Science.gov

Sample records for additional gene products

  1. Additive Manufactured Product Integrity

    NASA Technical Reports Server (NTRS)

    Waller, Jess; Wells, Doug; James, Steve; Nichols, Charles

    2017-01-01

    NASA is providing key leadership in an international effort linking NASA and non-NASA resources to speed adoption of additive manufacturing (AM) to meet NASA's mission goals. Participants include industry, NASA's space partners, other government agencies, standards organizations and academia. Nondestructive Evaluation (NDE) is identified as a universal need for all aspects of additive manufacturing.

  2. An Additional Regulatory Gene for Actinorhodin Production in Streptomyces lividans Involves a LysR-Type Transcriptional Regulator

    PubMed Central

    Martínez-Costa, Oscar H.; Martín-Triana, Angel J.; Martínez, Eduardo; Fernández-Moreno, Miguel A.; Malpartida, Francisco

    1999-01-01

    The sequence of a 4.8-kbp DNA fragment adjacent to the right-hand end of the actinorhodin biosynthetic (act) cluster downstream of actVB-orf6 from Streptomyces coelicolor A3(2) reveals six complete open reading frames, named orf7 to orf12. The deduced amino acid sequences from orf7, orf10, and orf11 show significant similarities with the following products in the databases: a putative protein from the S. coelicolor SCP3 plasmid, LysR-type transcriptional regulators, and proteins belonging to the family of short-chain dehydrogenases/reductases, respectively. The deduced product of orf8 reveals low similarities with several methyltransferases from different sources, while orf9 and orf12 products show no similarities with other known proteins. Disruptions of orf10 and orf11 genes in S. coelicolor appear to have no significant effect on the production of actinorhodin. Nevertheless, disruption or deletion of orf10 in Streptomyces lividans causes actinorhodin overproduction. The introduction of extra copies of orf10 and orf11 genes in an S. coelicolor actIII mutant restores the ability to produce actinorhodin. Transcriptional analysis and DNA footprinting indicate that Orf10 represses its own transcription and regulates orf11 transcription, expression of which might require the presence of an unknown inducer. No DNA target for Orf10 protein was found within the act cluster. PMID:10400594

  3. COMBINATION DOSE OF TWO PHTHALATES ADDITIVELY DEPRESSES TESTOSTERONE PRODUCTION AND INSL3 GENE EXPRESSION IN MALE RAT FETUSES

    EPA Science Inventory

    Diethylhexyl phthalate (DEHP) and di(n-butyl) phthalate (DBP) are phthalate esters used to modify plastic and polymer textures. Individually,DEHP and DBP reduce testosterone production, inhibit reproductive tract development, andinduce reproductive organ malformationsin male rats...

  4. Simvastatin and Dipentyl Phthalate Lower Ex vivo Testicular Testosterone Production and Exhibit Additive Effects on Testicular Testosterone and Gene Expression Via Distinct Mechanistic Pathways in the Fetal Rat

    EPA Science Inventory

    Sex differentiation of the male reproductive tract in mammals is driven, in part, by fetal androgen production. In utero, some phthalate esters (PEs) alter fetal Leydig cell differentiation, reducing the expression of several genes associated with steroid synthesis/transport, and...

  5. Additive manufacturing in production: challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Ahuja, Bhrigu; Karg, Michael; Schmidt, Michael

    2015-03-01

    Additive manufacturing, characterized by its inherent layer by layer fabrication methodology has been coined by many as the latest revolution in the manufacturing industry. Due to its diversification of Materials, processes, system technology and applications, Additive Manufacturing has been synonymized with terminology such as Rapid prototyping, 3D printing, free-form fabrication, Additive Layer Manufacturing, etc. A huge media and public interest in the technology has led to an innovative attempt of exploring the technology for applications beyond the scope of the traditional engineering industry. Nevertheless, it is believed that a critical factor for the long-term success of Additive Manufacturing would be its ability to fulfill the requirements defined by the traditional manufacturing industry. A parallel development in market trends and product requirements has also lead to a wider scope of opportunities for Additive Manufacturing. The presented paper discusses some of the key challenges which are critical to ensure that Additive Manufacturing is truly accepted as a mainstream production technology in the industry. These challenges would highlight on various aspects of production such as product requirements, process management, data management, intellectual property, work flow management, quality assurance, resource planning, etc. In Addition, changing market trends such as product life cycle, mass customization, sustainability, environmental impact and localized production will form the foundation for the follow up discussion on the current limitations and the corresponding research opportunities. A discussion on ongoing research to address these challenges would include topics like process monitoring, design complexity, process standardization, multi-material and hybrid fabrication, new material development, etc.

  6. Additives In Meat and Poultry Products

    MedlinePlus

    ... What is a food additive? What is a "direct" food additive? What is an 'indirect" food additive? ... convenience foods. [ Top of Page ] What is a “direct” food additive? According to the FDA, “Direct food ...

  7. Replacing and Additive Horizontal Gene Transfer in Streptococcus

    PubMed Central

    Choi, Sang Chul; Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Stanhope, Michael J.; Siepel, Adam

    2012-01-01

    The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage (“replacing HGT”) and events that result in the addition of substantial new genomic material (“additive HGT”). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S. dysgalactiae subspecies dysgalactiae (SDD). Using recently developed statistical models and computational methods, we find evidence for abundant gene flow of both kinds within each of the SPY and SDE clades and of reduced levels of exchange between SPY and SDD. In addition, our analysis strongly supports a pronounced asymmetry in SPY–SDE gene flow, favoring the SPY-to-SDE direction. This finding is of particular interest in light of the recent increase in virulence of pathogenic SDE. We find much stronger evidence for SPY–SDE gene flow among replacing than among additive transfers, suggesting a primary influence from homologous recombination between co-occurring SPY and SDE cells in human hosts. Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. The genes affected by additive HGTs are enriched for functions having to do with transposition, recombination, and DNA integration, consistent with previous findings, whereas replacing HGTs seen to influence a more diverse set of genes. Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes. PMID:22617954

  8. Nucleophilic 1,4-additions for natural product discovery.

    PubMed

    Cox, Courtney L; Tietz, Jonathan I; Sokolowski, Karol; Melby, Joel O; Doroghazi, James R; Mitchell, Douglas A

    2014-09-19

    Natural products remain an important source of drug candidates, but the difficulties inherent to traditional isolation, coupled with unacceptably high rates of compound rediscovery, limit the pace of natural product detection. Here we describe a reactivity-based screening method to rapidly identify exported bacterial metabolites that contain dehydrated amino acids (i.e., carbonyl- or imine-activated alkenes), a common motif in several classes of natural products. Our strategy entails the use of a commercially available thiol, dithiothreitol, for the covalent labeling of activated alkenes by nucleophilic 1,4-addition. Modification is easily discerned by comparing mass spectra of reacted and unreacted cell surface extracts. When combined with bioinformatic analysis of putative natural product gene clusters, targeted screening and isolation can be performed on a prioritized list of strains. Moreover, known compounds are easily dereplicated, effectively eliminating superfluous isolation and characterization. As a proof of principle, this labeling method was used to identify known natural products belonging to the thiopeptide, lanthipeptide, and linaridin classes. Further, upon screening a panel of only 23 actinomycetes, we discovered and characterized a novel thiopeptide antibiotic, cyclothiazomycin C.

  9. 40 CFR 300.920 - Addition of products to Schedule.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... additional information and/or a sample of the product in order to review and/or conduct validation sampling... not list the product. (3) Request for review of decision. (i) A manufacturer whose product was determined to be ineligible for listing on the NCP Product Schedule may request EPA's Administrator to...

  10. Additive Functions in Boolean Models of Gene Regulatory Network Modules

    PubMed Central

    Darabos, Christian; Di Cunto, Ferdinando; Tomassini, Marco; Moore, Jason H.; Provero, Paolo; Giacobini, Mario

    2011-01-01

    Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred Boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity

  11. Additive functions in boolean models of gene regulatory network modules.

    PubMed

    Darabos, Christian; Di Cunto, Ferdinando; Tomassini, Marco; Moore, Jason H; Provero, Paolo; Giacobini, Mario

    2011-01-01

    Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity

  12. A versatile element for gene addition in bacterial chromosomes

    PubMed Central

    Sibley, Marion H.; Raleigh, Elisabeth A.

    2012-01-01

    The increasing interest in genetic manipulation of bacterial host metabolic pathways for protein or small molecule production has led to a need to add new genes to a chromosome quickly and easily without leaving behind a selectable marker. The present report describes a vector and four-day procedure that enable site-specific chromosomal insertion of cloned genes in a context insulated from external transcription, usable once in a construction series. The use of rhamnose-inducible transcription from rhaBp allows regulation of the inserted genes independently of the commonly used IPTG and arabinose strategies. Using lacZ as a reporter, we first show that expression from the rhamnose promoter is tightly regulatable, exhibiting very low leakage of background expression compared with background, and moderate rhamnose-induced expression compared with IPTG-induced expression from lacp. Second, the expression of a DNA methyltransferase was used to show that rhamnose regulation yielded on-off expression of this enzyme, such that a resident high-copy plasmid was either fully sensitive or fully resistant to isoschizomer restriction enzyme cleavage. In both cases, growth medium manipulation allows intermediate levels of expression. The vehicle can also be adapted as an ORF-cloning vector. PMID:22123741

  13. Methods for detecting additional genes underlying Alzheimer disease

    SciTech Connect

    Locke, P.A.; Haines, J.L.; Ter-Minassian, M.

    1994-09-01

    Alzheimer`s disease (AD) is a complex inherited disorder with proven genetic heterogeneity. To date, genes on chromosome 21 (APP) and 14 (not yet identified) are associated with early-onset familial AD, while the APOE gene on chromosome 19 is associated with both late onset familial and sporadic AD and early onset sporadic AD. Although these genes likely account for the majority of AD, many familial cases cannot be traced to any of these genes. From a set of 127 late-onset multiplex families screened for APOE, 43 (34%) families have at least one affected individual with no APOE-4 allele, suggesting an alternative genetic etiology. Simulation studies indicated that additional loci could be identified through a genomic screen with a 10 cM sieve on a subset of 21 well documented, non-APOE-4 families. Given the uncertainties in the mode of inheritance, reliance on a single analytical method could result in a missed linkage. Therefore, we have developed a strategy of using multiple overlapping yet complementary methods to detect linkage. These include sib-pair analysis and affected-pedigree-member analysis, neither of which makes assumptions about mode of inheritance, and lod score analysis (using two predefined genetic models). In order for a marker to qualify for follow-up, it must fit at least two of three criteria. These are nominal P values of 0.05 or less for the non-parametric methods, and/or a lod score greater than 1.0. Adjacent markers each fulfilling a single criterion also warrant follow-up. To date, we have screened 61 markers on chromosomes 1, 2, 3, 18, 19, 21, and 22. One marker, D2S163, generated a lod score of 1.06 ({theta} = 0.15) and an APMT statistic of 3.68 (P < 0.001). This region is currently being investigated in more detail. Updated results of this region plus additional screening data will be presented.

  14. Metal-Catalyzed Asymmetric Michael Addition in Natural Product Synthesis.

    PubMed

    Hui, Chunngai; Pu, Fan; Xu, Jing

    2016-12-19

    Asymmetric catalysis for chiral compound synthesis is a rapidly growing field in modern organic chemistry. Asymmetric catalytic processes have been indispensable for the synthesis of enantioselective materials to meet demands from various fields. Michael addition has been used extensively for the construction of C-C bonds under mild conditions. With the discovery and development of organo- and metal-catalyzed asymmetric Michael additions, the synthesis of enantioselective and/or diastereoselective Michael adducts has become possible and increasingly prevalent in the literature. In particular, metal-catalyzed asymmetric Michael addition has been employed as a key reaction in natural product synthesis for the construction of contiguous quaternary stereogenic center(s), which is still a difficult task in organic synthesis. Previously reported applications of metal-catalyzed asymmetric Michael additions in natural product synthesis are presented here and discussed in depth.

  15. Biogas Production on Demand Regulated by Butyric Acid Addition

    NASA Astrophysics Data System (ADS)

    Kasper, K.; Schiffels, J.; Krafft, S.; Kuperjans, I.; Elbers, G.; Selmer, T.

    2016-03-01

    Investigating effects of volatile fatty acids on the biogas process it was observed that butyric acid can be used for transient stimulation of the methane production in biogas plants operating with low energy substrates like cattle manure. Upon addition of butyrate the methane output of the reactors doubled within 24 h and reached almost 3-times higher methane yields within 3-4 days. Butyrate was quantitatively eliminated and the reactors returned to the original productivity state within 3 days when application of butyrate was stopped. The opportunity to use butyrate feeding for increased biogas production on demand is discussed.

  16. New frontiers in the therapy of primary immunodeficiency: From gene addition to gene editing.

    PubMed

    Kohn, Donald B; Kuo, Caroline Y

    2017-03-01

    The most severe primary immune deficiency diseases (PIDs) have been successfully treated with allogeneic hematopoietic stem cell transplantation for more than 4 decades. However, such transplantations have the best outcomes when there is a well-matched donor available because immune complications, such as graft-versus-host disease, are greater without a matched sibling donor. Gene therapy has been developed as a method to perform autologous transplantations of a patient's own stem cells that are genetically corrected. Through an iterative bench-to-bedside-and-back process, methods to efficiently add new copies of the relevant gene to hematopoietic stem cells have led to safe and effective treatments for several PIDs, including forms of severe combined immune deficiency, Wiskott-Aldrich syndrome, and chronic granulomatous disease. New methods for gene editing might allow additional PIDs to be treated by gene therapy because they will allow the endogenous gene to be repaired and expressed under its native regulatory elements, which are essential for genes involved in cell processes of signaling, activation, and proliferation. Gene therapy is providing exciting new treatment options for patients with PIDs, and advances are sure to continue.

  17. Identification of genes and gene products necessary for bacterial bioluminescence.

    PubMed

    Engebrecht, J; Silverman, M

    1984-07-01

    Expression of luminescence in Escherichia coli was recently achieved by cloning genes from the marine bacterium Vibrio fischeri. One DNA fragment on a hybrid plasmid encoded regulatory functions and enzymatic activities necessary for light production. We report the results of a genetic analysis to identify the luminescence genes (lux) that reside on this recombinant plasmid. lux gene mutations were generated by hydroxylamine treatment, and these mutations were ordered on a linear map by complementation in trans with a series of polar transposon insertions on other plasmids. lux genes were defined by complementation of lux gene defects on pairs of plasmids in trans in E. coli. Hybrid plasmids were also used to direct the synthesis of polypeptides in the E. coli minicell system. Seven lux genes and the corresponding gene products were identified from the complementation analysis and the minicell programing experiments. These genes, in the order of their position on a linear map, and the apparent molecular weights of the gene products are luxR (27,000), luxI (25,000), luxC (53,000), luxD (33,000), luxA (40,000), luxB (38,000), and luxE (42,000). From the luminescence phenotypes of E. coli containing mutant plasmids, functions were assigned to these genes: luxA, luxB, luxC, luxD, and luxE encode enzymes for light production and luxR and luxI encode regulatory functions.

  18. Genetic evidence for an additional function of phage T4 gene 32 protein: interaction with ligase.

    PubMed

    Mosig, G; Breschkin, A M

    1975-04-01

    Gene 32 of bacteriophage T4 is essential for DNA replication, recombination, and repair. In an attempt to clarify the role of the corresponding gene product, we have looked for mutations that specifically inactivate one but not all of its functions and for compensating suppressor mutations in other genes. Here we describe a gene 32 ts mutant that does not produce progeny, but in contrast to an am mutant investigated by others, is capable of some primary and secondary DNA replication and of forming "joint" recombinational intermediates after infection of Escherichia coli B at the restrictive temperature. However, parental and progeny DNA strands are not ligated to covalently linked "recombinant" molecules, and single strands of vegetative DNA do not exceed unit length. Progeny production as well as capacity for covalent linkage in this gene 32 ts mutant are partially restored by additional rII mutations. Suppression by rII depends on functioning host ligase [EC 6.5.1.2; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)]. This gene 32 ts mutation (unlike some others) in turn suppresses the characteristic plaque morphology of rII mutants. We conclude that gene 32 protein, in addition to its role in DNA replication and in the formation of "joint" recombinational intermediates, interacts with T4 ligase [EC 6.5.1.1; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)] when recombining DNA strands are covalently linked. The protein of the mutant that we describe here is mainly defective in this interaction, thus inactivating T4 ligase in recombination. Suppressing rII mutations facilitate substitution of host ligase. There is suggestive evidence that these interactions occur at the membrane.

  19. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  20. Production scheduling with discrete and renewable additional resources

    NASA Astrophysics Data System (ADS)

    Kalinowski, K.; Grabowik, C.; Paprocka, I.; Kempa, W.

    2015-11-01

    In this paper an approach to planning of additional resources when scheduling operations are discussed. The considered resources are assumed to be discrete and renewable. In most research in scheduling domain, the basic and often the only type of regarded resources is a workstation. It can be understood as a machine, a device or even as a separated space on the shop floor. In many cases, during the detailed scheduling of operations the need of using more than one resource, required for its implementation, can be indicated. Resource requirements for an operation may relate to different resources or resources of the same type. Additional resources are most often referred to these human resources, tools or equipment, for which the limited availability in the manufacturing system may have an influence on the execution dates of some operations. In the paper the concept of the division into basic and additional resources and their planning method was shown. A situation in which sets of basic and additional resources are not separable - the same additional resource may be a basic resource for another operation is also considered. Scheduling of operations, including greater amount of resources can cause many difficulties, depending on whether the resource is involved in the entire time of operation, only in the selected part(s) of operation (e.g. as auxiliary staff at setup time) or cyclic - e.g. when an operator supports more than one machine, or supervises the execution of several operations. For this reason the dates and work times of resources participation in the operation can be different. Presented issues are crucial when modelling of production scheduling environment and designing of structures for the purpose of scheduling software development.

