cycle outside of containment facilities. Minigenome systems are used to model viral genome replication and transcription, whereas transcription and replication competent virus-like particle systems also model morphogenesis and budding as well as infection of target cells. As such, these modeling systems have tremendous potential to further the discovery and screening of new antivirals targeting hemorrhagic fever viruses. This review provides an overview of currently established reverse genetics systems for hemorrhagic fever-causing negative-sense RNA viruses, with a particular emphasis on filoviruses, and the potential application of these systems for antiviral research. PMID:21699921

  10. Intermediate-type vancomycin resistance (VISA) in genetically-distinct Staphylococcus aureus isolates is linked to specific, reversible metabolic alterations.

    PubMed

    Alexander, Elizabeth L; Gardete, Susana; Bar, Haim Y; Wells, Martin T; Tomasz, Alexander; Rhee, Kyu Y

    2014-01-01

    Intermediate (VISA-type) vancomycin resistance in Staphylococcus aureus has been associated with a range of physiologic and genetic alterations. Previous work described the emergence of VISA-type resistance in two clonally-distinct series of isolates. In both series (the first belonging to MRSA clone ST8-USA300, and the second to ST5-USA100), resistance was conferred by a single mutation in yvqF (a negative regulator of the vraSR two-component system associated with vancomycin resistance). In the USA300 series, resistance was reversed by a secondary mutation in vraSR. In this study, we combined systems-level metabolomic profiling with statistical modeling techniques to discover specific, reversible metabolic alterations associated with the VISA phenotype.

  11. Soma to germline inheritance of extrachromosomal genetic information via a LINE-1 reverse transcriptase-based mechanism.

    PubMed

    Spadafora, Corrado

    2016-08-01

    Mature spermatozoa are permeable to foreign DNA and RNA molecules. Here I propose a model, whereby extrachromosomal genetic information, mostly encoded in the form of RNA in somatic cells, can cross the Weismann barrier and reach epididymal spermatozoa. LINE-1 retrotransposon-derived reverse transcriptase (RT) can play key roles in the process by expanding the RNA-encoded information. Retrotransposon-encoded RT is stored in mature gametes, is highly expressed in early embryos and undifferentiated cells, and becomes downregulated in differentiated cells. In turn, RT plays a role in developmental control, as its inhibition arrests developmental progression of early embryos with globally altered transcriptomic profiles. Thus, sperm cells act as recipients, and transgenerational vectors of somatically derived genetic information which they pass to the next generation with the potential to modify the fate of the developing embryos. PMID:27315018

  12. 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

  13. 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.

  14. 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.

  15. Performance of a model cascade thrust reverser for short-haul applications

    NASA Technical Reports Server (NTRS)

    Dietrich, D. A.; Gutierrez, O. A.

    1974-01-01

    Aerodynamic and acoustic characteristics are presented for a cowlmounted, model cascade thrust reverser suitable for short-haul aircraft. Thrust reverser efficiency and the influence on fan performance were determined from isolated fan-driven models under static and forward velocity conditions. Cascade reverser noise characteristics were determined statically in an isolated pipe-flow test, while aerodynamic installation effects were determined with a wind-tunnel, fan-powered airplane model. Application of test results to short-haul aircraft calculations demonstrated that such a cascade thrust reverser may be able to meet both the performance and noise requirements for short-haul aircraft operation. However, aircraft installation effects can be quite significant.

  16. Generation of an Avian-Mammalian Rotavirus Reassortant by Using a Helper Virus-Dependent Reverse Genetics System

    PubMed Central

    Reetz, Jochen; Kaufer, Benedikt B.; Trojnar, Eva

    2015-01-01

    ABSTRACT The genetic diversity of rotavirus A (RVA) strains is facilitated in part by genetic reassortment. Although this process of genome segment exchange has been reported frequently among mammalian RVAs, it remained unknown if mammalian RVAs also could package genome segments from avian RVA strains. We generated a simian RVA strain SA11 reassortant containing the VP4 gene of chicken RVA strain 02V0002G3. To achieve this, we transfected BSR5/T7 cells with a T7 polymerase-driven VP4-encoding plasmid, infected the cells with a temperature-sensitive SA11 VP4 mutant, and selected the recombinant virus by increasing the temperature. The reassortant virus could be stably passaged and exhibited cytopathic effects in MA-104 cells, but it replicated less efficiently than both parental viruses. Our results show that avian and mammalian rotaviruses can exchange genome segments, resulting in replication-competent reassortants with new genomic and antigenic features. IMPORTANCE This study shows that rotaviruses of mammals can package genome segments from rotaviruses of birds. The genetic diversity of rotaviruses could be broadened by this process, which might be important for their antigenic variability. The reverse genetics system applied in the study could be useful for targeted generation and subsequent characterization of distinct rotavirus reassortant strains. PMID:26581988

  17. 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

  18. 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

  19. 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.

  20. Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses

    PubMed Central

    Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nuntawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

    2012-01-01

    Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate (A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby Canine Kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 29 HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. PMID:22230579

  1. Probing subcellular organic hydroperoxide formation via a genetically encoded ratiometric and reversible fluorescent indicator.

    PubMed

    Zhao, Boxuan Simen; Zhang, Gong; Zeng, Shizhe; He, Chuan; Chen, Peng R

    2013-12-01

    A ratiometric and reversible organic hydroperoxide (OHP) sensor, rOHSer, was developed with high sensitivity and selectivity for subcellular OHP visualization. Through targeting rOHSer to the nucleus, we demonstrated that high levels of D-glucose cause elevated OHP production in this compartment. Further utilization of rOHSer probe may allow more elucidation of unique roles of OHPs in diverse biological processes.

  2. Large-Scale Reverse Genetics in Arabidopsis: Case Studies from the Chloroplast 2010 Project1[C][W][OA

    PubMed Central

    Ajjawi, Imad; Lu, Yan; Savage, Linda J.; Bell, Shannon M.; Last, Robert L.

    2010-01-01

    Traditionally, phenotype-driven forward genetic plant mutant studies have been among the most successful approaches to revealing the roles of genes and their products and elucidating biochemical, developmental, and signaling pathways. A limitation is that it is time consuming, and sometimes technically challenging, to discover the gene responsible for a phenotype by map-based cloning or discovery of the insertion element. Reverse genetics is also an excellent way to associate genes with phenotypes, although an absence of detectable phenotypes often results when screening a small number of mutants with a limited range of phenotypic assays. The Arabidopsis Chloroplast 2010 Project (www.plastid.msu.edu) seeks synergy between forward and reverse genetics by screening thousands of sequence-indexed Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutants for a diverse set of phenotypes. Results from this project are discussed that highlight the strengths and limitations of the approach. We describe the discovery of altered fatty acid desaturation phenotypes associated with mutants of At1g10310, previously described as a pterin aldehyde reductase in folate metabolism. Data are presented to show that growth, fatty acid, and chlorophyll fluorescence defects previously associated with antisense inhibition of synthesis of the family of acyl carrier proteins can be attributed to a single gene insertion in Acyl Carrier Protein4 (At4g25050). A variety of cautionary examples associated with the use of sequence-indexed T-DNA mutants are described, including the need to genotype all lines chosen for analysis (even when they number in the thousands) and the presence of tagged and untagged secondary mutations that can lead to the observed phenotypes. PMID:19906890

  3. Effect of Host Genetic Variation on the Pharmacokinetics and Clinical Response of Non-nucleoside Reverse Transcriptase Inhibitors.

    PubMed

    Saitoh, Akihiko; Spector, Stephen A

    2008-01-01

    Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been used widely for treating human immunodeficiency virus type 1 (HIV-1) infected patients as a component of highly active antiretroviral therapy (HAART) and for the prevention of mother-to-child transmission (MTCT). Cytochrome P450 (CYP) 2B6 is an important hepatic isoenzyme responsible for the metabolism of NNRTIs including efavirenz and nevirapine. Recent pharmacogenetic studies have shown that CYP2B6 genetic variants alter hepatic CYP2B6 protein expression and function, and the pharmacokinetics of several CYP2B6 substrates. In particular, the CYP2B6-G516T polymorphism in exon 4 affects the pharmacokinetics of efavirenz. Other studies have shown associations of the CYP2B6-G516T genotype with nevirapine pharmacokinetics and central nervous system adverse effects related to efavirenz use. In total, CYP2B6 genetic variants are important determinants of efavirenz and nevirapine pharmacokinetics . Further studies are needed to identify the associations of CYP2B6 genetic variants with the development of NNRTI resistant viruses.

  4. 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

  5. In Situ Reverse Transcription, an Approach To Characterize Genetic Diversity and Activities of Prokaryotes

    PubMed Central

    Chen, F.; Gonzalez, J. M.; Dustman, W. A.; Moran, M. A.; Hodson, R. E.

    1997-01-01

    Reverse transcription of RNA molecules inside intact bacterial cells was carried out by using reverse transcriptase with a single oligonucleotide complementary to specific 16S rRNA or mRNA sequences. Fluorescently labeled nucleotides were incorporated into each transcribed cDNA inside cells. This protocol is termed in situ reverse transcription (ISRT). In this study, by using species-specific primers targeting unique regions of the 16S rRNA sequences, ISRT was used successfully to detect and enumerate the two lignin-degrading bacteria Microbulbifer hydrolyticus IRE-31 and Sagittula stellata E-37 in culture mixtures and complex enrichment communities selected for lignin degradation. Image analysis revealed that M. hydrolyticus IRE-31 and S. stellata E-37 accounted for approximately 30 and 2%, respectively, of the total bacterial cells in lignin enrichment communities. Populations estimated by ISRT were comparable to those estimated by in situ hybridization (ISH) techniques and to those estimated by hybridization against extracted community DNA. ISRT was also successfully used to detect Pseudomonas putida F1 expressing the todC1 gene in seawater exposed to toluene vapor. ISRT provided a higher signal intensity than ISH, especially when targeting mRNA. The calculated pixel intensities resulting from ISRT were up to 4.2 times greater than those from ISH. This suggests that multiple incorporation of fluorescently labeled nucleotides into cDNA provides a high sensitivity for phylogenetic identification of bacterial populations as well as detection of cells expressing a specific functional gene within complex bacterial communities. PMID:16535753

  6. Time-Reversal Imaging of seismic sources and application to recent large Earthquakes

    NASA Astrophysics Data System (ADS)

    Montagner, J.; Larmat, C.; Fink, M.; Capdeville, Y.; Tourin, A.

    2006-12-01

    The occurrence of the disastrous Sumatra-Andaman earthquake on dec. 26, 2004 makes it necessary to develop innovative techniques for studying the complex spatio-temporal characteristics of rupture. The concept of time-reversal (hereafter referred to as TR) was previously successfully applied for acoustic waves in many fields such as medical imaging, underwater acoustics and non destructive testing. The increasing power of computers and numerical methods (such as spectral element methods) enables one to simulate more and more accurately the propagation of seismic waves in heterogeneous media and to develop new applications, in particular time reversal in the three-dimensional Earth. We present here the first applications at the global scale of TR with associated reverse movies of seismic waves propagation by sending back time--reversed seismograms. We show that seismic wave energy is refocused at the right location and the right time of the earthquake. When TR is applied to the Sumatra-- Andaman earthquake (26 dec. 2004), the migration of the rupture from the south towards the north is retrieved. All corresponding movies can be downloaded at the following webpage: http://www.gps.caltech.edu/~carene Other applications to recent smaller earthquakes will be also shown. Therefore, the technique of TR is potentially interesting for automatically locating earthquakes in space and time and for constraining the spatio-temporal history of complex earthquakes .

  7. 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.

  8. Applications of graph theory to landscape genetics

    PubMed Central

    Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

    2008-01-01

    We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

  9. 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

  10. Blue light- and genetically-reversed gravitropic response in protonemata of the moss Ceratodon purpureus.

    PubMed

    Lamparter, T; Hughes, J; Hartmann, E

    1998-09-01

    In darkness, protonemal filaments of Ceratodon purpureus (Brid.) grow negatively gravitropically (upwards). Red light induces a positive phototropic response mediated by the photoreceptor phytochrome. A red light treatment also has an inhibitory effect on the gravitropic response, an effect also mediated by phytochrome. In this study the effects of blue light on phototropism and on gravitropism were analysed. Unilateral blue light resulted in only a weak phototropic response, but markedly randomised growth direction. Blue light given together with a gravitropic stimulus reversed the gravitropism, changing it from negative to positive (filaments grow downward). The effect of blue light was also analysed with the mutant ptr116, which is defective in the biosynthesis of the phytochrome chromophore, and in a newly isolated mutant wwr2, which is positively gravitropic in darkness. Blue light induced the same reversal of gravitropism in ptrll6 as in the wild type, indicating that phytochrome is not involved in this process. In wwr2 the direction of gravitropism was unaltered by the blue light treatment. Light also affects chlorophyll content and the size of plastids, potential statoliths for gravitropism. Red light induced an increase in plastid size and chlorophyll content in the wild type but not in ptr116. Blue light induced a similar change in wild type plastids. It seems as though light-induced alterations of gravitropism are not simply mediated by alterations in plastid properties, and that red light and blue light evoke fundamentally different responses. PMID:11536885

  11. Silica-based nanocomposites via reverse microemulsions: classifications, preparations, and applications.

    PubMed

    Wang, Jiasheng; Shah, Zameer Hussain; Zhang, Shufen; Lu, Rongwen

    2014-05-01

    Silica-based nanocomposites with amorphous silica as the matrix or carrier along with a functional component have been extensively investigated. These nanocomposites combine the advantages of both silica and the functional components, demonstrating great potential for various applications. To synthesize such composites, one of the most frequently used methods is reverse microemulsion due to its convenient control over the size, shape, and structures. The structures of the composites have a decisive significance for their properties and applications. In this review, we tried to categorize the silica-based nanocomposites via reverse microemulsions based on their structures, discussed the syntheses individually for each structure, summarized their applications, and made some perspectives based on the current progress of this field. PMID:24562100

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

    PubMed

    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 F(1) bulls, 113 F(1) dams, and 246 F(2) progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F(1) bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F(2) 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

  13. Silica-based nanocomposites via reverse microemulsions: classifications, preparations, and applications

    NASA Astrophysics Data System (ADS)

    Wang, Jiasheng; Shah, Zameer Hussain; Zhang, Shufen; Lu, Rongwen

    2014-04-01

    Silica-based nanocomposites with amorphous silica as the matrix or carrier along with a functional component have been extensively investigated. These nanocomposites combine the advantages of both silica and the functional components, demonstrating great potential for various applications. To synthesize such composites, one of the most frequently used methods is reverse microemulsion due to its convenient control over the size, shape, and structures. The structures of the composites have a decisive significance for their properties and applications. In this review, we tried to categorize the silica-based nanocomposites via reverse microemulsions based on their structures, discussed the syntheses individually for each structure, summarized their applications, and made some perspectives based on the current progress of this field.Silica-based nanocomposites with amorphous silica as the matrix or carrier along with a functional component have been extensively investigated. These nanocomposites combine the advantages of both silica and the functional components, demonstrating great potential for various applications. To synthesize such composites, one of the most frequently used methods is reverse microemulsion due to its convenient control over the size, shape, and structures. The structures of the composites have a decisive significance for their properties and applications. In this review, we tried to categorize the silica-based nanocomposites via reverse microemulsions based on their structures, discussed the syntheses individually for each structure, summarized their applications, and made some perspectives based on the current progress of this field. Electronic supplementary information (ESI) available: The structures of all the surfactants included in this review are listed. See DOI: 10.1039/c3nr06025j

  14. 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.

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

    PubMed Central

    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.

    2015-01-01

    Copy number variations have been frequently associated with developmental delay, intellectual disability, and autism spectrum disorders1. MECP2 duplication syndrome is one of the most common genomic rearrangements in males2 and is characterized by autism, intellectual disability, motor dysfunction, anxiety, epilepsy, recurrent respiratory tract infections, and early death3–5. 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, however, 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 disorders6–8, including loss of MeCP2 in Rett syndrome9, 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 hypothesized that restoration of normal MeCP2 levels in MECP2 duplication adult mice would rescue their phenotype. Therefore, we first generated and characterized a conditional Mecp2-overexpressing mouse model and showed that correction of MeCP2 levels largely reversed the behavioral, molecular, and electrophysiological deficits. Next, we sought a translational strategy to reduce MeCP2 and turned to antisense oligonucleotides (ASOs). ASOs are small modified nucleic acids that can selectively hybridize with mRNA transcribed from a target gene and silence it10,11, and have been successfully used to correct deficits in different mouse models12–18. We found that ASO treatment induced a broad phenotypic rescue in adult symptomatic transgenic MECP2

  16. 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.

  17. 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

  18. 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

  19. Reverse engineering of biochemical equations from time-course data by means of genetic programming.

    PubMed

    Sugimoto, Masahiro; Kikuchi, Shinichi; Tomita, Masaru

    2005-05-01

    Increased research aimed at simulating biological systems requires sophisticated parameter estimation methods. All current approaches, including genetic algorithms, need pre-existing equations to be functional. A generalized approach to predict not only parameters but also biochemical equations from only observable time-course information must be developed and a computational method to generate arbitrary equations without knowledge of biochemical reaction mechanisms must be developed. We present a technique to predict an equation using genetic programming. Our technique can search topology and numerical parameters of mathematical expression simultaneously. To improve the search ability of numeric constants, we added numeric mutation to the conventional procedure. As case studies, we predicted two equations of enzyme-catalyzed reactions regarding adenylate kinase and phosphofructokinase. Our numerical experimental results showed that our approach could obtain correct topology and parameters that were close to the originals. The mean errors between given and simulation-predicted time-courses were 1.6 x 10(-5)% and 2.0 x 10(-3)%, respectively. Our equation prediction approach can be applied to identify metabolic reactions from observable time-courses.

  20. Cardiovascular genetics: technological advancements and applicability for dilated cardiomyopathy.

    PubMed

    Kummeling, G J M; Baas, A F; Harakalova, M; van der Smagt, J J; Asselbergs, F W

    2015-07-01

    Genetics plays an important role in the pathophysiology of cardiovascular diseases, and is increasingly being integrated into clinical practice. Since 2008, both capacity and cost-efficiency of mutation screening of DNA have been increased magnificently due to the technological advancement obtained by next-generation sequencing. Hence, the discovery rate of genetic defects in cardiovascular genetics has grown rapidly and the financial threshold for gene diagnostics has been lowered, making large-scale DNA sequencing broadly accessible. In this review, the genetic variants, mutations and inheritance models are briefly introduced, after which an overview is provided of current clinical and technological applications in gene diagnostics and research for cardiovascular disease and in particular, dilated cardiomyopathy. Finally, a reflection on the future perspectives in cardiogenetics is given.

  1. 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

  2. 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

  3. Physiology and genetic traits of reverse osmosis membrane biofilms: a case study with Pseudomonas aeruginosa.

    PubMed

    Herzberg, Moshe; Elimelech, Menachem

    2008-02-01

    Biofilm formation of Pseudomonas aeruginosa on the surface of a reverse osmosis (RO) membrane was studied using a synthetic wastewater medium to simulate conditions relevant to reclamation of secondary wastewater effluent. P. aeruginosa biofilm physiology and spatial activity were analyzed following growth on the membrane using a short-life green fluorescent protein derivative expressed in a growth-dependent manner. As a consequence of the limiting carbon source prevailing in the suspended culture of the RO unit, a higher distribution of active cells was observed in the biofilm close to the membrane surface, likely due to the higher nutrient levels induced by concentration polarization effects. The faster growth of the RO-sessile cells compared to the planktonic cells in the RO unit was reflected by the transcriptome of the two cultures analyzed with DNA microarrays. In contrast to the findings recently reported in gene expression studies of P. aeruginosa biofilms, in the RO system, genes related to stress, adaptation, chemotaxis and resistance to antibacterial agents were induced in the planktonic cells. In agreement with the findings of previous P. aeruginosa biofilm studies, motility- and attachment-related genes were repressed in the RO P. aeruginosa biofilm. Supported by the microarray data, an increase in both motility and chemotaxis phenotypes was observed in the suspended cells. The increase in nutrient concentration in close proximity to the membrane is suggested to enhance biofouling by chemotaxis response of the suspended cells and their swimming toward the membrane surface.

  4. Genetic Modification of the Penicillin G Acylase Surface To Improve Its Reversible Immobilization on Ionic Exchangers▿

    PubMed Central

    Montes, Tamara; Grazú, Valeria; López-Gallego, Fernando; Hermoso, Juan A.; García, Jose L.; Manso, Isabel; Galán, Beatriz; González, Ramón; Fernández-Lafuente, Roberto; Guisán, José M.

    2007-01-01

    A new mutant of the industrial enzyme penicillin G acylase (PGA) from Escherichia coli has been designed to improve its reversible immobilization on anionic exchangers (DEAE- or polyethyleneimine [PEI]-coated agarose) by assembling eight new glutamic residues distributed homogeneously through the enzyme surface via site-directed mutagenesis. The mutant PGA is produced and processed in vivo as is the native enzyme. Moreover, it has a similar specific activity to and shows the same pH activity profile as native PGA; however, its isoelectric point decreased from 6.4 to 4.3. Although the new enzyme is adsorbed on both supports, the adsorption was even stronger when supports were coated with PEI, allowing us to improve the enzyme stability in organic cosolvents. The use of restrictive conditions during the enzyme adsorption on anionic exchangers (pH 5 and high ionic strength) permitted us to still further increase the strength of adsorption and the enzyme stability in the presence of organic solvents, suggesting that these conditions allow the penetration of the enzyme inside the polymeric beds, thus becoming fully covered with the polymer. After the enzyme inactivation, it can be desorbed to reuse the support. The possibility to improve the immobilization properties on an enzyme by site-directed mutagenesis of its surface opens a promising new scenario for enzyme engineering. PMID:17098917

  5. 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.

  6. 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.

  7. 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.

  8. [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.

  9. Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide.

    PubMed

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

    2006-11-15

    A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)(3)GY(GA)(3)GE(GA)(3)GH(GA)(3)GK, forms large beta-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of beta-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 beta-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125 degrees 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 approximately 1 and approximately 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 beta-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

  10. Application of Iterative Time-Reversal for Electromagnetic Wave Focusing in a Wave Chaotic System

    NASA Astrophysics Data System (ADS)

    Taddese, Biniyam; Antonsen, Thomas; Ott, Edward; Anlage, Steven

    2011-03-01

    Time-reversal mirrors exploit the time-reversal invariance of the wave equation to achieve spatial and temporal focusing, and they have been shown to be very effective sensors of perturbations to wave chaotic systems. The sensing technique is based on a classical analogue of the Loschmidt echo. However, dissipation results in an imperfect focusing, hence we created a sensing technique employing exponential amplification to overcome this limitation [1,2]. We now apply the technique of iterative time-reversal, which had been demonstrated in a dissipative acoustic system, to an electromagnetic time-reversal mirror, and experimentally demonstrate improved temporal focusing. We also use a numerical model of a network of transmission lines to demonstrate improved focusing by the iterative technique for various degrees and statistical distributions of loss in the system. The application of the iterative technique to improve the performance and practicality of our sensor is explored. This work is supported by an ONR MURI Grant No. N000140710734, AFOSR Grant No. FA95501010106, and the Maryland CNAM.

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

    PubMed

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

    2014-05-19

    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 focusing--with good reason--almost 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

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

    PubMed

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

    2014-05-19

    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 focusing--with good reason--almost 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.

  13. Establishing RNA interference as a reverse-genetic approach for gene functional analysis in protoplasts.

    PubMed

    Zhai, Zhiyang; Sooksa-nguan, Thanwalee; Vatamaniuk, Olena K

    2009-02-01

    Double-stranded (ds)RNA interference (RNAi) is widely used for functional analysis of plant genes and is achieved via generating stable transformants expressing dsRNA in planta. This study demonstrated that RNAi can also be utilized to examine gene functions in protoplasts. Because protoplasts are nongrowing cells, effective RNAi-triggered gene silencing depends not only on a depletion of gene transcripts but also on turnover rates of corresponding polypeptides. Herein, we tested if transient RNAi in protoplasts would result in the depletion of a targeted polypeptide and, because protoplasts have a limited life span, if functional assays of RNAi knockout genes would be feasible in protoplasts. We showed that protoplasts transfection with an in vitro-synthesized dsRNA against Arabidopsis (Arabidopsis thaliana) beta-glutamylcysteine synthase (ECS1), a key enzyme in the synthesis of glutathione, resulted in a 95% depletion of ECS1 transcript, a 72% decrease of ECS1 polypeptide, and a 60% drop in glutathione content. These results were comparable with those obtained upon analysis of Arabidopsis seedlings bearing the cad2-1 mutant allele of ECS1. We also improved the procedure for RNAi inactivation of several genes simultaneously. Finally, because we isolated protoplasts from tissues of 14-d-old seedlings instead of 1-month-old mature plants, the described procedure is rapid (as it only takes 20 d from seed planting to functional studies), suitable for analyzing multiple genes in parallel, and independent of cloning dsRNAs into plant expression vectors. Therefore, RNAi in protoplasts complements existing genetic tools, as it allows rapid, cost- and space-efficient initial screening and selection of genes for subsequent in planta studies.

  14. 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.