  1. Production of sodalite waste forms by addition of glass

    SciTech Connect

    Pereira, C.

    1995-05-01

    Spent nuclear fuel can be treated in a molten salt electrorefiner for conversion into metal and mineral waste forms for geologic disposal. Sodalite is one of the mineral waste forms under study. Fission products in the molten salt are ion-exchanged into zeolite A, which is converted to sodalite and consolidated. Sodalite can be formed directly from mixtures of salt and zeolite A at temperatures above 975 K; however, nepheline is usually produced as a secondary phase. Addition of small amounts of glass frit to the mixture reduced nepheline formation significantly. Loss of fission products was not observed for reaction below 1000 K. Hot-pressing of the sodalite powders yielded dense pellets ({approximately}2.3 g/cm{sup 3}) without any loss of fission product species. Normalized release rates were below 1 g/m{sup 2}{center_dot}day for pre-washed samples in 28-day leach tests based on standard MCC-1 tests but increased with the presence of free salt on the sodalite.

  2. Additive manufacturing. Continuous liquid interface production of 3D objects.

    PubMed

    Tumbleston, John R; Shirvanyants, David; Ermoshkin, Nikita; Janusziewicz, Rima; Johnson, Ashley R; Kelly, David; Chen, Kai; Pinschmidt, Robert; Rolland, Jason P; Ermoshkin, Alexander; Samulski, Edward T; DeSimone, Joseph M

    2015-03-20

    Additive manufacturing processes such as 3D printing use time-consuming, stepwise layer-by-layer approaches to object fabrication. We demonstrate the continuous generation of monolithic polymeric parts up to tens of centimeters in size with feature resolution below 100 micrometers. Continuous liquid interface production is achieved with an oxygen-permeable window below the ultraviolet image projection plane, which creates a "dead zone" (persistent liquid interface) where photopolymerization is inhibited between the window and the polymerizing part. We delineate critical control parameters and show that complex solid parts can be drawn out of the resin at rates of hundreds of millimeters per hour. These print speeds allow parts to be produced in minutes instead of hours.

  3. Human AZU-1 gene, variants thereof and expressed gene products

    DOEpatents

    Chen, Huei-Mei; Bissell, Mina

    2004-06-22

    A human AZU-1 gene, mutants, variants and fragments thereof. Protein products encoded by the AZU-1 gene and homologs encoded by the variants of AZU-1 gene acting as tumor suppressors or markers of malignancy progression and tumorigenicity reversion. Identification, isolation and characterization of AZU-1 and AZU-2 genes localized to a tumor suppressive locus at chromosome 10q26, highly expressed in nonmalignant and premalignant cells derived from a human breast tumor progression model. A recombinant full length protein sequences encoded by the AZU-1 gene and nucleotide sequences of AZU-1 and AZU-2 genes and variant and fragments thereof. Monoclonal or polyclonal antibodies specific to AZU-1, AZU-2 encoded protein and to AZU-1, or AZU-2 encoded protein homologs.

  4. Additive manufacturing techniques for the production of tissue engineering constructs.

    PubMed

    Mota, Carlos; Puppi, Dario; Chiellini, Federica; Chiellini, Emo

    2015-03-01

    'Additive manufacturing' (AM) refers to a class of manufacturing processes based on the building of a solid object from three-dimensional (3D) model data by joining materials, usually layer upon layer. Among the vast array of techniques developed for the production of tissue-engineering (TE) scaffolds, AM techniques are gaining great interest for their suitability in achieving complex shapes and microstructures with a high degree of automation, good accuracy and reproducibility. In addition, the possibility of rapidly producing tissue-engineered constructs meeting patient's specific requirements, in terms of tissue defect size and geometry as well as autologous biological features, makes them a powerful way of enhancing clinical routine procedures. This paper gives an extensive overview of different AM techniques classes (i.e. stereolithography, selective laser sintering, 3D printing, melt-extrusion-based techniques, solution/slurry extrusion-based techniques, and tissue and organ printing) employed for the development of tissue-engineered constructs made of different materials (i.e. polymeric, ceramic and composite, alone or in combination with bioactive agents), by highlighting their principles and technological solutions.

  5. Dose addition predicts the effects of a mixture of five phthalate esters to inhibit fetal testosterone production and gene expression, and postnatal reproductive development in the Sprague Dawley rat

    EPA Science Inventory

    Exposure to some phthalate esters (PE) during sexual differentiation induces reproductive malformations in male and female rats. In the fetal male, these lesions result from phthalate-induced reductions in testicular testosterone (T) production and insulin-like hormone 3 (insl3) ...

  6. Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data.

    PubMed

    Powell, Joseph E; Henders, Anjali K; McRae, Allan F; Kim, Jinhee; Hemani, Gibran; Martin, Nicholas G; Dermitzakis, Emmanouil T; Gibson, Greg; Montgomery, Grant W; Visscher, Peter M

    2013-05-01

    There is increasing evidence that heritable variation in gene expression underlies genetic variation in susceptibility to disease. Therefore, a comprehensive understanding of the similarity between relatives for transcript variation is warranted--in particular, dissection of phenotypic variation into additive and non-additive genetic factors and shared environmental effects. We conducted a gene expression study in blood samples of 862 individuals from 312 nuclear families containing MZ or DZ twin pairs using both pedigree and genotype information. From a pedigree analysis we show that the vast majority of genetic variation across 17,994 probes is additive, although non-additive genetic variation is identified for 960 transcripts. For 180 of the 960 transcripts with non-additive genetic variation, we identify expression quantitative trait loci (eQTL) with dominance effects in a sample of 339 unrelated individuals and replicate 31% of these associations in an independent sample of 139 unrelated individuals. Over-dominance was detected and replicated for a trans association between rs12313805 and ETV6, located 4MB apart on chromosome 12. Surprisingly, only 17 probes exhibit significant levels of common environmental effects, suggesting that environmental and lifestyle factors common to a family do not affect expression variation for most transcripts, at least those measured in blood. Consistent with the genetic architecture of common diseases, gene expression is predominantly additive, but a minority of transcripts display non-additive effects.

  7. Methods of cracking a crude product to produce additional crude products

    DOEpatents

    Mo, Weijian; Roes, Augustinus Wilhelmus Maria; Nair, Vijay

    2009-09-08

    A method for producing a crude product is disclosed. Formation fluid is produced from a subsurface in situ heat treatment process. The formation fluid is separated to produce a liquid stream and a first gas stream. The first gas stream includes olefins. The liquid stream is fractionated to produce one or more crude products. At least one of the crude products has a boiling range distribution from 38.degree. C. and 343.degree. C. as determined by ASTM Method D5307. The crude product having the boiling range distribution from 38.degree. C. and 343.degree. C. is catalytically cracked to produce one or more additional crude products. At least one of the additional crude products is a second gas stream. The second gas stream has a boiling point of at most 38.degree. C. at 0.101 MPa.

  8. Identification of the biosynthetic gene cluster and an additional gene for resistance to the antituberculosis drug capreomycin.

    PubMed

    Felnagle, Elizabeth A; Rondon, Michelle R; Berti, Andrew D; Crosby, Heidi A; Thomas, Michael G

    2007-07-01

    Capreomycin (CMN) belongs to the tuberactinomycin family of nonribosomal peptide antibiotics that are essential components of the drug arsenal for the treatment of multidrug-resistant tuberculosis. Members of this antibiotic family target the ribosomes of sensitive bacteria and disrupt the function of both subunits of the ribosome. Resistance to these antibiotics in Mycobacterium species arises due to mutations in the genes coding for the 16S or 23S rRNA but can also arise due to mutations in a gene coding for an rRNA-modifying enzyme, TlyA. While Mycobacterium species develop resistance due to alterations in the drug target, it has been proposed that the CMN-producing bacterium, Saccharothrix mutabilis subsp. capreolus, uses CMN modification as a mechanism for resistance rather than ribosome modification. To better understand CMN biosynthesis and resistance in S. mutabilis subsp. capreolus, we focused on the identification of the CMN biosynthetic gene cluster in this bacterium. Here, we describe the cloning and sequence analysis of the CMN biosynthetic gene cluster from S. mutabilis subsp. capreolus ATCC 23892. We provide evidence for the heterologous production of CMN in the genetically tractable bacterium Streptomyces lividans 1326. Finally, we present data supporting the existence of an additional CMN resistance gene. Initial work suggests that this resistance gene codes for an rRNA-modifying enzyme that results in the formation of CMN-resistant ribosomes that are also resistant to the aminoglycoside antibiotic kanamycin. Thus, S. mutabilis subsp. capreolus may also use ribosome modification as a mechanism for CMN resistance.

  9. Microstructure-controllable Laser Additive Manufacturing Process for Metal Products

    NASA Astrophysics Data System (ADS)

    Huang, Wei-Chin; Chuang, Chuan-Sheng; Lin, Ching-Chih; Wu, Chih-Hsien; Lin, De-Yau; Liu, Sung-Ho; Tseng, Wen-Peng; Horng, Ji-Bin

    Controlling the cooling rate of alloy during solidification is the most commonly used method for varying the material microstructure. However, the cooling rate of selective laser melting (SLM) production is constrained by the optimal parameter settings for a dense product. This study proposes a method for forming metal products via the SLM process with electromagnetic vibrations. The electromagnetic vibrations change the solidification process for a given set of SLM parameters, allowing the microstructure to be varied via magnetic flux density. This proposed method can be used for creating microstructure-controllable bio-implant products with complex shapes.

  10. Solutol and cremophor products as new additives in suppository formulation.

    PubMed

    Berkó, Szilvia; Regdon, Géza; Erös, István

    2002-01-01

    Our research has a double purpose. On the one hand, doctors have expressed the need to formulate a rectal suppository dosage form from diuretic ethacrynic acid, which would add to the choice of treatment methods and thereby increase the possibilities of individual cure. On the other hand, the liberation and thereby the bioavailability of poorly-soluble ethacrynic acid needs to be enhanced, and for this purpose solubility-increasing additives new to rectal therapy were used. Solutol HS 15, Cremophor RH 40, and Cremophor RH 60 were used as additives in concentrations of 1, 3, 5, and 10%. The quantity of drug released changed as a function of additive concentration. Depending on the acceptor phase, the best results were achieved with an additive concentration of 1-3%, which is related to the optimal additive quantity accumulated on the boundary surface.

  11. Extracellular complementation and the identification of additional genes involved in aerial mycelium formation in Streptomyces coelicolor.

    PubMed

    Nodwell, J R; Yang, M; Kuo, D; Losick, R

    1999-02-01

    Morphogenesis in the bacterium Streptomyces coelicolor involves the formation of a lawn of hair-like aerial hyphae on the colony surface that stands up in the air and differentiates into chains of spores. bld mutants are defective in the formation of this aerial mycelium and grow as smooth, hairless colonies. When certain pairs of bld mutants are grown close to one another on rich sporulation medium, they exhibit extracellular complementation such that one mutant restores aerial mycelium formation to the other. The extracellular complementation relationships of most of the previously isolated bld mutants placed them in a hierarchy of extracellular complementation groups. We have screened for further bld mutants with precautions intended to maximize the discovery of additional genes. Most of the 50 newly isolated mutant strains occupy one of three of the previously described positions in the hierarchy, behaving like bldK, bldC, or bldD mutants. We show that the mutations in some of the strains that behave like bldK are bldK alleles but that others fall in a cluster at a position on the chromosome distinct from that of any known bld gene. We name this locus bldL. By introducing cloned genes into the strains that exhibit bldC or bldD-like extracellular complementation phenotypes, we show that most of these strains are likely to contain mutations in genes other than bldC or bldD. These results indicate that the genetic control of aerial mycelium formation is more complex than previously recognized and support the idea that a high proportion of bld genes are directly or indirectly involved in the production of substances that are exchanged between cells during morphological differentiation.

  12. Extracellular complementation and the identification of additional genes involved in aerial mycelium formation in Streptomyces coelicolor.

    PubMed Central

    Nodwell, J R; Yang, M; Kuo, D; Losick, R

    1999-01-01

    Morphogenesis in the bacterium Streptomyces coelicolor involves the formation of a lawn of hair-like aerial hyphae on the colony surface that stands up in the air and differentiates into chains of spores. bld mutants are defective in the formation of this aerial mycelium and grow as smooth, hairless colonies. When certain pairs of bld mutants are grown close to one another on rich sporulation medium, they exhibit extracellular complementation such that one mutant restores aerial mycelium formation to the other. The extracellular complementation relationships of most of the previously isolated bld mutants placed them in a hierarchy of extracellular complementation groups. We have screened for further bld mutants with precautions intended to maximize the discovery of additional genes. Most of the 50 newly isolated mutant strains occupy one of three of the previously described positions in the hierarchy, behaving like bldK, bldC, or bldD mutants. We show that the mutations in some of the strains that behave like bldK are bldK alleles but that others fall in a cluster at a position on the chromosome distinct from that of any known bld gene. We name this locus bldL. By introducing cloned genes into the strains that exhibit bldC or bldD-like extracellular complementation phenotypes, we show that most of these strains are likely to contain mutations in genes other than bldC or bldD. These results indicate that the genetic control of aerial mycelium formation is more complex than previously recognized and support the idea that a high proportion of bld genes are directly or indirectly involved in the production of substances that are exchanged between cells during morphological differentiation. PMID:9927452

  13. [Immune response genes products in human physiology].

    PubMed

    Khaitov, R M; Alekseev, L P

    2012-09-01

    Current data on physiological role of human immune response genes' proteomic products (antigens) are discussed. The antigens are specified by a very high level of diversity that mediates a wide specter ofphysiological functions. They actually provide integrity and biological stability of human as species. These data reveal new ideas on many pathological processes as well as drafts new approaches for prophylaxis and treatment.

  14. Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II {beta} subunit (CSNK2B)

    SciTech Connect

    Albertella, M.R.; Jones, H.; Thomson, W.

    1996-09-01

    A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the central 1100-kb class III region, making it important to characterize this region fully for the presence of novel genes. An {approximately}220-kb segment of DNA in the class III region separating the Hsp70 (HSPA1L) and BAT1 (D6S8IE) genes, which was previously known to contain 14 genes. Genomic DNA fragments spanning the gaps between the known genes were used as probes to isolate cDNAs corresponding to five new genes within this region. Evidence from Northern blot analysis and exon trapping experiments that suggested the presence of at least two more new genes was also obtained. Partial cDNA and complete exonic genomic sequencing of one of the new genes has identified it as the casein kinase II{beta} subunit (CSNK2B). Two of the other novel genes lie within a region syntenic to that implicated in susceptibility to experimental allergic orchitis in the mouse, an autoimmune disease of the testis, and represent additional candidates for the Orch-1 locus associated with this disease. In addition, characterization of the 13-kb intergenic gap separating the RD (D6545) and G11 (D6S60E) genes has revealed the presence of a gene encoding a 1246-amino-acid polypeptide that shows significant sequence similarity to the yeast anti-viral Ski2p gene product. 49 refs., 8 figs.

  15. 40 CFR 300.920 - Addition of products to Schedule.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... manufacturer of his decision in writing. (b) Surface washing agents, surface collecting agents, bioremediation... collecting agent, bioremediation agent, or miscellaneous oil spill control agent to the NCP Product Schedule... collecting agent, bioremediation agent, or miscellaneous oil spill control agent. On the basis of this...

  16. 40 CFR 300.920 - Addition of products to Schedule.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... manufacturer of his decision in writing. (b) Surface washing agents, surface collecting agents, bioremediation... collecting agent, bioremediation agent, or miscellaneous oil spill control agent to the NCP Product Schedule... collecting agent, bioremediation agent, or miscellaneous oil spill control agent. On the basis of this...

  17. 40 CFR 300.920 - Addition of products to Schedule.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... manufacturer of his decision in writing. (b) Surface washing agents, surface collecting agents, bioremediation... collecting agent, bioremediation agent, or miscellaneous oil spill control agent to the NCP Product Schedule... collecting agent, bioremediation agent, or miscellaneous oil spill control agent. On the basis of this...

  18. 40 CFR 300.920 - Addition of products to Schedule.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... manufacturer of his decision in writing. (b) Surface washing agents, surface collecting agents, bioremediation... collecting agent, bioremediation agent, or miscellaneous oil spill control agent to the NCP Product Schedule... collecting agent, bioremediation agent, or miscellaneous oil spill control agent. On the basis of this...

  19. Additives initiate selective production of chemicals from biomass pyrolysis.

    PubMed

    Leng, Shuai; Wang, Xinde; Wang, Lei; Qiu, Huizhe; Zhuang, Guilin; Zhong, Xing; Wang, Jianguo; Ma, Fengyun; Liu, Jingmei; Wang, Qiang

    2014-03-01

    To improve chemicals selectivity under low temperature, a new method that involves the injection of additives into biomass pyrolysis is introduced. This method allows biomass pyrolysis to achieve high selectivity to chemicals under low temperature (300°C), while nothing was obtained in typical pyrolysis under 300°C. However, by using the new method, the first liquid drop emerged at the interval between 140°C and 240°C. Adding methanol to mushroom scrap pyrolysis obtained high selectivity to acetic acid (98.33%), while adding ethyl acetate gained selectivity to methanol (65.77%) in bagasse pyrolysis and to acetone (72.51%) in corncob pyrolysis. Apart from basic chemicals, one high value-added chemical (2,3-dihydrobenzofuran) was also detected, which obtained the highest selectivity (10.33%) in corncob pyrolysis through the addition of ethyl acetate. Comparison of HZSM-5 and CaCO3 catalysis showed that benzene emerged in the liquid because of the larger degree of cracking and hydrodeoxygenation over HZSM-5.

  20. Use of Galerina marginata genes and proteins for peptide production

    DOEpatents

    Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.; Luo, Hong

    2017-03-21

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptides and cyclic peptide production in mushrooms. In particular, the present invention relates to using genes and proteins from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making small peptides and small cyclic peptides including peptides similar to amanitin. Further, the present inventions relate to providing kits for making small peptides.

  1. Use of Galerina marginata genes and proteins for peptide production

    DOEpatents

    Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.; Luo, Hong

    2016-03-01

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptides and cyclic peptide production in mushrooms. In particular, the present invention relates to using genes and proteins from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making small peptides and small cyclic peptides including peptides similar to amanitin. Further, the present inventions relate to providing kits for making small peptides.

  2. 15 CFR 713.4 - Advance declaration requirements for additionally planned production, processing, or consumption...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 2 CHEMICALS § 713.4 Advance declaration requirements for additionally planned production... additionally planned production, processing, or consumption of Schedule 2 chemicals. 713.4 Section...

  3. 15 CFR 713.4 - Advance declaration requirements for additionally planned production, processing, or consumption...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 2 CHEMICALS § 713.4 Advance declaration requirements for additionally planned production... additionally planned production, processing, or consumption of Schedule 2 chemicals. 713.4 Section...

  4. 15 CFR 713.4 - Advance declaration requirements for additionally planned production, processing, or consumption...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 2 CHEMICALS § 713.4 Advance declaration requirements for additionally planned production... additionally planned production, processing, or consumption of Schedule 2 chemicals. 713.4 Section...

  5. 15 CFR 713.4 - Advance declaration requirements for additionally planned production, processing, or consumption...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 2 CHEMICALS § 713.4 Advance declaration requirements for additionally planned production... additionally planned production, processing, or consumption of Schedule 2 chemicals. 713.4 Section...

  6. Additional duplicated Hox genes in the earthworm: Perionyx excavatus Hox genes consist of eleven paralog groups.

    PubMed

    Cho, Sung-Jin; Vallès, Yvonne; Kim, Kyong Min; Ji, Seong Chul; Han, Seock Jung; Park, Soon Cheol

    2012-02-10

    Annelida is a lophotrochozoan phylum whose members have a high degree of diversity in body plan morphology, reproductive strategies and ecological niches among others. Of the two traditional classes pertaining to the phylum Annelida (Polychaete and Clitellata), the structure and function of the Hox genes has not been clearly defined within the Oligochaeta class. Using a PCR-based survey, we were able to identify five new Hox genes from the earthworm Perionyx excavatus: a Hox3 gene (Pex-Hox3b), two Dfd genes (Pex-Lox6 and Pex-Lox18), and two posterior genes (Pex-post1 and -post2a). Our result suggests that the eleven earthworm Hox genes contain at least four paralog groups (PG) that have duplicated. We found the clitellates-diagnostic signature residues and annelid signature motif. Also, we show by semi-quantitative RT-PCR that duplicated Hox gene orthologs are differentially expressed in six different anterior-posterior body regions. These results provide essential data for comparative evolution of the Hox cluster within the Annelida.

  7. Additive Manufacturing in Production: A Study Case Applying Technical Requirements

    NASA Astrophysics Data System (ADS)

    Ituarte, Iñigo Flores; Coatanea, Eric; Salmi, Mika; Tuomi, Jukka; Partanen, Jouni

    Additive manufacturing (AM) is expanding the manufacturing capabilities. However, quality of AM produced parts is dependent on a number of machine, geometry and process parameters. The variability of these parameters affects the manufacturing drastically and therefore standardized processes and harmonized methodologies need to be developed to characterize the technology for end use applications and enable the technology for manufacturing. This research proposes a composite methodology integrating Taguchi Design of Experiments, multi-objective optimization and statistical process control, to optimize the manufacturing process and fulfil multiple requirements imposed to an arbitrary geometry. The proposed methodology aims to characterize AM technology depending upon manufacturing process variables as well as to perform a comparative assessment of three AM technologies (Selective Laser Sintering, Laser Stereolithography and Polyjet). Results indicate that only one machine, laser-based Stereolithography, was feasible to fulfil simultaneously macro and micro level geometrical requirements but mechanical properties were not at required level. Future research will study a single AM system at the time to characterize AM machine technical capabilities and stimulate pre-normative initiatives of the technology for end use applications.

  8. 75 FR 33824 - Pharmaceutical Products and Chemical Intermediates, Fourth Review: Advice Concerning the Addition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-15

    ... COMMISSION Pharmaceutical Products and Chemical Intermediates, Fourth Review: Advice Concerning the Addition of Certain Products to the Pharmaceutical Appendix to the HTS AGENCY: United States International... (Commission) instituted investigation No. 332-520, Pharmaceutical Products and Chemical Intermediates,...

  9. Inverse gene-for-gene interactions contribute additively to tan spot susceptibility in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the world. The disease system is known to involve at least three fungal-produced necrotrophic effectors (NEs) that interact with corresponding host sensitivity (S) genes in an inv...

  10. Random transposon mutagenesis of the Saccharopolyspora erythraea genome reveals additional genes influencing erythromycin biosynthesis

    PubMed Central

    Fedashchin, Andrij; Cernota, William H.; Gonzalez, Melissa C.; Leach, Benjamin I.; Kwan, Noelle; Wesley, Roy K.; Weber, J. Mark

    2015-01-01

    A single cycle of strain improvement was performed in Saccharopolyspora erythraea mutB and 15 genotypes influencing erythromycin production were found. Genotypes generated by transposon mutagenesis appeared in the screen at a frequency of ∼3%. Mutations affecting central metabolism and regulatory genes were found, as well as hydrolases, peptidases, glycosyl transferases and unknown genes. Only one mutant retained high erythromycin production when scaled-up from micro-agar plug fermentations to shake flasks. This mutant had a knockout of the cwh1 gene (SACE_1598), encoding a cell-wall-associated hydrolase. The cwh1 knockout produced visible growth and morphological defects on solid medium. This study demonstrated that random transposon mutagenesis uncovers strain improvement-related genes potentially useful for strain engineering. PMID:26468041

  11. Deduced products of C4-dicarboxylate transport regulatory genes of Rhizobium leguminosarum are homologous to nitrogen regulatory gene products.

    PubMed Central

    Ronson, C W; Astwood, P M; Nixon, B T; Ausubel, F M

    1987-01-01

    We have sequenced two genes dctB and dctD required for the activation of the C4-dicarboxylate transport structural gene dctA in free-living Rhizobium leguminosarum. The hydropathic profile of the dctB gene product (DctB) suggested that its N-terminal region may be located in the periplasm and its C-terminal region in the cytoplasm. The C-terminal region of DctB was strongly conserved with similar regions of the products of several regulatory genes that may act as environmental sensors, including ntrB, envZ, virA, phoR, cpxA, and phoM. The N-terminal domains of the products of several regulatory genes thought to be transcriptional activators, including ntrC, ompR, virG, phoB and sfrA. In addition, the central and C-terminal regions of DctD were strongly conserved with the products of ntrC and nifA, transcriptional activators that require the alternate sigma factor rpoN (ntrA) as co-activator. The central region of DctD also contained a potential ATP-binding domain. These results are consistent with recent results that show that rpoN product is required for dctA activation, and suggest that DctB plus DctD-mediated transcriptional activation of dctA may be mechanistically similar to NtrB plus NtrC-mediated activation of glnA in E. coli. PMID:3671068

  12. Toxicological safety assessment of genetically modified Bacillus thuringiensis with additional N-acyl homoserine lactonase gene.

    PubMed

    Peng, Donghai; Zhou, Chenfei; Chen, Shouwen; Ruan, Lifang; Yu, Ziniu; Sun, Ming

    2008-01-01

    The aim of the present study is to evaluate the toxicology safety to mammals of a genetically modified (GM) Bacillus thuringiensis with an additional N-acyl homoserine lactones gene (aiiA), which possesses insecticidal activity together with restraint of bacterial pathogenicity and is intended for use as a multifunctional biopesticide. Safety assessments included an acute oral toxicity test and 28-d animal feeding study in Wistar rats, primary eye and dermal irritation in Zealand White rabbits, and delayed contact hypersensitivity in guinea pigs. Tests were conducted using spray-dried powder preparation. This GM product showed toxicity neither in oral acute toxicity test nor in 28-d animal feeding test at a dose of 5,000 mg/kg body weight. During the animal feeding test, there were no significant differences in growth, food and water consumption, hematology, blood biochemical indices, organ weights, and histopathology finding between rats in controls and tested groups. Tested animals in primary eye and dermal irritation and delayed contact hypersensitivity test were also devoid of any toxicity compared to controls. All the above results demonstrated that the GM based multifunctional B. thuringiensis has low toxicity and low eye and dermal irritation and would not cause hypersensitivity to laboratory mammals and therefore could be regarded as safe for use as a pesticide.

  13. Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products

    SciTech Connect

    Kuchka, M.R.

    1992-01-01

    The following is a review of research accomplished in the first two years of funding for the above mentioned project. The work performed is a molecular characterization of nuclear mutants of Chlamydomonas reinhardtii which are deficient in different stages in the post-transcriptional expression of a single chloroplast encoded polypeptide, the D2 protein of Photosystem II. Our long-term goals are to understand the molecular mechanisms by which nuclear gene products affect the expression of chloroplast genes. Specifically, we which to understand how specific nuclear gene products affect the turnover rate of the D2 encoding mRNA (psbD), how other nuclear encoded factors work to promote the translation of psbD mRNA and/or stabilize the D2 protein, and what the role of the D2 protein itself is in Photosystem II assembly and in the control of expression of other chloroplast genes. This progress report will be organized into four major sections concerning (I) The characterization of nuclear mutants affected in D2 translation/turnover, (II) The study of trans-acting factors which associate with the 5{prime} end of the psbD mRNA, (III) In vitro mutagenesis of the psbD gene, and (IV) Additional studies.

  14. Polymorphisms of Saccharomyces cerevisiae genes involved in wine production.

    PubMed

    Vigentini, Ileana; Fracassetti, Daniela; Picozzi, Claudia; Foschino, Roberto

    2009-03-01

    The setting up of new molecular methods for Saccharomyces cerevisiae typing is valuable in enology. Actually, the ability to discriminate different strains in wine making can have a benefit both for the control of the fermentation process and for the preservation of wine typicity. This study focused on the screening of single-nucleotide polymorphisms in genes involved in wine production that could evolve rapidly considering the selective pressure of the isolation environment. Preliminary screening of 30 genes in silico was performed, followed by the selection of 10 loci belonging to 8 genes. The sequence analysis showed a low polymorphism and a degree of heterozygosity. However, a new potential molecular target was recognized in the TPS1 gene coding for the trehalose-6-phosphate synthase enzyme involved in the ethanol resistance mechanism. This gene showed a 1.42% sequence diversity with seven different nucleotide substitutions. Moreover, classic techniques were applied to a collection of 50 S. cerevisiae isolates, mostly with enologic origin. Our results confirmed that the wine making was not carried out only by the inoculated commercial starter because indigenous strains of S. cerevisiae present during fermentation were detected. In addition, a high genetic relationship among some commercial cultures was found, highlighting imprecision or fraudulent practices by starter manufacturers.

  15. Regulation of photoreceptor gene transcription via a highly conserved transcriptional regulatory element by vsx gene products

    PubMed Central

    Pan, Yi; Comiskey, Daniel F.; Kelly, Lisa E.; Chandler, Dawn S.

    2016-01-01

    Purpose The photoreceptor conserved element-1 (PCE-1) sequence is found in the transcriptional regulatory regions of many genes expressed in photoreceptors. The retinal homeobox (Rx or Rax) gene product functions by binding to PCE-1 sites. However, other transcriptional regulators have also been reported to bind to PCE-1. One of these, vsx2, is expressed in retinal progenitor and bipolar cells. The purpose of this study is to identify Xenopus laevis vsx gene products and characterize vsx gene product expression and function with respect to the PCE-1 site. Methods X. laevis vsx gene products were amplified with PCR. Expression patterns were determined with in situ hybridization using whole or sectioned X. laevis embryos and digoxigenin- or fluorescein-labeled antisense riboprobes. DNA binding characteristics of the vsx gene products were analyzed with electrophoretic mobility shift assays (EMSAs) using in vitro translated proteins and radiolabeled oligonucleotide probes. Gene transactivation assays were performed using luciferase-based reporters and in vitro transcribed effector gene products, injected into X. laevis embryos. Results We identified one vsx1 and two vsx2 gene products. The two vsx2 gene products are generated by alternate mRNA splicing. We verified that these gene products are expressed in the developing retina and that expression resolves into distinct cell types in the mature retina. Finally, we found that vsx gene products can bind the PCE-1 site in vitro and that the two vsx2 isoforms have different gene transactivation activities. Conclusions vsx gene products are expressed in the developing and mature neural retina. vsx gene products can bind the PCE-1 site in vitro and influence the expression of a rhodopsin promoter-luciferase reporter gene. The two isoforms of vsx have different gene transactivation activities in this reporter gene system. PMID:28003732

  16. Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation.

    PubMed

    Bemer, Marian; van Dijk, Aalt D J; Immink, Richard G H; Angenent, Gerco C

    2017-01-01

    Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein-protein interactions between members of a particular plant TF family has long been recognised; however, a significant number of interfamily TF interactions has recently been reported. The biological implications and the molecular mechanisms involved in cross-family interactions have now started to be elucidated and the examples illustrate potential roles in the bridging of biological processes. Hence, cross-family TF interactions expand the molecular toolbox for plants with additional mechanisms to control and fine-tune robust gene expression patterns and to adapt to their continuously changing environment.

  17. Orsomucoid: A new variant and additional duplicated ORM1 gene in Qatari population

    SciTech Connect

    Sebetan, I.M.; Alali, K.A.; Alzaman, A.

    1994-09-01

    A new genetically determined ORM2 variant and additional duplicated ORM1 gene were observed in Qatari population using isoelectric focusing in ultra thin layer polyacrylamide gels. The studied population samples indicate occurence of six ORM1 alleles and three ORM2 ones. A simple reliable method for separation of orsomucoid variations with comparison of different reported methods will be presented.

  18. Antagonistic control of a dual-input mammalian gene switch by food additives

    PubMed Central

    Xie, Mingqi; Ye, Haifeng; Hamri, Ghislaine Charpin-El; Fussenegger, Martin

    2014-01-01

    Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies. PMID:25030908

  19. Antagonistic control of a dual-input mammalian gene switch by food additives.

    PubMed

    Xie, Mingqi; Ye, Haifeng; Hamri, Ghislaine Charpin-El; Fussenegger, Martin

    2014-08-01

    Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies.

  20. 75 FR 55776 - Request for Comments on Vaccine Production and Additional Planning for Future Possible Pandemic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-14

    ... International Trade Administration Request for Comments on Vaccine Production and Additional Planning for Future... comments from the public and relevant industries on vaccine production and additional planning for future... such. ADDRESSES: You may submit comments by any of the following methods: E-mail:...

  1. 15 CFR 714.3 - Advance declaration requirements for additionally planned production of Schedule 3 chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... additionally planned production of Schedule 3 chemicals. 714.3 Section 714.3 Commerce and Foreign Trade... COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 3 CHEMICALS § 714.3 Advance declaration requirements for additionally planned production of Schedule 3 chemicals. (a)...

  2. Reaction products of amido-amine and epoxide useful as fuel additives

    SciTech Connect

    Efner, H.F.

    1988-04-12

    A method for reducing engine deposits in an internal combustion engine is described comprising the addition of a detergent fuel additive package to a hydrocarbon fuel for the engine. The fuel detergent is added in an amount effective to reduce deposits and the hydrocarbon fuel is used with detergent additive as fuel in an internal combustion engine. The detergent fuel additive package comprises: (1) a fuel detergent additive that is the reaction product prepared by reacting (a) vegetable oil or (b) higher carboxylic acid chosen from (i) aliphatic fatty acids having 10-25 carbon atoms and (ii) aralkyl acids having 12-42 carbon atoms with (c) multiamine to obtain a fist product mixture with the first product mixture reacted with alklylene oxide to produce a second product mixture and (2) a fuel detergent additive solvent compatible with the fuels.

  3. Effect of Periodic Water Addition on Citric Acid Production in Solid State Fermentation

    NASA Astrophysics Data System (ADS)

    Utpat, Shraddha S.; Kinnige, Pallavi T.; Dhamole, Pradip B.

    2013-09-01

    Water addition is one of the methods used to control the moisture loss in solid state fermentation (SSF). However, none of the studies report the timing of water addition and amount of water to be added in SSF. Therefore, this work was undertaken with an objective to evaluate the performance of periodic water addition on citric acid production in SSF. Experiments were conducted at different moistures (50-80 %) and temperatures (30-40 °C) to simulate the conditions in a fermenter. Citric acid production by Aspergillus niger (ATCC 9029) using sugarcane baggase was chosen as a model system. Based on the moisture profile, citric acid and sugar data, a strategy was designed for periodic addition of water. Water addition at 48, 96, 144 and 192 h enhanced the citric acid production by 62 % whereas water addition at 72, 120, and 168 h increased the citric acid production by just 17 %.

  4. Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis.