  15. Genetic Ablation of Vitamin D Activation Pathway Reverses Biochemical and Skeletal Anomalies in Fgf-23-Null Animals

    PubMed Central

    Sitara, Despina; Razzaque, Mohammed S.; St-Arnaud, René; Huang, Wei; Taguchi, Takashi; Erben, Reinhold G.; Lanske, Beate

    2006-01-01

    Fibroblast growth factor-23 (FGF-23) is one of the circulating phosphaturic factors associated with renal phosphate wasting. Fgf-23−/− animals show extremely high serum levels of phosphate and 1,25-dihydroxyvitamin D3, along with abnormal bone mineralization and soft tissue calcifications. To determine the role of vitamin D in mediating altered phosphate homeostasis and skeletogenesis in the Fgf-23−/− mice, we generated mice lacking both the Fgf-23 and 1α-hydroxylase genes (Fgf-23−/−/1α(OH)ase−/−). In the current study, we have identified the cellular source of Fgf-23 in adult mice. In addition, loss of vitamin D activities from Fgf-23−/− mice reverses the severe hyperphosphatemia to hypophosphatemia, attributable to increased urinary phosphate wasting in Fgf-23−/−/1α(OH)ase−/− mice, possibly as a consequence of decreased expression of NaPi2a. Ablation of vitamin D from Fgf-23−/− mice resulted in further reduction of total bone mineral content and bone mineral density and reversed ectopic calcification of skeleton and soft tissues, suggesting that abnormal mineral ion homeostasis and impaired skeletogenesis in Fgf-23−/− mice are mediated through enhanced vitamin D activities. In conclusion, using genetic manipulation studies, we have provided evidence for an in vivo inverse correlation between Fgf-23 and vitamin D activities and for the severe skeletal and soft tissue abnormalities of Fgf-23−/− mice being mediated through vitamin D. PMID:17148678

  16. 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.

  17. [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

  18. [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.

  19. Characterization of influenza virus NS1 protein by using a novel helper-virus-free reverse genetic system.

    PubMed

    Enami, M; Enami, K

    2000-06-01

    We have developed a novel helper-virus-free reverse genetic system to genetically manipulate influenza A viruses. The RNPs, which were purified from the influenza A/WSN/33 (WSN) virus, were treated with RNase H in the presence of NS (nonstructural) cDNA fragments. This specifically digested the NS RNP. The NS-digested RNPs thus obtained were transfected into cells together with the in vitro-reconstituted NS RNP. The NS-digested RNPs alone did not rescue viruses; however, cotransfection with the NS RNP did. This protocol was also used to rescue the NP transfectant. We obtained two NS1 mutants, dl12 and N110, using this protocol. The dl12 NS gene contains a deletion of 12 amino acids at positions 66 to 77 near the N terminus. This virus was temperature sensitive in Madin-Darby bovine kidney (MDBK) cells as well as in Vero cells. The translation of all viral proteins as well as cellular proteins was significantly disrupted during a later time of infection at the nonpermissive temperature of 39 degrees C. The N110 mutant consists of 110 amino acids which are the N-terminal 48% of the WSN virus NS1 protein. Growth of this virus was significantly reduced at any temperature. In the virus-infected cells, translation of the M1 protein was reduced to 10 to 20% of that of the wild-type virus; however, the translation of neither the nucleoprotein nor NS1 was significantly interfered with, indicating the important role of NS1 in translational stimulation of the M1 protein.

  20. Development and application of biological technologies in fish genetic breeding.

    PubMed

    Xu, Kang; Duan, Wei; Xiao, Jun; Tao, Min; Zhang, Chun; Liu, Yun; Liu, ShaoJun

    2015-02-01

    Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology. PMID:25595050

  1. Development and application of biological technologies in fish genetic breeding.

    PubMed

    Xu, Kang; Duan, Wei; Xiao, Jun; Tao, Min; Zhang, Chun; Liu, Yun; Liu, ShaoJun

    2015-02-01

    Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology.

  2. Combining Telomerase Reverse Transcriptase Genetic Variant rs2736100 with Epidemiologic Factors in the Prediction of Lung Cancer Susceptibility

    PubMed Central

    Wang, Xu; Ma, Kewei; Chi, Lumei; Cui, Jiuwei; Jin, Lina; Hu, Ji-Fan; Li, Wei

    2016-01-01

    Genetic variants from a considerable number of susceptibility loci have been identified in association with cancer risk, but their interaction with epidemiologic factors in lung cancer remains to be defined. We sought to establish a forecasting model for identifying individuals with high-risk of lung cancer by combing gene single-nucleotide polymorphisms with epidemiologic factors. Genotyping and clinical data from 500 lung cancer cases and 500 controls were used for developing the logistic regression model. We found that lung cancer was associated with telomerase reverse transcriptase (TERT) rs2736100 single-nucleotide polymorphism. The TERT rs2736100 model was still significantly associated with lung cancer risk when combined with environmental and lifestyle factors, including lower education, lower BMI, COPD history, heavy cigarettes smoking, heavy cooking emission, and dietary factors (over-consumption of meat and deficiency in fish/shrimp, vegetables, dairy products, and soybean products). These data suggest that combining TERT SNP and epidemiologic factors may be a useful approach to discriminate high and low-risk individuals for lung cancer. PMID:27162544

  3. Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of Arabidopsis thaliana.

    PubMed

    Takenaka, Mizuki; Verbitskiy, Daniil; Zehrmann, Anja; Brennicke, Axel

    2010-08-27

    RNA editing in flowering plant mitochondria post-transcriptionally alters several hundred nucleotides from C to U, mostly in mRNAs. Several factors required for specific RNA-editing events in plant mitochondria and plastids have been identified, all of them PPR proteins of the PLS subclass with a C-terminal E-domain and about half also with an additional DYW domain. Based on this information, we here probe the connection between E-PPR proteins and RNA editing in plant mitochondria. We initiated a reverse genetics screen of T-DNA insertion lines in Arabidopsis thaliana and investigated 58 of the 150 E-PPR-coding genes for a function in RNA editing. Six genes were identified to be involved in mitochondrial RNA editing at specific sites. Homozygous mutants of the five genes MEF18-MEF22 display no gross disturbance in their growth or development patterns, suggesting that the editing sites affected are not crucial at least in the greenhouse. These results show that a considerable percentage of the E-PPR proteins are involved in the functional processing of site-specific RNA editing in plant mitochondria.

  4. Protective efficacy of a high-growth reassortant swine H3N2 inactivated vaccine constructed by reverse genetic manipulation

    PubMed Central

    Wen, Feng; Ma, Ji-Hong; Yang, Fu-Ru; Huang, Meng; Zhou, Yan-Jun; Li, Ze-Jun

    2014-01-01

    Novel reassortant H3N2 swine influenza viruses (SwIV) with the matrix gene from the 2009 H1N1 pandemic virus have been isolated in many countries as well as during outbreaks in multiple states in the United States, indicating that H3N2 SwIV might be a potential threat to public health. Since southern China is the world's largest producer of pigs, efficient vaccines should be developed to prevent pigs from acquiring H3N2 subtype SwIV infections, and thus limit the possibility of SwIV infection at agricultural fairs. In this study, a high-growth reassortant virus (GD/PR8) was generated by plasmid-based reverse genetics and tested as a candidate inactivated vaccine. The protective efficacy of this vaccine was evaluated in mice by challenging them with another H3N2 SwIV isolate [A/Swine/Heilongjiang/1/05 (H3N2) (HLJ/05)]. Prime and booster inoculation with GD/PR8 vaccine yielded high-titer serum hemagglutination inhibiting antibodies and IgG antibodies. Complete protection of mice against H3N2 SwIV was observed, with significantly reduced lung lesion and viral loads in vaccine-inoculated mice relative to mock-vaccinated controls. These results suggest that the GD/PR8 vaccine may serve as a promising candidate for rapid intervention of H3N2 SwIV outbreaks in China. PMID:24675833

  5. Reverse Genetic Morpholino Approach Using Cardiac Ventricular Injection to Transfect Multiple Difficult-to-target Tissues in the Zebrafish Larva

    PubMed Central

    Konantz, Judith; Antos, Christopher L.

    2014-01-01

    The zebrafish is an important model to understand the cell and molecular biology of organ and appendage regeneration. However, molecular strategies to employ reverse genetics have not yet been adequately developed to assess gene function in regeneration or tissue homeostasis during larval stages after zebrafish embryogenesis, and several tissues within the zebrafish larva are difficult to target. Intraventricular injections of gene-specific morpholinos offer an alternative method for the current inability to genomically target zebrafish genes in a temporally controlled manner at these stages. This method allows for complete dispersion and subsequent incorporation of the morpholino into various tissues throughout the body, including structures that were formerly impossible to reach such as those in the larval caudal fin, a structure often used to noninvasively research tissue regeneration. Several genes activated during larval finfold regeneration are also present in regenerating adult vertebrate tissues, so the larva is a useful model to understand regeneration in adults. This morpholino dispersion method allows for the quick and easy identification of genes required for the regeneration of larval tissues as well as other physiological phenomena regulating tissue homeostasis after embryogenesis. Therefore, this delivery method provides a currently needed strategy for temporal control to the evaluation of gene function after embryogenesis.  PMID:24961304

  6. Reverse genetic morpholino approach using cardiac ventricular injection to transfect multiple difficult-to-target tissues in the zebrafish larva.

    PubMed

    Konantz, Judith; Antos, Christopher L

    2014-01-01

    The zebrafish is an important model to understand the cell and molecular biology of organ and appendage regeneration. However, molecular strategies to employ reverse genetics have not yet been adequately developed to assess gene function in regeneration or tissue homeostasis during larval stages after zebrafish embryogenesis, and several tissues within the zebrafish larva are difficult to target. Intraventricular injections of gene-specific morpholinos offer an alternative method for the current inability to genomically target zebrafish genes in a temporally controlled manner at these stages. This method allows for complete dispersion and subsequent incorporation of the morpholino into various tissues throughout the body, including structures that were formerly impossible to reach such as those in the larval caudal fin, a structure often used to noninvasively research tissue regeneration. Several genes activated during larval finfold regeneration are also present in regenerating adult vertebrate tissues, so the larva is a useful model to understand regeneration in adults. This morpholino dispersion method allows for the quick and easy identification of genes required for the regeneration of larval tissues as well as other physiological phenomena regulating tissue homeostasis after embryogenesis. Therefore, this delivery method provides a currently needed strategy for temporal control to the evaluation of gene function after embryogenesis. 

  7. [Engineering by reverse genetics and characterization of the new reassortant influenza virus strain H5N1].

    PubMed

    Zeberezhnyĭ, A D; Grebennikova, T V; Vorkunova, G K; Yuzhakov, A G; Kostina, L V; Norkina, S N; Aliper, T I; Nepoklonov, E A; Lvov, D K

    2014-01-01

    Reverse genetics was applied to engineering of the reassortantvaccine candidate strain against highly pathogenic avian influenza viruses (HPAIVs) of the H5 subtype. The new strain recPR8-H5N1 contains the HA gene from the Russian HPAIV A/Kurgan/05/2005 (H5N1), the NA and internal genes from A/Puerto Rico/8/34 (H1N1). The strain recPR8-H5N1 demonstrated the antigenic specificity (H5), high proliferation rate in 12 days chicken embryos, and was lethal for the embryos in 36 hours. An inactivated emulsified vaccine based on the strain recPR8-H5N1 elicited high antibody titers and protected 6-week-old chickens from lethal challenge with the HPAIV A/Kurgan/05/2005 (H5N1) on day 21 after single immunization. Infection of non-vaccinated birds with the strain recPR8-H5N1 did not cause any pathology, and the virus was not detected using PCR in blood and cloacal swabs on day 7 p.i. Specific weak seroconversion caused by infection with the strain recPR8-H5N1 was detected on day 14 p.i. As a result, a new influenza virus strain was obtained with modified properties.

  8. Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation.

    PubMed

    Posavi, Marijan; Gelembiuk, Gregory William; Larget, Bret; Lee, Carol Eunmi

    2014-11-01

    Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions. PMID:25135455

  9. Application of genetically modified and cloned pigs in translational research.

    PubMed

    Matsunari, Hitomi; Nagashima, Hiroshi

    2009-06-01

    Pigs are increasingly being recognized as good large-animal models for translational research, linking basic science to clinical applications in order to establish novel therapeutics. This article reviews the current status and future prospects of genetically modified and cloned pigs in translational studies. It also highlights pigs specially designed as disease models, for xenotransplantation or to carry cell marker genes. Finally, use of porcine somatic stem and progenitor cells in preclinical studies of cell transplantation therapy is also discussed.

  10. Experimental studies of applications of time-reversal acoustics to noncoherent underwater communications

    NASA Astrophysics Data System (ADS)

    Heinemann, M.; Larraza, A.; Smith, K. B.

    2003-06-01

    The most difficult problem in shallow underwater acoustic communications is considered to be the time-varying multipath propagation because it impacts negatively on data rates. At high data rates the intersymbol interference requires adaptive algorithms on the receiver side that lead to computationally intensive and complex signal processing. A novel technique called time-reversal acoustics (TRA) can environmentally adapt the acoustic propagation effects of a complex medium in order to focus energy at a particular target range and depth. Using TRA, the multipath structure is reduced because all the propagation paths add coherently at the intended target location. This property of time-reversal acoustics suggests a potential application in the field of noncoherent acoustic communications. This work presents results of a tank scale experiment using an algorithm for rapid transmission of binary data in a complex underwater environment with the TRA approach. A simple 15-symbol code provides an example of the simplicity and feasibility of the approach. Covert coding due to the inherent scrambling induced by the environment at points other than the intended receiver is also investigated. The experiments described suggest a high potential in data rate for the time-reversal approach in underwater acoustic communications while keeping the computational complexity low.

  11. Isolation of Mutations in the Drosophila Homologues of the Human Neurofibromatosis 2 and Yeast Cdc42 Genes Using a Simple and Efficient Reverse-Genetic Method

    PubMed Central

    Fehon, R. G.; Oren, T.; LaJeunesse, D. R.; Melby, T. E.; McCartney, B. M.

    1997-01-01

    Reverse genetic analysis in Drosophila has been greatly aided by a growing collection of lethal P transposable element insertions that provide molecular tags for the identification of essential genetic loci. However, because the screens performed to date primarily have generated autosomal P-element insertions, this collection has not been as useful for performing reverse genetic analysis of X-linked genes. We have designed a reverse genetic screen that takes advantage of the hemizygosity of the X chromosome in males together with a cosmid-based transgene that serves as an autosomally linked duplication of a small region of the X chromosome. The efficacy and efficiency of this method is demonstrated by the isolation of mutations in Drosophila homologues of two well-studied genes, the human Neurofibromatosis 2 tumor suppressor and the yeast CDC42 gene. The method we describe should be of general utility for the isolation of mutations in other X-linked genes, and should also provide an efficient method for the isolation of new alleles of existing X-linked or autosomal mutations in Drosophila. PMID:9136014

  12. The strains recommended for use in the bacterial reverse mutation test (OECD guideline 471) can be certified as non-genetically modified organisms.

    PubMed

    Sugiyama, Kei-Ichi; Yamada, Masami; Awogi, Takumi; Hakura, Atsushi

    2016-01-01

    The bacterial reverse mutation test, commonly called Ames test, is used worldwide. In Japan, the genetically modified organisms (GMOs) are regulated under the Cartagena Domestic Law, and organisms obtained by self-cloning and/or natural occurrence would be exempted from the law case by case. The strains of Salmonella typhimurium and Escherichia coli recommended for use in the bacterial reverse mutation test (OECD guideline 471), have been considered as non-GMOs because they can be constructed by self-cloning or naturally occurring bacterial strains, or do not disturb the biological diversity. The present article explains the reasons why these tester strains should be classified as non-GMOs.

  13. 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.

  14. 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.

  15. 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.

  16. Next generation sequencing and its applications in forensic genetics.

    PubMed

    Børsting, Claus; Morling, Niels

    2015-09-01

    It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs, insertion/deletions, mRNA) that cannot be analyzed simultaneously with the standard PCR-CE methods used today. The true variation in core forensic STR loci has been uncovered, and previously unknown STR alleles have been discovered. The detailed sequence information may aid mixture interpretation and will increase the statistical weight of the evidence. In this review, we will give an introduction to NGS and single-molecule sequencing, and we will discuss the possible applications of NGS in forensic genetics.

  17. Reversible polymorphism-aware phylogenetic models and their application to tree inference.

    PubMed

    Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin

    2016-10-21

    We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction. PMID:27480613

  18. Time-Reversal Acoustic Focusing with Liquid Resonator for Medical Applications

    NASA Astrophysics Data System (ADS)

    Sinelnikov, Yegor D.; Sutin, Alexandre Y.; Sarvazyan, Armen P.

    2007-05-01

    Time Reversal Acoustic (TRA) focusing system based on the use of liquid filled resonators with single or few transducers is demonstrated to effectively converge acoustic energy in space and time. Because the wavelength in liquid is typically smaller than in solids, liquid based TRA focusing resonators can have smaller dimensions than solid resonators. The efficiency of liquid-based TRA focusing resonators to transmit acoustic power to soft tissues is improved by impedance matching of the acoustic transducer assembly to the surrounding liquid. Experiments were conducted to understand the properties of TRA focusing with the liquid-filled resonators and possible application of the TRA systems for biomedical applications. The factors defining the efficiency of liquid based TRA focusing resonators were explored. In media with high attenuation, the binary mode of ultrasound delivery yielded noticeably narrower focusing of ultrasound than conventional analog focusing.

  19. Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof

    PubMed Central

    Nolden, T.; Pfaff, F.; Nemitz, S.; Freuling, C. M.; Höper, D.; Müller, T.; Finke, Stefan

    2016-01-01

    Reverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache’s reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level. PMID:27046474

  20. 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)+λV 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(γ,t|γ',t')=P˜(γ',t'|γ,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.

  1. 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

  2. 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.

  3. [Genetic biomarkers and personalized medicine: application in cardiovascular pharmacology].

    PubMed

    Carrillo Norte, Juan Antonio

    2013-01-01

    Not all patients respond to drug therapy in a uniform and beneficial fashion. The goal of this article is to describe the contribution of genetic variation to drug response, with a focus on drugs used in cardiovascular therapy. The rapid development of techniques in the area of genome analysis has facilitated identification of new pharmacogenomic biomarkers that can provide predictive tools for improvement of drug response and fewer incidence of adverse drug reactions. Such biomarkers mainly originate from genes encoding drug-metabolizing enzymes, drug transporters, drug targets and human leukocyte antigens. However, despite significant progress in pharmacogenomic research, only a few drugs require a pharmacogenetic test before prescription. Among the several gaps that limit the application of pharmacogenetics, it deserves to be mentioned the complex nature of drug response, that makes difficult to disentangle the interplay between genetics and environment leading to pharmacological phenotype. We have to spare no effort in the identification of genetic biomarkers related to the pathogenesis of the diseases and therapeutic targets. It may help clinicians to individualize dosing drug regimen, maximize drug efficacy and enhance drug safety with certain drugs and populations at risk.

  4. 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

  5. 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.

  6. Photochemically reversible liquefaction and solidification of multiazobenzene sugar-alcohol derivatives and application to reworkable adhesives.

    PubMed

    Akiyama, Haruhisa; Kanazawa, Satoshi; Okuyama, Yoko; Yoshida, Masaru; Kihara, Hideyuki; Nagai, Hideki; Norikane, Yasuo; Azumi, Reiko

    2014-05-28

    Multiazobenzene compounds, hexakis-O-[4-(phenylazo)phenoxyalkylcarboxyl]-D-mannitols and hexakis-O-[4-(4-hexylphenylazo)phenoxyalkylcarboxyl]-D-mannitols, exhibit photochemically reversible liquefaction and solidification at room temperature. Their photochemical and thermal phase transitions were investigated in detail through thermal analysis, absorption spectroscopy, and dynamic viscoelasticity measurements, and were compared with those of other sugar-alcohol derivatives. Tensile shear strength tests were performed to determine the adhesions of the compounds sandwiched between two glass slides to determine whether the compounds were suitable for application as adhesives. The adhesions were varied by alternately irradiating the compounds with ultraviolet and visible light to photoinduce phase transitions. The azobenzene hexyl tails, lengths of the methylene spacers, and differences in the sugar-alcohol structures affected the photoresponsive properties of the compounds.

  7. Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues

    PubMed Central

    McDonagh, Brian; Martínez-Acedo, Pablo; Vázquez, Jesús; Padilla, C. Alicia; Sheehan, David; Bárcena, José Antonio

    2012-01-01

    Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. Reversible cysteine modifications allow for potential redox regulation of proteins. Traditional measurement of the relative absolute quantity of a protein between two samples is not always necessarily proportional to the activity of the protein. We propose application of iTRAQ reagents in combination with a previous thiol selection method to relatively quantify the redox state of cysteines both within and between samples in a single analysis. Our method allows for the identification of the proteins, identification of redox-sensitive cysteines within proteins, and quantification of the redox status of individual cysteine-containing peptides. As a proof of principle, we applied this technique to yeast alcohol dehydrogenase-1 exposed in vitro to H2O2 and also in vivo to the complex proteome of the Gram-negative bacterium Bacillus subtilis. PMID:22844595

  8. 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.

  9. 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.

  10. 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

  11. Examination of time-reversal acoustics in shallow water and applications to noncoherent underwater communications

    NASA Astrophysics Data System (ADS)

    Smith, Kevin B.; Abrantes, Antonio A. M.; Larraza, Andres

    2003-06-01

    The shallow water acoustic communication channel is characterized by strong signal degradation caused by multipath propagation and high spatial and temporal variability of the channel conditions. At the receiver, multipath propagation causes intersymbol interference and is considered the most important of the channel distortions. This paper examines the application of time-reversal acoustic (TRA) arrays, i.e., phase-conjugated arrays (PCAs), that generate a spatio-temporal focus of acoustic energy at the receiver location, eliminating distortions introduced by channel propagation. This technique is self-adaptive and automatically compensates for environmental effects and array imperfections without the need to explicitly characterize the environment. An attempt is made to characterize the influences of a PCA design on its focusing properties with particular attention given to applications in noncoherent underwater acoustic communication systems. Due to the PCA spatial diversity focusing properties, PC arrays may have an important role in an acoustic local area network. Each array is able to simultaneously transmit different messages that will focus only at the destination receiver node.

  12. The Tricentennial People: Human Applications of the New Genetics.

    ERIC Educational Resources Information Center

    Neumann, Marguerite, Ed.

    This symposium focused on the social, political, and ethical implications of the current trends in genetic research. Four papers are presented here along with transcripts of the accompanying discussions. The topics include: (1) genetics and the biological basis of the human condition; (2) the pros and cons of genetic counseling; (3) genetics and…

  13. 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.

  14. The strains recommended for use in the bacterial reverse mutation test (OECD guideline 471) can be certified as non-genetically modified organisms.

    PubMed

    Sugiyama, Kei-Ichi; Yamada, Masami; Awogi, Takumi; Hakura, Atsushi

    2016-01-01

    The bacterial reverse mutation test, commonly called Ames test, is used worldwide. In Japan, the genetically modified organisms (GMOs) are regulated under the Cartagena Domestic Law, and organisms obtained by self-cloning and/or natural occurrence would be exempted from the law case by case. The strains of Salmonella typhimurium and Escherichia coli recommended for use in the bacterial reverse mutation test (OECD guideline 471), have been considered as non-GMOs because they can be constructed by self-cloning or naturally occurring bacterial strains, or do not disturb the biological diversity. The present article explains the reasons why these tester strains should be classified as non-GMOs. PMID:27350822

  15. 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

  16. 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.

  17. Genetics

    MedlinePlus

    ... 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 ...

  18. Genetic engineering of the chloroplast: novel tools and new applications.

    PubMed

    Bock, Ralph

    2014-04-01

    The plastid genome represents an attractive target of genetic engineering in crop plants. Plastid transgenes often give high expression levels, can be stacked in operons and are largely excluded from pollen transmission. Recent research has greatly expanded our toolbox for plastid genome engineering and many new proof-of-principle applications have highlighted the enormous potential of the transplastomic technology in both crop improvement and the development of plants as bioreactors for the sustainable and cost-effective production of biopharmaceuticals, enzymes and raw materials for the chemical industry. This review describes recent technological advances with plastid transformation in seed plants. It focuses on novel tools for plastid genome engineering and transgene expression and summarizes progress with harnessing the potential of plastid transformation in biotechnology.

  19. Genetic engineering of the chloroplast: novel tools and new applications.

    PubMed

    Bock, Ralph

    2014-04-01

    The plastid genome represents an attractive target of genetic engineering in crop plants. Plastid transgenes often give high expression levels, can be stacked in operons and are largely excluded from pollen transmission. Recent research has greatly expanded our toolbox for plastid genome engineering and many new proof-of-principle applications have highlighted the enormous potential of the transplastomic technology in both crop improvement and the development of plants as bioreactors for the sustainable and cost-effective production of biopharmaceuticals, enzymes and raw materials for the chemical industry. This review describes recent technological advances with plastid transformation in seed plants. It focuses on novel tools for plastid genome engineering and transgene expression and summarizes progress with harnessing the potential of plastid transformation in biotechnology. PMID:24679252

  20. 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

  1. [The study of tomato fruit weight quantitative trait locus and its application in genetics teaching].

    PubMed

    Wang, Haiyan

    2015-08-01

    The classical research cases, which have greatly promoted the development of genetics in history, can be combined with the content of courses in genetics teaching to train students' ability of scientific thinking and genetic analysis. The localization and clone of gene controlling tomato fruit weight is a pioneer work in quantitative trait locus (QTL) studies and represents a complete process of QTL research in plants. Application of this integrated case in genetics teaching, which showed a wonderful process of scientific discovery and the fascination of genetic research, has inspired students' interest in genetics and achieved a good teaching effect.

  2. 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.

  3. Application of statistical design for the optimization of amino acid separation by reverse-phase HPLC.

    PubMed

    Gheshlaghi, R; Scharer, J M; Moo-Young, M; Douglas, P L

    2008-12-01

    Modified resolution and overall separation factors used to quantify the separation of complex chromatography systems are described. These factors were proven to be applicable to the optimization of amino acid resolution in reverse-phase (RP) HPLC chromatograms. To optimize precolumn derivatization with phenylisothiocyanate, a 2(5-1) fractional factorial design in triplicate was employed. The five independent variables for optimizing the overall separation factor were triethylamine content of the aqueous buffer, pH of the aqueous buffer, separation temperature, methanol/acetonitrile concentration ratio in the organic eluant, and mobile phase flow rate. Of these, triethylamine concentration and methanol/acetonitrile concentration ratio were the most important. The methodology captured the interaction between variables. Temperature appeared in the interaction terms; consequently, it was included in the hierarchic model. The preliminary model based on the factorial experiments was not able to explain the response curvature in the design space; therefore, a central composite design was used to provide a quadratic model. Constrained nonlinear programming was used for optimization purposes. The quadratic model predicted the optimal levels of the variables. In this study, the best levels of the five independent variables that provide the maximum modified resolution for each pair of consecutive amino acids appearing in the chromatograph were determined. These results are of utmost importance for accurate analysis of a subset of amino acids.

  4. 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.

  5. 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.

  6. A Class of Random Walks in Reversible Dynamic Environments: Antisymmetry and Applications to the East Model

    NASA Astrophysics Data System (ADS)

    Avena, Luca; Blondel, Oriane; Faggionato, Alessandra

    2016-10-01

    We introduce via perturbation a class of random walks in reversible dynamic environments having a spectral gap. In this setting one can apply the mathematical results derived in Avena et al. (L^2-Perturbed Markov processes and applications to random walks in dynamic random environments, Preprint, 2016). As first results, we show that the asymptotic velocity is antisymmetric in the perturbative parameter and, for a subclass of random walks, we characterize the velocity and a stationary distribution of the environment seen from the walker as suitable series in the perturbative parameter. We then consider as a special case a random walk on the East model that tends to follow dynamical interfaces between empty and occupied regions. We study the asymptotic velocity and density profile for the environment seen from the walker. In particular, we determine the sign of the velocity when the density of the underlying East process is not 1 / 2, and we discuss the appearance of a drift in the balanced setting given by density 1 / 2.

  7. 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

  8. Reversible Size Modulation of Aqueous Microgels via Orthogonal or Combined Application of Thermo- and Phototriggers.

    PubMed

    Phua, Dazril I; Herman, Krisztian; Balaceanu, Andreea; Zakrevski, Juri; Pich, Andrij

    2016-04-26

    Aqueous microgels that respond orthogonally to external temperature and light stimuli and to a combination of both stimuli were developed. N-Vinylcaprolactam (VCL) was copolymerized with small feed amounts (<5 mol %) of 4-[(4-methacryloyloxy)phenylazo] benzenesulfonic acid (ABSA) and cross-linked with N,N'-methylenebis(acrylamide) (BIS) to synthesize monodisperse and colloidally stable P(VCL-BIS-ABSA) microgels. The volume phase transition information on the microgels under both orthogonal and combined application of temperature and light stimuli was investigated in situ by dynamic light scattering (DLS) instrument. Modeling of this information by the Flory-Rehner theory describes and aids the preliminary understanding of the main features in the volume phase transition of these photoresponsive microgels. Interestingly, the microgels rapidly deswell upon UV irradiation (λ = 365 nm), even as the trans-ABSA pendant groups are converted to the more polar cis state. The variation in the content of the pendant azobenzene groups in the microgels allows for reversible modulation of the phototriggered volume change. We propose that the approach of the sulfonic acid groups of cis-ABSA toward the polymer backbone causes the disruption of hydrogen bonding interactions between water molecules and the carbonyl groups of VCL. PMID:26974267

  9. 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

  10. Reverse genetics vaccine seeds for influenza: Proof of concept in the source of PB1 as a determinant factor in virus growth and antigen yield.

    PubMed

    Gíria, Marta; Santos, Luís; Louro, João; Rebelo de Andrade, Helena

    2016-09-01

    Growth deficits of reverse genetics vaccine seeds have compromised effective immunization. The impairment has been attributed to sub-optimal protein interactions. Some level of dependence may exist between PB1 and antigenic glycoproteins, however, further research is necessary to clarify the extent to which it can be used in favor of seed production. Our objective was to establish proof of concept on the phenotypic outcome of PB1 source in the PR8: A(H1N1)pdm09 reassortants. Reassortants were generated with the gene constellation of the classical 6:2 PR8: HA, NApdm09 seed prototype and the 5:3 reassortant PR8: HA, NA, PB1pdm09. Viral growth and antigen yield were evaluated 12-60h post-infection. The 5:3 reassortant presented statistically significant growth and antigen yield improvements when compared to the 6:2. We believe these findings to be of promising value to vaccine research towards an improvement of reverse genetic seeds, an overall more cost-effective vaccine manufacture and timely delivery. PMID:27240145

  11. 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

  12. 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

  13. Finite element analysis/hydroburst test data correlation for reverse dome integrated stage application

    NASA Astrophysics Data System (ADS)

    Burson, K. S.; Nowakowski, M.; Tiwari, S.

    1993-02-01

    The U.S. Army's Missile Integrated Stage ('MIST') program has undertaken the development of an advanced strategic interceptor booster's solid-fueled rocket motor. The primary structural components of this booster are a composite case with full-diameter aft closure opening, a titanium reverse dome, and a forced-deflection nozzle plug housing. Attention is presently given to the correlation between the analytical models used in this program and the hydroburst test data obtained for the MIST reverse dome. It is found that the reverse dome exceeded the minimum required burst pressure of 2300 psig.

  14. Development of a reverse-genetics system for murine norovirus 3: long-term persistence occurs in the caecum and colon

    PubMed Central

    Bailey, Dalan; Chaudhry, Yasmin

    2012-01-01

    Human noroviruses (HuNoV) are a major cause of viral gastroenteritis worldwide, yet, due to the inability to propagate HuNoV in cell culture, murine norovirus (MNV) is typically used as a surrogate to study norovirus biology. MNV-3 represents an attractive strain to study norovirus infections in vivo because it establishes persistence in wild-type mice, yet causes symptoms resembling gastroenteritis in immune-compromised STAT1−/− mice. The lack of reverse-genetics approaches to recover genetically defined MNV-3 has limited further studies on the identification of viral sequences that contribute to persistence. Here we report the establishment of a combined DNA-based reverse-genetics and mouse-model system to study persistent MNV-3 infections in wild-type (C57BL/6) mice. Viral RNA and infectious virus were detected in faeces for at least 56 days after inoculation. Strikingly, the highest concentrations of viral RNA during persistence were detected in the caecum and colon, suggesting that viral persistence is maintained in these tissues. Possible adaptive changes arising during persistence in vivo appeared to accumulate in the minor capsid protein (VP2) and the viral polymerase (NS7), in contrast with adaptive mutations selected during cell-culture passages in RAW264.7 cells that appeared in the major capsid protein (VP1) and non-structural protein NS4. This system provides an attractive model that can be readily used to identify viral sequences that contribute to persistence in an immunocompetent host and to more acute infection in an immunocompromised host, providing new insights into the biology of norovirus infections. PMID:22495235

  15. 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

  16. Hospital infection caused by non-typable Staphylococcus aureus: application of reverse typing.

    PubMed Central

    Martín-Bourgon, C.; Berrón, S.; Casal, J.

    1985-01-01

    Hospital infections caused by strains of Staphylococcus aureus non-typable (NT) by phages have occurred in three Spanish hospitals since 1981. Reverse typing allowed characterization of the strains in all three cases. PMID:3157742

  17. 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.

  18. Genetic algorithm and the application for job shop group scheduling

    NASA Astrophysics Data System (ADS)

    Mao, Jianzhong; Wu, Zhiming

    1995-08-01

    Genetic algorithm (GA) is a heuristic and random search technique mimicking nature. This paper first presents the basic principle of GA, the definition and the function of the genetic operators, and the principal character of GA. On the basis of these, the paper proposes using GA as a new solution method of the job-shop group scheduling problem, discusses the coded representation method of the feasible solution, and the particular limitation to the genetic operators.

  19. Genetics and psychiatry: a proposal for the application of the precautionary principle.

    PubMed

    Porteri, Corinna

    2013-08-01

    The paper suggests an application of the precautionary principle to the use of genetics in psychiatry focusing on scientific uncertainty. Different levels of uncertainty are taken into consideration--from the acknowledgement that the genetic paradigm is only one of the possible ways to explain psychiatric disorders, via the difficulties related to the diagnostic path and genetic methods, to the value of the results of studies carried out in this field. Considering those uncertainties, some measures for the use of genetics in psychiatry are suggested. Some of those measures are related to the conceptual limits of the genetic paradigm; others are related to present knowledge and should be re-evaluated.

  20. 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

  1. 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

  2. Application of Reverse Transcription-PCR and Real-Time PCR in Nanotoxicity Research

    PubMed Central

    Mo, Yiqun; Wan, Rong; Zhang, Qunwei

    2016-01-01

    Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq® DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix. PMID:22975959

  3. Bloat free genetic programming: application to human oral bioavailability prediction.

    PubMed

    Silva, Sara; Vanneschi, Leonardo

    2012-01-01

    Being able to predict the human oral bioavailability for a potential new drug is extremely important for the drug discovery process. This problem has been addressed by several prediction tools, with Genetic Programming providing some of the best results ever achieved. In this paper we use the newest developments of Genetic Programming, in particular the latest bloat control method, Operator Equalisation, to find out how much improvement we can achieve on this problem. We show examples of some actual solutions and discuss their quality, comparing them with previously published results. We identify some unexpected behaviours related to overfitting, and discuss the way for further improving the practical usage of the Genetic Programming approach.

  4. 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.

  5. 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

  6. [Application of ISSR technology in genetic diversity detection of jute].

    PubMed

    Qi, Jianmin; Zhou, Dongxin; Wu, Weiren; Lin, Lihui; Wu, Jianmei; Fang, Pingping

    2003-09-01

    The genetic diversity among 27 accessions of Corchorus, including 10 Jute species, was investigated with ISSR technique. 283 DNA bands were amplified with 25 ISSR primers, among which, 263 (92.85%) were polymorphic, with 10.48 bands per primer in average. A further systemic cluster analysis indicated that the accessions could be clustered into three groups, and the group II (including two cultispecies and their close wild species) was obviously genetically different from the groups I and III (including eight wild species). Moreover, 16 accessions in group II presented a higher intraspecific genetic resemblance, while 11 accessions among groups I & III showed an abundant interspecific genetic diversity. After synthesized the relevant findings of morphology and DNA classification, it's found that C. urticifolius could be one of the original wild species, C. tilaculariszic was a variation of C. tilaculari, and Tian Jute could be an untitled wild species.

  7. A field-reversed magnetic configuration and applications of high-temperature FRC plasma

    SciTech Connect

    Ryzhkov, S. V.

    2011-12-15

    As applied to a tokomak, a magnetic trap for confinement of a plasma with an inverted field or a magnetic field reversed configuration (FRC) is one of the most promising alternatives of the systems with high {beta}. A brief review of the latest data on FRC and potential directions of using such configurations in addition to energy generation in thermonuclear reactors (TNRs) is proposed.

  8. Development of a full-length cDNA-derived enterovirus A71 vaccine candidate using reverse genetics technology.

    PubMed

    Yang, Ya-Ting; Chow, Yen-Hung; Hsiao, Kuang-Nan; Hu, Kai-Chieh; Chiang, Jen-Ron; Wu, Suh-Chin; Chong, Pele; Liu, Chia-Chyi

    2016-08-01

    Enterovirus A71 (EV-A71) is responsible for epidemics of hand, foot and mouth disease (HFMD) in young children. To circumvent difficulties in obtaining clinical enterovirus isolates that might be contaminated with other viruses, a platform technology was developed to quickly generate vaccine virus strains based on the published enterovirus genomic sequences. A recombinant plasmid containing the full-length infectious cDNA clone of EV-A71 vaccine strain E59 was directly generated after transfecting the recombinant plasmid into Vero, RD or HEK293A cells, and phenotypic characteristics similar to the parental strain were observed. The cDNA-derived infectious EV-A71 virus grown in Vero cells produced relatively stable virus titers in both T-flasks and microcarrier culture systems. To evaluate the genetic stability of the cDNA-derived EV-A71 viruses, the immunodominant structural proteins, VP1 and VP2, of the recombinant EV-A71 viruses were sequenced and analyzed. The cDNA-derived EV-A71 virus showed weak pathogenicity in a human SCARB2 mouse model. These results show the successful generation of a recombinant virus derived from a published viral genomic sequence that demonstrated good genetic stability and viral yields, which could represent an efficient and safe vaccine strain for cGMP-grade manufacturing. PMID:27387826

  9. The K65R mutation in HIV-1 reverse transcriptase: genetic barriers, resistance profile and clinical implications.

    PubMed

    Brenner, Bluma G; Coutsinos, Dimitrios

    2009-11-01

    Resistance to antiviral therapy is the limiting factor in the successful management of HIV. In general, the K65R mutation is rarely selected (1.7-4%) with tenofovir disoproxil fumarate (TDF), abacavir (ABC), didanosine (ddI), and stavudine (d4T), as compared with the high incidence (>40%) of thymidine analog mutations associated with zidovudine and d4T. The high barrier to the development of K65R may reflect a combination of factors, including the high potency of K65R-selecting drugs, including recommended TDF/emtricitabine and ABC/lamivudine (ABC/3TC) combinations; the partial (low-intermediate level) profile of cross-resistance conferred by K65R to TDF, ABC and 3TC; the favorable viral fitness constraint imposed by K65R and the 3TC/emtricitabine-associated M184V mutations; the bidirectional antagonism between the K65R and thymidine analog mutation pathways; and unique RNA structural considerations in the region surrounding codon 65. Nevertheless, surprisingly high levels of treatment failures and K65R resistance may be associated with triple nucleoside analog regimens. The use of TDF + ABC, TDF + ddI and ABC + d4T in combination with 3TC or emtricitabine should be avoided. This selection of K65R may be reduced by the inclusion of zidovudine in two-four nucleoside reverse-transcriptase regimens. Clinical studies have demonstrated an increased frequency of K65R in association with suboptimal d4T and ddI regimens, as well as nevirapine and its resistance mutations Y181C and G190A. The potential for the development of the K65R mutation in subtype C is particularly problematic wherein a signature KKK nucleotide motif, at codons 64, 65 and 66 in reverse transcriptase, appear to lead to template pausing, facilitating the selection of K65R. Optimizing regimens may attenuate the emergence of K65R, leading to better long-term treatment management in different geographic settings. TDF-based regimens are the leading candidates for first- and second-line therapy, microbicides

  10. 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

  11. 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

  12. Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events.

    PubMed

    Monjane, Adérito L; Martin, Darren P; Lakay, Francisco; Muhire, Brejnev M; Pande, Daniel; Varsani, Arvind; Harkins, Gordon; Shepherd, Dionne N; Rybicki, Edward P

    2014-07-01

    Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own "lethally recombinant." Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. Importance: Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk

  13. Reverse Genetics of Drosophila RNA Polymerase II: Identification and Characterization of Rpii140, the Genomic Locus for the Second-Largest Subunit

    PubMed Central

    Hamilton, B. J.; Mortin, M. A.; Greenleaf, A. L.

    1993-01-01

    We have used a reverse genetics approach to isolate genes encoding two subunits of Drosophila melanogaster RNA polymerase II. RpII18 encodes the 18-kDa subunit and maps cytogenetically to polytene band region 83A. RpII140 encodes the 140-kDa subunit and maps to polytene band region 88A10:B1,2. Focusing on RpII140, we used in situ hybridization to map this gene to a small subinterval defined by the endpoints of a series of deficiencies impinging on the 88A/B region and showed that it does not represent a previously known genetic locus. Two recently defined complementation groups, A5 and Z6, reside in the same subinterval and thus were candidates for the RpII140 locus. Phenotypes of A5 mutants suggested that they affect RNA polymerase II, in that the lethal phase and the interaction with developmental loci such as Ubx resemble those of mutants in the gene for the largest subunit, RpII215. Indeed, we have achieved complete genetic rescue of representative recessive lethal mutations of A5 with a P-element construct containing a 9.1-kb genomic DNA fragment carrying RpII140. Interestingly, the initial construct also rescued lethal alleles in the neighboring complementation group, Z6, revealing that the 9.1-kb insert carries two genes. Deleting coding region sequences of RpII140, however, yielded a transformation vector that failed to rescue A5 alleles but continued to rescue Z6 alleles. These results strongly support the conclusion that the A5 complementation group is equivalent to the genomic RpII140 locus. PMID:8325487

  14. Reversal of Refractory Ulcerative Colitis and Severe Chronic Fatigue Syndrome Symptoms Arising from Immune Disturbance in an HLADR/DQ Genetically Susceptible Individual with Multiple Biotoxin Exposures

    PubMed Central

    Gunn, Shelly R.; Gibson Gunn, G.; Mueller, Francis W.

    2016-01-01

    Patient: Male, 25 Final Diagnosis: Ulcerative colitis and chronic fatigue syndrome Symptoms: Colitis • profound fatigue • multi-joint pain • cognitive impairment • corneal keratitis Medication: — Clinical Procedure: VIP replacement therapy Specialty: Family Medicine Objective: Unusual clinical course Background: Patients with multisymptom chronic conditions, such as refractory ulcerative colitis (RUC) and chronic fatigue syndrome (CFS), present diagnostic and management challenges for clinicians, as well as the opportunity to recognize and treat emerging disease entities. In the current case we report reversal of co-existing RUC and CFS symptoms arising from biotoxin exposures in a genetically susceptible individual. Case Report: A 25-year-old previously healthy male with new-onset refractory ulcerative colitis (RUC) and chronic fatigue syndrome (CFS) tested negative for autoimmune disease biomarkers. However, urine mycotoxin panel testing was positive for trichothecene group and air filter testing from the patient’s water-damaged rental house identified the toxic mold Stachybotrys chartarum. HLA-DR/DQ testing revealed a multisusceptible haplotype for development of chronic inflammation, and serum chronic inflammatory response syndrome (CIRS) biomarker testing was positive for highly elevated TGF-beta and a clinically undetectable level of vasoactive intestinal peptide (VIP). Following elimination of biotoxin exposures, VIP replacement therapy, dental extractions, and implementation of a mind body intervention-relaxation response (MBI-RR) program, the patient’s symptoms resolved. He is off medications, back to work, and resuming normal exercise. Conclusions: This constellation of RUC and CFS symptoms in an HLA-DR/DQ genetically susceptible individual with biotoxin exposures is consistent with the recently described CIRS disease pathophysiology. Chronic immune disturbance (turbatio immuno) can be identified with clinically available CIRS biomarkers and

  15. 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

  16. 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.

  17. Applications of nanoparticle drug delivery systems for the reversal of multidrug resistance in cancer

    PubMed Central

    HUANG, YINGHONG; COLE, SUSAN P.C.; CAI, TIANGE; CAI, YU

    2016-01-01

    Multidrug resistance (MDR) to chemotherapy presents a major obstacle in the treatment of cancer patients, which directly affects the clinical success rate of cancer therapy. Current research aims to improve the efficiency of chemotherapy, whilst reducing toxicity to prolong the lives of cancer patients. As with good biocompatibility, high stability and drug release targeting properties, nanodrug delivery systems alter the mechanism by which drugs function to reverse MDR, via passive or active targeting, increasing drug accumulation in the tumor tissue or reducing drug elimination. Given the potential role of nanodrug delivery systems used in multidrug resistance, the present study summarizes the current knowledge on the properties of liposomes, lipid nanoparticles, polymeric micelles and mesoporous silica nanoparticles, together with their underlying mechanisms. The current review aims to provide a reliable basis and useful information for the development of new treatment strategies of multidrug resistance reversal using nanodrug delivery systems. PMID:27347092

  18. Harnessing reversible oxidative addition: application of diiodinated aromatic compounds in the carboiodination process.

    PubMed

    Petrone, David A; Lischka, Matthias; Lautens, Mark

    2013-09-27

    An I for an I: Conditions for the intramolecular carboiodination and the simultaneous convergent intramolecular carboiodination/intermolecular Heck reaction of various diiodoarenes were developed. The ability of the Pd(0)/QPhos catalyst/ligand combination to undergo reversible oxidative addition allows these reactions to proceed well, thus increasing both the appeal and utility of this class of substrates in site-selective cross-coupling reactions.

  19. 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.

  20. Application of real-time polymerase chain reaction in the clinical genetic practice.

    PubMed

    Nagy, Bálint

    2013-03-01

    The development of polymerase chain reaction revolutionized the molecular genetics and diagnostics. Technical improvements helped to make more specific and sensitive target determinations. Introduction of real-time polymerase chain reaction makes possible several applications in clinical genetics like detection of gene mutations, single nucleotide polymorphisms, deletions, measurement of gene expressions, micro ribonucleic acids, free nucleic acids and microbial genomes. Here I discuss a few examples for specific applications in prenatal clinical genetic practice. These are the detection of microbial genomes, deletions, trisomies, mutations, single nucleotide polymorphisms and free nucleic acids. PMID:27625833

  1. Application of real-time polymerase chain reaction in the clinical genetic practice

    PubMed Central

    Nagy, Bálint

    2013-01-01

    The development of polymerase chain reaction revolutionized the molecular genetics and diagnostics. Technical improvements helped to make more specific and sensitive target determinations. Introduction of real-time polymerase chain reaction makes possible several applications in clinical genetics like detection of gene mutations, single nucleotide polymorphisms, deletions, measurement of gene expressions, micro ribonucleic acids, free nucleic acids and microbial genomes. Here I discuss a few examples for specific applications in prenatal clinical genetic practice. These are the detection of microbial genomes, deletions, trisomies, mutations, single nucleotide polymorphisms and free nucleic acids.

  2. Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications.

    PubMed

    Pandey, Gunjan; Paul, Debarati; Jain, Rakesh K

    2005-02-18

    Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s). PMID:15649393

  3. Application of Carbonate Reservoir using waveform inversion and reverse-time migration methods

    NASA Astrophysics Data System (ADS)

    Kim, W.; Kim, H.; Min, D.; Keehm, Y.

    2011-12-01

    Recent exploration targets of oil and gas resources are deeper and more complicated subsurface structures, and carbonate reservoirs have become one of the attractive and challenging targets in seismic exploration. To increase the rate of success in oil and gas exploration, it is required to delineate detailed subsurface structures. Accordingly, migration method is more important factor in seismic data processing for the delineation. Seismic migration method has a long history, and there have been developed lots of migration techniques. Among them, reverse-time migration is promising, because it can provide reliable images for the complicated model even in the case of significant velocity contrasts in the model. The reliability of seismic migration images is dependent on the subsurface velocity models, which can be extracted in several ways. These days, geophysicists try to obtain velocity models through seismic full waveform inversion. Since Lailly (1983) and Tarantola (1984) proposed that the adjoint state of wave equations can be used in waveform inversion, the back-propagation techniques used in reverse-time migration have been used in waveform inversion, which accelerated the development of waveform inversion. In this study, we applied acoustic waveform inversion and reverse-time migration methods to carbonate reservoir models with various reservoir thicknesses to examine the feasibility of the methods in delineating carbonate reservoir models. We first extracted subsurface material properties from acoustic waveform inversion, and then applied reverse-time migration using the inverted velocities as a background model. The waveform inversion in this study used back-propagation technique, and conjugate gradient method was used in optimization. The inversion was performed using the frequency-selection strategy. Finally waveform inversion results showed that carbonate reservoir models are clearly inverted by waveform inversion and migration images based on the

  4. 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

  5. Genetic studies in chronic kidney disease: interpretation and clinical applicability.

    PubMed

    Witasp, Anna; Nordfors, Louise; Carrero, Juan Jesus; Luttropp, Karin; Lindholm, Bengt; Schalling, Martin; Stenvinkel, Peter

    2012-01-01

    The tools of modern molecular biology are evolving rapidly, resulting in vastly more efficient approaches to illuminating human genetic variations and their effects on common multifactorial disorders such as chronic kidney disease (CKD). Indeed, candidate gene association studies and genome-wide association studies (GWASs) have generated novel genetic variants in previously unrecognized biological pathways, highlighting disease mechanisms with a potential role in CKD etiology, morbidity and mortality. Nephrologists now need to find ways to make use of these advancements and meet the increasingly stringent requirements for valid study design, data handling and interpretation of genetic studies. Adding to our prior article in this journal, which introduced the basics of genotype-phenotype association studies in CKD, this second article focuses on how to ascertain robust and reproducible findings by applying adequate methodological and statistical approaches to genotype-phenotype studies in CKD populations. Moreover, this review will briefly discuss genotype-based risk prediction, pharmacotherapy, drug target identification and individualized treatment solutions, specifically highlighting potentially important findings in CKD patients. This increased knowledge will hopefully facilitate the exciting transition from conventional clinical medicine to gene-based medicine. However, before this can be accomplished, unsolved issues regarding the complex human genetic architecture as well technical and clinically oriented obstacles will have to be overcome. Additionally, new policies and standardized risk evaluations for genetic testing in the clinical setting will have to be established to guarantee that CKD patients are provided with high-quality genotype-guided counseling that will help to improve their poor outcomes.