    PubMed

    Guo, Mei; Rupe, Mary A; Yang, Xiaofeng; Crasta, Oswald; Zinselmeier, Christopher; Smith, Oscar S; Bowen, Ben

    2006-09-01

    Heterosis, or hybrid vigor, has been widely exploited in plant breeding for many decades, but the molecular mechanisms underlying the phenomenon remain unknown. In this study, we applied genome-wide transcript profiling to gain a global picture of the ways in which a large proportion of genes are expressed in the immature ear tissues of a series of 16 maize hybrids that vary in their degree of heterosis. Key observations include: (1) the proportion of allelic additively expressed genes is positively associated with hybrid yield and heterosis; (2) the proportion of genes that exhibit a bias towards the expression level of the paternal parent is negatively correlated with hybrid yield and heterosis; and (3) there is no correlation between the over- or under-expression of specific genes in maize hybrids with either yield or heterosis. The relationship of the expression patterns with hybrid performance is substantiated by analysis of a genetically improved modern hybrid (Pioneer hybrid 3394) versus a less improved older hybrid (Pioneer hybrid 3306) grown at different levels of plant density stress. The proportion of allelic additively expressed genes is positively associated with the modern high yielding hybrid, heterosis and high yielding environments, whereas the converse is true for the paternally biased gene expression. The dynamic changes of gene expression in hybrids responding to genotype and environment may result from differential regulation of the two parental alleles. Our findings suggest that differential allele regulation may play an important role in hybrid yield or heterosis, and provide a new insight to the molecular understanding of the underlying mechanisms of heterosis.

  5. Identification of the neurofibromatosis type 1 gene product

    SciTech Connect

    Gutmann, D.H.; Wood, D.L.; Collins, F.S. )

    1991-11-01

    The gene for neurofibromatosis type 1 (NF1) was recently identified by positional cloning. The complete cDNA encodes a polypeptide of 2818 amino acids. To study the NF1 gene product, antibodies were raised against both fusion proteins and synthetic peptides. Initial characterization of two anti-peptide antibodies and one fusion-protein antibody demonstrated a specific protein of {approx}250 kDa by both immunoprecipitation and immunoblotting. This protein was found in all tissues and cell lines examined and is detected in human, rat, and mouse tissues. To demonstrate that these antibodies specifically recognize the NF1 protein, additional fusion proteins containing the sequence specific to the synthetic peptide were generated. Both peptide antisera recognize the proper specific fusion proteins so generated. Immunoprecipitates using the peptide antisera were shown to recognize the same protein detected by immunoblotting with either the other peptide antiserum or the fusion-protein antiserum. Immunoblotting using antiserum specific to spatially distinct epitopes conducted on tissue homogenates demonstrated the NF1 protein in all adult tissues. Based on the homology between the NF1 gene product and members of the GTPase-activating protein (GAP) superfamily, the name NF1-GAP-related protein (NF1GRP) is suggested.

  6. Effect of urea addition on giant reed ensilage and subsequent methane production by anaerobic digestion.

    PubMed

    Liu, Shan; Ge, Xumeng; Liew, Lo Niee; Liu, Zhe; Li, Yebo

    2015-09-01

    The effect of urea addition on giant reed ensilage and sequential anaerobic digestion (AD) of the ensiled giant reed was evaluated. The dry matter loss during ensilage (up to 90 days) with or without urea addition was about 1%. Addition of 2% urea enhanced production of lactic acid by about 4 times, and reduced production of propionic acid by 2-8 times. Besides, urea addition reduced degradation of cellulose and hemicellulose, and increased degradation of lignin in giant reed during ensilage. Ensilage with or without urea addition had no significant effects on the enzymatic digestibility of giant reed, but ensilage with urea addition achieved a cumulative methane yield of 173 L/kg VS, which was 18% higher than that of fresh giant reed. The improved methane yield of giant reed could be attributed to the production of organic acids and ethanol during ensilage.

  7. Alphavirus vectors: applications for DNA vaccine production and gene expression.

    PubMed

    Lundstrom, K

    2000-01-01

    Replication-deficient alphavirus vectors have been developed for efficient high-level transgene expression. The broad host range of alphaviruses has allowed infection of a wide variety of mammalian cell lines and primary cultures. Particularly, G protein-coupled receptors have been expressed at high levels and subjected to binding and functional studies. Expression in suspension cultures has greatly facilitated production of large quantities of recombinant proteins for structural studies. Injection of recombinant alphavirus vectors into rodent brain resulted in local reporter gene expression. Highly neuron-specific expression was obtained in hippocampal slice cultures in vivo. Additionally, preliminary studies in animal models suggest that alphavirus vectors can be attractive candidates for gene therapy applications. Traditionally alphavirus vectors, either attenuated strains or replication-deficient particles, have been used to elicit efficient immune responses in animals. Recently, the application of alphaviruses has been extended to naked nucleic acids. Injection of DNA as well as RNA vectors has demonstrated efficient antigen production. In many cases, protection against lethal challenges has been obtained after immunization with alphavirus particles or nucleic acid vectors. Alphavirus vectors can therefore be considered as potentially promising vectors for vaccine production.

  8. Determination of seven certified color additives in food products using liquid chromatography.

    PubMed

    Harp, Bhakti Petigara; Miranda-Bermudez, Enio; Barrows, Julie N

    2013-04-17

    This study describes a new method for determining FD&C Blue No. 1, FD&C Blue No. 2, FD&C Green No. 3, FD&C Red No. 3, FD&C Red No. 40, FD&C Yellow No. 5, and FD&C Yellow No. 6 in food products. These seven color additives are water-soluble dyes that are required to be batch certified by the U.S. Food and Drug Administration (FDA) before they may be used in food and other FDA-regulated products. In the new method, the color additives are extracted from a product using one of two procedures developed for various product types, isolated from the noncolored components, and analyzed by liquid chromatography with photodiode array detection. The method was validated by determining linearity, range, precision, recovery from various matrices, limit of detection, limit of quantitation, and relative standard deviation for each color additive. A survey of 44 food products, including beverages, frozen treats, powder mixes, gelatin products, candies, icings, jellies, spices, dressings, sauces, baked goods, and dairy products, found total color additives ranging from 1.9 to 1221 mg/kg. FDA intends to use the new method for conducting a rigorous, comprehensive dietary exposure assessment of certified color additives in products likely to be consumed by children.

  9. Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.

    PubMed

    Kulyté, Agné; Belarbi, Yasmina; Lorente-Cebrián, Silvia; Bambace, Clara; Arner, Erik; Daub, Carsten O; Hedén, Per; Rydén, Mikael; Mejhert, Niklas; Arner, Peter

    2014-04-01

    Adipose tissue inflammation is present in insulin-resistant conditions. We recently proposed a network of microRNAs (miRNAs) and transcription factors (TFs) regulating the production of the proinflammatory chemokine (C-C motif) ligand-2 (CCL2) in adipose tissue. We presently extended and further validated this network and investigated if the circuits controlling CCL2 can interact in human adipocytes and macrophages. The updated subnetwork predicted that miR-126/-193b/-92a control CCL2 production by several TFs, including v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) (ETS1), MYC-associated factor X (MAX), and specificity protein 12 (SP1). This was confirmed in human adipocytes by the observation that gene silencing of ETS1, MAX, or SP1 attenuated CCL2 production. Combined gene silencing of ETS1 and MAX resulted in an additive reduction in CCL2 production. Moreover, overexpression of miR-126/-193b/-92a in different pairwise combinations reduced CCL2 secretion more efficiently than either miRNA alone. However, although effects on CCL2 secretion by co-overexpression of miR-92a/-193b and miR-92a/-126 were additive in adipocytes, the combination of miR-126/-193b was primarily additive in macrophages. Signals for miR-92a and -193b converged on the nuclear factor-κB pathway. In conclusion, TF and miRNA-mediated regulation of CCL2 production is additive and partly relayed by cell-specific networks in human adipose tissue that may be important for the development of insulin resistance/type 2 diabetes.

  10. Flue gas desulfurization by-products additions to acid soil: alfalfa productivity and environmental quality.

    PubMed

    Chen, L; Dick, W A; Nelson, S

    2001-01-01

    Flue gas desulfurization (FGD) by-products are created when coal is burned and SO2 is removed from the flue gases. These FGD by-products are often alkaline and contain many plant nutrients. Land application of FGD by-products is encouraged but little information is available related to plant responses and environmental impacts concerning such use. Agricultural lime (ag-lime) and several new types of FGD by-products which contain either vermiculite or perlite were applied at 0, 0.5, 1.0, and 2.0 times the soil's lime requirement (LR) rate to an acidic soil (Wooster silt loam). The highest FGD by-products application rate was equivalent to 75.2 Mg ha(-1). Growth of alfalfa (Medicago sativa L.) was significantly increased compared to the untreated control in the second year after treatment with yields for the 1 x LR rate of FGD approximately 7-8 times greater compared to the untreated control and 30% greater than for the commercial ag-lime. Concentrations of Mo in alfalfa were significantly increased by FGD by-products application, compared to the untreated control, while compared to the ag-lime treatment, concentrations of B increased and Ba decreased. No soil contamination problems were observed, even at the 2xLR rate, indicating these materials can be safely applied to agricultural soils.

  11. The effects of flue gas desulfurization (FGD) system additives on solid by-products. Final report

    SciTech Connect

    Huyck, K.A.; Tatum, G.S.; DeKraker, D.P.

    1995-12-01

    This study was designed to examine characteristics of by-products from flue gas desulfurization (FGD) systems that use performance-enhancing additives. The by-products were evaluated for handling, disposal, properties, and utilization potential. This study was designed to identify potential operation-limiting consequences (fatal flaws) caused by using FGD system additives. It was not intended to be an all-encompassing study of the possible process, environmental, and utilization circumstances at each plant. Seven utilities conducting additive testing agreed to provide samples for this study both before and during their testing. Solid samples were collected from FGD systems using the following additives: di-basic acid (DBA), which is a mixture of succinic, glutaric, and adipic acids; formate; sulfur; ethylene diamine tetraacetic acid (EDTA); and chloride. Changes in handling properties that may alter process operations were observed at sites where DBS was used. Changes in leaching behavior, permeability and unconfined compressive strength (properties that affect by-product disposal properties) showed no clear trend for additive or system type. The intent of this study is to provide an overall assessment of potential system-limiting effects of FGD additive use. There were no overriding problems relating to disposal with the use of additives. However, properties of solids produced with and without additives should be tested at each site prior to use of an FGD system additive. This is necessary because of the variability in state disposal and permitting requirements and the influence of specific operating conditions on by-product properties.

  12. An Inventory of Methods for the Assessment of Additive Increased Addictiveness of Tobacco Products

    PubMed Central

    van de Nobelen, Suzanne; Kienhuis, Anne S.

    2016-01-01

    Background: Cigarettes and other forms of tobacco contain the addictive drug nicotine. Other components, either naturally occurring in tobacco or additives that are intentionally added during the manufacturing process, may add to the addictiveness of tobacco products. As such, these components can make cigarette smokers more easily and heavily dependent. Efforts to regulate tobacco product dependence are emerging globally. Additives that increase tobacco dependence will be prohibited under the new European Tobacco Product Directive. Objective: This article provides guidelines and recommendations for developing a regulatory strategy for assessment of increase in tobacco dependence due to additives. Relevant scientific literature is summarized and criteria and experimental studies that can define increased dependence of tobacco products are described. Conclusions: Natural tobacco smoke is a very complex matrix of components, therefore analysis of the contribution of an additive or a combination of additives to the level of dependence on this product is challenging. We propose to combine different type of studies analyzing overall tobacco product dependence potential and the functioning of additives in relation to nicotine. By using a combination of techniques, changes associated with nicotine dependence such as behavioral, physiological, and neurochemical alterations can be examined to provide sufficient information. Research needs and knowledge gaps will be discussed and recommendations will be made to translate current knowledge into legislation. As such, this article aids in implementation of the Tobacco Product Directive, as well as help enable regulators and researchers worldwide to develop standards to reduce dependence on tobacco products. Implications: This article provides an overall view on how to assess tobacco product constituents for their potential contribution to use and dependence. It provides guidelines that help enable regulators worldwide to

  13. 39 CFR 3055.6 - Addition of new market dominant products or changes to existing market dominant products.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 39 Postal Service 1 2011-07-01 2011-07-01 false Addition of new market dominant products or changes to existing market dominant products. 3055.6 Section 3055.6 Postal Service POSTAL REGULATORY COMMISSION PERSONNEL SERVICE PERFORMANCE AND CUSTOMER SATISFACTION REPORTING Annual Reporting of...

  14. Use of phytogenic products as feed additives for swine and poultry.

    PubMed

    Windisch, W; Schedle, K; Plitzner, C; Kroismayr, A

    2008-04-01

    This article summarizes the experimental knowledge on efficacy, possible modes of action, and aspects of application of phytogenic products as feed additives for swine and poultry. Phytogenic feed additives comprise a wide variety of herbs, spices, and products derived thereof, and are mainly essential oils. The assumption that phytogenic compounds might improve the palatability of feed has not yet been confirmed by choice-feeding studies. Although numerous studies have demonstrated antioxidative and antimicrobial efficacy in vitro, respective experimental in vivo evidence is still quite limited. The same applies to the supposition that phytogenic compounds may specifically enhance activities of digestive enzymes and nutrient absorption. Nevertheless, a limited number of experimental comparisons of phytogenic feed additives with antibiotics and organic acids have suggested similar effects on the gut, such as reduced bacterial colony counts, fewer fermentation products (including ammonia and biogenic amines), less activity of the gut-associated lymphatic system, and a greater prececal nutrient digestion, probably reflecting an overall improved gut equilibrium. In addition, some phytogenic compounds seem to promote intestinal mucus production. Such effects may explain a considerable number of practical studies with swine and poultry reporting improved production performance after providing phytogenic feed additives. In total, available evidence indicates that phytogenic feed additives may add to the set of nonantibiotic growth promoters for use in livestock, such as organic acids and probiotics. However, a systematic approach toward the efficacy and safety of phytogenic compounds used as feed additives for swine and poultry is still missing.

  15. A test strategy for the assessment of additive attributed toxicity of tobacco products.

    PubMed

    Kienhuis, Anne S; Staal, Yvonne C M; Soeteman-Hernández, Lya G; van de Nobelen, Suzanne; Talhout, Reinskje

    2016-08-01

    The new EU Tobacco Product Directive (TPD) prohibits tobacco products containing additives that are toxic in unburnt form or that increase overall toxicity of the product. This paper proposes a strategy to assess additive attributed toxicity in the context of the TPD. Literature was searched on toxicity testing strategies for regulatory purposes from tobacco industry and governmental institutes. Although mainly traditional in vivo testing strategies have been applied to assess toxicity of unburnt additives and increases in overall toxicity of tobacco products due to additives, in vitro tests combined with toxicogenomics and validated using biomarkers of exposure and disease are most promising in this respect. As such, tests are needed that are sensitive enough to assess additive attributed toxicity above the overall toxicity of tobacco products, which can associate assay outcomes to human risk and exposure. In conclusion, new, sensitive in vitro assays are needed to conclude whether comparable testing allows for assessment of small changes in overall toxicity attributed to additives. A more pragmatic approach for implementation on a short-term is mandated lowering of toxic emission components. Combined with risk assessment, this approach allows assessment of effectiveness of harm reduction strategies, including banning or reducing of additives.

  16. Fc-receptor and M-protein genes of group A streptococci are products of gene duplication.

    PubMed Central

    Heath, D G; Cleary, P P

    1989-01-01

    The partial nucleotide sequence for an Fc-receptor gene from an M-type 76 group A streptococcus was determined. DNA sequence analysis revealed considerable sequence similarity between the Fc-receptor and M-protein genes in their proposed promoter regions, signal sequences, and 3' termini. Additional analysis indicated that the deduced Fc-receptor protein contains a proline-rich region and membrane anchor region highly similar to that of M protein. In view of these results, we postulated that Fc-receptor and M-protein genes of group A streptococci are the products of gene duplication from a common ancestral gene. It is proposed that DNA sequence similarity between these two genes may allow for extragenic homologous recombination as a means of generating antigenic diversity in these two surface proteins. PMID:2660147

  17. Fine Mapping of Two Additive Effect Genes for Awn Development in Rice (Oryza sativa L.)

    PubMed Central

    Li, Jinjie; Yao, Guoxin; Pan, Huiqiao; Hu, Guanglong; Chen, Chao; Zhang, Hongliang; Li, Zichao

    2016-01-01

    Awns, important domestication and agronomic traits in rice (Oryza sativa L.), are conferred by polygenes and the environment. Near isogenic line (NIL) pairs BM33 and BM38 were constructed from crosses between awnless japonica cv Nipponbare as recurrent parent, and lines SLG or Funingxiaohongmang (awned japonica accessions), respectively, as donors. In order to study the genetic and molecular mechanism of awning, two unknown, independent genes with additive effects were identified in a cross between the NILs. To map and clone the two genes, a BC4F4 population of 8,103 individuals and a BC4F6 population of 11,206 individuals were constructed. Awn3-1 was fine mapped to a 101.13 kb genomic region between Indel marker In316 and SNP marker S9-1 on chromosome 3. Nine predicted genes in the interval were annotated in the Rice Annotation Project Database (RAP-DB), and Os03g0418600 was identified as the most likely candidate for Awn3-1 through sequence comparisons and RT-PCR assays. Awn4-2 was fine mapped to a 62.4 kb genomic region flanked by simple sequence repeat (SSR) marker M1126 and Indel maker In73 on chromosome 4L. This region contained the previously reported gene An-1 that regulates awn development. Thus, An-1 may be the candidate gene of Awn4-2. These results will facilitate cloning of the awn genes and thereby provide an understanding of the molecular basis of awn development. PMID:27494628

  18. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases

    PubMed Central

    Moehle, Erica A.; Rock, Jeremy M.; Lee, Ya-Li; Jouvenot, Yann; DeKelver, Russell C.; Gregory, Philip D.; Urnov, Fyodor D.; Holmes, Michael C.

    2007-01-01

    Efficient incorporation of novel DNA sequences into a specific site in the genome of living human cells remains a challenge despite its potential utility to genetic medicine, biotechnology, and basic research. We find that a precisely placed double-strand break induced by engineered zinc finger nucleases (ZFNs) can stimulate integration of long DNA stretches into a predetermined genomic location, resulting in high-efficiency site-specific gene addition. Using an extrachromosomal DNA donor carrying a 12-bp tag, a 900-bp ORF, or a 1.5-kb promoter-transcription unit flanked by locus-specific homology arms, we find targeted integration frequencies of 15%, 6%, and 5%, respectively, within 72 h of treatment, and with no selection for the desired event. Importantly, we find that the integration event occurs in a homology-directed manner and leads to the accurate reconstruction of the donor-specified genotype at the endogenous chromosomal locus, and hence presumably results from synthesis-dependent strand annealing repair of the break using the donor DNA as a template. This site-specific gene addition occurs with no measurable increase in the rate of random integration. Remarkably, we also find that ZFNs can drive the addition of an 8-kb sequence carrying three distinct promoter-transcription units into an endogenous locus at a frequency of 6%, also in the absence of any selection. These data reveal the surprising versatility of the specialized polymerase machinery involved in double-strand break repair, illuminate a powerful approach to mammalian cell engineering, and open the possibility of ZFN-driven gene addition therapy for human genetic disease. PMID:17360608

  19. Additive effects of serotonin transporter and tryptophan hydroxylase-2 gene variation on emotional processing.

    PubMed

    Herrmann, Martin J; Huter, Theresa; Müller, Frauke; Mühlberger, Andreas; Pauli, Paul; Reif, Andreas; Renner, Tobias; Canli, Turhan; Fallgatter, Andreas J; Lesch, Klaus-Peter

    2007-05-01

    Prior studies reported that functional variants of both the serotonin transporter (5-HTT) and tryptophan hydroxylase-2 genes (TPH2), 2 key regulators of the serotonergic signaling pathway, modulate amygdala activation during emotional processing. We addressed the question whether these 2 gene variants modulate each other, using an emotional picture-processing task. Specifically, we measured event-related potentials (ERPs) during a passive emotional picture perception task, focusing on ERPs for the early posterior negativity (EPN) around 240 ms and for the slow wave starting at 315 ms. We found evidence for increased neural activity at 240 ms in individuals who carried 1 or 2 copies of the low-expression short variant of the 5-HTT. Carriers of T variant of the TPH2 also showed a tendency toward increased neural activity at 240 ms. Moreover, we observed an additive effect of both genotypes for EPN, with highest neural activity to emotional stimuli in individuals carrying combination of both short variant of 5-HTT and T variant of TPH2. Our results indicate that both the 5-HTT and the TPH2 genotypes modulate the sensory encoding of affective stimuli during early steps of visual processing and reveal additive effects of 2 genes in the serotonergic control of emotion regulation.

  20. An additional Meyerozyma guilliermondii IMH3 gene confers mycophenolic acid resistance in fungal CTG clade species.

    PubMed

    Defosse, Tatiana A; Mélin, Céline; Clastre, Marc; Besseau, Sébastien; Lanoue, Arnaud; Glévarec, Gaëlle; Oudin, Audrey; Dugé de Bernonville, Thomas; Vandeputte, Patrick; Linder, Tomas; Bouchara, Jean-Philippe; Courdavault, Vincent; Giglioli-Guivarc'h, Nathalie; Papon, Nicolas

    2016-09-01

    The fungal CTG clade comprises a number of well-known yeasts that impact human health or with high biotechnological potential. To further extend the set of molecular tools dedicated to these microorganisms, the initial focus of this study was to develop a mycophenolic acid (MPA) resistance cassette. Surprisingly, while we were carrying out preliminary susceptibility testing experiments in a set of yeast species, Meyerozyma guilliermondii, although not being a MPA producer, was found to be primarily resistant toward this drug, whereas a series of nine related species were susceptible to MPA. Using comparative and functional genomic approaches, we demonstrated that all MPA-susceptible CTG clade species display a single gene, referred to as IMH3.1, encoding the MPA target inosine monophosphate dehydrogenase (IMPDH) and that MPA resistance relies on the presence in the M. guilliermondii genome of an additional IMPDH-encoding gene (IMH3.2). The M. guilliermondii IMH3.2 gene displays marked differences compared to IMH3.1 including the lack of intron, a roughly 160-fold higher transcription level and a serine residue at position 251. Placed under the control of the M. guilliermondii actin 1 gene promoter, IMH3.2 was successfully used to transform Lodderomyces elongisporus, Clavispora lusitaniae, Scheffersomyces stipitis and Candida parapsilosis.

  1. LASS6, an additional member of the longevity assurance gene family.

    PubMed

    Weinmann, Arndt; Galle, Peter R; Teufel, Andreas

    2005-11-01

    Longevity assurance genes (LAGs) represent a subgroup of the homeobox gene family. Five mammalian homologs have been reported, and the corresponding proteins have previously been investigated with respect to their key role in ceramide synthesis. However, members of the LAG family have been shown to be involved in cell growth regulation and cancer differentiation. In an effort to characterize additional members of the LAG family, we have screened the latest releases of genomic databases and report on the bioinformatic characterization of yet another member, LAG1 longevity assurance homolog 6 (LASS6). Like other LAG family members, the LASS6 protein contained a homeodomain and LAG1 domain. In phylogenetic analyses, it displayed highest homology to LASS5. The corresponding gene was localized to human chromosome 2q24.3, spanning a rather large genomic region of 318 kb. Orthologous sequences in mouse and zebrafish suggested a conservation of LASS6 in vertebrates as the protein and corresponding genomic sequences were highly conserved. LASS6 expression was analyzed in silico, and the gene was shown to be broadly expressed in a wide range of tissues. Furthermore, available microarray data suggested a role in cancer differentiation and early embryonic development.

  2. Product versus additive threshold models for analysis of reproduction outcomes in animal genetics.

    PubMed

    David, I; Bodin, L; Gianola, D; Legarra, A; Manfredi, E; Robert-Granié, C

    2009-08-01

    The phenotypic observation of some reproduction traits (e.g., insemination success, interval from lambing to insemination) is the result of environmental and genetic factors acting on 2 individuals: the male and female involved in a mating couple. In animal genetics, the main approach (called additive model) proposed for studying such traits assumes that the phenotype is linked to a purely additive combination, either on the observed scale for continuous traits or on some underlying scale for discrete traits, of environmental and genetic effects affecting the 2 individuals. Statistical models proposed for studying human fecundability generally consider reproduction outcomes as the product of hypothetical unobservable variables. Taking inspiration from these works, we propose a model (product threshold model) for studying a binary reproduction trait that supposes that the observed phenotype is the product of 2 unobserved phenotypes, 1 for each individual. We developed a Gibbs sampling algorithm for fitting a Bayesian product threshold model including additive genetic effects and showed by simulation that it is feasible and that it provides good estimates of the parameters. We showed that fitting an additive threshold model to data that are simulated under a product threshold model provides biased estimates, especially for individuals with high breeding values. A main advantage of the product threshold model is that, in contrast to the additive model, it provides distinct estimates of fixed effects affecting each of the 2 unobserved phenotypes.

  3. Correlating information contents of gene ontology terms to infer semantic similarity of gene products.

    PubMed

    Gan, Mingxin

    2014-01-01

    Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson's correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

  4. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    SciTech Connect

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  5. Shift in metabolism towards ethanol production in Saccharomyces cerevisiae by addition of metabolic inhibitors

    SciTech Connect

    Hahn-Haegerdal, B.; Mattiasson, B.

    1982-01-01

    The future exploitation of fermentation processes for the production of bulk chemicals will very much depend on whether product yield and product concentration can be improved. At the present time the cost for the raw material and the product upgrading limits the competitiveness of fermentation processes in relation to petrochemical processes. Much effort is put into selecting microbial strains with higher product yields as well as improved tolerance towards increased product concentrations. This approach is rather laborious and time-consuming and the overall goal will be beneficial if it is complemented with other techniques. This investigation will describe how productivity migh be improved by addition of a specific metabolic inhibitor, sodium azide, which inhibits the cytochrome oxidase of the respiratory chain. As a model for these studies Saccaromyces cerevisiae fermenting glucose to ethanol was chosen.

  6. Determination and validation of principal gene products

    PubMed Central

    Tress, Michael L.; Wesselink, Jan-Jaap; Frankish, Adam; López, Gonzalo; Goldman, Nick; Löytynoja, Ari; Massingham, Tim; Pardi, Fabio; Whelan, Simon; Harrow, Jennifer; Valencia, Alfonso

    2009-01-01

    Motivation Alternative splicing has the potential to generate a wide range of protein isoforms. For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear. Results We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. The five methods used were the conservation of exonic structure, the detection of non-neutral evolution, the conservation of functional residues, the existence of a known protein structure and the abundance of vertebrate orthologues. The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants. PMID:18006548

  7. Effect of product form upon fatigue-crack growth behavior in Alloy 718: additional results

    SciTech Connect

    James, L A

    1980-08-01

    A previous study had characterized the fatigue-crack growth behavior of four wrought product forms (sheet, plate, bar and forging) from a single heat of Alloy 718 and concluded that there were no consistent trends in the crack growth rate results that could be attributed to product form variability. The present study adds one additional product form (gas-tungsten-arc weldments) from the same heat, and compares the behavior to that exhibited by the wrought product forms. Two different precipitation heat-treatments were employed at each of five test temperatures (24, 316, 427, 538, and 649{sup 0}C).

  8. The effect of product form upon fatigue-crack growth behavior in Alloy 718: Additional results

    SciTech Connect

    James, L.A.

    1980-08-01

    A previous study had characterized the fatigue-crack growth behavior of four wrought product forms (sheet, plate, bar and forging) from a single heat of Alloy 718 and concluded that there were no consistent trends in the crack growth rate results that could be attributed to product form variability. The present study adds one additional product form (gas-tungsten-arc weldments) from the same heat, and compares the behavior to that exhibited by the wrought product forms. Two different precipitation heat-treatments were employed at each of five test temperatures. 11 refs., 5 figs., 3 tabs.

  9. Older paternal age and fresh gene mutation: data on additional disorders.

    PubMed

    Jones, K L; Smith, D W; Harvey, M A; Hall, B D; Quan, L

    1975-01-01

    Older paternal age has previously been documented as a factor in sporadic fresh mutational cases of several autosomal dominant disorders. In this collaborative study, an older mean paternal age has been documented in sporadic cases of at least five additional dominantly inheritable disorders; the basal cell nevus syndrome, the Waardenburg syndrome, the Crouzon syndrome, the oculo-dental-digital sysdrome, and the Treacher-Collins syndrome. It was also found to be a factor in acrodysostosis and progeria, suggesting a fresh mutant gene etiology for these two conditions in which virtually all cases have been sporadic and the mode of genetic etiology has been unknown.

  10. Enhanced photo-fermentative H2 production using Rhodobacter sphaeroides by ethanol addition and analysis of soluble microbial products

    PubMed Central

    2014-01-01

    Background Biological fermentation routes can provide an environmentally friendly way of producing H2 since they use renewable biomass as feedstock and proceed under ambient temperature and pressure. In particular, photo-fermentation has superior properties in terms of achieving high H2 yield through complete degradation of substrates. However, long-term H2 production data with stable performance is limited, and this data is essential for practical applications. In the present work, continuous photo-fermentative H2 production from lactate was attempted using the purple non-sulfur bacterium, Rhodobacter sphaeroides KD131. As a gradual drop in H2 production was observed, we attempted to add ethanol (0.2% v/v) to the medium. Results As continuous operation went on, H2 production was not sustained and showed a negligible H2 yield (< 0.5 mol H2/mol lactateadded) within two weeks. Electron balance analysis showed that the reason for the gradual drop in H2 production was ascribed to the increase in production of soluble microbial products (SMPs). To see the possible effect of ethanol addition, a batch test was first conducted. The presence of ethanol significantly increased the H2 yield from 1.15 to 2.20 mol H2/mol lactateadded, by suppressing the production of SMPs. The analysis of SMPs by size exclusion chromatography showed that, in the later period of fermentation, more than half of the low molecular weight SMPs (< 1 kDa) were consumed and used for H2 production when ethanol had been added, while the concentration of SMPs continuously increased in the absence of ethanol. It was found that the addition of ethanol facilitated the utilization of reducing power, resulting in an increase in the cellular levels of NAD+ and NADP+. In continuous operation, ethanol addition was effective, such that stable H2 production was attained with an H2 yield of 2.5 mol H2/mol lactateadded. Less than 15% of substrate electrons were used for SMP production, whereas 35% were used in

  11. Rheological behavior and organoleptic effects of ovalbumin addition in yogurt mousse production.

    PubMed

    Menéndez, M; Paredes, B; Iglesias, O; Rendueles, M; Díaz, M

    2006-03-01

    Yogurt mousse is a novel, high added-value dairy product that has been well received by the market. This paper presents a study of the effect of the addition of ovalbumin to the product on its rheological and organoleptic qualities. The ovalbumin was previously separated from egg white with a high grade of purity using an ion exchange resin synthesized by the authors. Diverse rheological tests at different temperatures and corresponding sensorial assessments were conducted to compare samples without and with added ovalbumin. The obtained results confirm that the product is viscoelastic and combines the properties of foams and emulsions; the elastic component is greater than the viscous component. Moreover, at temperatures ranging from 5 to 15 degrees C, a usual interval of consumption, the product behaves rheologically in a similar way. Conversely, the addition of ovalbumin under the assayed conditions also makes the elastic character of the product increase at a given temperature. Finally, the sensorial assessment tests and determinations of stability and volume yield enabled us to verify that the addition of ovalbumin at an amount of 1.3% hardly alters the stability, resistance to shear stress, or the texture and improves the degree of foaming. Therefore, the product with additive is of good commercial quality.

  12. Inducible product gene expression technology tailored to bioprocess engineering.

    PubMed

    Weber, Wilfried; Fussenegger, Martin

    2007-10-01

    Bioprocess engineering has developed as a discipline to design optimal culture conditions and bioreactor operation protocols for production cell lines engineered for constitutive expression of desired protein pharmaceuticals. With the advent of heterologous gene regulation systems it has become possible to fine-tune expression of difficult-to-produce protein pharmaceuticals to optimal levels and to conditionally engineer cell metabolism for the best production performance. However, most of the small-molecules used to trigger expression of product or metabolic engineering product genes are incompatible with downstream processing regulations or process economics. Recent progress in product gene control design has resulted in the development of bioprocess-compatible regulation systems, which are responsive to physical parameters such as temperature or physiologic trigger molecules that are either an inherent part of host cell metabolism or intrinsic components of licensed protein-free cell culture media, such as redox status, vitamin H and gaseous acetaldehyde. While all of these systems have been shown to fine-tune product gene expression independent of the host cell metabolism some of them can be plugged into metabolic networks to capture critical physiologic parameters and convert them into an optimal production response. Assembly of individual product gene control modalities into synthetic networks has recently enabled construction of autonomously regulated time-delay or cell density-sensitive gene circuits, which trigger population-wide induction of product gene expression at a predefined time or culture density. We provide a comprehensive overview on the latest developments in the design of bioprocess-compatible product gene control systems.

  13. [Effects of menthol as an additive in tobacco products and the need for regulation].

    PubMed

    Kahnert, S; Nair, U; Mons, U; Pötschke-Langer, M

    2012-03-01

    Menthol is the most widely used and the most prominent tobacco additive in tobacco products advertised and marketed by the tobacco industry. Besides its characteristic flavor, it possesses a variety of pharmacological properties facilitating tobacco smoke inhalation and potentiating dependence. These properties of menthol not only favor tobacco initiation and consumption but can also prevent smoking cessation. This article summarizes the effect of menthol as an additive in tobacco products and its effect on tobacco consumption that causes a number of chronic diseases and premature death and, therefore, counteracts tobacco control measures. Currently, there is no legislative regulation in Germany that considers the health hazard, addiction-enhancing and attractiveness-increasing properties of additives permitted in tobacco products. Effective regulation or even a ban could contribute to a reduction of tobacco consumption and, hence, save many people from a long-lasting tobacco dependence.

  14. Arrays in rays: terminal addition in echinoderms and its correlation with gene expression.

    PubMed

    Mooi, Rich; David, Bruno; Wray, Gregory A

    2005-01-01

    The echinoderms are deuterostomes that superimpose radial symmetry upon bilateral larval morphology. Consequently, they are not the first animals that come to mind when the concepts of segmentation and terminal addition are being discussed. However, it has long been recognized that echinoderms have serial elements along their radii formed in accordance with the ocular plate rule (OPR). The OPR is a special case of terminal growth, forming elements of the ambulacra that define the rays in echinoderms. New elements are added at the terminus of the ray, which may or may not be marked by a calcified element called the terminal plate (the "ocular" of sea urchins). The OPR operates in every echinoderm, from the occasionally bizarre fossils of the Cambrian to the most familiar extant taxa. Using the OPR and other criteria of recognition, echinoderm body wall can be divided into two main regions: extraxial components are associated with the somatocoels, axial components (formed in accordance with the OPR) with the hydrocoel. We compare patterns of development in axial regions of echinoderms with those found in the anterior-posterior axes of the earliest echinoderms as well as other invertebrates. Although axial and extraxial skeletons appear to be composed of the same biomineral matrix, the genes involved in patterning these two skeletal components are likely distinct. During development of the axial skeleton, for instance, the genes engrailed and orthodenticle are expressed in spatial and temporal patterns consistent with the OPR. Other genes such as distal-less seem to demarcate early ontogenetic boundaries between the axial rudiment and the extraxial larval body. There is a complex and pervasive reorganization of gene expression domains to produce the highly divergent morphologies seen in the Echinodermata. We integrate morphological and genetic information, particularly with respect to the origins of radial symmetry in the rudiment, and the concomitant development of

  15. Functions of the gene products of Escherichia coli.

    PubMed Central

    Riley, M

    1993-01-01

    A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome. PMID:7508076

  16. Detection in vivo of a new gene product (gene III) of cauliflower mosaic virus

    PubMed Central

    Xiong, C.; Lebeurier, G.; Hirth, L.