  6. Molecular evolutionary genetics of isozymes: pattern, theory, and application.

    PubMed

    Nevo, E

    1990-01-01

    Isozyme studies at the population genetics-ecology interface conducted at the Institute of Evolution, University of Haifa, during 15 years, 1974-1989, are reviewed in terms of the evidence, theoretical, and practical implications. These studies involve numerous individuals, populations, species, and higher taxa in nature of plants, animals, and humans tested for variation at 15 to 50 primary isozyme loci. The isozyme studies have been conducted mainly in individuals sampled in natural populations at the local, regional, and global levels. Two of the species studied were wild cereals, the progenitors of wheat and barley in the Near East Fertile Crescent. These studies have been complemented by laboratory controlled a priori experimentation of inorganic and organic pollution biology. The human genetics laboratory compared isozyme structure of Jewish and non-Jewish populations. Our results indicate that: (i) isozyme diversity in nature in abundant, at least partly adaptive, and is oriented and maintained primarily by ecological factors. (ii) Natural selection in action is highlighted by stresses involving among others thermal, chemical, and climatic factors. (iii) Speciation can occur with little change in isozyme diversity. (iv) Jews from diverse countries, and in spite of 2,000 years of Diaspora, retain in the frequencies of some isozymes their Near Eastern origins. (v) Wild cereals harbor rich genetic resources exploitable in breeding either directly as adaptive structures, or indirectly as genetic markers for genotypic production of elite agronomic traits. (vi) Isozymes have been utilized as genetic monitors of marine pollution thereby contributing to environmental quality and conservation. (vii) Isozymes can substantially contribute to conservation biology. (viii) Isozymes have been successfully utilized in constructing molecular phylogenies and in revealing new sibling species. (ix) Future theoretical and practical directions of isozyme studies at the protein

  7. Molecular evolutionary genetics of isozymes: pattern, theory, and application.

    PubMed

    Nevo, E

    1990-01-01

    Isozyme studies at the population genetics-ecology interface conducted at the Institute of Evolution, University of Haifa, during 15 years, 1974-1989, are reviewed in terms of the evidence, theoretical, and practical implications. These studies involve numerous individuals, populations, species, and higher taxa in nature of plants, animals, and humans tested for variation at 15 to 50 primary isozyme loci. The isozyme studies have been conducted mainly in individuals sampled in natural populations at the local, regional, and global levels. Two of the species studied were wild cereals, the progenitors of wheat and barley in the Near East Fertile Crescent. These studies have been complemented by laboratory controlled a priori experimentation of inorganic and organic pollution biology. The human genetics laboratory compared isozyme structure of Jewish and non-Jewish populations. Our results indicate that: (i) isozyme diversity in nature in abundant, at least partly adaptive, and is oriented and maintained primarily by ecological factors. (ii) Natural selection in action is highlighted by stresses involving among others thermal, chemical, and climatic factors. (iii) Speciation can occur with little change in isozyme diversity. (iv) Jews from diverse countries, and in spite of 2,000 years of Diaspora, retain in the frequencies of some isozymes their Near Eastern origins. (v) Wild cereals harbor rich genetic resources exploitable in breeding either directly as adaptive structures, or indirectly as genetic markers for genotypic production of elite agronomic traits. (vi) Isozymes have been utilized as genetic monitors of marine pollution thereby contributing to environmental quality and conservation. (vii) Isozymes can substantially contribute to conservation biology. (viii) Isozymes have been successfully utilized in constructing molecular phylogenies and in revealing new sibling species. (ix) Future theoretical and practical directions of isozyme studies at the protein

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Reverse genetics based rgH5N2 vaccine provides protection against high dose challenge of H5N1 avian influenza virus in chicken.

    PubMed

    Bhatia, S; Khandia, R; Sood, R; Bhat, S; Siddiqui, A; Jahagirdhar, G; Mishra, S; Mishra, A; Pateriya, A K; Kulkarni, D D

    2016-08-01

    An inactivated vaccine was developed using the rgH5N2 virus (6 + 2 reassortant) generated by plasmid based reverse genetics system (RGS) with WSN/33/H1N1 as backbone virus. Following mutation of the basic amino acid cleavage site RRRKKR*GLF to IETR*GLF, the H5-HA (haemagglutinin) gene of the selected donor H5N1 virus (A/chicken/West Bengal/80995/2008) of antigenic clade 2.2 was used along with the N2-NA gene from H9N2 field isolate (A/chicken/Uttar Pradesh/2543/2004) for generation of the rgH5N2 virus. A single dose (0.5 ml/bird) of the inactivated rgH5N2 vaccine protected 100% of the vaccinated chickens (n = 10) on 28(th) dpv (early challenge) and 90% of the vaccinated chickens (n = 10) on 200(th) dpv (late challenge) against high dose challenge with HPAI virus (10(9) EID50/bird). Challenge virus shedding via oropharynx and cloaca of the vaccinated chickens was detectable by realtime RT-PCR during 1-5 dpc and 1-9 days dpc in the early and the late challenge, respectively. The protective level of antibodies (mean HI titre > 128) was maintained without booster vaccination for 200 days. The present study provides the experimental evidence about the extent of protection provided by a reverse genetics based vaccine for clade 2.2 H5N1 viruses against challenge with high dose of field virus at two different time points (28 dpv and 200 dpv). The challenge study is uniquely different from the previous similar experiments on account of 1000 times higher dose of challenge and protection at 200 dpv. The protection and virus shedding data of the study may be useful for countries planning to use H5 vaccine in poultry especially against the clade 2.2 H5N1 viruses. PMID:27296706

  13. 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

  14. Application of the Time Reversed Acoustic Concept to Earthquake Location and Focal Depth Determination

    NASA Astrophysics Data System (ADS)

    Toksoz, M.; Lu, R.; Pearce, F.; Sarkar, S.

    2007-12-01

    Local and regional seismograms have long codas due to strong scattering of seismic waves in the crust. Accurate identification of individual phases (P, pP, PmP, S, sS, etc.) is difficult because the scattered arrivals complicate the local seismograms and introduce errors in picking phases and their arrival times. These, in turn, introduce errors in hypocenter parameters. Strong scattering, that is a detriment to picking individual phases, makes it possible to apply the Time Reversed Acoustic (TRA) concept to local earthquake location and focal depth determination. The basic idea in TRA is to time reverse the recorded signals (seismograms) and to inject them into the earth. If the earth structure is known, the back-propagated signals could focus at the source. We demonstrate this by synthetic (numerical) examples and with seismograms from earthquakes. Foci, determined by TRA and by traditional methods with arrival times from close-in stations, agree very well. Independently, we present a method based on the TRA concept for earthquake focal depth determination. In a highly scattering medium, the source time function determination and pP identification can be accomplished simply, by autocorrelation of the seismograms.

  15. An application of time-reversed acoustics to the imaging of a salt-dome flank

    NASA Astrophysics Data System (ADS)

    Willis, M. E.; Lu, R.; Campman, X.; Toksöz, N.; Zhang, Y.; de Hoop, M. V.

    2005-12-01

    We present results of applying the concept of time-reversed acoustics (TRA) to the imaging of a salt-dome flank in a v(z) medium. A simulated multi-level walk-away VSP survey with sources at the surface and receivers in the borehole can be sorted into an equivalent reverse VSP (RVSP) with effective downhole sources and surface receivers. We apply the TRA process to the RVSP traces and create a zero offset seismic section as if it had been collected from collocated downhole sources and receivers. This procedure effectively redatums the wavefield from the surface to the borehole, eliminating the need for any complicated processing. The redatummed traces are created by summing the autocorrelations of the traces in the RVSP common shot gather. Theory says that each shot gather should be from receivers which completely surround the source. From practical considerations, we only have available the RVSP common receivers on the earth's surface, so we obtain an approximate zero offset section. Even with this restriction, our example shows that the results are encouraging. The image of the salt dome flank is created from the redatummed traces using a standard post-stack depth migration algorithm. This image compares favorably with the salt dome flank model.

  16. 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.

  17. Unequal representation of genetic variation across ancestry groups creates healthcare inequality in the application of precision medicine.

    PubMed

    Petrovski, Slavé; Goldstein, David B

    2016-07-14

    An important application of modern genomics is diagnosing genetic disorders. We use the largest publicly available exome sequence database to show that this key clinical service can currently be performed much more effectively in individuals of European genetic ancestry.

  18. Exploitation of genetically modified inoculants for industrial ecology applications.

    PubMed

    Morrissey, John P; Walsh, Ultan F; O'Donnell, Anne; Moënne-Loccoz, Yvan; O'Gara, Fergal

    2002-08-01

    The major growth seen in the biotechnology industry in recent decades has largely been driven by the exploitation of genetic engineering techniques. The initial benefits have been predominantly in the biomedical area, with products such as vaccines and hormones that have received broad public approval. In the environmental biotechnology and industrial ecology sectors, biotechnology has the potential to make significant advances through the use of genetically modified (GM) microbial inoculants that can reduce agri-chemical usage or remediate polluted environments. Although many GM inoculants have been developed and tested under laboratory conditions, commercial exploitation has lagged behind. Here, we review scientific and regulatory requirements that must be satisfied as part of that exploitation process. Particular attention is paid to new European Union (EU) regulations (Directives) that govern the testing and release of genetically modified organisms and microbial plant protection inoculants in the EU. With regard to the release of GM inoculants, the impact of the inoculant and the fate of modified genes are important concerns. Long term monitoring of release sites is necessary to address these issues. Data are reported from the monitoring of a site 6 years after release of GM Sinorhizobium meliloti strains. It was found that despite the absence of a host plant, the GM strains persisted in the soil for at least 6 years. Horizontal transfer and microevolution of a GM plasmid between S. meliloti strains was also observed. These data illustrate the importance of assessing the long-term persistence of GM inoculants. PMID:12448755

  19. Barriers to application of genetically modified lactic acid bacteria.

    PubMed

    Verrips, C T; van den Berg, D J

    1996-10-01

    To increase the acceptability of food products containing genetically modified microorganisms it is necessary to provide in an early stage to the consumers that the product is safe and that the product provide a clear benefit to the consumer. To comply with the first requirement a systematic approach to analyze the probability that genetically modified lactic acid bacteria will transform other inhabitants of the gastro- intestinal (G/I) tract or that these lactic acid bacteria will pick up genetic information of these inhabitants has been proposed and worked out to some degree. From this analysis it is clear that reliable data are still missing to carry out complete risk assessment. However, on the basis of present knowledge, lactic acid bacteria containing conjugative plasmids should be avoided. Various studies show that consumers in developed countries will accept these products when they offer to them health or taste benefits or a better keepability. For the developing countries the biggest challenge for scientists is most likely to make indigenous fermented food products with strongly improved microbiological stability due to broad spectra bacteriocins produced by lactic acid bacteria. Moreover, these lactic acid bacteria may contribute to health.

  20. A survey of application: genomics and genetic programming, a new frontier.

    PubMed

    Khan, Mohammad Wahab; Alam, Mansaf

    2012-08-01

    The aim of this paper is to provide an introduction to the rapidly developing field of genetic programming (GP). Particular emphasis is placed on the application of GP to genomics. First, the basic methodology of GP is introduced. This is followed by a review of applications in the areas of gene network inference, gene expression data analysis, SNP analysis, epistasis analysis and gene annotation. Finally this paper concluded by suggesting potential avenues of possible future research on genetic programming, opportunities to extend the technique, and areas for possible practical applications.

  1. Genetic variants in telomerase reverse transcriptase (TERT) and telomerase-associated protein 1 (TEP1) and the risk of male infertility.

    PubMed

    Yan, Lifeng; Wu, Shengmin; Zhang, Shenghu; Ji, Guixiang; Gu, Aihua

    2014-01-25

    Telomeres are critical in maintaining genomic stability and integrity, and telomerase expression in spermatogonial stem cells is responsible for the maintenance of telomere length in the human male germline. Genetic variants in telomere-associated pathway genes might affect telomere length and chromosomal stability, and subsequently disease susceptibility. Thus, we hypothesize that single nucleotide polymorphisms (SNPs) in this pathway could contribute to male infertility risk. In a case-control study of 580 male infertility cases and 580 matched controls, 8 common SNPs in telomerase reverse transcriptase (TERT) and telomerase-associated protein 1 (TEP1) were genotyped. Overall, we found that TERT rs2736100 was inversely associated with male infertility risk (adjusted odds ratio (OR)=0.66, 95% confidence interval (CI): 0.47-0.92; Ptrend=0.011), whereas TEP1 rs1713449 was positively associated with risk of male infertility (adjusted OR=1.39, 95% CI: 1.20-1.62; Ptrend<0.001). In addition, subjects carrying risk genotypes of these both loci had a two-fold (95% CI: 1.34-3.15) increase in the risk of male infertility, indicating a significant gene-gene interaction between these two loci (P for multiplicative interaction=0.009). Moreover, linear regression analysis showed that individuals carrying the TEP1 rs1713419 variants have significantly higher levels of sperm DNA fragmentation (β=2.243, P=0.016). In conclusion, our results give the first evidence that genetic variations of TERT rs2736100 and TEP1 rs1713449 were associated with susceptibility to male infertility.

  2. 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 ...

  3. 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...

  4. 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

  5. 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

  6. 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.

  7. Application of Reverse Engineering Template for the Correction of Asymmetric Deformity of Maxillofacial Fibrous Dysplasia.

    PubMed

    Pan, Jianwei; Ye, Bin; Hu, Jing; Li, Xiang; Zhang, Yiqun; Li, Jihua

    2016-03-01

    Facial asymmetry deformity is the most common symptom of patients with fibrous dysplasia. This study provides a novel method based on computed tomography scan data, mirror-imaged reverse engineering and rapid prototyping for design and manufacture of an individual template guiding accurately the extent and quantity of partial resection of hyperplastic tissues to reshape the affected bones during operation. Ten adult patients with unilateral facial fibrous dysplasia accepted these treatments, the postoperative appearances showed that the protrusions were effectively reduced; bilateral faces were basically symmetric with no serious complications. This method shorts operation time, decreases surgical risk, and guarantees the aesthetic symmetry. Apparent recurrence was not observed during the follow-up period, and the final outcomes were satisfactory for both surgeons and patients.

  8. Application of reverse micelle extraction process for amylase recovery using response surface methodology.

    PubMed

    Bera, Manav B; Panesar, Parmjit S; Panesar, Reeba; Singh, Bahadur

    2008-06-01

    The effect of different process variables of reverse micelle extraction process like pH, addition of surfactant (AOT) concentration and potassium chloride (KCl) concentration on amylase recovery has been studied and analysed. Solid-state fermentation was used for the production of amylase enzyme. Response surface methodology (RSM) using central composite rotatable design (CCRD) was employed to analyse and optimize the enzyme extraction process. The regression analysis indicates that the effect of AOT concentration, and KCl concentration were significant, whereas the effect of pH was non-significant on enzyme recovery. For the maximum recovery of enzyme, the optimum operating condition for pH, AOT concentration (M) and KCl concentration were 10.43, 0.05 and 1.00, respectively. Under these optimal conditions, the enzyme recovery was 83.16%.

  9. An invariance principle for reversible Markov processes. Applications to random motions in random environments

    SciTech Connect

    De Masi, A.; Ferrari, P.A.; Goldstein, S.; Wick, W.D. )

    1989-05-01

    The authors present an invariance principle for antisymmetric functions of a reversible Markov process which immediately implies convergence to Brownian motion for a wide class of random motions in random environments. They apply it to establish convergence to Brownian motion (i) for a walker moving in the infinite cluster of the two-dimensional bond percolation model, (ii) for a d-dimensional walker moving in a symmetric random environment under very mild assumptions on the distribution of the environment, (iii) for a tagged particle in a d-dimensional symmetric lattice gas which allows interchanges, (iv) for a tagged particle in a d-dimensional system of interacting Brownian particles. Their formulation also leads naturally to bounds on the diffusion constant.

  10. Genetic algorithms and their application to in silico evolution of genetic regulatory networks.

    PubMed

    Knabe, Johannes F; Wegner, Katja; Nehaniv, Chrystopher L; Schilstra, Maria J

    2010-01-01

    A genetic algorithm (GA) is a procedure that mimics processes occurring in Darwinian evolution to solve computational problems. A GA introduces variation through "mutation" and "recombination" in a "population" of possible solutions to a problem, encoded as strings of characters in "genomes," and allows this population to evolve, using selection procedures that favor the gradual enrichment of the gene pool with the genomes of the "fitter" individuals. GAs are particularly suitable for optimization problems in which an effective system design or set of parameter values is sought.In nature, genetic regulatory networks (GRNs) form the basic control layer in the regulation of gene expression levels. GRNs are composed of regulatory interactions between genes and their gene products, and are, inter alia, at the basis of the development of single fertilized cells into fully grown organisms. This paper describes how GAs may be applied to find functional regulatory schemes and parameter values for models that capture the fundamental GRN characteristics. The central ideas behind evolutionary computation and GRN modeling, and the considerations in GA design and use are discussed, and illustrated with an extended example. In this example, a GRN-like controller is sought for a developmental system based on Lewis Wolpert's French flag model for positional specification, in which cells in a growing embryo secrete and detect morphogens to attain a specific spatial pattern of cellular differentiation. PMID:20835807

  11. 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.

  12. Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days

    PubMed Central

    Aubry, Fabien; Gould, Ernest A.; de Lamballerie, Xavier

    2016-01-01

    Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines. PMID:27548676

  13. 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

  14. Optimization of influenza A vaccine virus by reverse genetic using chimeric HA and NA genes with an extended PR8 backbone.

    PubMed

    Medina, Julie; Boukhebza, Houda; De Saint Jean, Amélie; Sodoyer, Régis; Legastelois, Isabelle; Moste, Catherine

    2015-08-20

    The yield of influenza antigen production may significantly vary between vaccine strains; for example the A/California/07/09 (H1N1)-X179A vaccine virus, prepared during 2009 influenza pandemic, presented a low antigen yield in eggs compared to other seasonal H1N1 reassortants. In this study a bi-chimeric virus expressing HA and NA genes with A/Puerto Rico/8/34 (H1N1) (PR8) and X179A domains was rescued by reverse genetics using a mixture of Vero/CHOK1 cell lines (Medina et al. [7]). The bi-chimeric virus obtained demonstrated to yield much larger amounts of HA than X179A in eggs as measured by single-radial-immunodiffusion (SRID), the reference method to quantify HA protein in influenza vaccine. Such kind of optimized virus using PR8 backbone derived chimeric glycoproteins could be used as improved seed viruses for vaccine production. PMID:26206270

  15. Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days.

    PubMed

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

    2016-01-01

    Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines.

  16. Potassium channel openers increase aortic elastic fiber formation and reverse the genetically determined elastin deficit in the BN rat.

    PubMed

    Slove, Séverin; Lannoy, Morgane; Behmoaras, Jacques; Pezet, Mylène; Sloboda, Natacha; Lacolley, Patrick; Escoubet, Brigitte; Buján, Julia; Jacob, Marie-Paule

    2013-10-01

    Hypertension is a cardiovascular disorder that appears in more than half of the patients with Williams-Beuren syndrome, hemizygous for the elastin gene among 26 to 28 other genes. It was shown that the antihypertensive drug minoxidil, an ATP-dependent potassium channel opener, enhances elastic fiber formation; however, no wide clinical application was developed because of its adverse side effects. The Brown Norway rat was used here as an arterial elastin-deficient model. We tested 3 different potassium channel openers, minoxidil, diazoxide, and pinacidil, and 1 potassium channel blocker, glibenclamide, on cultured smooth muscle cells from Brown Norway rat aorta. All tested potassium channel openers increased mRNAs encoding proteins and enzymes involved in elastic fiber formation, whereas glibenclamide had the opposite effect. The higher steady-state level of tropoelastin mRNA in minoxidil-treated cells was attributable to an increase in both transcription and mRNA stability. Treatment of Brown Norway rats for 10 weeks with minoxidil or diazoxide increased elastic fiber content and decreased cell number in the aortic media, without changing collagen content. The minoxidil-induced cardiac hypertrophy was reduced when animals simultaneously received irbesartan, an angiotensin II-receptor antagonist. This side effect of minoxidil was not observed in diazoxide-treated animals. In conclusion, diazoxide, causing less undesirable side effects than minoxidil, or coadministration of minoxidil and irbesartan, increases elastic fiber content, decreases cell number in the aorta and, thus, could be suitable for treating vascular pathologies characterized by diminished arterial elastin content and simultaneous hypertension. PMID:23918751

  17. Application of Genetic Algorithms in Nonlinear Heat Conduction Problems

    PubMed Central

    Khan, Waqar A.

    2014-01-01

    Genetic algorithms are employed to optimize dimensionless temperature in nonlinear heat conduction problems. Three common geometries are selected for the analysis and the concept of minimum entropy generation is used to determine the optimum temperatures under the same constraints. The thermal conductivity is assumed to vary linearly with temperature while internal heat generation is assumed to be uniform. The dimensionless governing equations are obtained for each selected geometry and the dimensionless temperature distributions are obtained using MATLAB. It is observed that GA gives the minimum dimensionless temperature in each selected geometry. PMID:24695517

  18. [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

  19. [Application of genetic polymorphisms in blood to forensic anthropology].

    PubMed

    Misawa, S

    1991-08-01

    1. The Ainu subjects and, as controls, Wajin subjects obtained in the District of Hokkaido, were studied for blood groups, serum groups and red cell enzyme groups. The high n gene and r" gene frequencies seem to be characteristic in the distribution of the Ainu. In considering the high frequencies of Fya and Agx genes, low incidence K gene and Rh negative type, and existence of Di (a+) type, it is conceivable that the distribution of these blood group in the Ainu are closer to those in Mongoloid than to those in Caucasoid. The results of genetic distance analysis were in full agreement with the genetic affinity of the Ainu to the Mongoloid racial stock. According to the phylogenetic tree constructed on the basis of 16 polymorphic loci, it may be concluded that the Ainu are derived from the common stock of Mongoloids, which in turn has common ancestry with American Indians. The Negritos which are thought to be oldest living aborigines of southeast Asia and the western pacific. We investigated for grouping some genetic polymorphic traits from Negrito blood samples collected in the Philippines. A total of more than 500 samples were examined for 20 genetic traits. The most outstanding features of Negritos were as follows: Di (a+) type was found and all individuals were Lu (a-b +) and K-k+ types. Mia, Wra and Jsa genes were absent and all samples were U+ type. The existence of Dia gene and absence of both Lua and K genes are thought to suggest that the distribution of Negritos is quite close to that of Mongoloid populations. Fy (a-b-) and Js (a+) types are not found in our study. These results do not suggest similarity between Negritos and African. 2. The tandem repeat of a 28-base-pair (bp) sequence downstream of the human c-Ha-ras-1 oncogene was studied as a probe for DNA fingerprinting. Multiple hypervariable patterns were observed by Southern hybridization at low stringency. The patterns were specific to individuals, indicating the availability of the 28-bp repeat

  20. [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.

  1. [Initiative of introducing the applications of genetics for public health purposes in Poland].

    PubMed

    Lutyńska, Anna; Krzysztof, Kuszewski; Wysocki, Mirosław J

    2012-01-01

    An integration of scientific associations involved in public health and genetics to apply genetics achievements might create new perspectives of public health and health promotion in Poland and allow to apply genomic applications that are currently in transition from research to public health practice. Activities might enable to undertake preventive actions as population screening programs based on genome-based knowledge and technologies as targeted preventive interventions. The achievements in the field of public health genetics or genomics have been taking place in several countries and have begun to have an impact on population health status.

  2. 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)-β-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)-β-glucan synthase gene, HvCslF6, was down-regulated by RNA interference. Neither cell wall thickness nor the levels of grain (1,3;1,4)-β-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

  3. 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.

  4. A “Reverse-Schur” Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design

    PubMed Central

    Bardhan, Jaydeep P.; Altman, Michael D.

    2009-01-01

    We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule’s electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts–in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method. PMID:23055839

  5. 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…

  6. 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

  7. Control of nonlinear systems using periodic parametric perturbations with application to a reversed field pinch

    NASA Astrophysics Data System (ADS)

    Mirus, Kevin Andrew

    In this thesis, the possibility of controlling low- and high-dimensional chaotic systems by periodically driving an accessible system parameter is examined. This method has been carried out on several numerical systems and the MST Reversed Field Pinch. The numerical systems investigated include the logistic equation, the Lorenz equations, the Rossler equations, a coupled lattice of logistic equations, a coupled lattice of Lorenz equations, the Yoshida equations, which model tearing mode fluctuations in a plasma, and a neural net model for magnetic fluctuations on MST. This method was tested on the MST by sinusoidally driving a magnetic flux through the toroidal gap of the device. Numerically, periodic drives were found to be most effective at producing limit cycle behavior or significantly reducing the dimension of the system when the perturbation frequency was near natural frequencies of unstable periodic orbits embedded in the attractor of the unperturbed system. Several different unstable periodic orbits have been stabilized in this way for the low-dimensional numerical systems, sometimes with perturbation amplitudes that were less than 5% of the nominal value of the parameter being perturbed. In high- dimensional systems, limit cycle behavior and significant decreases in the system dimension were also achieved using perturbations with frequencies near the natural unstable periodic orbit frequencies. Results for the MST were not this encouraging, most likely because of an insufficient drive amplitude, the extremely high dimension of the plasma behavior, large amounts of noise, and a lack of stationarity in the transient plasma pulses.

  8. Control of nonlinear systems using periodic parametric perturbations with application to a reversed field pinch

    SciTech Connect

    Mirus, K.A.

    1998-06-01

    In this thesis, the possibility of controlling low- and high-dimensional chaotic systems by periodically driving an accessible system parameter is examined. This method has been carried out on several numerical systems and the MST Reversed Field Pinch. The numerical systems investigated include the logistic equation, the Lorenz equations, the Roessler equations, a coupled lattice of logistic equations, a coupled lattice of Lorenz equations, the Yoshida equations, which model tearing mode fluctuations in a plasma, and a neural net model for magnetic fluctuations on MST. This method was tested on the MST by sinusoidally driving a magnetic flux through the toroidal gap of the device. Numerically, periodic drives were found to be most effective at producing limit cycle behavior or significantly reducing the dimension of the system when the perturbation frequency was near natural frequencies of unstable periodic orbits embedded in the attractor of the unperturbed system. Several different unstable periodic orbits have been stabilized in this way for the low-dimensional numerical systems, sometimes with perturbation amplitudes that were less than 5% of the nominal value of the parameter being perturbed. In high-dimensional systems, limit cycle behavior and significant decreases in the system dimension were also achieved using perturbations with frequencies near the natural unstable periodic orbit frequencies. Results for the MST were not this encouraging, most likely because of an insufficient drive amplitude, the extremely high dimension of the plasma behavior, large amounts of noise, and a lack of stationarity in the transient plasma pulses.

  9. 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.

  10. Molecular Imprinting of Silica Nanoparticle Surfaces via Reversible Addition-Fragmentation Polymerization for Optical Biosensing Applications

    NASA Astrophysics Data System (ADS)

    Oluz, Zehra; Nayab, Sana; Kursun, Talya Tugana; Caykara, Tuncer; Yameen, Basit; Duran, Hatice

    Azo initiator modified surface of silica nanoparticles were coated via reversible addition-fragmentation polymerization (RAFT) of methacrylic acid and ethylene glycol dimethacrylate using 2-phenylprop 2-yl dithobenzoate as chain transfer agent. Using L-phenylalanine anilide as template during polymerization led molecularly imprinted nanoparticles. RAFT polymerization offers an efficient control of grafting process, while molecularly imprinted polymers shows enhanced capacity as sensor. L-phenylalanine anilide imprinted silica particles were characterized by X-Ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM). Performances of the particles were followed by surface plasmon resonance spectroscopy (SPR) after coating the final product on gold deposited glass substrate against four different analogous of analyte molecules: D-henylalanine anilide, L-tyrosine, L-tryptophan and L-phenylalanine. Characterizations indicated that silica particles coated with polymer layer do contain binding sites for L-phenylalanine anilide, and are highly selective for the molecule of interest. This project was supported by TUBITAK (Project No:112M804).

  11. Spatial and temporal evolution of organic foulant layers on reverse osmosis membranes in wastewater reuse applications.

    PubMed

    Farias, Elizabeth L; Howe, Kerry J; Thomson, Bruce M

    2014-07-01

    Advanced treatment to remove trace constituents and emerging contaminants is an important consideration for wastewater treatment for potable reuse, and reverse osmosis (RO) can be a suitable technology to provide the necessary level of treatment. However, membrane fouling by biological and organic matter is a concern. This research examined the development of the RO membrane fouling layer using a bench-scale membrane bioreactor operating at different solids retention times (SRTs), followed by a custom-designed RO test cell. The RO test cell contained stacked plates that sandwich five sheets of RO membrane material, which can be extracted for autopsy at separate times over the course of an experiment without disturbing the remaining membranes. The MBR-RO system was run continuously for 2 weeks at each SRT. The RO membranes were stained for live and dead cells, protein, and carbohydrate-like materials, and visualized using confocal laser scanning microscopy. Images of the stained foulant layers were obtained at different depths within the foulant layer at each time point for all SRT conditions. As the RO foulant layer developed, changes occurred in the distribution and morphology of the live cells and carbohydrates, but not the proteins. These trends were similar for all three SRT conditions tested. RO membrane fouling increased with increased MBR SRT, and the highest SRT had the highest ratios of live to dead cells and carbohydrate-like material to dead cells. The autopsied membranes were also analyzed for protein and carbohydrate content, and it was found that the carbohydrate concentration on the membranes after 14 days increased as the SRT increased.

  12. Exfoliative toxin detection using reversed passive latex agglutination: clinical and epidemiologic applications.

    PubMed Central

    Kawabata, A; Ichiyama, S; Iinuma, Y; Hasegawa, Y; Ohta, M; Shimokata, K

    1997-01-01

    A rapid and simple method for detecting exfoliative toxin serotypes A and B from clinical isolates has been developed as a test kit (EXT-RPLA; Denka Seiken Co. Ltd., Niigata, Japan). This method is based on reversed passive latex agglutination. The detection limit of the EXT-RPLA observed for purified exfoliative toxin serotypes A and B was 1 ng/ml. We evaluated the clinical and epidemiologic uses of the EXT-RPLA. A total of 381 isolates of Staphylococcus aureus, 292 from various clinical specimens and 89 from the skin of dermatologic patients, were studied. The EXT-RPLA detected 19 exfoliative toxin producers, including 16 serotype A producers and 3 serotype B producers, but no double producers. The sensitivity and specificity of the EXT-RPLA were confirmed by the newborn mouse bioassay and a PCR assay for the structural genes for exfoliative toxin serotypes A and B (eta and etb, respectively). The overall positivity rate of exfoliative toxin producers was 5.0% (19 of 381), including 16 serotype A isolates and 3 serotype B isolates. Of the 89 isolates from the skin of dermatologic patients, 12 (13.5%) were positive for exfoliative toxin production. Only 2 (1.3%) of the 153 methicillin-resistant S. aureus isolates produced exfoliative toxin, while 17 (7.5%) of the 228 methicillin-sensitive isolates produced exfoliative toxin. The EXT-RPLA assay is a simple and reliable method for detecting exfoliative toxin, and we recommend its use for the rapid diagnosis of staphylococcal scalded skin syndrome. We also recommend its use for detection of this syndrome so that effective control measures can be taken against the spread of this syndrome. PMID:9230367

  13. 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.

  14. Modelling liquid crystal elastomers and potential application as a reversibly switchable adhesive

    NASA Astrophysics Data System (ADS)

    Adams, James

    2013-03-01

    Liquid crystal elastomers (LCEs) are rubbery materials that composed of liquid crystalline polymers (LCPs) crosslinked into a network. The rod-like mesogens incorporated into the LCPs are have random orientations in the high temperature isotropic phase, but can adopt the canonical liquid crystalline phases as the temperature is lowered. Smectic liquid crystal elastomers have highly anisotropic mechanical behaviour. This arises in side chain smectic-A systems because the smectic layers behave as if they are embedded in the rubber matrix. The macroscopic mechanical behaviour of these solids is sensitive to the buckling of the layers, so is a multiscale problem. A coarse grained free energy that includes the fine-scale buckling of the layers has been developed, which enables continuum modelling of these systems. In the first part of this talk I present a model of the mechanical behaviour of side chain smectic elastomers. The properties of nematic LCEs, such as their high loss tangent, and mechanical strain hardening, might enable them to be used as reversibly switchable pressure sensitive adhesive (PSA). PSAs are typically made from viscoelastic polymers. The quality of their adhesion can be measured by the tack energy, which is the work required to separate two bodies. To obtain a high tack energy a PSA should be capable of a large strain. It should strain soften at low strain to produce crack blunting, and then strain harden at high strain to stiffen the fibrils formed late in the debonding process. I will present a model of the tack energy of weakly crosslinked nematic polymers. To describe the constitutive properties of this system the nematic dumbbell model of Maffettone et al. was used. This constutitive model was then combined with the block model of Yamaguchi et al. describing PSAs. It was found that the parallel orientation of the nematic has a higher tack energy than both the isotropic and the perpendicular director orientation. This work is supported by

  15. Olfactory bulb recovery following reversible deafferentation with repeated detergent application in the adult zebrafish.

    PubMed

    Paskin, T R; Iqbal, T R; Byrd-Jacobs, C A

    2011-11-24

    The neuroplasticity and regenerative properties of the olfactory system make it a useful model for studying the ability of the nervous system to recover from damage. We have developed a novel method for examining the effects of long-term deafferentation and regeneration of the olfactory organ and resulting influence on the olfactory bulb in adult zebrafish. To test the hypothesis that repeated damage to the olfactory epithelium causes reduced olfactory bulb afferent input and cessation of treatment allows recovery, we chronically ablated the olfactory organ every 2-3 days for 3 weeks with the detergent Triton X-100 while another group was allowed 3 weeks of recovery following treatment. Animals receiving chronic treatment showed severe morphological disruption of the olfactory organ, although small pockets of epithelium remained. These pockets were labeled by anti-calretinin, indicating the presence of mature olfactory sensory neurons (OSNs). Following a recovery period, the epithelium was more extensive and neuronal labeling increased, with three different morphologies of sensory neurons observed. Repeated peripheral exposure to Triton X-100 also affected the olfactory bulb. Bulb volumes and anti-tyrosine hydroxylase-like immunoreactivity, which is an indicator of afferent activity, were diminished in the olfactory bulb of the chronically treated group compared to the control side. In the recovery group, there was little difference in bulb volume or antibody staining. These results suggest that repeated, long-term nasal irrigation with Triton X-100 eliminates a substantial number of mature OSNs and reduces afferent input to the olfactory bulb. It also appears that these effects are reversible and regeneration will occur in both the peripheral olfactory organ and the olfactory bulb when given time to recover following cessation of treatment. We report here a new method that allows observation not only of the effects of deafferentation on the olfactory bulb but also

  16. Rejection of emerging organic micropollutants in nanofiltration-reverse osmosis membrane applications.

    PubMed

    Xu, Pei; Drewes, Jörg E; Bellona, Christopher; Amy, Gary; Kim, Tae-Uk; Adam, Marc; Heberer, Thomas

    2005-01-01

    The rejection of emerging trace organics by a variety of commercial reverse osmosis (RO), nanofiltration (NF), and ultra-low-pressure RO (ULPRO) membranes was investigated using TFC-HR, NF-90, NF-200, TFC-SR2, and XLE spiral membrane elements (Koch Membrane Systems, Wilmington, Massachusetts) to simulate operational conditions for drinking-water treatment and wastewater reclamation. In general, the presence of effluent organic matter (EfOM) improved the rejection of ionic organics by tight NF and RO membranes, as compared to a type-II water matrix (adjusted by ionic strength and hardness), likely as a result of a decreased negatively charged membrane surface. Rejection of ionic pharmaceutical residues and pesticides exceeded 95% by NF-90, XLE, and TFC-HR membranes and was above 89% for the NF-200 membrane. Hydrophobic nonionic compounds, such as bromoform and chloroform, exhibited a high initial rejection, as a result of both hydrophobic-hydrophobic solute-membrane interactions and steric exclusion, but rejection decreased significantly after 10 hours of operation because of partitioning of solutes through the membranes. This resulted in a partial removal of disinfection byproducts by the RO membrane TFC-HR. In a type-II water matrix, the effect of increasing feed water recoveries on rejection of hydrophilic ionic and nonionic compounds was compound-dependent and not consistent for different membranes. The presence of EfOM, however, could neutralize the effect of hydrodynamic operating condition on rejection performance. The ULPRO and tight NF membranes were operated at lower feed pressure, as compared to the TFC-HR, and provided a product water quality similar to a conventional RO membrane, regarding trace organics of interest.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. Justice and Reverse Discrimination.

    ERIC Educational Resources Information Center

    Goldman, Alan H.

    Defining reverse discrimination as hiring or admissions decisions based on normally irrelevant criteria, this book develops principles of rights, compensation, and equal opportunity applicable to the reverse discrimination issue. The introduction defines the issue and discusses deductive and inductive methodology as applied to reverse…

  4. 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

  5. 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

    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 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

  6. 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.

  7. 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.

  8. 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...

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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)

  14. Using Reverse Engineering for Automated Usability Evaluation of Gui-Based Applications

    NASA Astrophysics Data System (ADS)

    Memon, Atif M.

    Graphical user interfaces (GUIs) are important parts of today’s software and their usability ensures the usefulness of the overall software. A popular technique to check the usability of GUIs is by performing usability evaluations either manually or automatically using tools. While manual evaluation is resource intensive, performing automatic usability evaluation usually involves the creation of a model of the GUI, a significant resource-intensive step that intimidates many practitioners and prevents the application of the automated techniques. This chapter presents “GUI ripping,” a new process that automatically recovers models of the GUI by dynamically “traversing” all its windows and extracting all the widgets, properties, and values. The usefulness of this process is demonstrated by recovering a structural model called a GUI forest and dynamic models called event-flow graphs and integration trees. Results of case studies show that GUI ripping is effective and requires very little human intervention.

  15. 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

  16. The application of a genetic algorithm for solving crystal structures from powder diffraction data

    NASA Astrophysics Data System (ADS)

    Kariuki, Benson M.; Serrano-González, Heliodoro; Johnston, Roy L.; Harris, Kenneth D. M.

    1997-12-01

    We report the successful application of a genetic algorithm to tackle crystal structure solution from powder diffraction data in the case of a previously unknown structure — ortho-thymotic acid. In the structure solution calculation, the structural fragment was subjected to combined translation and rotation within the unit cell, together with variation of selected intramolecular degrees of freedom under the control of a genetic algorithm, in which a population of trial structures is allowed to evolve subject to well-defined procedures for mating, mutation and natural selection. Importantly, the genetic algorithm approach adopts the `direct-space' philosophy for structure solution, and implicitly avoids the problematic step of extracting the intensities of individual reflections from the powder diffraction data. The structure solution was found efficiently in the genetic algorithm calculation, and was then used as the initial structural model in Rietveld refinement calculations. The work reported in this Letter paves the way for the future application of the genetic algorithm approach to a much wider array of structural problems.

  17. Magnetic logging: Detection of the earth's magnetic field reversals and application to borehole magnetostratigraphy

    SciTech Connect

    Bouisset, P.; Lalanne, B.; Augustin, A. ); Pages, G. )

    1991-03-01

    TOTAL CFP and CEA (the French Atomic Energy Commission) designed and developed two magnetic logging tools for precise and reliable in-situ magnetic measurements in the low magnetized sedimentary formations encountered when drilling for oil. The tools, measuring respectively the magnetic field and the magnetic susceptibility of the rocks, are operated as standard logging tools, and logs are recorded during standard logging operations. A proper combination of these magnetic respectively the magnetic field and the magnetic susceptibility of the rocks, are operated as standard logging tools, and logs are recorded during standard logging operations. A proper combination of these magnetic measurements leads to the determination, every meter, of natural remanent magnetization polarity, from which the direction of the Earth's magnetic field at the time of sedimentation is derived. A magnetostratigraphic sequence is obtained for each well and appears to be similar to the magnetostratigraphic reference scale. Application of this method to wells in the North Sea gives good results for correlations and absolute age determination, as well as facies diachronism. Further comparison of results obtained from magnetic measurements and from sequence stratigraphy applied to conventional logs shows that third-order sequence boundaries can be diachronous in wells 80 km apart. Although the potential of magnetic measurements is still under investigation, the first encouraging results clearly show that the new dating method presented in this paper can be very helpful in petroleum geology.

  18. Clostridium perfringens Enterotoxin: Action, Genetics, and Translational Applications

    PubMed Central

    Freedman, John C.; Shrestha, Archana; McClane, Bruce A.

    2016-01-01

    Clostridium perfringens enterotoxin (CPE) is responsible for causing the gastrointestinal symptoms of several C. perfringens food- and nonfood-borne human gastrointestinal diseases. The enterotoxin gene (cpe) is located on either the chromosome (for most C. perfringens type A food poisoning strains) or large conjugative plasmids (for the remaining type A food poisoning and most, if not all, other CPE-producing strains). In all CPE-positive strains, the cpe gene is strongly associated with insertion sequences that may help to assist its mobilization and spread. During disease, CPE is produced when C. perfringens sporulates in the intestines, a process involving several sporulation-specific alternative sigma factors. The action of CPE starts with its binding to claudin receptors to form a small complex; those small complexes then oligomerize to create a hexameric prepore on the membrane surface. Beta hairpin loops from the CPE molecules in the prepore assemble into a beta barrel that inserts into the membrane to form an active pore that enhances calcium influx, causing cell death. This cell death results in intestinal damage that causes fluid and electrolyte loss. CPE is now being explored for translational applications including cancer therapy/diagnosis, drug delivery, and vaccination. PMID:26999202

  19. 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

  20. 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

  1. 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.

  2. 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

  3. Identification and Biotechnological Application of Novel Regulatory Genes Involved in Streptomyces Polyketide Overproduction through Reverse Engineering Strategy

    PubMed Central

    Nah, Ji-Hye; Kim, Hye-Jin; Lee, Han-Na; Lee, Mi-Jin; Choi, Si-Sun; Kim, Eung-Soo

    2013-01-01

    Polyketide belongs to a family of abundant natural products typically produced by the filamentous soil bacteria Streptomyces. Similar to the biosynthesis of most secondary metabolites produced in the Streptomyces species, polyketide compounds are synthesized through tight regulatory networks in the cell, and thus extremely low levels of polyketides are typically observed in wild-type strains. Although many Streptomyces polyketides and their derivatives have potential to be used as clinically important pharmaceutical drugs, traditional strain improvement strategies such as random recursive mutagenesis have long been practiced with little understanding of the molecular basis underlying enhanced polyketide production. Recently, identifying, understanding, and applying a novel polyketide regulatory system identified from various Omics approaches, has become an important tool for rational Streptomyces strain improvement. In this paper, DNA microarray-driven reverse engineering efforts for improving titers of polyketides are briefly summarized, primarily focusing on our recent results of identification and application of novel global regulatory genes such as wblA, SCO1712, and SCO5426 in Streptomyces species. Sequential targeted gene manipulation involved in polyketide biosynthetic reguation synergistically provided an efficient and rational strategy for Streptomyces strain improvement. Moreover, the engineered regulation-optimized Streptomyces mutant strain was further used as a surrogate host for heterologous expression of polyketide pathway. PMID:23555090

  4. Reversal of Acute Complex Regional Pain Syndrome Using the Practical Application of Neurodiagnostic Evaluation Process: A Case Study

    PubMed Central

    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

  5. 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

  6. 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.

  7. 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

  8. Genetic Algorithms Application for the Photoacoustic Signal Temporal Shape Analysis and Energy Density Spatial Distribution Calculation

    NASA Astrophysics Data System (ADS)

    Lukić, M.; Ćojbašić, Ž.; Rabasović, M. D.; Markushev, D. D.; Todorović, D. M.

    2013-09-01

    Recently, a few numerical methods based on the photoacoustic (PA) signal temporal shape analysis and energy density spatial distribution calculation, which is directly related to the laser beam spatial profile, have been presented. It has been shown that these methods allow a precise reproduction of the spatial profile and the radius of the laser beam, determining the vibrational-to-translational (V-T) relaxation time with good accuracy. Their applicability has been shown and confirmed for the analysis of an arbitrary symmetric laser beam spatial profile in cylindrical geometry. Here, the application of genetic optimization for solving the problem of a simultaneous laser beam spatial profile and V-T relaxation time determination by pulsed PAs is presented. Real-coded genetic algorithms are used to calculate the mentioned relaxation time by fitting the experimental signal with the theoretical one. The aim is to find combinations of PA signal parameters, namely, the radius of the laser beam and the V-T relaxation time that provide the best match with the given signal. A calculated PA signal with a known profile is used to simulate an experimental signal, and the sum of the square deviations representing deviations of the given and fitted signals is minimized by means of genetic optimization. In that way, the genetic algorithms are used to simultaneously estimate the radius of the laser beam and the V-T relaxation time efficiently and with high accuracy. Compared to previous methods, the presented method is much simpler and requires less time to compute.

  9. 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.

  10. 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

  11. Statistical genetics with application to population-based study design: a primer for clinicians.

    PubMed

    Beyene, Joseph; Pare, Guillaume

    2014-02-01

    With the completion of the entire human genome sequence and remarkable advances in genotyping technologies, there has been an increased interest in the application of genetics and genomics in biomedical research over the last decade. Large-scale population-based genetic association studies have now become routine and their application to several multifactorial diseases such as cardiovascular disorders has led to the identification of a number of novel susceptibility genes. However, to be able to interpret results from such studies, clinicians need to have a basic understanding of unique concepts and issues related to this fast-moving area of research. In this primer, we provide a broad overview of design, analysis, and methodological issues with a focus on population-based study design.

  12. 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)

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

    NASA Astrophysics Data System (ADS)

    Masucci, A. P.; Kalampokis, A.; Eguíluz, V. M.; Hernández-García, 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.

  14. 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.

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

    DOE PAGES

    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

  16. 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.

  17. Controlled reverse pulse electrosynthesized spike-piece-structured Ni/Ni(OH)2 interlayer nanoplates for electrochemical pseudocapacitor applications.

    PubMed

    Pavul Raj, R; Mohan, S; Jha, Shailendra K

    2016-01-31

    An ultrathin Ni/Ni(OH)2 hybrid electrode has been synthesized using a controlled reverse pulse modulated electrochemical approach and demonstrated as an advanced pseudocapacitor material having a remarkable specific capacitance and excellent cycling performance.

  18. Plant artificial chromosome technology and its potential application in genetic engineering.

    PubMed

    Yu, Weichang; Yau, Yuan-Yeu; Birchler, James A

    2016-05-01

    Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands.

  19. 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

  20. Plant artificial chromosome technology and its potential application in genetic engineering.

    PubMed

    Yu, Weichang; Yau, Yuan-Yeu; Birchler, James A

    2016-05-01

    Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands. PMID:26369910

  1. Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

    PubMed

    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.

  2. 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

  3. New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background

    PubMed Central

    Penco, Silvana; Buscema, Massimo; Patrosso, Maria Cristina; Marocchi, Alessandro; Grossi, Enzo

    2008-01-01

    -480 C/T; endothelial nitric oxide synthase 690 C/T and glu298asp; vitamin K-dependent coagulation factor seven arg353glu, glycoprotein Ia/IIa 873 G/A and E-selectin ser128arg. Conclusion This study provides an alternative and reliable method to approach complex diseases. Indeed, the application of a novel artificial intelligence-based method offers a new insight into genetic markers of sporadic ALS pointing out the existence of a strong genetic background. PMID:18513389

  4. TANTAMOUNT TO FRAUD?: EXPLORING NON-DISCLOSURE OF GENETIC INFORMATION IN LIFE INSURANCE APPLICATIONS AS GROUNDS FOR POLICY RESCISSION.

    PubMed

    Prince, Anya E R

    2016-01-01

    Many genetic counselors recommend that individuals secure desired insurance policies, such as life insurance, prior to undergoing predictive genetic testing. It has been argued, however, that this practice is "tantamount to fraud" and that failure to disclose genetic test results, or conspiring to secure a policy before testing, opens an individual up to legal recourse. This debate traps affected individuals in a Catch-22. If they apply for life insurance and disclose a genetic test result, they may be denied. If they apply without disclosing the information, they may have committed fraud. The consequences of life insurance fraud are significant: If fraud is found on an application, a life insurer can rescind the policy, in some cases even after the individual has passed away. Such a rescission could leave family members or beneficiaries without the benefits of the life insurance policy payment after the individual's death and place them in in economic difficulty. Although it is clear that lying in response to a direct question about genetic testing would be tantamount to fraud, few, if any, life insurance applications currently include broad questions about genetic testing. This paper investigates whether non-disclosure of unasked for genetic information constitutes fraud and explores varying types of insurance questions that could conceivably be interpreted as seeking genetic information. Life insurance applicants generally have no duty to disclose unasked for information, including genetic information, on an application. However, given the complexities of genetic information, individuals may be exposed to fraud and rescission of their life insurance policy despite honest attempts to truthfully and completely answer all application questions. PMID:27263254

  5. TANTAMOUNT TO FRAUD?: EXPLORING NON-DISCLOSURE OF GENETIC INFORMATION IN LIFE INSURANCE APPLICATIONS AS GROUNDS FOR POLICY RESCISSION.