    1984-01-01

    Cauliflower mosaic virus DNA contains six major open reading frames (ORFs). As only the mRNA corresponding to the transcription of gene VI and its translation product have been isolated, the identification in infected plants of products corresponding to the five other putative genes remains to be established. The present paper reports the detection of an ORF III product by means of antibodies raised against an NH2-terminal synthetic peptide of 19 amino acids corresponding to a sequence predicted from the nucleotide sequence of ORF III. The detection of this gene product raises the question of the mechanism of its expression. Images PMID:16593524

  17. The Wilms’ Tumor Suppressor Gene (wt1) Product Regulates Dax-1 Gene Expression during Gonadal Differentiation

    PubMed Central

    Kim, Jungho; Prawitt, Dirk; Bardeesy, Nabeel; Torban, Elena; Vicaner, Caroline; Goodyer, Paul; Zabel, Bernard; Pelletier, Jerry

    1999-01-01

    Gonadal differentiation is dependent upon a molecular cascade responsible for ovarian or testicular development from the bipotential gonadal ridge. Genetic analysis has implicated a number of gene products essential for this process, which include Sry, WT1, SF-1, and DAX-1. We have sought to better define the role of WT1 in this process by identifying downstream targets of WT1 during normal gonadal development. We have noticed that in the developing murine gonadal ridge, wt1 expression precedes expression of Dax-1, a nuclear receptor gene. We document here that the spatial distribution profiles of both proteins in the developing gonad overlap. We also demonstrate that WT1 can activate the Dax-1 promoter. Footprinting analysis, transient transfections, promoter mutagenesis, and mobility shift assays suggest that WT1 regulates Dax-1 via GC-rich binding sites found upstream of the Dax-1 TATA box. We show that two WT1-interacting proteins, the product of a Denys-Drash syndrome allele of wt1 and prostate apoptosis response-4 protein, inhibit WT1-mediated transactivation of Dax-1. In addition, we demonstrate that WT1 can activate the endogenous Dax-1 promoter. Our results indicate that the WT1–DAX-1 pathway is an early event in the process of mammalian sex determination. PMID:10022915

  18. Cheese whey as substrate of batch hydrogen production: effect of temperature and addition of buffer.

    PubMed

    Muñoz-Páez, K M; Poggi-Varaldo, H M; García-Mena, J; Ponce-Noyola, M T; Ramos-Valdivia, A C; Barrera-Cortés, J; Robles-González, I V; Ruiz-Ordáz, N; Villa-Tanaca, L; Rinderknecht-Seijas, N

    2014-05-01

    The aim of this work was to evaluate the effect of buffer addition and process temperature (ambient and 35°C) on H2 production in batch fermentation of cheese whey (CW). When the H2 production reached a plateau, the headspace of the reactors were flushed with N2 and reactors were re-incubated. Afterwards, only the reactors with phosphate buffer showed a second cycle of H2 production and 48% more H2 was obtained. The absence of a second cycle in non-buffered reactors could be related to a lower final pH than in the buffered reactors; the low pH could drive the fermentation to solvents production. Indeed a high solvent production was observed in non-buffered bioreactors as given by low ρ ratios (defined as the ratio between sum of organic acid production and sum of solvents production). Regarding the process temperatures, no significant difference between the H2 production of reactors incubated at ambient temperature and at 35°C was described. After flushing the headspace of bioreactors with N2 at the end of the second cycle, the H2 production did not resume (in all reactors).

  19. 15 CFR 714.3 - Advance declaration requirements for additionally planned production of Schedule 3 chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... additionally planned production of Schedule 3 chemicals. 714.3 Section 714.3 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 3 CHEMICALS § 714.3...

  20. 15 CFR 714.3 - Advance declaration requirements for additionally planned production of Schedule 3 chemicals.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... additionally planned production of Schedule 3 chemicals. 714.3 Section 714.3 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 3 CHEMICALS § 714.3...

  1. 15 CFR 714.3 - Advance declaration requirements for additionally planned production of Schedule 3 chemicals.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... additionally planned production of Schedule 3 chemicals. 714.3 Section 714.3 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 3 CHEMICALS § 714.3...

  2. 15 CFR 714.3 - Advance declaration requirements for additionally planned production of Schedule 3 chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... additionally planned production of Schedule 3 chemicals. 714.3 Section 714.3 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS ACTIVITIES INVOLVING SCHEDULE 3 CHEMICALS § 714.3...

  3. 21 CFR 1304.26 - Additional recordkeeping requirements applicable to drug products containing gamma-hydroxybutyric...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Additional recordkeeping requirements applicable to drug products containing gamma-hydroxybutyric acid. 1304.26 Section 1304.26 Food and Drugs DRUG... accordance with an application under section 505 of the Federal Food, Drug, and Cosmetic Act must...

  4. Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products

    SciTech Connect

    Kuchka, M.R.

    1992-01-01

    Many individual chloroplast genes require the products of a collection of nuclear genes for their successful expression. These nuclear gene products apparently work with great specificity, each committed to the expression of a single chloroplast gene. We have chosen as a model nuclear mutants of Chlamydomonas affected in different stages in the expression of the chloroplast encoded Photosystem II polypeptide, D2. We have made the progress in understanding how nuclear gene products affect the translation of the D2 encoding MRNA. Two nuclear genes are required for this process which have been mapped genetically. In contrast to other examples of nuclear control of translation in the chloroplast, these nuclear gene products appear to be required either for specific stages in translation elongation or for the post-translational stabilization of the nascent D2 protein. Pseudoreversion analysis has led us to a locus which may be directly involved in D2 expression. We have made considerable progress in pursuing the molecular basis of psbd MRNA stabilization. psbD 5' UTR specific transcripts have been synthesized in vitro and used in gel mobility shift assays. UV-crosslinking studies are underway to identify the transacting factors which bind to these sequences. The continued examination of these mutants will help us to understand how nuclear gene products work in this specific case of chloroplast gene expression, and will elucidate how two distinct genomes can interact generally.

  5. Effects of resource addition on recovery of production and plant functional composition in degraded semiarid grasslands.

    PubMed

    Chen, Qing; Hooper, David U; Li, Hui; Gong, Xiao Ying; Peng, Fei; Wang, Hong; Dittert, Klaus; Lin, Shan

    2017-02-28

    Degradation of semiarid ecosystems from overgrazing threatens a variety of ecosystem services. Rainfall and nitrogen commonly co-limit production in semiarid grassland ecosystems; however, few studies have reported how interactive effects of precipitation and nitrogen addition influence the recovery of grasslands degraded by overgrazing. We conducted a 6-year experiment manipulating precipitation (natural precipitation and simulated wet year precipitation) and nitrogen (0, 25 and 50 kg N ha(-1)) addition at two sites with different histories of livestock grazing (moderately and heavily grazed) in Inner Mongolian steppe. Our results suggest that recovery of plant community composition and recovery of production can be decoupled. Perennial grasses provide long-term stability of high-quality forage production in this system. Supplemental water combined with exclosures led, in the heavily grazed site, to the strongest recovery of perennial grasses, although widespread irrigation of rangeland is not a feasible management strategy in many semiarid and arid regions. N fertilization combined with exclosures, but without water addition, increased dominance of unpalatable annual species, which in turn retarded growth of perennial species and increased inter-annual variation in primary production at both sites. Alleviation of grazing pressure alone allowed recovery of desired perennial species via successional processes in the heavily grazed site. Our experiments suggest that recovery of primary production and desirable community composition are not necessarily correlated. The use of N fertilization for the management of overgrazed grassland needs careful and systematic evaluation, as it has potential to impede, rather than aid, recovery.

  6. Expression QTL analysis of top loci from GWAS meta-analysis highlights additional schizophrenia candidate genes.

    PubMed

    de Jong, Simone; van Eijk, Kristel R; Zeegers, Dave W L H; Strengman, Eric; Janson, Esther; Veldink, Jan H; van den Berg, Leonard H; Cahn, Wiepke; Kahn, René S; Boks, Marco P M; Ophoff, Roel A

    2012-09-01

    There is genetic evidence that schizophrenia is a polygenic disorder with a large number of loci of small effect on disease susceptibility. Genome-wide association studies (GWASs) of schizophrenia have had limited success, with the best finding at the MHC locus at chromosome 6p. A recent effort of the Psychiatric GWAS consortium (PGC) yielded five novel loci for schizophrenia. In this study, we aim to highlight additional schizophrenia susceptibility loci from the PGC study by combining the top association findings from the discovery stage (9394 schizophrenia cases and 12 462 controls) with expression QTLs (eQTLs) and differential gene expression in whole blood of schizophrenia patients and controls. We examined the 6192 single-nucleotide polymorphisms (SNPs) with significance threshold at P<0.001. eQTLs were calculated for these SNPs in a sample of healthy controls (n=437). The transcripts significantly regulated by the top SNPs from the GWAS meta-analysis were subsequently tested for differential expression in an independent set of schizophrenia cases and controls (n=202). After correction for multiple testing, the eQTL analysis yielded 40 significant cis-acting effects of the SNPs. Seven of these transcripts show differential expression between cases and controls. Of these, the effect of three genes (RNF5, TRIM26 and HLA-DRB3) coincided with the direction expected from meta-analysis findings and were all located within the MHC region. Our results identify new genes of interest and highlight again the involvement of the MHC region in schizophrenia susceptibility.

  7. Four Additional Cases of Diphyllobothrium nihonkaiense Infection Confirmed by Analysis of COX1 Gene in Korea

    PubMed Central

    Park, Sang Hyun; Jeon, Hyeong Kyu; Kim, Jin Bong

    2015-01-01

    Most of the diphyllobothriid tapeworms isolated from human samples in the Republic of Korea (= Korea) have been identified as Diphyllobothrium nihonkaiense by genetic analysis. This paper reports confirmation of D. nihonkaiense infections in 4 additional human samples obtained between 1995 and 2014, which were analyzed at the Department of Parasitology, Hallym University College of Medicine, Korea. Analysis of the mitochondrial cytochrome c oxidase 1 (cox1) gene revealed a 98.5-99.5% similarity with a reference D. nihonkaiense sequence in GenBank. The present report adds 4 cases of D. nihonkaiense infections to the literature, indicating that the dominant diphyllobothriid tapeworm species in Korea is D. nihonkaiense but not D. latum. PMID:25748716

  8. Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling.

    PubMed

    Wu, Hulin; Lu, Tao; Xue, Hongqi; Liang, Hua

    2014-04-02

    The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method.

  9. Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling

    PubMed Central

    Wu, Hulin; Lu, Tao; Xue, Hongqi; Liang, Hua

    2014-01-01

    Summary The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method. PMID:25061254

  10. Cloning and characterization of a gene involved in triacylglycerol biosynthesis and identification of additional homologous genes in the oleaginous bacterium Rhodococcus opacus PD630.

    PubMed

    Alvarez, Adrian F; Alvarez, Héctor M; Kalscheuer, Rainer; Wältermann, Marc; Steinbüchel, Alexander

    2008-08-01

    The oleaginous bacterium Rhodococus opacus strain PD630 serves as a model organism to investigate the metabolism of storage triacylglycerols (TAGs) in bacteria. The key enzyme catalysing the last step of TAG biosynthesis in bacteria is a promiscuous acyltransferase (Atf), exhibiting acyl-CoA acyltransferase activity to both diacylglycerols (DGAT activity) and fatty alcohols (wax ester synthase, WS activity). An 800 bp PCR product was obtained from chromosomal DNA of strain PD630 by using degenerate primers designed from conserved stretches of Atf proteins of Acinetobacter baylyi strain ADP1 and Mycobacterium smegmatis mc(2)155. The atf fragment was used as a probe on a strain PD630 gene library, resulting in the identification of a 3948 bp chromosomal DNA fragment containing the complete atf1 gene. An atf1 disruption mutant of strain PD630 exhibited a TAG-leaky phenotype and accumulated up to 50 % less fatty acids than the wild-type, with significantly reduced oleic acid content when cultivated in the presence of gluconate or oleic acid. Whereas DGAT activity was drastically reduced in comparison to the wild-type, WS activity remained almost unchanged in the mutant. RT-PCR analysis of gluconate-grown cells of strain PD630 showed that there is expression of atf1 under conditions of TAG synthesis. To identify additional Atfs in strain PD630, PCR employing non-degenerate primers deduced from Rhodococcus jostii RHA1 sequence data was used. This yielded nine additional atf-homologous genes exhibiting 88-99 % sequence identity to the corresponding strain RHA1 enzymes. Besides Atf1 only Atf2 exhibited high DGAT and/or WS activity when heterologously expressed in Escherichia coli.

  11. Effect of combined herbal feed additives on methane, total gas production and rumen fermentation

    PubMed Central

    Chaturvedi, Indu; Dutta, Tapas Kumar; Singh, Pawan Kumar; Sharma, Ashwani

    2015-01-01

    The present study was to evaluate effect of herbal feed additives on methane and total gas production during the rumen fermentation for environment and animal health concern. Different parts of the five medicinal plants were selected such as leaf and small stems of Ocimum sanctum (Tulsi), roots of Curcuma longa (Haldi), fruits of Emblica officinalis (Amla), leaves of Azadirachta indica (Neem) and leaves and small stem of Clerodendrum phlomidis (Arni) for our study. Addition of different herbal additive combinations did not influence IVDMD and total gas production however methane production (mg/g of substrate DM) was significantly (P<0.05) reduced in Amla: Neem and Neem: Arni combinations. Total nitrogen significantly (P<0.01) increased in the combinations of Tulsi: Haldi and Amla: Neem. TCA–ppt-N is significantly (P<0.01) increased in Tulsi: Haldi, Haldi: Amla, Amla: Neem and Neem: Arni however NH3-N (mg/dl) significantly decreased in all treatments. We conclude that the screening of plant combinations, Amla: Neem and Neem: Arni have potential to decrease methane production and our herbal feed supplements have no side-effects on the ruminant in small amount. PMID:26124571

  12. The Role of Cocoa as a Cigarette Additive: Opportunities for Product Regulation

    PubMed Central

    Kennedy, Ryan David; Connolly, Gregory N.

    2014-01-01

    Introduction: The 2009 Family Smoking Prevention and Tobacco Control Act prohibited the use of characterizing flavors in cigarettes; however, some of these flavors are still used in cigarettes at varying levels. We reviewed tobacco industry internal documents to investigate the role of one of these flavors, cocoa, with the objective of understanding its relationship to sensory and risk perception, promotion of dependence, and enhancement of attractiveness and acceptability. Methods: We used the Legacy Tobacco Documents Library to identify documents relevant to our research questions. Initial search terms were generated following an examination of published literature on cocoa, other cigarette additives, and sensory and risk perception. Further research questions and search terms were generated based on review of documents generated from the initial search terms. Results: Cocoa is widely applied to cigarettes and has been used by the tobacco industry as an additive since the early 20th century. Cocoa can alter the sensory properties of cigarette smoke, including by providing a more appealing taste and decreasing its harshness. The tobacco industry has experimented with manipulating cocoa levels as a means of achieving sensory properties that appeal to women and youth. Conclusions: Although cocoa is identified as a flavor on tobacco industry Web sites, it may serve other sensory purposes in cigarettes as well. Eliminating cocoa as an additive from tobacco products may affect tobacco product abuse liability by altering smokers’ perceptions of product risk, and decreasing product appeal, especially among vulnerable populations. PMID:24610479

  13. Emerging role of phenolic compounds as natural food additives in fish and fish products.

    PubMed

    Maqsood, Sajid; Benjakul, Soottawat; Shahidi, Fereidoon

    2013-01-01

    Chemical and microbiological deteriorations are principal causes of quality loss of fish and fish products during handling, processing, and storage. Development of rancid odor and unpleasant flavor, changes of color and texture as well as lowering nutritional value in fish can be prevented by appropriate use of additives. Due to the potential health hazards of synthetic additives, natural products, especially antioxidants and antimicrobial agents, have been intensively examined as safe alternatives to synthetic compounds. Polyphenols (PP) are the natural antioxidants prevalent in fruits, vegetables, beverages (tea, wine, juices), plants, seaweeds, and some herbs and show antioxidative and antimicrobial activities in different fish and fish products. The use of phenolic compounds also appears to be a good alternative for sulphiting agent for retarding melanosis in crustaceans. Phenolic compounds have also been successfully employed as the processing aid for texture modification of fish mince and surimi. Thus, plant polyphenolic compounds can serve as potential additives for preventing quality deterioration or to retain the quality of fish and fish products.

  14. Qualitative identification of permitted and non-permitted colour additives in food products.

    PubMed

    Harp, Bhakti Petigara; Miranda-Bermudez, Enio; Baron, Carolina I; Richard, Gerald I

    2012-01-01

    Colour additives are dyes, pigments or other substances that can impart colour when added or applied to food, drugs, cosmetics, medical devices, or the human body. The substances must be pre-approved by the US Food and Drug Administration (USFDA) and listed in Title 21 of the US Code of Federal Regulations before they may be used in products marketed in the United States. Some also are required to be batch certified by the USFDA prior to their use. Both domestic and imported products sold in interstate commerce fall under USFDA jurisdiction, and the USFDA's district laboratories use a combination of analytical methods for identifying or confirming the presence of potentially violative colour additives. We have developed a qualitative method for identifying 17 certifiable, certification exempt, and non-permitted colour additives in various food products. The method involves extracting the colour additives from a product and isolating them from non-coloured components with a C(18) Sep-Pak cartridge. The colour additives are then separated and identified by liquid chromatography (LC) with photodiode array detection, using an Xterra RP18 column and gradient elution with aqueous ammonium acetate and methanol. Limits of detection (LODs) ranged from 0.02 to 1.49 mg/l. This qualititative LC method supplements the visible spectrophotometric and thin-layer chromatography methods currently used by the USFDA's district laboratories and is less time-consuming and requires less solvent compared to the other methods. The extraction step in the new LC method is a simple and an efficient process that can be used for most food types.

  15. Regulation of Cell and Gene Therapy Medicinal Products in Taiwan.

    PubMed

    Lin, Yi-Chu; Wang, Po-Yu; Tsai, Shih-Chih; Lin, Chien-Liang; Tai, Hsuen-Yung; Lo, Chi-Fang; Wu, Shiow-Ing; Chiang, Yu-Mei; Liu, Li-Ling

    2015-01-01

    Owing to the rapid and mature development of emerging biotechnology in the fields of cell culture, cell preservation, and recombinant DNA technology, more and more cell or gene medicinal therapy products have been approved for marketing, to treat serious diseases which have been challenging to treat with current medical practice or medicine. This chapter will briefly introduce the Taiwan Food and Drug Administration (TFDA) and elaborate regulation of cell and gene therapy medicinal products in Taiwan, including regulatory history evolution, current regulatory framework, application and review procedures, and relevant jurisdictional issues. Under the promise of quality, safety, and efficacy of medicinal products, it is expected the regulation and environment will be more flexible, streamlining the process of the marketing approval of new emerging cell or gene therapy medicinal products and providing diverse treatment options for physicians and patients.

  16. Innovations in value-addition of edible meat by-products.

    PubMed

    Toldrá, Fidel; Aristoy, M-Concepción; Mora, Leticia; Reig, Milagro

    2012-11-01

    While muscle foods are the more commonly consumed portion of an animal, meat by-products such as the entrails and internal organs are also widely consumed. Considered high-priced delicacies or waste material to be tossed away, the use and value of offal-edible and inedible meat by-products depend entirely on the culture and country in question. The skin, blood, bones, meat trimmings, fatty tissues, horns, hoofs, feet, skull, and internal organs of harvested animals comprise a wide variety of products including human or pet food or processed materials in animal feed, fertilizer, or fuel. Industry is using science and innovation to add value to animal by-products far beyond its usual profitability. Regardless of the final product's destination, it is still necessary to employ the most up-to-date and effective tools to analyze these products for nutritional properties, to search for key active molecules in nutrition like bioactive peptides, food safety (antimicrobial peptides), medicine, cosmetics or other fields, to develop new technological applications and to continue innovation towards advanced value-addition of meat by-products.

  17. Effect of the chlortetracycline addition method on methane production from the anaerobic digestion of swine wastewater.

    PubMed

    Huang, Lu; Wen, Xin; Wang, Yan; Zou, Yongde; Ma, Baohua; Liao, Xindi; Liang, Juanboo; Wu, Yinbao

    2014-10-01

    Effects of antibiotic residues on methane production in anaerobic digestion are commonly studied using the following two antibiotic addition methods: (1) adding manure from animals that consume a diet containing antibiotics, and (2) adding antibiotic-free animal manure spiked with antibiotics. This study used chlortetracycline (CTC) as a model antibiotic to examine the effects of the antibiotic addition method on methane production in anaerobic digestion under two different swine wastewater concentrations (0.55 and 0.22mg CTC/g dry manure). The results showed that CTC degradation rate in which manure was directly added at 0.55mg CTC/g (HSPIKE treatment) was lower than the control values and the rest of the treatment groups. Methane production from the HSPIKE treatment was reduced (p<0.05) by 12% during the whole experimental period and 15% during the first 7days. The treatments had no significant effect on the pH and chemical oxygen demand value of the digesters, and the total nitrogen of the 0.55mg CTC/kg manure collected from mediated swine was significantly higher than the other values. Therefore, different methane production under different antibiotic addition methods might be explained by the microbial activity and the concentrations of antibiotic intermediate products and metabolites. Because the primary entry route of veterinary antibiotics into an anaerobic digester is by contaminated animal manure, the most appropriate method for studying antibiotic residue effects on methane production may be using manure from animals that are given a particular antibiotic, rather than adding the antibiotic directly to the anaerobic digester.

  18. Gene analogue finder: a GRID solution for finding functionally analogous gene products

    PubMed Central

    Tulipano, Angelica; Donvito, Giacinto; Licciulli, Flavio; Maggi, Giorgio; Gisel, Andreas

    2007-01-01

    Background To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO). Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources. Results We have developed a tool, GENe AnaloGue FINdEr (ENGINE) that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. Conclusion ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non-model organisms that often have

  19. Additive Effects of Alcohols, Their Acidic By-Products, and Temperature on the Yeast Pachysolen tannophilus.

    PubMed

    Barbosa, M de F; Lee, H; Collins-Thompson, D L

    1990-02-01

    The effects of alcohols on the growth and fermentation of the yeast Pachysolen tannophilus were investigated at both 30 and 35 degrees C. Addition of alcohols to the culture medium decreased both the growth rate and the final cell yield in a dose-dependent manner, and this decrease was more severe at 35 degrees C. The concentration for 50% growth rate inhibition decreased as the chain length of the alcohol increased. In fermentations using a high initial cell density, production of acids was always observed when the medium was supplemented with alcohols. Supplementation of the culture medium with a short-chain alcohol plus the corresponding acid was shown to exert an additive deleterious effect on fermentation, and this effect increased with temperature. Production of acids was associated with the presence of alcohol dehydrogenase activity in cell extracts.

  20. Regulation of gene expression by tobacco product preparations in cultured human dermal fibroblasts

    SciTech Connect

    Malpass, Gloria E.; Arimilli, Subhashini; Prasad, G.L.; Howlett, Allyn C.

    2014-09-01

    Skin fibroblasts comprise the first barrier of defense against wounds, and tobacco products directly contact the oral cavity. Cultured human dermal fibroblasts were exposed to smokeless tobacco extract (STE), total particulate matter (TPM) from tobacco smoke, or nicotine at concentrations comparable to those found in these extracts for 1 h or 5 h. Differences were identified in pathway-specific genes between treatments and vehicle using qRT-PCR. At 1 h, IL1α was suppressed significantly by TPM and less significantly by STE. Neither FOS nor JUN was suppressed at 1 h by tobacco products. IL8, TNFα, VCAM1, and NFκB1 were suppressed after 5 h with STE, whereas only TNFα and NFκB1 were suppressed by TPM. At 1 h with TPM, secreted levels of IL10 and TNFα were increased. Potentially confounding effects of nicotine were exemplified by genes such as ATF3 (5 h), which was increased by nicotine but suppressed by other components of STE. Within 2 h, TPM stimulated nitric oxide production, and both STE and TPM increased reactive oxygen species. The biological significance of these findings and utilization of the gene expression changes reported herein regarding effects of the tobacco product preparations on dermal fibroblasts will require additional research. - Highlights: • Tobacco product preparations (TPPs) alter gene expression in dermal fibroblasts. • Some immediate early genes critical to the inflammatory process are affected. • Different TPPs produce differential responses in certain pro-inflammatory genes.

  1. New architecture of fast parallel multiplier using fast parallel counter with FPA (first partial product addition)

    NASA Astrophysics Data System (ADS)

    Lee, Mike M.; Cho, Byung Lok

    2001-11-01

    In this paper, we proposed a new First Partial product Addition (FPA) architecture with new compressor (or parallel counter) to CSA tree built in the process of adding partial product for improving speed in the fast parallel multiplier to improve the speed of calculating partial product by about 20% compared with existing parallel counter using full Adder. The new circuit reduces the CLA bit finding final sum by N/2 using the novel FPA architecture. A 5.14ns of multiplication speed of the 16X16 multiplier is obtained using 0.25um CMOS technology. The architecture of the multiplier is easily opted for pipeline design and demonstrates high speed performance.

  2. 3D Machine Vision and Additive Manufacturing: Concurrent Product and Process Development

    NASA Astrophysics Data System (ADS)

    Ilyas, Ismet P.

    2013-06-01

    The manufacturing environment rapidly changes in turbulence fashion. Digital manufacturing (DM) plays a significant role and one of the key strategies in setting up vision and strategic planning toward the knowledge based manufacturing. An approach of combining 3D machine vision (3D-MV) and an Additive Manufacturing (AM) may finally be finding its niche in manufacturing. This paper briefly overviews the integration of the 3D machine vision and AM in concurrent product and process development, the challenges and opportunities, the implementation of the 3D-MV and AM at POLMAN Bandung in accelerating product design and process development, and discusses a direct deployment of this approach on a real case from our industrial partners that have placed this as one of the very important and strategic approach in research as well as product/prototype development. The strategic aspects and needs of this combination approach in research, design and development are main concerns of the presentation.

  3. Dropwise Additive Manufacturing of Pharmaceutical Products for Amorphous and Self Emulsifying Drug Delivery Systems.

    PubMed

    Içten, Elçin; Purohit, Hitesh S; Wallace, Chelsey; Giridhar, Arun; Taylor, Lynne S; Nagy, Zoltan K; Reklaitis, Gintaras V

    2017-04-02

    The improvements in healthcare systems and the advent of the precision medicine initiative have created the need to develop more innovative manufacturing methods for the delivery and production of individualized dosing and personalized treatments. In accordance with the changes observed in healthcare systems towards more innovative therapies, this paper presents dropwise additive manufacturing of pharmaceutical products (DAMPP) for small scale, distributed manufacturing of individualized dosing as an alternative to conventional manufacturing methods A dropwise additive manufacturing process for amorphous and self-emulsifying drug delivery systems is reported, which utilizes drop-on-demand printing technology for automated and controlled deposition of melt-based formulations onto inert tablets. The advantages of drop on demand technology include reproducible production of droplets with adjustable sizing and high placement accuracy, which enable production of individualized dosing even for low dose and high potency drugs. Flexible use of different formulations, such as lipid-based formulations, allows enhancement of the solubility of poorly water soluble and highly lipophilic drugs with DAMPP. Here, DAMPP is used to produce solid oral dosage forms from melts of an active pharmaceutical ingredient and a surfactant. The dosage forms are analyzed to show the amorphous nature, self-emulsifying drug delivery system characteristics and dissolution behavior of these formulations.

  4. Hydrogen sulfide production by sulfate-reducing bacteria utilizing additives eluted from plastic resins.

    PubMed

    Tsuchida, Daisuke; Kajihara, Yusuke; Shimidzu, Nobuhiro; Hamamura, Kengo; Nagase, Makoto

    2011-06-01

    In the present study it was demonstrated that organic additives eluted from plastic resins could be utilized as substrates by sulfate-reducing bacteria. Two laboratory-scale experiments, a microcosm experiment and a leaching experiment, were conducted using polyvinyl chloride (PVC) as a model plastic resin. In the former experiment, the conversion of sulfate to sulfide was evident in microcosms that received plasticized PVC as the sole carbon source, but not in those that received PVC homopolymer. Additionally, dissolved organic carbon accumulated only in microcosms that received plasticized PVC, indicating that the dissolved organic carbon originated from additives. In the leaching experiment, phenol and bisphenol A were found in the leached solutions. These results suggest that the disposal of waste plastics in inert waste landfills may result in the production of H(2)S.

  5. Improving aerobic stability and biogas production of maize silage using silage additives.

    PubMed

    Herrmann, Christiane; Idler, Christine; Heiermann, Monika

    2015-12-01

    The effects of air stress during storage, exposure to air at feed-out, and treatment with silage additives to enhance aerobic stability on methane production from maize silage were investigated at laboratory scale. Up to 17% of the methane potential of maize without additive was lost during seven days exposure to air on feed-out. Air stress during storage reduced aerobic stability and further increased methane losses. A chemical additive containing salts of benzoate and propionate, and inoculants containing heterofermentative lactic acid bacteria were effective to increase aerobic stability and resulted in up to 29% higher methane yields after exposure to air. Exclusion of air to the best possible extent and high aerobic stabilities should be primary objectives when ensiling biogas feedstocks.

  6. Identification and distribution of products from novel tryptopyrokinin genes in the locust, Locusta migratoria.

    PubMed

    Redeker, Jana; Bläser, Marcel; Neupert, Susanne; Predel, Reinhard

    2017-04-22

    A recent analysis of the genome of Locusta migratoria indicated the presence of four novel insect neuropeptide genes encoding for multiple tryptopyrokinin peptides (tryptoPKs); hitherto only known from pyrokinin or capa genes. In our study, mature products of tryptoPK genes 1 and 2 were identified by mass spectrometry; precursor sequences assigned to the tryptoPK genes 3 and 4 are likely partial sequences of a single precursor. The expression of tryptoPK genes 1 and 2 is restricted to two cells in the subesophageal ganglion, exhibiting not only a unique neuropeptidome but also a very distinctive axonal projection. Comparative neuroendocrinology revealed that homologous cells in other insects also produce tryptoPKs but use other genes to generate this pattern. Since capa and pyrokinin genes are discussed as ancestors of the tryptoPK genes, we completed the hitherto only partially known precursor sequences of these genes by means of transcriptome analyses. The distribution of mature products of CAPA and pyrokinin precursors in the CNS is compared with that of tryptoPKs. In addition, a novel pyrokinin-like precursor is described.

  7. ROS production during symbiotic infection suppresses pathogenesis-related gene expression.

    PubMed

    Peleg-Grossman, Smadar; Melamed-Book, Naomi; Levine, Alex

    2012-03-01

    Leguminous plants have exclusive ability to form symbiotic relationship with soil bacteria of the genus Rhizobium. Symbiosis is a complex process that involves multiple molecular signaling activities, such as calcium fluxes, production of reactive oxygen species (ROS) and synthesis of nodulation genes. We analyzed the role of ROS in defense gene expression in Medicago truncatula during symbiosis and pathogenesis. Studies in Arabidopsis thaliana showed that the induction of pathogenesis-related (PR) genes during systemic acquired resistance (SAR) is regulated by NPR1 protein, which resides in the cytoplasm as an oligomer. After oxidative burst and return of reducing conditions, the NPR1 undergoes monomerization and becomes translocated to the nucleus, where it functions in PR genes induction. We show that ROS production is both stronger and longer during symbiotic interactions than during interactions with pathogenic, nonhost or common nonpathogenic soil bacteria. Moreover, root cells inoculated with Sinorhizobium meliloti accumulated ROS in the cytosol but not in vacuoles, as opposed to Pseudomonas putida inoculation or salt stress treatment. Furthermore, increased ROS accumulation by addition of H₂O₂ reduced the PR gene expression, while catalase had an opposite effect, establishing that the PR gene expression is opposite to the level of cytoplasmic ROS. In addition, we show that salicylic acid pretreatment significantly reduced ROS production in root cells during symbiotic interaction.

  8. Dropwise additive manufacturing of pharmaceutical products for melt-based dosage forms.

    PubMed

    Içten, Elçin; Giridhar, Arun; Taylor, Lynne S; Nagy, Zoltan K; Reklaitis, Gintaras V

    2015-05-01

    The US Food and Drug Administration introduced the quality by design approach and process analytical technology guidance to encourage innovation and efficiency in pharmaceutical development, manufacturing, and quality assurance. As part of this renewed emphasis on the improvement of manufacturing, the pharmaceutical industry has begun to develop more efficient production processes with more intensive use of online measurement and sensing, real-time quality control, and process control tools. Here, we present dropwise additive manufacturing of pharmaceutical products (DAMPP) as an alternative to conventional pharmaceutical manufacturing methods. This mini-manufacturing process for the production of pharmaceuticals utilizes drop on demand printing technology for automated and controlled deposition of melt-based formulations onto edible substrates. The advantages of drop-on-demand technology, including reproducible production of small droplets, adjustable drop sizing, high placement accuracy, and flexible use of different formulations, enable production of individualized dosing even for low-dose and high-potency drugs. In this work, DAMPP is used to produce solid oral dosage forms from hot melts of an active pharmaceutical ingredient and a polymer. The dosage forms are analyzed to show the reproducibility of dosing and the dissolution behavior of different formulations.