    PubMed

    Prince, Anya E R

    2016-01-01

    Many genetic counselors recommend that individuals secure desired insurance policies, such as life insurance, prior to undergoing predictive genetic testing. It has been argued, however, that this practice is "tantamount to fraud" and that failure to disclose genetic test results, or conspiring to secure a policy before testing, opens an individual up to legal recourse. This debate traps affected individuals in a Catch-22. If they apply for life insurance and disclose a genetic test result, they may be denied. If they apply without disclosing the information, they may have committed fraud. The consequences of life insurance fraud are significant: If fraud is found on an application, a life insurer can rescind the policy, in some cases even after the individual has passed away. Such a rescission could leave family members or beneficiaries without the benefits of the life insurance policy payment after the individual's death and place them in in economic difficulty. Although it is clear that lying in response to a direct question about genetic testing would be tantamount to fraud, few, if any, life insurance applications currently include broad questions about genetic testing. This paper investigates whether non-disclosure of unasked for genetic information constitutes fraud and explores varying types of insurance questions that could conceivably be interpreted as seeking genetic information. Life insurance applicants generally have no duty to disclose unasked for information, including genetic information, on an application. However, given the complexities of genetic information, individuals may be exposed to fraud and rescission of their life insurance policy despite honest attempts to truthfully and completely answer all application questions.

  6. 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)

  7. 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.

  8. The medical examination in United States immigration applications: the potential use of genetic testing leads to heightened privacy concerns.

    PubMed

    Burroughs, A Maxwell

    2005-01-01

    The medical examination has been an integral part of the immigration application process since the passing of the Immigration Act of 1891. Failing the medical examination can result in denial of the application. Over the years the medical examination has been expanded to include questioning about diseases that are scientifically shown to be rooted in an individual's genetic makeup. Recent advances in the fields of genomics and bioinformatics are making accurate and precise screening for these conditions a reality. Government policymakers will soon be faced with decisions regarding whether or not to sanction the use of these newly-developed genetic tests in the immigration application procedure. The terror threat currently facing the United States may ultimately bolster the argument in favor of genetic testing and/or DNA collection of applicants. However, the possibility of a government mandate requiring genetic testing raises a host of ethical issues; including the threat of eugenics and privacy concerns. Genetic testing has the ability to uncover a wealth of sensitive medical information about an individual and currently there are no medical information privacy protections afforded to immigration applicants. This article examines the potential for genetic testing in the immigration application process and the ethical issues surrounding this testing. In particular, this article explores the existing framework of privacy protections afforded to individuals living in the United States and how this and newly-erected standards like those released by the Health and Human Services (HHS) might apply to individuals seeking to immigrate to the United States. PMID:16619448

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

    PubMed

    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

  10. Gene genealogies for genetic association mapping, with application to Crohn's disease.

    PubMed

    Burkett, Kelly M; Greenwood, Celia M T; McNeney, Brad; Graham, Jinko

    2013-01-01

    A gene genealogy describes relationships among haplotypes sampled from a population. Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also has potential application in finding disease-predisposing genetic variants. As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies conditional on data at multiple genetic markers. We previously implemented an MCMC algorithm to sample from an approximation to the distribution of the gene genealogy conditional on haplotype data. Our approach samples ancestral trees, recombination and mutation rates at a genomic focal point. In this work, we describe how our sampler can be used to find disease-predisposing genetic variants in samples of cases and controls. We use a tree-based association statistic that quantifies the degree to which case haplotypes are more closely related to each other around the focal point than control haplotypes, without relying on a disease model. As the ancestral tree is a latent variable, so is the tree-based association statistic. We show how the sampler can be used to estimate the posterior distribution of the latent test statistic and corresponding latent p-values, which together comprise a fuzzy p-value. We illustrate the approach on a publicly-available dataset from a study of Crohn's disease that consists of genotypes at multiple SNP markers in a small genomic region. We estimate the posterior distribution of the tree-based association statistic and the recombination rate at multiple focal points in the region. Reassuringly, the posterior mean recombination rates estimated at the different focal points are consistent with previously published estimates. The tree-based association approach finds multiple sub-regions where the case haplotypes are more genetically related than the control haplotypes, and that there may be one or multiple disease-predisposing loci. PMID

  11. 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

  12. 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

  13. Enhanced conjugation of Candida rugosa lipase onto multiwalled carbon nanotubes using reverse micelles as attachment medium and application in nonaqueous biocatalysis.

    PubMed

    Raghavendra, Tripti; Vahora, Uzma; Shah, Amita R; Madamwar, Datta

    2014-01-01

    Three liquid phases (viz. aqueous, nonaqueous, and reverse micelles) were scrutinized as medium for attachment of the enzyme Candida rugosa lipase (CRL) onto multiwalled carbon nanotubes (CNTs). The nanotubes were functionalized to attain carboxyl and amino groups on their surfaces before enzyme conjugation. Transmission electron microscopy and Fourier transformation infrared spectroscopic studies were used for characterization of the nanotubes during the course of functionalization. High enzyme loadings associated with the functionalized CNTs were observed when reverse micelles were used as the attachment medium. In addition, high activity in terms of ester synthesis in organic solvents was also observed while using those preparations. The nanobioconjugates prepared using reverse micelles were found to be highly sturdy and exhibited appreciable operational stability of around 95 ± 3% at 20th cycle (in case of carboxylated nanotubes) and 90 ± 5% at 10th cycle (in case of aminated nanotubes) for esterification. This shows the potential application of reverse micelles as the attachment medium for surface active enzymes such as CRL onto CNTs.

  14. Optimality and stability of symmetric evolutionary games with applications in genetic selection.

    PubMed

    Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

    2015-06-01

    Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

  15. Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application.

    PubMed

    Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru; Langridge, Peter

    2016-01-01

    Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat. PMID:27459317

  16. First successful application of preimplantation genetic diagnosis and haplotyping for congenital hyperinsulinism.

    PubMed

    Qubbaj, Wafa; Al-Swaid, Abdulrahman; Al-Hassan, Saad; Awartani, Khalid; Deek, Hesham; Coskun, Serdar

    2011-01-01

    Congenital hyperinsulinism is the most common cause of persistent hypoglycaemia in infancy. Early surgical intervention is usually required to prevent brain damage. The prevention of the transmission to the offspring is important in families carrying the mutated gene. Preimplantation genetic diagnosis (PGD) is an early genetic testing procedure for couples at risk of transmitting inherited diseases. A 36-year-old Saudi woman married to her first cousin with four affected children was referred for PGD. The hyperinsulinism disease was caused by a novel homozygous mutation in the KCNJ11 gene, an arginine 301 to proline (R301P) substitution.PGD was achieved by whole genome amplification followed by mutation detection combined with short tandem repeat identifier analysis in the first cycle and with haplotyping in the second cycle. The first and second cycles resulted in the births of healthy twin girls and a boy, respectively. As far as is known, this is the first application of PGD to hyperinsulinism. A feasible strategy including whole genome amplification followed by direct mutation detection combined with haplotyping is described.Utilizing haplotyping increases the efficiency of PGD diagnosis as well as confirming the genetic diagnosis. It reveals the parental origin of each inherited chromosome.

  17. 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.

  18. Application of SNPscan in Genetic Screening for Common Hearing Loss Genes

    PubMed Central

    Ke, Jia; Li, Tao; Hu, Ping; Song, Yu; Xu, Chiyu; Wang, Jie; Cheng, Jing; Zhang, Lei; Duan, Hong; Yuan, Huijun; Ma, Furong

    2016-01-01

    The current study reports the successful application of a fast and efficient genetic screening system for common hearing loss (HL) genes based on SNPscan genotyping technology. Genetic analysis of 115 variants in common genes related to HL, GJB2, SLC26A4 and MT-RNR, was performed on 695 subjects with non-syndromic hearing loss (NSHL) from the Northern China. The results found that 38.7% (269/695) of cases carried bi-allelic pathogenic variants in GJB2 and SLC26A4 and 0.7% (5/695) of cases carried homoplasmic MT-RNR1 variants. The variant allele frequency of GJB2, SLC26A4 and MT-RNR1 was 19.8% (275/1390), 21.9% (304/1390), and 0.86% (6/695), respectively. This approach can explain ~40% of NSHL cases and thus is a useful tool for establishing primary molecular diagnosis of NSHL in clinical genetics. PMID:27792752

  19. Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application

    PubMed Central

    Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru

    2016-01-01

    Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat. PMID:27459317

  20. Insights into the biology of Borrelia burgdorferi gained through the application of molecular genetics.

    PubMed

    Groshong, Ashley M; Blevins, Jon S

    2014-01-01

    Borrelia burgdorferi, the vector-borne bacterium that causes Lyme disease, was first identified in 1982. It is known that much of the pathology associated with Lyme borreliosis is due to the spirochete's ability to infect, colonize, disseminate, and survive within the vertebrate host. Early studies aimed at defining the biological contributions of individual genes during infection and transmission were hindered by the lack of adequate tools and techniques for molecular genetic analysis of the spirochete. The development of genetic manipulation techniques, paired with elucidation and annotation of the B. burgdorferi genome sequence, has led to major advancements in our understanding of the virulence factors and the molecular events associated with Lyme disease. Since the dawn of this genetic era of Lyme research, genes required for vector or host adaptation have garnered significant attention and highlighted the central role that these components play in the enzootic cycle of this pathogen. This chapter covers the progress made in the Borrelia field since the application of mutagenesis techniques and how they have allowed researchers to begin ascribing roles to individual genes. Understanding the complex process of adaptation and survival as the spirochete cycles between the tick vector and vertebrate host will lead to the development of more effective diagnostic tools as well as identification of novel therapeutic and vaccine targets. In this chapter, the Borrelia genes are presented in the context of their general biological roles in global gene regulation, motility, cell processes, immune evasion, and colonization/dissemination.

  1. 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…

  2. 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…

  3. 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...

  4. Photoinduced reversible changes in morphology of plasmonic Ag nanorods on TiO2 and application to versatile photochromism.

    PubMed

    Kazuma, Emiko; Tatsuma, Tetsu

    2012-02-01

    We achieved reversible changes in length and spectrum of Ag nanorods based on plasmon-induced photoelectrochemical reactions. The changes are applied to multi-wavelength and dual-polarization photochromism in visible-infrared regions. It allows display of invisible images viewable only by infrared cameras. Also possible is display of superimposed visible and invisible images.

  5. 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...

  6. Molecular genetics of meningiomas: from basic research to potential clinical applications.

    PubMed

    Simon, Matthias; Boström, Jan P; Hartmann, Christian

    2007-05-01

    To review our current understanding of the molecular pathogenesis of meningiomas, to suggest topics for future investigations, and to present perspectives for clinical application. Significant progress has been made in recent years in delineating the molecular mechanisms involved in meningioma formation, growth, and malignant progression. However, many questions remain unanswered. Mutations in the NF2 gene probably account for the formation of more than half of all meningiomas. On the other hand, the molecular events underlying the initiation of meningiomas without NF2 mutations have yet to be identified. Investigating hereditary conditions associated with an increased meningioma incidence and the mechanisms underlying the development of radiation-induced meningiomas could potentially yield relevant insights. Meningioma growth is sustained by the dysregulated expression of steroid hormones, growth factors, their receptors, and activation of signal transduction cascades. The underlying genetic causes are unknown. Malignant progression of meningiomas probably involves the inactivation of tumor suppressor genes on chromosomes 1p, 9p, 10q, and 14q. However, with the possible exception of INK4A/INK4B, the actual targets of these chromosomal losses have remained largely elusive. Cell cycle dysregulation and telomerase activation have been recognized as important steps in meningioma progression. Telomere dynamics, cell cycle control, and the mechanisms responsible for deoxyribonucleic acid damage control are tightly interwoven. Investigating genes involved in the maintenance of genomic integrity might significantly deepen the understanding of meningioma progression. An area that has received relatively little attention thus far is the genetic background of meningioma spread and invasion. Possible clinical applications of the molecular data available may include a meningioma grading system based on genetic alterations, as well as therapeutic strategies for refractory

  7. Linear score tests for variance components in linear mixed models and applications to genetic association studies.

    PubMed

    Qu, Long; Guennel, Tobias; Marshall, Scott L

    2013-12-01

    Following the rapid development of genome-scale genotyping technologies, genetic association mapping has become a popular tool to detect genomic regions responsible for certain (disease) phenotypes, especially in early-phase pharmacogenomic studies with limited sample size. In response to such applications, a good association test needs to be (1) applicable to a wide range of possible genetic models, including, but not limited to, the presence of gene-by-environment or gene-by-gene interactions and non-linearity of a group of marker effects, (2) accurate in small samples, fast to compute on the genomic scale, and amenable to large scale multiple testing corrections, and (3) reasonably powerful to locate causal genomic regions. The kernel machine method represented in linear mixed models provides a viable solution by transforming the problem into testing the nullity of variance components. In this study, we consider score-based tests by choosing a statistic linear in the score function. When the model under the null hypothesis has only one error variance parameter, our test is exact in finite samples. When the null model has more than one variance parameter, we develop a new moment-based approximation that performs well in simulations. Through simulations and analysis of real data, we demonstrate that the new test possesses most of the aforementioned characteristics, especially when compared to existing quadratic score tests or restricted likelihood ratio tests. PMID:24328714

  8. Technological Advances in Bifidobacterial Molecular Genetics: Application to Functional Genomics and Medical Treatments

    PubMed Central

    FUKIYA, Satoru; HIRAYAMA, Yosuke; SAKANAKA, Mikiyasu; KANO, Yasunobu; YOKOTA, Atsushi

    2012-01-01

    Bifidobacteria are well known as beneficial intestinal bacteria that exert health-promoting effects in humans. In addition to physiological and immunological investigations, molecular genetic technologies have been developed and have recently started to be applied to clarify the molecular bases of host-Bifidobacterium interactions. These technologies include transformation technologies and Escherichia coli-Bifidobacterium shuttle vectors that enable heterologous gene expression. In this context, a plasmid artificial modification method that protects the introduced plasmid from the restriction system in host bifidobacteria has recently been developed to increase transformation efficiency. On the other hand, targeted gene inactivation systems, which are vital for functional genomics, seemed far from being practically applicable in bifidobacteria. However, remarkable progress in this technology has recently been achieved, enabling functional genomics in bifidobacteria. Integrated use of these molecular genetic technologies with omics-based analyses will surely boost characterization of the molecular basis underlying beneficial effects of bifidobacteria. Applications of recombinant bifidobacteria to medical treatments have also progressed. PMID:24936345

  9. Genetics and evolution: an iOS application to supplement introductory courses in transmission and evolutionary genetics.

    PubMed

    Myers, Russell B; Millman, Brandon; Noor, Mohamed A F

    2014-04-11

    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.

  10. 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.

  11. Application of automation and information systems to forensic genetic specimen processing.

    PubMed

    Leclair, Benoît; Scholl, Tom

    2005-03-01

    During the last 10 years, the introduction of PCR-based DNA typing technologies in forensic applications has been highly successful. This technology has become pervasive throughout forensic laboratories and it continues to grow in prevalence. For many criminal cases, it provides the most probative evidence. Criminal genotype data banking and victim identification initiatives that follow mass-fatality incidents have benefited the most from the introduction of automation for sample processing and data analysis. Attributes of offender specimens including large numbers, high quality and identical collection and processing are ideal for the application of laboratory automation. The magnitude of kinship analysis required by mass-fatality incidents necessitates the application of computing solutions to automate the task. More recently, the development activities of many forensic laboratories are focused on leveraging experience from these two applications to casework sample processing. The trend toward increased prevalence of forensic genetic analysis will continue to drive additional innovations in high-throughput laboratory automation and information systems.

  12. Testing whether Genetic Variation Explains Correlation of Quantitative Measures of Gene Expression, and Application to Genetic Network Analysis

    PubMed Central

    Yu, Zhaoxia; Wang, Leiwei; Hildebrandt, Michelle A.T.; Schaid, Daniel J.

    2009-01-01

    SUMMARY Genetic networks for gene expression data are often built by graphical models, which in turn are built from pairwise correlations of gene expression levels. A key feature of building graphical models is evaluation of conditional independence of two traits, given other traits. When conditional independence can be assumed, the traits that are conditioned on are considered to “explain” the correlation of a pair of traits, allowing efficient building and interpretation of a network. Overlaying genetic polymorphisms, such as single nucleotide polymorphisms (SNPs), on quantitative measures of gene expression provides a much richer set of data to build a genetic network, because it is possible to evaluate whether sets of SNPs “explain” the correlation of gene expression levels. However, there is strong evidence that gene expression levels are controlled by multiple interacting genes, suggesting that it will be difficult to reduce the partial correlation completely to zero. Ignoring the fact that some set of SNPs can explain at least part of the correlation between gene expression levels, if not all, might miss important clues on the genetic control of gene expression. To enrich the assessment of the causes of correlation between gene expression levels, we develop methods to evaluate whether a set of covariates (e.g., SNPs, or even a set of quantitative expression transcripts), explains at least some of the correlation of gene expression levels. These methods can be used to assist the interpretation of regulation of gene expression and the construction of gene regulation networks. PMID:18444230

  13. 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

  14. 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

  15. 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.

  16. Hypospadias in a male (78,XY; SRY-positive) dog and sex reversal female (78,XX; SRY-negative) dogs: clinical, histological and genetic studies.

    PubMed

    Switonski, M; Payan-Carreira, R; Bartz, M; Nowacka-Woszuk, J; Szczerbal, I; Colaço, B; Pires, M A; Ochota, M; Nizanski, W

    2012-01-01

    Hypospadias is rarely reported in dogs. In this study we pre-sent 2 novel cases of this disorder of sexual development and, in addition, a case of hereditary sex reversal in a female with an enlarged clitoris. The first case was a male Moscow watchdog with a normal karyotype (78,XY) and the presence of the SRY gene. In this dog, perineal hypospadias, bilateral inguinal cryptorchidism and testes were observed. The second case, representing the Cocker spaniel breed, had a small penis with a hypospadic orifice of the urethra, bilateral cryptorchidism, testis and a rudimentary gonad inside an ovarian bursa, a normal female karyotype (78,XX) and a lack of the SRY gene. This animal was classified as a compound sex reversal (78,XX, SRY-negative) with the hypospadias syndrome. The third case was a Cocker spaniel female with an enlarged clitoris and internally located ovotestes. Cytogenetic and molecular analyses revealed a normal female karyotype (78,XX) and a lack of the SRY gene, while histology of the gonads showed an ovotesticular structure. This case was classified as a typical hereditary sex reversal syndrome (78,XX, SRY-negative). Molecular studies were focused on coding sequences of the SRY gene (case 1) and 2 candidates for monogenic hypospadias, namely MAMLD1 (mastermind-like domain containing 1) and SRD5A2 (steroid-5-alpha-reductase, alpha polypeptide 2). Sequencing of the entire SRY gene, including 5'- and 3'-flanking regions, did not reveal any mutation. The entire coding sequence of MAMLD1 and SRD5A2 was analyzed in all the intersexes, as well as in 4 phenotypically normal control dogs (3 females and 1 male). In MAMLD1 2 SNPs, including 1 missense substitution in exon 1 (c.128A>G, Asp43Ser), were identified, whereas in SRD5A2 7 polymorphisms, including 1 missense SNP (c.358G>A, Ala120Thr), were found. None of the identified polymorphisms cosegregated with the intersexual phenotype, thus, we cannot confirm that hypospadias may be associated with polymorphism

  17. 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)

  18. A simian-human immunodeficiency virus carrying the rt gene from Chinese CRF01_AE strain of HIV is sensitive to nucleoside reverse transcriptase inhibitors and has a highly genetic stability in vivo.

    PubMed

    Wang, Wei; Yao, Nan; Ju, Bin; Dong, Zhihui; Cong, Zhe; Jiang, Hong; Qin, Chuan; Wei, Qiang

    2014-06-01

    Human immunodeficiency virus (HIV)-1 subtype CRF01_AE is one of the major HIV-1 subtypes that dominate the global epidemic. However, its drug resistance, associated mutations, and viral fitness have not been systemically studied, because available chimeric simian-HIVs (SHIVs) usually express the HIV-1 reverse transcriptase (rt) gene of subtype B HIV-1, which is different from subtype CRF01_AE HIV-1. In this study, a recombinant plasmid, pRT-SHIV/AE, was constructed to generate a chimeric RT-SHIV/AE by replacing the rt gene of simian immunodeficiency virus (SIVmac239) with the counterpart of Chinese HIV-1 subtype CRF01_AE. The infectivity, replication capacity, co-receptor tropism, drug sensitivity, and genetic stability of RT-SHIV/AE were characterized. The new chimeric RT-SHIV/AE effectively infected and replicated in human T cell line and rhesus peripheral blood mononuclear cells (rhPBMC). The rt gene of RT-SHIV/AE lacked the common mutation (T215I) associated with drug resistance. RT-SHIV-AE retained infectivity and immunogenicity, similar to that of its counterpart RT-SHIV/TC virus following intravenous inoculation in Chinese rhesus macaque. RT-SHIV-AE was more sensitive to nucleoside reverse transcriptase inhibitors (NRTIs) than the RT-SHIV/TC. RT-SHIV/AE was genetically stable in Chinese rhesus macaque. The new chimeric RT-SHIV/AE may be a valuable tool for evaluating the efficacy of the rt-based antiviral drugs against the subtype CRF01_AE HIV-1.

  19. 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

  20. 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.

  1. [Integrating genetic and gene expression data: methods and applications of eQTL mapping].

    PubMed

    Liu, Gang; Peng, Hui-Ru; Ni, Zhong-Fu; Qin, Dan-Dan; Song, Fang-Wei; Song, Guang-Shu; Sun, Qi-Xin

    2008-09-01

    The availability of high-throughput genotyping technologies and microarray assays has allowed researchers to investigate genetic variations that influence levels of gene expression. Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression. Similar to traditional QTL studies, the main goal of eQTL is to identify the genomic locations to which the expression traits are linked. Although microarrays provide the expression data of thousands of transcripts, standard QTL mapping methods, which are able to handle at most tens of traits, cannot be applied directly. As a result, it is necessary to consider the statistical principles involved in the design and analysis of these experiments. In this paper, we reviewed individual selection, experimental design of microarray, normalization of gene expression data, mapping methods, and explaining of results and proposed potential methodological problems for such analyses. Finally, we discussed the applications of this integrative genomic approach to estimate heritability of transcripts, identify candidate genes, construct gene networks, and understand interactions between genes, genes and environments.

  2. Power Calculation of Multi-step Combined Principal Components with Applications to Genetic Association Studies.

    PubMed

    Li, Zhengbang; Zhang, Wei; Pan, Dongdong; Li, Qizhai

    2016-01-01

    Principal component analysis (PCA) is a useful tool to identify important linear combination of correlated variables in multivariate analysis and has been applied to detect association between genetic variants and human complex diseases of interest. How to choose adequate number of principal components (PCs) to represent the original system in an optimal way is a key issue for PCA. Note that the traditional PCA, only using a few top PCs while discarding the other PCs, might significantly lose power in genetic association studies if all the PCs contain non-ignorable signals. In order to make full use of information from all PCs, Aschard and his colleagues have proposed a multi-step combined PCs method (named mCPC) recently, which performs well especially when several traits are highly correlated. However, the power superiority of mCPC has just been illustrated by simulation, while the theoretical power performance of mCPC has not been studied yet. In this work, we attempt to investigate theoretical properties of mCPC and further propose a novel and efficient strategy to combine PCs. Extensive simulation results confirm that the proposed method is more robust than existing procedures. A real data application to detect the association between gene TRAF1-C5 and rheumatoid arthritis further shows good performance of the proposed procedure. PMID:27189724

  3. Large resistive 2D Micromegas with genetic multiplexing and some imaging applications

    NASA Astrophysics Data System (ADS)

    Bouteille, S.; Attié, D.; Baron, P.; Calvet, D.; Magnier, P.; Mandjavidze, I.; Procureur, S.; Riallot, M.

    2016-10-01

    The performance of the first large resistive Micromegas detectors with 2D readout and genetic multiplexing is presented. These detectors have a 50 × 50cm2 active area and are equipped with 1024 strips both in X- and Y-directions. The same genetic multiplexing pattern is applied on both coordinates, resulting in the compression of signals on 2 × 61 readout channels. Four such detectors have been built at CERN, and extensively tested with cosmics. The resistive strip film allows for very high gain operation, compensating for the charge spread on the 2 dimensions as well as the S / N loss due to the huge, 1 nF input capacitance. This film also creates a significantly different signal shape in the X- and Y-coordinates due to the charge evacuation along the resistive strips. All in all a detection efficiency above 95% is achieved with a 1 cm drift gap. Though not yet optimal, the measured 300 μm spatial resolution allows for very precise imaging in the field of muon tomography, and some applications of these detectors are presented.

  4. Harnessing a High Cargo-Capacity Transposon for Genetic Applications in Vertebrates

    PubMed Central

    Balciunas, Darius; Bell, Jason; Geurts, Aron; Sivasubbu, Sridhar; Wang, Xin; Hackett, Perry B; Largaespada, David A; McIvor, R. Scott; Ekker, Stephen C

    2006-01-01

    Viruses and transposons are efficient tools for permanently delivering foreign DNA into vertebrate genomes but exhibit diminished activity when cargo exceeds 8 kilobases (kb). This size restriction limits their molecular genetic and biotechnological utility, such as numerous therapeutically relevant genes that exceed 8 kb in size. Furthermore, a greater payload capacity vector would accommodate more sophisticated cis cargo designs to modulate the expression and mutagenic risk of these molecular therapeutics. We show that the Tol2 transposon can efficiently integrate DNA sequences larger than 10 kb into human cells. We characterize minimal sequences necessary for transposition (miniTol2) in vivo in zebrafish and in vitro in human cells. Both the 8.5-kb Tol2 transposon and 5.8-kb miniTol2 engineered elements readily function to revert the deficiency of fumarylacetoacetate hydrolase in an animal model of hereditary tyrosinemia type 1. Together, Tol2 provides a novel nonviral vector for the delivery of large genetic payloads for gene therapy and other transgenic applications. PMID:17096595

  5. 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.

  6. 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

  7. Antenatal diagnosis of anophthalmia by three-dimensional ultrasound: a novel application of the reverse face view.

    PubMed

    Wong, H S; Parker, S; Tait, J; Pringle, K C

    2008-07-01

    The prenatal diagnosis of anophthalmia can be made on the demonstration of absent eye globe and lens on the affected side(s) on two-dimensional ultrasound examination, but when the fetal head position is unfavorable three-dimensional (3D) ultrasound may reveal additional diagnostic sonographic features, including sunken eyelids and small or hypoplastic orbit on the affected side(s). We present two cases of isolated anophthalmia diagnosed on prenatal ultrasound examination in which 3D ultrasound provided additional diagnostic information. The reverse face view provides valuable information about the orbits and the eyeballs for prenatal diagnosis and assessment of anophthalmia.

  8. 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.

  9. 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.

  10. Optimisation of halogenase enzyme activity by application of a genetic algorithm.

    PubMed

    Muffler, Kai; Retzlaff, Marco; van Pée, 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%.

  11. Using distance covariance for improved variable selection with application to learning genetic risk models.

    PubMed

    Kong, Jing; Wang, Sijian; Wahba, Grace

    2015-05-10

    Variable selection is of increasing importance to address the difficulties of high dimensionality in many scientific areas. In this paper, we demonstrate a property for distance covariance, which is incorporated in a novel feature screening procedure together with the use of distance correlation. The approach makes no distributional assumptions for the variables and does not require the specification of a regression model and hence is especially attractive in variable selection given an enormous number of candidate attributes without much information about the true model with the response. The method is applied to two genetic risk problems, where issues including uncertainty of variable selection via cross validation, subgroup of hard-to-classify cases, and the application of a reject option are discussed.

  12. Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays.

    PubMed

    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.

  13. 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

  14. 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.

  15. Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit.

    PubMed

    Mora, Leticia; Bramley, Peter M; Fraser, Paul D

    2013-06-01

    A key global challenge for plant biotechnology is addressing food security, whereby provision must be made to feed 9 billion people with nutritional feedstuffs by 2050. To achieve this step change in agricultural production new crop varieties are required that are tolerant to environmental stresses imposed by climate change, have better yields, are more nutritious and require less resource input. Genetic modification (GM) and marker-assisted screening will need to be fully utilised to deliver these new crop varieties. To evaluate these varieties both in terms of environmental and food safety and the rational design of traits a systems level characterisation is necessary. To link the transcriptome to the metabolome, quantitative proteomics is required. Routine quantitative proteomics is an important challenge. Gel-based densitometry and MS analysis after stable isotope labeling have been employed. In the present article, we describe the application of a label-free approach that can be used in combination with SDS-PAGE and reverse-phase chromatography to evaluate the changes in the proteome of new crop varieties. The workflow has been optimised for protein coverage, accuracy and robustness, then its application demonstrated using a GM tomato variety engineered to deliver nutrient dense fruit.

  16. First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize.

    PubMed

    Fantozzi, Anna; Ermolli, Monica; Marini, Massimiliano; Scotti, Domenico; Balla, Branko; Querci, Maddalena; Langrell, Stephen R H; Van den Eede, Guy

    2007-02-21

    An innovative covalent microsphere immunoassay, based on the usage of fluorescent beads coupled to a specific antibody, was developed for the quantification of the endotoxin Cry1Ab present in MON810 and Bt11 genetically modified (GM) maize lines. In particular, a specific protocol was developed to assess the presence of Cry1Ab in a very broad range of GM maize concentrations, from 0.1 to 100% [weight of genetically modified organism (GMO)/weight]. Test linearity was achieved in the range of values from 0.1 to 3%, whereas fluorescence signal increased following a nonlinear model, reaching a plateau at 25%. The limits of detection and quantification were equal to 0.018 and 0.054%, respectively. The present study describes the first application of quantitative high-throughput immunoassays in GMO analysis.

  17. First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize.

    PubMed

    Fantozzi, Anna; Ermolli, Monica; Marini, Massimiliano; Scotti, Domenico; Balla, Branko; Querci, Maddalena; Langrell, Stephen R H; Van den Eede, Guy

    2007-02-21

    An innovative covalent microsphere immunoassay, based on the usage of fluorescent beads coupled to a specific antibody, was developed for the quantification of the endotoxin Cry1Ab present in MON810 and Bt11 genetically modified (GM) maize lines. In particular, a specific protocol was developed to assess the presence of Cry1Ab in a very broad range of GM maize concentrations, from 0.1 to 100% [weight of genetically modified organism (GMO)/weight]. Test linearity was achieved in the range of values from 0.1 to 3%, whereas fluorescence signal increased following a nonlinear model, reaching a plateau at 25%. The limits of detection and quantification were equal to 0.018 and 0.054%, respectively. The present study describes the first application of quantitative high-throughput immunoassays in GMO analysis. PMID:17300145

  18. 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

  19. Examination of a genetic algorithm for the application in high-throughput downstream process development.

    PubMed

    Treier, Katrin; Berg, Annette; Diederich, Patrick; Lang, Katharina; Osberghaus, Anna; Dismer, Florian; Hubbuch, Jürgen

    2012-10-01

    Compared to traditional strategies, application of high-throughput experiments combined with optimization methods can potentially speed up downstream process development and increase our understanding of processes. In contrast to the method of Design of Experiments in combination with response surface analysis (RSA), optimization approaches like genetic algorithms (GAs) can be applied to identify optimal parameter settings in multidimensional optimizations tasks. In this article the performance of a GA was investigated applying parameters applicable in high-throughput downstream process development. The influence of population size, the design of the initial generation and selection pressure on the optimization results was studied. To mimic typical experimental data, four mathematical functions were used for an in silico evaluation. The influence of GA parameters was minor on landscapes with only one optimum. On landscapes with several optima, parameters had a significant impact on GA performance and success in finding the global optimum. Premature convergence increased as the number of parameters and noise increased. RSA was shown to be comparable or superior for simple systems and low to moderate noise. For complex systems or high noise levels, RSA failed, while GA optimization represented a robust tool for process optimization. Finally, the effect of different objective functions is shown exemplarily for a refolding optimization of lysozyme.

  20. 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.

  1. 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

  2. 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

  3. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.).

    PubMed

    Cheng, Jiaowen; Qin, Cheng; Tang, Xin; Zhou, Huangkai; Hu, Yafei; Zhao, Zicheng; Cui, Junjie; Li, Bo; Wu, Zhiming; Yu, Jiping; Hu, Kailin

    2016-01-01

    The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum. PMID:27623541

  4. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.)

    PubMed Central

    Cheng, Jiaowen; Qin, Cheng; Tang, Xin; Zhou, Huangkai; Hu, Yafei; Zhao, Zicheng; Cui, Junjie; Li, Bo; Wu, Zhiming; Yu, Jiping; Hu, Kailin

    2016-01-01

    The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum. PMID:27623541

  5. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.).

    PubMed

    Cheng, Jiaowen; Qin, Cheng; Tang, Xin; Zhou, Huangkai; Hu, Yafei; Zhao, Zicheng; Cui, Junjie; Li, Bo; Wu, Zhiming; Yu, Jiping; Hu, Kailin

    2016-01-01

    The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum.

  6. 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.

  7. 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

  8. Visual & reversible sensing of cyanide in real samples by an effective ratiometric colorimetric probe & logic gate application.

    PubMed

    Bhardwaj, Shubhrajyotsna; Singh, Ashok Kumar

    2015-10-15

    A novel anion probe 3 (2,4-di-tert-butyl-6-((2(2,4-dinitrophenyl) hydrazono) methyl) phenol) has been unveiled as an effective ratiometric and colorimetric sensor for selective and rapid detection of cyanide. The sensing behavior was demonstrated by UV-vis experiments and NMR studies. This sensory system exhibited prominent visual color change toward cyanide ion over other testing anions in DMSO (90%) solvent, with a 1:1 binding stoichiometry and a detection limit down to 3.6×10(-8) mol L(-1). Sensor reveals specific anti-jamming activity and reversible in the presence of Cu(2+) ions. This concept has been applied to design a logic gate circuit at the molecular level. Further we developed coated graphite electrode using probe 3 as ionophore and studied the performance characteristics of electrode. The sensitivity of ratiometric-based colorimetric assay is below the 1.9 μM, accepted by the World Health Organization as the highest permissible cyanide concentration in drinking water. So it can be applied for both quantitative determination and qualitative supervising of cyanide concentrations in real samples.

  9. Improvement of influenza A/Fujian/411/02 (H3N2) virus growth in embryonated chicken eggs by balancing the hemagglutinin and neuraminidase activities, using reverse genetics.

    PubMed

    Lu, Bin; Zhou, Helen; Ye, Dan; Kemble, George; Jin, Hong

    2005-06-01

    The H3N2 influenza A/Fujian/411/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A/Fujian/411/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A/Fujian/411/02 virus was examined in this study by the reverse genetics technology. Two antigenically related strains that replicated well in embryonated chicken eggs, A/Sendai-H/F4962/02 and A/Wyoming/03/03, were compared with the prototype A/Fujian/411/02 virus. A/Sendai differed from A/Fujian by three amino acids in the neuraminidase (NA), whereas A/Wyoming differed from A/Fujian by five amino acids in the hemagglutinin (HA). The HA and NA segments of these three viruses were reassorted with cold-adapted A/Ann Arbor/6/60, the master donor virus for the live attenuated type A influenza vaccines (FluMist). The HA and NA residues differed between these three H3N2 viruses evaluated for their impact on virus replication in MDCK cells and in embryonated chicken eggs. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. Thus, the balance between the HA and NA activities is critical for influenza virus replication in a different host system. The HA or NA changes that increased A/Fujian/411/02 virus replication in embryonated chicken eggs were found to have no significant impact on antigenicity of these recombinant viruses. This study demonstrated that the reverse genetics technology could be used to

  10. 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.

  11. [Application of reversed-phase ion-pair chromatography for universal estimation of octanol-water partition coefficients of acid, basic and amphoteric drugs].

    PubMed

    Zhu, Hui; Yang, Ri-Fang; Yun, Liu-Hong; Jiang, Yu; Li, Jin

    2009-09-01

    This paper is to establish a reversed-phase ion-pair chromatography (RP-IPC) method for universal estimation of the octanol/water partition coefficients (logP) of a wide range of structurally diverse compounds including acidic, basic, neutral and amphoteric species. The retention factors corresponding to 100% water (logk(w)) were derived from the linear part of the logk'/phi relationship, using at least four isocratic logk' values containing different organic compositions. The logk(w) parameters obtained were close to the corresponding logP values obtained with the standard "shake flask" methods. The mean deviation for test drugs is 0.31. RP-IPC with trifluoroacetic acid as non classic ion-pair agents can be applicable to determine the logP values for a variety of drug-like molecules with increased accuracy.

  12. Genetically Modified Networks: A Genetic Algorithm contribution to Space Geodesy. Application to the transformation of SLR and DORIS EOP time series into ITRF2005.

    NASA Astrophysics Data System (ADS)

    Coulot, D.; Collilieux, X.; Pollet, A.; Berio, P.; Gobinddass, M. L.; Soudarin, L.; Willis, P.

    2009-04-01

    In this study, we apply Genetic Algorithms (GAs) in order to optimize the referencing (and consequently the precision - stability - and the accuracy) of the EOPs with respect to ITRF2005. These EOPs are derived from SLR or DORIS data at a daily sampling, simultaneously with weekly station positions. GAs are evolutionary algorithms, i.e. stochastic algorithms based on the evolution theory and using some genetic operators such as chromosome crossover and gene mutations. They are currently used for a broad spectrum of activities, from medicine to defence to finance. They have also been used in Earth and Space sciences (remote sensing, geophysics, meteorology, astrophysics, astronomy, etc.) since the early nineties. But, as far as we know, the present work is the first application of GAs in the framework of Space Geodesy. In this work, we use an algorithm based on GAs to find weekly optimal sub-networks over which applying minimum constraints in order to reference EOPs. Each week, the three rotations of the involved terrestrial frames are forced to be zero with respect to ITRF2005 through minimum constraints applied over these sub-networks, which are called Genetically Modified Networks (GMNs). The reference system effects are used as objectives to optimize with GAs. Regarding SLR, our approach provides an improvement of 10 % in accuracy for polar motion in comparison to the results obtained with the network specially designed for EOP referencing by the Analysis Working Group of the International Laser Ranging Service. This improvement of nearly 25 as represents 50 % of the current precision of the IERS 05 C04 reference series. We also show preliminary results regarding such GMNs for the DORIS technique using two different solutions (IGN and CNES/CLS solutions). Finally, for practical applications, we also test, for the SLR and the DORIS techniques, the possible emergence of global core networks to be used for EOP referencing on the basis of GAs.

  13. 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

    2012-01-01

    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.

  14. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

    PubMed Central

    Cui, Chenghua; Shu, Wei; Li, Peining

    2016-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH

  15. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications.

    PubMed

    Cui, Chenghua; Shu, Wei; Li, Peining

    2016-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH

  16. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

    PubMed Central

    Cui, Chenghua; Shu, Wei; Li, Peining

    2016-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH

  17. 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.

  18. 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

  19. 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.

  20. 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, Tõnu; 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 in vivo. 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.

  1. Construction and application of a protein and genetic interaction network (yeast interactome)

    PubMed Central

    Stuart, Gregory R.; Copeland, William C.; Strand, Micheline K.

    2009-01-01

    Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome. PMID:19273534

  2. Functional, fractal nonlinear response with application to rate processes with memory, allometry, and population genetics

    PubMed Central

    Vlad, Marcel O.; Morán, Federico; Popa, Vlad T.; Szedlacsek, Stefan E.; Ross, John

    2007-01-01

    We give a functional generalization of fractal scaling laws applied to response problems as well as to probability distributions. We consider excitations and responses, which are functions of a given state vector. Based on scaling arguments, we derive a general nonlinear response functional scaling law, which expresses the logarithm of a response at a given state as a superposition of the values of the logarithms of the excitations at different states. Such a functional response law may result from the balance of different growth processes, characterized by variable growth rates, and it is the first order approximation of a perturbation expansion similar to the phase expansion. Our response law is a generalization of the static fractal scaling law and can be applied to the study of various problems from physics, chemistry, and biology. We consider some applications to heterogeneous and disordered kinetics, organ growth (allometry), and population genetics. Kinetics on inhomogeneous reconstructing surfaces leads to rate equations described by our nonlinear scaling law. For systems with dynamic disorder with random energy barriers, the probability density functional of the rate coefficient is also given by our scaling law. The relative growth rates of different biological organs (allometry) can be described by a similar approach. Our scaling law also emerges by studying the variation of macroscopic phenotypic variables in terms of genotypic growth rates. We study the implications of the causality principle for our theory and derive a set of generalized Kramers–Kronig relationships for the fractal scaling exponents. PMID:17360340

  3. Genetic recombination pathways and their application for genome modification of human embryonic stem cells.

    PubMed

    Nieminen, Mikko; Tuuri, Timo; Savilahti, Harri

    2010-10-01

    Human embryonic stem cells are pluripotent cells derived from early human embryo and retain a potential to differentiate into all adult cell types. They provide vast opportunities in cell replacement therapies and are expected to become significant tools in drug discovery as well as in the studies of cellular and developmental functions of human genes. The progress in applying different types of DNA recombination reactions for genome modification in a variety of eukaryotic cell types has provided means to utilize recombination-based strategies also in human embryonic stem cells. Homologous recombination-based methods, particularly those utilizing extended homologous regions and those employing zinc finger nucleases to boost genomic integration, have shown their usefulness in efficient genome modification. Site-specific recombination systems are potent genome modifiers, and they can be used to integrate DNA into loci that contain an appropriate recombination signal sequence, either naturally occurring or suitably pre-engineered. Non-homologous recombination can be used to generate random integrations in genomes relatively effortlessly, albeit with a moderate efficiency and precision. DNA transposition-based strategies offer substantially more efficient random strategies and provide means to generate single-copy insertions, thus potentiating the generation of genome-wide insertion libraries applicable in genetic screens.

  4. Construction and application of a protein and genetic interaction network (yeast interactome).

    PubMed

    Stuart, Gregory R; Copeland, William C; Strand, Micheline K

    2009-04-01

    Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome.

  5. 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

  6. 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.

  7. [Novel methods and their applicability in the evaluation of the genetic background of endocrine system tumours].

    PubMed

    Patócs, Attila; Likó, István; Butz, Henriett; Baghy, Kornélia; Rácz, Károly

    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.

  8. [Application of case-based method in genetics and eugenics teaching].

    PubMed

    Li, Ya-Xuan; Zhao, Xin; Zhang, Fei-Xiong; Hu, Ying-Kao; Yan, Yue-Ming; Cai, Min-Hua; Li, Xiao-Hui

    2012-05-01

    Genetics and Eugenics is a cross-discipline between genetics and eugenics. It is a common curriculum in many Chinese universities. In order to increase the learning interest, we introduced case teaching method and got a better teaching effect. Based on our teaching practices, we summarized some experiences about this subject. In this article, the main problem of case-based method applied in Genetics and Eugenics teaching was discussed.

  9. The 'new genetics' in blood and cardiovascular research: applications to prevention and treatment.

    PubMed

    Motulsky, A G

    1984-11-01

    Genetic approaches have become an important component of both fundamental and disease-oriented research. Certain diseases of the blood--the hemoglobinopathies--have been elucidated by the spectacular methods of molecular genetics. Some of these advances have already been incorporated in disease management. Often, common conditions such as coronary heart disease and hypertension show familial aggregation. Genetic analysis of these diseases together with biochemical and molecular methods are likely to be useful for further understanding and ultimate prevention and control.

  10. 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

  11. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    PubMed

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed. PMID:27100228

  12. [Genetic polymorphism of FIBRA,DHFRP2 and ACTBP2 and their forensic application in Yunnan Han population].

    PubMed

    Jing, Qiang; Nie, Sheng-Jie

    2002-09-01

    To investigate the genetic polymorphism of FIBRA,DHFRP2 and ACTBP2 in Yunnan Han population as well as their application in forensic science, EDTA-blood specimens were collected from 200 healthy individuals. The DNA were extracted either by the Chloro form, phenol method or by the Chelex-100 method. The PCR products were analyzed by PAG vertical electrophoresis,following by silver staining. All gene frequencies, discrimination power (DP), exclusion of paternity probability (EPP), heterozygosity (H),polymorphisms information content (PIC),matching probability (PM) as well as the Hardy-Weinberg test were calculated. The obtained data are beneficial in the understanding of population genetics of the three STR loci in Yunnan Han population and the results suggest that these loci are valuable genetic markers for paternity testing and personal identification in forensic science practice.

  13. 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.

  14. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    PubMed

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  15. Genetic engineering of probiotic Escherichia coli Nissle 1917 for clinical application.

    PubMed

    Ou, Bingming; Yang, Ying; Tham, Wai Liang; Chen, Lin; Guo, Jitao; Zhu, Guoqiang

    2016-10-01

    Escherichia coli strain Nissle 1917 (EcN) has been used as a probiotic. Genetic engineering has enhanced the utility of EcN in several vaccine and pharmaceutical preparations. We discuss in this mini review the genetics and physical properties of EcN. We also discuss the numerous genetic engineering strategies employed for EcN-based vaccine development, including recombinant plasmid transfer, genetic engineering of cryptic plasmids or the EcN chromosome, EcN bacterial ghosts and its outer membrane vesicles. We also provide a current update on the progress and the challenges regarding the use of EcN in vaccine development.

  16. Genetic engineering of probiotic Escherichia coli Nissle 1917 for clinical application.

    PubMed

    Ou, Bingming; Yang, Ying; Tham, Wai Liang; Chen, Lin; Guo, Jitao; Zhu, Guoqiang

    2016-10-01

    Escherichia coli strain Nissle 1917 (EcN) has been used as a probiotic. Genetic engineering has enhanced the utility of EcN in several vaccine and pharmaceutical preparations. We discuss in this mini review the genetics and physical properties of EcN. We also discuss the numerous genetic engineering strategies employed for EcN-based vaccine development, including recombinant plasmid transfer, genetic engineering of cryptic plasmids or the EcN chromosome, EcN bacterial ghosts and its outer membrane vesicles. We also provide a current update on the progress and the challenges regarding the use of EcN in vaccine development. PMID:27640192

  17. 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 60°C 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 60°C 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

  18. 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

  19. Novel Applications of Multi-task Learning and Multiple Output Regression to Multiple Genetic Trait Prediction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait predicti...

  20. Application of restriction site amplified polymorphism (RSAP) to genetic diversity in Saccharina japonica

    NASA Astrophysics Data System (ADS)

    Zhao, Cui; Liu, Cui; Li, Wei; Chi, Shan; Feng, Rongfang; Liu, Tao

    2013-07-01

    Restriction site amplified polymorphism (RSAP) was used, for the first time, to analyze the genetic structure and diversity of four, mainly cultivated, varieties of the brown alga, Saccharina japonica. Eighty-eight samples from varieties " Rongfu ", " Fujian ", " Ailunwan " and " Shengchanzhong " were used for the genetic analyses. One hundred and ninety-eight bands were obtained using eight combinations of primers. One hundred and ninety-one (96.46%) were polymorphic bands. Nei's genetic diversity was 0.360, and the coefficient of genetic differentiation was 0.357. No inbreeding-type recession was found in the four brown alga varieties and the results of the " Ailunwan " variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program. Genetic diversity and cluster analyses results were consistent with these genetic relationships. The results show the RSAP method is suitable for genetic analysis. Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.

  1. [Application of the Barr body case in teaching practice of genetics].

    PubMed

    Chen, Fan-Guo; Hou, Bing-Kai

    2012-04-01

    There are three classical problems at the chromosome level in cytogenetics, namely the formation mechanisms and effects of Barr body, polytenic chromosome, and lampbrush chromosome. Teachers and researchers keep sustaining attention to the Barr body because of the relationships between Barr body and the X chromosome dosage compensation effect in mammals, the human sex identification, and some human diseases. In our genetics teaching practice, we tried the case-based teaching method. We introduced the classical problems and research progress of the Barr body, as a line, into partial sections of our genetics teaching contents such as sex-linked genetic analysis, eukaryotic gene expression regulation, cancer genetic analysis, and genetic experiments. Finally, it will form a comprehensive summary of related knowledge of genetics through class discussion on the Barr body. We found that this teaching method can not only optimize the teaching contents of genetics, consolidate and widen students' basic knowledge, and help student to form the systemic and developmental views of a classical genetics problem, but also inspire students' interest in life sciences. Good teaching results have been achieved.

  2. 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…

  3. The Application of Bone Marrow Transplantation to the Treatment of Genetic Diseases

    NASA Astrophysics Data System (ADS)

    Parkman, Robertson

    1986-06-01

    Genetic diseases can be treated by transplantation of either normal allogeneic bone marrow or, potentially, autologous bone marrow into which the normal gene has been inserted in vitro (gene therapy). Histocompatible allogeneic bone marrow transplantation is used for the treatment of genetic diseases whose clinical expression is restricted to lymphoid or hematopoietic cells. The therapeutic role of bone marrow transplantation in the treatment of generalized genetic diseases, especially those affecting the central nervous system, is under investigation. The response of a generalized genetic disease to allogeneic bone marrow transplantation may be predicted by experiments in vitro. Gene therapy can be used only when the gene responsible for the disease has been characterized. Success of gene therapy for a specific genetic disease may be predicted by its clinical response to allogeneic bone marrow transplantation.

  4. 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

  5. [Advances in understanding Drosophila salivary gland polytene chromosome and its applications in genetics teaching].

    PubMed

    Gang, Li; Fanguo, Chen

    2015-06-01

    Drosophila salivary gland polytene chromosome, one of the three classical chromosomes with remarkable characteristics, has been used as an outstanding model for a variety of genetic studies since 1934. The greatest contribution of this model to genetics has been providing extraordinary angle of view in studying interphase chromosome structure and gene expression regulation. Additionally, it has been extensively used to understand some special genetic phenomena, such as dosage compensation and position-effect variegation. In this paper, we briefly review the advances in the study of Drosophila salivary gland chromosome, and try to systematically and effectively introduce this model system into genetics teaching practice in order to steer and inspire students' interest in genetics.

  6. Applications of genetic data to improve management and conservation of river fishes and their habitats

    USGS Publications Warehouse

    Scribner, Kim T; Lowe, Winsor H.; Landguth, Erin L.; Luikart, Gordon; Infante, Dana M.; Whelan, Gary; Muhlfeld, Clint C.

    2015-01-01

    Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthropogenic effects, and detect impairments to underlying processes. We show that by combining taxonomic, demographic, and genetic data of species in complex riverscapes, managers can better understand the spatial and temporal scales over which environmental processes and disturbance influence biodiversity. We describe how population genetic models using empirical or simulated genetic data quantify effects of environmental processes affecting species diversity and distribution. Our summary shows that aquatic assessment initiatives that use standardized data sets to direct management actions can benefit from integration of genetic data to improve the predictability of disturbance–response relationships of river fishes and their habitats over a broad range of spatial and temporal scales.

  7. Rapid detection of poliovirus by reverse transcription and polymerase chain amplification: application for differentiation between poliovirus and nonpoliovirus enteroviruses.

    PubMed Central

    Abraham, R; Chonmaitree, T; McCombs, J; Prabhakar, B; Lo Verde, P T; Ogra, P L

    1993-01-01

    This report describes a rapid method of detection of poliovirus from viral isolates of clinical specimens using a single set of primers selected from the conserved 5' noncoding region of the poliovirus genome. Of the 144 clinical viral isolates examined, 81 were positive for polioviruses and 50 were positive for nonpoliovirus enteroviruses by tissue culture neutralization and infectivity. All 81 (100%) of the viral isolates identified as poliovirus by tissue culture infectivity were also positive by polymerase chain reaction. Of 50 nonpoliovirus enterovirus isolates found to be negative for poliovirus by tissue culture neutralization and infectivity, 48 were also negative by polymerase chain reaction. The high sensitivity (100%) and specificity (96%) of the primer set indicate that this assay has potential clinical applicability in the diagnosis of nonpoliovirus enterovirus infection. Images PMID:7679404

  8. A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications

    PubMed Central

    Liang, Qian; He, Rong L.; Yau, Stephen S.-T.

    2011-01-01

    Background Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences. Methodology To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses. Conclusions Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve. PMID:21399690

  9. A Genetic Algorithm Variational Approach to Data Assimilation and Application to Volcanic Emissions

    NASA Astrophysics Data System (ADS)

    Schmehl, Kerrie J.; Haupt, Sue Ellen; Pavolonis, Michael J.

    2012-03-01

    Variational data assimilation methods optimize the match between an observed and a predicted field. These methods normally require information on error variances of both the analysis and the observations, which are sometimes difficult to obtain for transport and dispersion problems. Here, the variational problem is set up as a minimization problem that directly minimizes the root mean squared error of the difference between the observations and the prediction. In the context of atmospheric transport and dispersion, the solution of this optimization problem requires a robust technique. A genetic algorithm (GA) is used here for that solution, forming the GA-Variational (GA-Var) technique. The philosophy and formulation of the technique is described here. An advantage of the technique includes that it does not require observation or analysis error covariances nor information about any variables that are not directly assimilated. It can be employed in the context of either a forward assimilation problem or used to retrieve unknown source or meteorological information by solving the inverse problem. The details of the method are reviewed. As an example application, GA-Var is demonstrated for predicting the plume from a volcanic eruption. First the technique is employed to retrieve the unknown emission rate and the steering winds of the volcanic plume. Then that information is assimilated into a forward prediction of its transport and dispersion. Concentration data are derived from satellite data to determine the observed ash concentrations. A case study is made of the March 2009 eruption of Mount Redoubt in Alaska. The GA-Var technique is able to determine a wind speed and direction that matches the observations well and a reasonable emission rate.

  10. 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

  11. Reverse immunoaffinity chromatography: application to the purification of the 60- to 90-kDa gastric parietal cell autoantigen associated with autoimmune gastritis.

    PubMed

    Goldkorn, I; Gleeson, P A; Toh, B H

    1991-05-01

    Previous attempts to purify autoantigens by affinity chromatography using the total IgG from autoantibody-positive sera have not been very successful. We describe here a novel method using parietal cell autoantibodies, isolated on a crude autoantigen immunoabsorbent column, for the purification of the 60- to 90-kDa gastric parietal cell antigen targeted in autoimmune gastritis. The 60- to 90-kDa parietal cell antigen was first enriched 2.5-fold from a 0.5% Triton X-100 extract of total pig gastric mucosal membranes by DEAE-Sepharose 4B chromatography. The fraction containing the 60- to 90-kDa antigen was directly coupled to CNBr-activated Sepharose 4B to produce an immunoadsorbent column for the "reverse" purification of the specific parietal cell autoantibodies from pooled gastric parietal cell autoantibody-positive human sera. A 0.5% Triton X-100 extract of pig gastric mucosal membranes was initially precleared by sequential passage through Protein A-Sepharose 4B and normal human Ig-Sepharose 4B columns. The 60- to 90-kDa gastric parietal cell antigen (approximately 10 micrograms) was then purified from this precleared Triton X-100 membrane extract by affinity chromatography on a 1-ml column of purified autoantibody-Sepharose 4B, followed by preparative sodium dodecyl sulfate-polyacrylamide gel electrophonesis. This method, incorporating a "reverse" immunoaffinity chromatography step, has general applicability for the purification of tissue autoantigens using highly specific autoantibodies present in the sera of humans and experimental animals with a variety of other autoimmune diseases.

  12. 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 (940 mbar) 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 (50 cm, 41.5 cm in effective length, 50 μm i.d.), and the background electrolyte was composed of 20 mmol L(-1) sodium tetraborate in 10 % of methanol, pH 9.3. For the reverse polarity, -25 kV/35 s was applied followed by application of +30 kV for the electrophoretic run. Temperature was set at 20 °C, and all analytes were monitored at 297 nm. The method showed acceptable linearity (r (2) > 0.997) in the studied range of 0.1-5.0 mg L(-1), limits of detection below 0.017 mg L(-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.

  13. Critical overview of applications of genetic testing in sport talent identification.

    PubMed

    Roth, Stephen M

    2012-12-01

    Talent identification for future sport performance is of paramount interest for many groups given the challenges of finding and costs of training potential elite athletes. Because genetic factors have been implicated in many performance- related traits (strength, endurance, etc.), a natural inclination is to consider the addition of genetic testing to talent identification programs. While the importance of genetic factors to sport performance is generally not disputed, whether genetic testing can positively inform talent identification is less certain. The present paper addresses the science behind the genetic tests that are now commercially available (some under patent protection) and aimed at predicting future sport performance potential. Also discussed are the challenging ethical issues that emerge from the availability of these tests. The potential negative consequences associated with genetic testing of young athletes will very likely outweigh any positive benefit for sport performance prediction at least for the next several years. The paper ends by exploring the future possibilities for genetic testing as the science of genomics in sport matures over the coming decade(s).

  14. Molecular Genetic Analysis of Chlamydia Species.

    PubMed

    Sixt, Barbara S; Valdivia, Raphael H

    2016-09-01

    Species of Chlamydia are the etiologic agent of endemic blinding trachoma, the leading cause of bacterial sexually transmitted diseases, significant respiratory pathogens, and a zoonotic threat. Their dependence on an intracellular growth niche and their peculiar developmental cycle are major challenges to elucidating their biology and virulence traits. The last decade has seen tremendous advances in our ability to perform a molecular genetic analysis of Chlamydia species. Major achievements include the generation of large collections of mutant strains, now available for forward- and reverse-genetic applications, and the introduction of a system for plasmid-based transformation enabling complementation of mutations; expression of foreign, modified, or reporter genes; and even targeted gene disruptions. This review summarizes the current status of the molecular genetic toolbox for Chlamydia species and highlights new insights into their biology and new challenges in the nascent field of Chlamydia genetics. PMID:27607551

  15. Genetic algorithms optimization approach supported by the first-order derivative and Newton-Raphson methods: Application to fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Fisz, J. J.; Buczkowski, M.; Budziński, M. P.; Kolenderski, P.

    2005-05-01

    The application of genetic algorithms (GA) optimization approach supported by the first-order derivative (FOD) and Newton-Raphson (NR) methods to time-resolved polarized fluorescence spectroscopy, is discussed. It is demonstrated that the application of both methods to χ2 function reduces the number of adjustable model parameters. The combination of GA-optimizer with the FOD and NR methods improves considerably the efficiency of global analysis of kinetic and polarized fluorescence decays for solutions and organized media, including the case of excited-state processes.

  16. The apt/6-Methylpurine Counterselection System and Its Applications in Genetic Studies of the Hyperthermophilic Archaeon Sulfolobus islandicus

    PubMed Central

    Bi, Hongkai; Whitaker, Rachel J.

    2016-01-01

    ABSTRACT Sulfolobus islandicus serves as a model for studying archaeal biology as well as linking novel biology to evolutionary ecology using functional population genomics. In the present study, we developed a new counterselectable genetic marker in S. islandicus to expand the genetic toolbox for this species. We show that resistance to the purine analog 6-methylpurine (6-MP) in S. islandicus M.16.4 is due to the inactivation of a putative adenine phosphoribosyltransferase encoded by M164_0158 (apt). The application of the apt gene as a novel counterselectable marker was first illustrated by constructing an unmarked α-amylase deletion mutant. Furthermore, the 6-MP counterselection feature was employed in a forward (loss-of-function) mutation assay to reveal the profile of spontaneous mutations in S. islandicus M.16.4 at the apt locus. Moreover, the general conservation of apt genes in the crenarchaea suggests that the same strategy can be broadly applied to other crenarchaeal model organisms. These results demonstrate that the apt locus represents a new tool for genetic manipulation and sequence analysis of the hyperthermophilic crenarchaeon S. islandicus. IMPORTANCE Currently, the pyrEF/5-fluoroorotic acid (5-FOA) counterselection system remains the sole counterselection marker in crenarchaeal genetics. Since most Sulfolobus mutants constructed by the research community were derived from genetic hosts lacking the pyrEF genes, the pyrEF/5-FOA system is no longer available for use in forward mutation assays. Demonstration of the apt/6-MP counterselection system for the Sulfolobus model renders it possible to again study the mutation profiles in mutants that have already been constructed by the use of strains with a pyrEF-deficient background. Furthermore, additional counterselectable markers will allow us to conduct more sophisticated genetic studies, i.e., investigate mechanisms of chromosomal DNA transfer and quantify recombination frequencies among S

  17. 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

    2015-10-09

    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.

  18. Reversible DNA compaction.

    PubMed

    González-Pérez, 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

  19. Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

    PubMed Central

    Tian, Hong-Xia; Zhang, Xu-Chao; Wang, Zhen; Chen, Jian-Guang; Chen, Shi-Liang; Guo, Wei-Bang; Wu, Yi-Long

    2016-01-01

    Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena iPLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on MassARRAY mass spectrometry platform. Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of 99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a LungCartaTM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases. Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with LungCartaTM kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively. Conclusions: The proposed MassARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues. PMID:27144063

  20. 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)

  1. Genetic regulation of platelet receptor expression and function: application in clinical practice and drug development.

    PubMed

    Williams, Marlene S; Weiss, Ethan J; Sabatine, Marc S; Simon, Daniel I; Bahou, Wadie F; Becker, Lewis C; Parise, Leslie V; Dauerman, Harold L; French, Patricia A; Smyth, Susan S; Becker, Richard C

    2010-12-01

    Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering (1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, (2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and (3) the role of platelet function/genetic testing in guiding antiplatelet therapy.

  2. Genetics of Type 2 Diabetes: Insights into the Pathogenesis and Its Clinical Application

    PubMed Central

    Sun, Xue; Yu, Weihui; Hu, Cheng

    2014-01-01

    With rapidly increasing prevalence, diabetes has become one of the major causes of mortality worldwide. According to the latest studies, genetic information makes substantial contributions towards the prediction of diabetes risk and individualized antidiabetic treatment. To date, approximately 70 susceptibility genes have been identified as being associated with type 2 diabetes (T2D) at a genome-wide significant level (P < 5 × 10−8). However, all the genetic loci identified so far account for only about 10% of the overall heritability of T2D. In addition, how these novel susceptibility loci correlate with the pathophysiology of the disease remains largely unknown. This review covers the major genetic studies on the risk of T2D based on ethnicity and briefly discusses the potential mechanisms and clinical utility of the genetic information underlying T2D. PMID:24864266

  3. Analysis of genetic variation and potential applications in genome-scale metabolic modeling.

    PubMed

    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.

  4. Genetic activity profiles--application in assessing potential carcinogenicity of complex environmental mixtures.

    PubMed

    Waters, M D; Claxton, L D; Stack, H F; Graedel, T E

    1990-01-01

    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. The expanded genetic activity profile (GAP) data-base provides a computer-generated graphic representation of genetic bioassay data as a function of dose of the substance tested. In addition, the atmospheric chemical compound (ACC) data-base contains information on chemical structures, properties, detection methods and sources of chemicals found in ambient air. Using the combined data-bases, information on the quantity of an individual chemical present within a mixture or fraction of a mixture may be related to the quantity (lowest effective dose; LED) of the chemical required to demonstrate a positive response in one or more genetic bioassays. Alternatively, quantitative information on the carcinogenic potency of each individual compound (TD50 value) may be related to the quantity present in the mixture or mixture fraction and used to calculate the percent human exposure dose/rodent potency dose (HERP) for the chemical. Using an additivity assumption, a conservative estimate of potential carcinogenic hazard for the mixture may be calculated based on the HERP indices for its chemical components. This conceptual approach is limited by the relatively small number of chemicals identified in complex mixtures for which genetic toxicology and animal cancer data exist.

  5. Using needs-based frameworks for evaluating new technologies: an application to genetic tests.

    PubMed

    Rogowski, Wolf H; Schleidgen, Sebastian

    2015-02-01

    Given the multitude of newly available genetic tests in the face of limited healthcare budgets, the European Society of Human Genetics assessed how genetic services can be prioritized fairly. Using (health) benefit maximizing frameworks for this purpose has been criticized on the grounds that rather than maximization, fairness requires meeting claims (e.g. based on medical need) equitably. This study develops a prioritization score for genetic tests to facilitate equitable allocation based on need-based claims. It includes attributes representing health need associated with hereditary conditions (severity and progression), a genetic service's suitability to alleviate need (evidence of benefit and likelihood of positive result) and costs to meet the needs. A case study for measuring the attributes is provided and a suggestion is made how need-based claims can be quantified in a priority function. Attribute weights can be informed by data from discrete-choice experiments. Further work is needed to measure the attributes across the multitude of genetic tests and to determine appropriate weights. The priority score is most likely to be considered acceptable if developed within a decision process which meets criteria of procedural fairness and if the priority score is interpreted as "strength of recommendation" rather than a fixed cut-off value. PMID:25488566

  6. 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

  7. 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.

  8. Reverse Genetics of Respiratory Syncytial Virus.

    PubMed

    Stobart, Christopher C; Hotard, Anne L; Meng, Jia; Moore, Martin L

    2016-01-01

    Respiratory syncytial virus (RSV) is a negative-strand RNA virus that is associated with severe lower respiratory tract infections in young infants and the elderly. RSV remains a leading cause worldwide of infant mortality, and despite the high clinical and economic burden of the virus there are currently no available vaccines. Here, we describe the methods for recovery of recombinant RSV viruses using a bacterial artificial chromosome and methods related to procurement and expansion of stocks of RSV mutants. PMID:27464692

  9. Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).

    PubMed

    Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, 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.

  10. Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)

    PubMed Central

    Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, 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. Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.

    PubMed

    Allnutt, T R; Roper, K; Henry, C

    2008-01-23

    A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed.

  12. Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.

    PubMed

    Allnutt, T R; Roper, K; Henry, C

    2008-01-23

    A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed. PMID:18092752

  13. Dendritic cell delivery of plasmid DNA. Applications for controlled genetic immunization.

    PubMed

    Mumper, R J; Ledebur, H C

    2001-09-01

    Positive human clinical data using biolistic-mediated gene transfer (i.e., gene gun) to administer a nucleic acid-based Hepatitis B vaccine has validated genetic immunization as an effective clinical vaccine modality. Although the precise mechanism of action has yet to be determined, preclinical studies using jet injection have indicated that direct targeting of resident antigen presenting cells (Langerhan's cells) in the skin as the primary immunological driving force for the potent and long-lived immune response. Moreover, positive results with topical delivery of genetic vaccines and ex vivo loading of dendritic cells with antigen has strengthened the movement toward directly targeting antigen presenting cells as a means to amplify, control, and mediate the immunological consequences of prophylactic and/or therapeutic genetic vaccines. Despite these encouraging results with the gene gun, it is unclear whether this technology will translate into commercially available vaccines due to potential product development barriers such as cost and convenience. It is clear that safety concerns in using genetic approaches to treat and prevent disease have highlighted the need for strict product requirements for genetic vaccines. A plausible strategy to meet these requirements is to combine controlled plasmid delivery systems with tissue-specific gene expression systems.

  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 (αs2-, β-, and κ-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: αs2-casein A = 2.9 ± 0.8 g/L and F = 1.8 ± 0.4 g/L; β-casein C = 3.0 ± 0.8 g/L and C1 = 2.0 ± 0.7 g/L and κ-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 αs2-casein genetic variants A and F, and β-casein C and C1 with other previously described method. The main important result was obtained for κ-casein because, till now, no data were available on quantification of single genetic variants for this protein. PMID:26304408

  15. 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 (αs2-, β-, and κ-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: αs2-casein A = 2.9 ± 0.8 g/L and F = 1.8 ± 0.4 g/L; β-casein C = 3.0 ± 0.8 g/L and C1 = 2.0 ± 0.7 g/L and κ-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 αs2-casein genetic variants A and F, and β-casein C and C1 with other previously described method. The main important result was obtained for κ-casein because, till now, no data were available on quantification of single genetic variants for this protein.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish.

    PubMed

    Tong, JinGou; Sun, XiaoWen

    2015-02-01

    The traits of cultured fish must continually be genetically improved to supply high-quality animal protein for human consumption. Economically important fish traits are controlled by multiple gene quantitative trait loci (QTL), most of which have minor effects, but a few genes may have major effects useful for molecular breeding. In this review, we chose relevant studies on some of the most intensively cultured fish and concisely summarize progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades. The potential applications of these major-effect genes and their associated markers in marker-assisted selection and molecular breeding, as well as future research directions are also discussed. These genetic and genomic analyses will be valuable for elucidating the mechanisms modulating economically important traits and to establish more effective molecular breeding techniques in fish.

  3. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora.

    PubMed

    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

  4. A novel genetic score approach using instruments to investigate interactions between pathways and environment: application to air pollution.

    PubMed

    Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

    2014-01-01

    Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999-2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (p(interaction) = 0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (p(interaction) = 0.12), CRP (p(interaction) = 0.02), and ICAM-1 (pinteraction = 0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.

  5. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora.

    PubMed

    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.

  6. 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

  7. Genetic engineering of mesenchymal stem cells and its application in human disease therapy.

    PubMed

    Hodgkinson, Conrad P; Gomez, José A; Mirotsou, Maria; Dzau, Victor J

    2010-11-01

    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.

  8. Preimplantation genetic diagnosis: technological advances to improve accuracy and range of applications.

    PubMed

    Kuliev, Anver; Verlinsky, Yury

    2008-04-01

    Preimplantation genetic diagnosis (PGD) is an option for couples who are at risk that enables them to have unaffected progeny without facing the risk of pregnancy termination after prenatal diagnosis as currently practiced. It is also one of the practical tools used in assisted reproduction technology to improve the chance of conception for infertility cases with poor prognosis. Because PGD is performed using a single biopsied cell, technological advances are important to improving PGD accuracy. This has contributed to the avoidance of misdiagnosis in PGD for single gene disorders, and extensive experience in PGD for chromosomal disorders suggests strategies for more reliable evaluation of the chromosomal status of the preimplantation embryo. This paper describes the present status of PGD for genetic and chromosomal disorders, its accuracy and range, and how PGD is an integral part of IVF and genetic practices.

  9. 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

  10. 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

  11. 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.

  12. Genetic vectors as a tool in association studies: definitions and application for study of rheumatoid arthritis.

    PubMed

    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. Cost-effectiveness of MODY genetic testing: translating genomic advances into practical health applications.

    PubMed

    Naylor, Rochelle N; John, Priya M; Winn, Aaron N; Carmody, David; Greeley, Siri Atma W; Philipson, Louis H; Bell, Graeme I; Huang, Elbert S

    2014-01-01

    OBJECTIVE To evaluate the cost-effectiveness of a genetic testing policy for HNF1A-, HNF4A-, and GCK-MODY in a hypothetical cohort of type 2 diabetic patients 25-40 years old with a MODY prevalence of 2%. RESEARCH DESIGN AND METHODS We used a simulation model of type 2 diabetes complications based on UK Prospective Diabetes Study data, modified to account for the natural history of disease by genetic subtype to compare a policy of genetic testing at diabetes diagnosis versus a policy of no testing. Under the screening policy, successful sulfonylurea treatment of HNF1A-MODY and HNF4A-MODY was modeled to produce a glycosylated hemoglobin reduction of -1.5% compared with usual care. GCK-MODY received no therapy. Main outcome measures were costs and quality-adjusted life years (QALYs) based on lifetime risk of complications and treatments, expressed as the incremental cost-effectiveness ratio (ICER) (USD/QALY). RESULTS The testing policy yielded an average gain of 0.012 QALYs and resulted in an ICER of 205,000 USD. Sensitivity analysis showed that if the MODY prevalence was 6%, the ICER would be ~50,000 USD. If MODY prevalence was >30%, the testing policy was cost saving. Reducing genetic testing costs to 700 USD also resulted in an ICER of ~50,000 USD. CONCLUSIONS Our simulated model suggests that a policy of testing for MODY in selected populations is cost-effective for the U.S. based on contemporary ICER thresholds. Higher prevalence of MODY in the tested population or decreased testing costs would enhance cost-effectiveness. Our results make a compelling argument for routine coverage of genetic testing in patients with high clinical suspicion of MODY.

  14. Genetic determinants of breast cancer risk: a review of current literature and issues pertaining to clinical application.

    PubMed

    Njiaju, Uchenna O; Olopade, Olufunmilayo I

    2012-09-01

    Despite major advances in breast cancer therapy, annual mortality remains significant with a sizeable proportion of patients eventually succumbing to metastatic disease. Clearly, optimizing approaches for identification and management of women at heightened risk for breast cancer will reduce overall morbidity and mortality from the disease. Over the past few decades, advances in molecular genetics and linkage analyses have allowed for the identification of specific germline mutations underlying a significant fraction of hereditary breast cancer. Genome-wide association studies have been developed as a powerful tool in identifying lower penetrance mutations, and it is believed that such genome-level variations may act in concert to give rise to the majority of inherited breast cancer risk. Controversies and uncertainties remain in clinical application of newly identified genomic loci that confer genetic susceptibility. This article reviews the well-characterized breast cancer susceptibility genes, highlights recent publications pertaining to the less well known and lower penetrance genetic polymorphisms, summarizes challenges in translating research findings to the clinical scenario, and offers some recommendations for clinical practice.

  15. 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 .

  16. 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

  17. Evaluation of Residual Static Corrections by Hybrid Genetic Algorithm Steepest Ascent Autostatics Inversion.Application southern Algerian fields

    NASA Astrophysics Data System (ADS)

    Eladj, Said; bansir, fateh; ouadfeul, sid Ali

    2016-04-01

    The application of genetic algorithm starts with an initial population of chromosomes representing a "model space". Chromosome chains are preferentially Reproduced based on Their fitness Compared to the total population. However, a good chromosome has a Greater opportunity to Produce offspring Compared To other chromosomes in the population. The advantage of the combination HGA / SAA is the use of a global search approach on a large population of local maxima to Improve Significantly the performance of the method. To define the parameters of the Hybrid Genetic Algorithm Steepest Ascent Auto Statics (HGA / SAA) job, we Evaluated by testing in the first stage of "Steepest Ascent," the optimal parameters related to the data used. 1- The number of iterations "Number of hill climbing iteration" is equal to 40 iterations. This parameter defines the participation of the algorithm "SA", in this hybrid approach. 2- The minimum eigenvalue for SA '= 0.8. This is linked to the quality of data and S / N ratio. To find an implementation performance of hybrid genetic algorithms in the inversion for estimating of the residual static corrections, tests Were Performed to determine the number of generation of HGA / SAA. Using the values of residual static corrections already calculated by the Approaches "SAA and CSAA" learning has Proved very effective in the building of the cross-correlation table. To determine the optimal number of generation, we Conducted a series of tests ranging from [10 to 200] generations. The application on real seismic data in southern Algeria allowed us to judge the performance and capacity of the inversion with this hybrid method "HGA / SAA". This experience Clarified the influence of the corrections quality estimated from "SAA / CSAA" and the optimum number of generation hybrid genetic algorithm "HGA" required to have a satisfactory performance. Twenty (20) generations Were enough to Improve continuity and resolution of seismic horizons. This Will allow

  18. 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, François; 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; Maréchal, Valérie; 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.

  19. Use of Embryos Extracted from Individual Cannabis sativa Seeds for Genetic Studies and Forensic Applications.

    PubMed

    Soler, Salvador; Borràs, Dionís; Vilanova, Santiago; Sifres, Alicia; Andújar, Isabel; Figàs, Maria R; Llosa, Ernesto R; Prohens, Jaime

    2016-03-01

    Legal limits on the psychoactive tetrahydrocannabinol (THC) content in Cannabis sativa plants have complicated genetic and forensic studies in this species. However, Cannabis seeds present very low THC levels. We developed a method for embryo extraction from seeds and an improved protocol for DNA extraction and tested this method in four hemp and six marijuana varieties. This embryo extraction method enabled the recovery of diploid embryos from individual seeds. An improved DNA extraction protocol (CTAB3) was used to obtain DNA from individual embryos at a concentration and quality similar to DNA extracted from leaves. DNA extracted from embryos was used for SSR molecular characterization in individuals from the 10 varieties. A unique molecular profile for each individual was obtained, and a clear differentiation between hemp and marijuana varieties was observed. The combined embryo extraction-DNA extraction methodology and the new highly polymorphic SSR markers facilitate genetic and forensic studies in Cannabis. PMID:27404624

  20. 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