  9. GABA Production in Lactococcus lactis Is Enhanced by Arginine and Co-addition of Malate

    PubMed Central

    Laroute, Valérie; Yasaro, Chonthicha; Narin, Waranya; Mazzoli, Roberto; Pessione, Enrica; Cocaign-Bousquet, Muriel; Loubière, Pascal

    2016-01-01

    Lactococcus lactis NCDO 2118 was previously selected for its ability to decarboxylate glutamate to γ-aminobutyric acid (GABA), an interesting nutritional supplement able to improve mood and relaxation. Amino acid decarboxylation is generally considered as among the biochemical systems allowing lactic acid bacteria to counteracting acidic stress and obtaining metabolic energy. These strategies also include arginine deiminase pathway and malolactic fermentation but little is known about their possible interactions of with GABA production. In the present study, the effects of glutamate, arginine, and malate (i.e., the substrates of these acid-resistance pathways) on L. lactis NCDO 2118 growth and GABA production performances were analyzed. Both malate and arginine supplementation resulted in an efficient reduction of acidity and improvement of bacterial biomass compared to glutamate supplementation. Glutamate decarboxylation was limited to narrow environmental conditions (pH < 5.1) and physiological state (stationary phase). However, some conditions were able to improve GABA production or activate glutamate decarboxylation system even outside of this compass. Arginine clearly stimulated glutamate decarboxylation: the highest GABA production (8.6 mM) was observed in cultures supplemented with both arginine and glutamate. The simultaneous addition of arginine, malate, and glutamate enabled earlier GABA production (i.e., during exponential growth) at relatively high pH (6.5). As far as we know, no previous study has reported GABA production in such conditions. Although further studies are needed to understand the molecular basis of these phenomena, these results represent important keys suitable of application in GABA production processes. PMID:27458444

  10. Additive loss-of-function proteasome subunit mutations in CANDLE/PRAAS patients promote type I IFN production

    PubMed Central

    Brehm, Anja; Liu, Yin; Sheikh, Afzal; Marrero, Bernadette; Omoyinmi, Ebun; Zhou, Qing; Montealegre, Gina; Biancotto, Angelique; Reinhardt, Adam; Almeida de Jesus, Adriana; Pelletier, Martin; Tsai, Wanxia L.; Remmers, Elaine F.; Kardava, Lela; Hill, Suvimol; Kim, Hanna; Lachmann, Helen J.; Megarbane, Andre; Chae, Jae Jin; Brady, Jilian; Castillo, Rhina D.; Brown, Diane; Casano, Angel Vera; Gao, Ling; Chapelle, Dawn; Huang, Yan; Stone, Deborah; Chen, Yongqing; Sotzny, Franziska; Lee, Chyi-Chia Richard; Kastner, Daniel L.; Torrelo, Antonio; Zlotogorski, Abraham; Moir, Susan; Gadina, Massimo; McCoy, Phil; Wesley, Robert; Rother, Kristina; Hildebrand, Peter W.; Brogan, Paul; Krüger, Elke; Aksentijevich, Ivona; Goldbach-Mansky, Raphaela

    2015-01-01

    Autosomal recessive mutations in proteasome subunit β 8 (PSMB8), which encodes the inducible proteasome subunit β5i, cause the immune-dysregulatory disease chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE), which is classified as a proteasome-associated autoinflammatory syndrome (PRAAS). Here, we identified 8 mutations in 4 proteasome genes, PSMA3 (encodes α7), PSMB4 (encodes β7), PSMB9 (encodes β1i), and proteasome maturation protein (POMP), that have not been previously associated with disease and 1 mutation in PSMB8 that has not been previously reported. One patient was compound heterozygous for PSMB4 mutations, 6 patients from 4 families were heterozygous for a missense mutation in 1 inducible proteasome subunit and a mutation in a constitutive proteasome subunit, and 1 patient was heterozygous for a POMP mutation, thus establishing a digenic and autosomal dominant inheritance pattern of PRAAS. Function evaluation revealed that these mutations variably affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. Moreover, defects in proteasome formation and function were recapitulated by siRNA-mediated knockdown of the respective subunits in primary fibroblasts from healthy individuals. Patient-isolated hematopoietic and nonhematopoietic cells exhibited a strong IFN gene-expression signature, irrespective of genotype. Additionally, chemical proteasome inhibition or progressive depletion of proteasome subunit gene transcription with siRNA induced transcription of type I IFN genes in healthy control cells. Our results provide further insight into CANDLE genetics and link global proteasome dysfunction to increased type I IFN production. PMID:26524591

  11. Complete sequence of a plasmid from a bovine methicillin-resistant Staphylococcus aureus harbouring a novel ica-like gene cluster in addition to antimicrobial and heavy metal resistance genes.

    PubMed

    Feßler, Andrea T; Zhao, Qin; Schoenfelder, Sonja; Kadlec, Kristina; Brenner Michael, Geovana; Wang, Yang; Ziebuhr, Wilma; Shen, Jianzhong; Schwarz, Stefan

    2017-02-01

    The multiresistance plasmid pAFS11, obtained from a bovine methicillin-resistant Staphylococcus aureus (MRSA) isolate, was completely sequenced and analysed for its structure and organisation. Moreover, the susceptibility to the heavy metals cadmium and copper was determined by broth macrodilution. The 49,189-bp plasmid harboured the apramycin resistance gene apmA, two copies of the macrolide/lincosamide/streptogramin B resistance gene erm(B) (both located on remnants of a truncated transposon Tn917), the kanamycin/neomycin resistance gene aadD, the tetracycline resistance gene tet(L) and the trimethoprim resistance gene dfrK. The latter three genes were part of a 7,284-bp segment which was bracketed by two copies of IS431. In addition, the cadmium resistance operon cadDX as well as the copper resistance genes copA and mco were located on the plasmid and mediated a reduced susceptibility to cadmium and copper. Moreover, a complete novel ica-like gene cluster of so far unknown genetic origin was detected on this plasmid. The ica-like gene cluster comprised four different genes whose products showed 64.4-76.9% homology to the Ica proteins known to be involved in biofilm formation of the S. aureus strains Mu50, Mu3 and N315. However, 96.2-99.4% homology was seen to proteins from S. sciuri NS1 indicating an S. sciuri origin. The finding of five different antibiotic resistance genes co-located on a plasmid with heavy metal resistance genes and an ica-like gene cluster is alarming. With the acquisition of this plasmid, antimicrobial multiresistance, heavy metal resistances and potential virulence properties may be co-selected and spread via a single horizontal gene transfer event.

  12. Indications of Transformation Products from Hydraulic Fracturing Additives in Shale Gas Wastewater

    NASA Astrophysics Data System (ADS)

    Elsner, Martin; Hoelzer, Kathrin; Sumner, Andrew J.; Karatum, Osman; Nelson, Robert K.; Drollette, Brian D.; O'Connor, Megan P.; D'Ambro, Emma; Getzinger, Gordon J.; Ferguson, P. Lee; Reddy, Christopher M.; Plata, Desiree L.

    2016-04-01

    Unconventional natural gas development (UNGD) generates large volumes of wastewater, whose detailed composition must be known for adequate risk assessment and treatment. In particular, there is a need to elucidate the structures of organic chemical additives, extracted geogenic compounds, and transformation products. This study investigated six Fayetteville Shale UNGD wastewater samples for their organic composition using purge-and-trap gas chromatography-mass spectrometry (P&T-GC-MS) in combination with liquid-liquid extraction with comprehensive two-dimensional gas chromatography-time of flight-mass spectrometry (GCxGC-TOF-MS). Following application of strict compound identification confidence criteria, we classified compounds according to their putative origin. Samples displayed distinct chemical distributions composed of typical geogenic substances (hydrocarbons), disclosed UNGD additives (e.g., hydrocarbons, phthalates, such as diisobutyl phthalate, and radical initiators, such as azobisisobutyronitrile), and undisclosed compounds (e.g., halogenated hydrocarbons, such as 2-bromohexane or 4-bromoheptane). Undisclosed chloromethyl alkanoates (chloromethyl propanoate, pentanoate, and octanoate) were identified as putative delayed acids (those that release acidic moieties only after hydrolytic cleavage, whose rate could potentially be controlled), suggesting they were deliberately introduced to react in the subsurface. Identification of halogenated methanes and acetones, in contrast, suggested they were formed as unintended by-products. Our study highlights the possibility that UNGD operations generate transformation products, knowledge of which is crucial for risk assessment and treatment strategies, and underscores the value of disclosing potential precursors that are injected into the subsurface.

  13. Indications of Transformation Products from Hydraulic Fracturing Additives in Shale-Gas Wastewater.

    PubMed

    Hoelzer, Kathrin; Sumner, Andrew J; Karatum, Osman; Nelson, Robert K; Drollette, Brian D; O'Connor, Megan P; D'Ambro, Emma L; Getzinger, Gordon J; Ferguson, P Lee; Reddy, Christopher M; Elsner, Martin; Plata, Desiree L

    2016-08-02

    Unconventional natural gas development (UNGD) generates large volumes of wastewater, the detailed composition of which must be known for adequate risk assessment and treatment. In particular, transformation products of geogenic compounds and disclosed additives have not been described. This study investigated six Fayetteville Shale wastewater samples for organic composition using a suite of one- and two-dimensional gas chromatographic techniques to capture a broad distribution of chemical structures. Following the application of strict compound-identification-confidence criteria, we classified compounds according to their putative origin. Samples displayed distinct chemical distributions composed of typical geogenic substances (hydrocarbons and hopane biomarkers), disclosed UNGD additives (e.g., hydrocarbons, phthalates such as diisobutyl phthalate, and radical initiators such as azobis(isobutyronitrile)), and undisclosed compounds (e.g., halogenated hydrocarbons, such as 2-bromohexane or 4-bromoheptane). Undisclosed chloromethyl alkanoates (chloromethyl propanoate, pentanoate, and octanoate) were identified as potential delayed acids (i.e., those that release acidic moieties only after hydrolytic cleavage, the rate of which could be potentially controlled), suggesting they were deliberately introduced to react in the subsurface. In contrast, the identification of halogenated methanes and acetones suggested that those compounds were formed as unintended byproducts. Our study highlights the possibility that UNGD operations generate transformation products and underscores the value of disclosing additives injected into the subsurface.

  14. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    PubMed

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

  15. Effect of acid additives on sugarcane bagasse pyrolysis: Production of high yields of sugars.

    PubMed

    David, Geraldo Ferreira; Perez, Victor Haber; Rodriguez Justo, Oselys; Garcia-Perez, Manuel

    2017-01-01

    The aim of this work was to improve sugarcane bagasse thermochemical conversion to pyrolytic sugars production, particularly to levoglucosan. The experiments were carried out evaluating the effect of acid washing with HNO3 (0.1wt.%) followed by H2SO4 addition (0.1, 0.2 and 0.3wt.%) at pyrolysis temperatures of 350, 400, 450, 500, 550 and 600°C was studied by Py-GC/MS. The experimental results showed that HNO3 washing, followed by H2SO4 concentration of 0.2wt.% at 350°C resulted in an increase in levoglucosan yield between 5 and 7 times the yield obtained when the raw bagasse was processed. Thus, these results are very attractive to improve pyrolytic sugars production in sugarcane bagasse by previously acid treatment to pyrolysis technology.

  16. Dextransucrase production using cashew apple juice as substrate: effect of phosphate and yeast extract addition.

    PubMed

    Chagas, Clarice M A; Honorato, Talita L; Pinto, Gustavo A S; Maia, Geraldo A; Rodrigues, Sueli

    2007-05-01

    Cashew apples are considered agriculture excess in the Brazilian Northeast because cashew trees are cultivated primarily with the aim of cashew nut production. In this work, the use of cashew apple juice as a substrate for Leuconostoc mesenteroides cultivation was investigated. The effect of yeast extract and phosphate addition was evaluated using factorial planning tools. Both phosphate and yeast extract addition were significant factors for biomass growth, but had no significant effect on maximum enzyme activity. The enzyme activities found in cashew apple juice assays were at least 3.5 times higher than the activity found in the synthetic medium. Assays with pH control (pH = 6.5) were also carried out. The pH-controlled fermentation enhanced biomass growth, but decreased the enzyme activity. Crude enzyme free of cells produced using cashew apple juice was stable for 16 h at 30 degrees C at a pH of 5.0.

  17. Environmental behavior of cement-based stabilized foundry sludge products incorporating additives.

    PubMed

    Ruiz, M C; Irabien, A

    2004-06-18

    A series of experiments were conducted to stabilize the inorganic and organic pollutants in a foundry sludge from a cast iron activity using Portland cement as binder and three different types of additives, organophilic bentonite, lime and coal fly ash. Ecotoxicological and chemical behavior of stabilized mixes of foundry sludge were analyzed to assess the feasibility to immobilize both types of contaminants, all determined on the basis of compliance leaching tests. The incorporation of lime reduces the ecotoxicity of stabilized mixes and enhances stabilization of organic pollutants obtaining better results when a 50% of cement is replaced by lime. However, the alkalinity of lime increases slightly the leached zinc up to concentrations above the limit set under neutral conditions by the European regulations. The addition of organophilic bentonite and coal fly ash can immobilize the phenolic compounds but are inefficient to reduce the ecotoxicity and mobility of zinc of final products.

  18. Assessment of production performance in 2 breeds of broilers fed prebiotics as feed additives.

    PubMed

    Hanning, I; Clement, A; Owens, C; Park, S H; Pendleton, S; Scott, E E; Almeida, G; Gonzalez Gil, F; Ricke, S C

    2012-12-01

    Pasture-flock-raised poultry are becoming an increasingly popular product, but only limited options are currently available for maintaining gut health. For these producers, prebiotics are an attractive option because they are generally recognized as safe (GRAS) and can be mixed into the feed and thus do not require adjustments to production protocols. However, if prebiotic treatments reduce production performance, they would not be useful to producers. Thus, the objective of this study was to measure performance of pasture-raised broilers fed 1 of 3 prebiotic treatments. For these trials, 2 breeds of birds were used: Naked Neck slow-growing breeds and Cornish White Rock cross fast-growing breeds. The experimental design was replicated for each breed. A total of 340 birds were split into 4 groups, each group fed one feed additive: 1) galactoligosaccharides (2% wt/wt), 2) fructooligosaccharides (1% wt/wt), 3) plum fibers (1% wt/wt), or 4) no additives. During the 8-wk rearing period, 10 birds from each group were collected and euthanized to take small intestine samples. Histological preparations were made from the small intestine tissue, and 4 measurements of villi height and crypt depth from each cross section were taken. Throughout the study, mortality was monitored and BW measurements were taken at 2-wk intervals. For the Cornish White Rock cross, the group receiving the feed supplemented with fructooligosaccharides had higher (P < 0.05) 8-wk BW than those fed Plum; control and birds fed galactoligosaccharides were intermediate. For the Naked Neck breed, the group receiving the plum fibers had the highest final BW. It appears that all 3 feed supplements offered some protective effect for alterations in villi length and crypt depth due to feed withdrawal, but only for the Naked Neck breed. The data indicate the 3 prebiotics utilized in this study could be used without risk of decreasing production performance, but only for Naked Neck breeds.

  19. RNA-seq validation of RNAi identifies additional gene connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    RNA interference (RNAi) is a functional genomics tool to validate phenotypes by delivering targeted, gene-specific, and complementary dsRNA into a host via injection, feeding, or other means in order to reduce gene expression. RNAi in the red flour beetle, Tribolium castaneum, has been successful du...

  20. Expanded natural product diversity revealed by analysis of lanthipeptide-like gene clusters in actinobacteria.

    PubMed

    Zhang, Qi; Doroghazi, James R; Zhao, Xiling; Walker, Mark C; van der Donk, Wilfred A

    2015-07-01

    Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptide-like biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities.

  1. Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

    PubMed Central

    Zhang, Qi; Doroghazi, James R.; Zhao, Xiling; Walker, Mark C.

    2015-01-01

    Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptide-like biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities. PMID:25888176

  2. Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat

    SciTech Connect

    Kenney, S.; Kamine, J.; Markovitz, D.; Fenrick, R.; Pagano, J.

    1988-03-01

    Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, the authors demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.

  3. Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm.

    PubMed

    Bassene, J B; Froelicher, Y; Dubois, C; Ferrer, R M; Navarro, L; Ollitrault, P; Ancillo, G

    2010-09-01

    Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin'+C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.

  4. Artificial stimulation of soil amine production by addition of organic carbon and nitrogen transforming enzymes

    NASA Astrophysics Data System (ADS)

    Kieloaho, Antti-Jussi; Parshintsev, Jevgeni; Riekkola, Marja-Liisa; Kulmala, Markku; Pumpanen, Jukka; Heinonsalo, Jussi

    2013-04-01

    The major part of nitrogen (N) in boreal forest soil is in organic form (Soil Organic Nitrogen, SON). One of the main pathways for amine production is the decay of SON in soil. Amino acids react with specific decarboxylase enzymes which transform them to amines. Amino acid turnover time in forest soil is relatively fast (in hours) because amino acids can be used as N and C source by plants and microbes. Therefore, amino acid production by protease enzymes might be the critical step for amine production and release from forest soil. The aim of the study was to artificially introduce enzymes responsible for protein transformation into amino acids (proteases) as well as soil organic matter (SOM) decomposition (laccase and manganese peroxidase) in order to increase SON transformation and amine synthesis. Glucose addition has been shown to induce natural soil protease activity. Bovine serum albumin (BSA) was used as control protein. Treatments were conducted both in Scots pine seedlings containing as well as non-planted microcosms. N transformations were examined, as well as amine concentration in soil. The experiment consisted of eight different treatments; two as controls concerning enzyme addition, four treatments were planted with one year old nursery grown Scots pine (Pinus sylvestris L.) seedlings and four were non-planted. The experiment lasted approximately six months and the treatments with the additions were conducted within one more month. The protease activity was discovered more commonly after the treatment with protease or glucose additions. In planted BSA-control some natural protease activity was found but not in non-planted controls. Different substrate additions did not cause any differences in total N percentage, but the presence of the seedlings diminished soil N% by approximately 20%. In addition, the same effect was clearly seen in dissolved N, NH4+ and NO3-. Plant has exploited the soluble N forms almost entirely from the system, irrespective of

  5. Evaluating leachate recirculation with cellulase addition to enhance waste biostabilisation and landfill gas production.

    PubMed

    Frank, R R; Davies, S; Wagland, S T; Villa, R; Trois, C; Coulon, F

    2016-09-01

    The effect of leachate recirculation with cellulase augmentation on municipal solid waste (MSW) biostabilisation and landfill gas production was investigated using batch bioreactors to determine the optimal conditions of moisture content, temperature and nutrients. Experimentation was thereafter scaled-up in 7L bioreactors. Three conditions were tested including (1) leachate recirculation only, (2) leachate recirculation with enzyme augmentation and (3) no leachate recirculation (control). Cumulative biogas production of the batch tests indicated that there was little difference between the leachate and control test conditions, producing on average 0.043m(3)biogaskg(-1) waste. However the addition of cellulase at 15×10(6)Utonne(-1) waste doubled the biogas production (0.074m(3)biogaskg(-1) waste). Similar trend was observed with the bioreactors. Cellulase addition also resulted in the highest COD reduction in both the waste and the leachate samples (47% and 42% COD reduction, respectively). In both cases, the quantity of biogas produced was closer to the lower value of theoretical and data-based biogas prediction indicators (0.05-0.4m(3)biogaskg(-1) waste). This was likely due to a high concentration of heavy metals present in the leachate, in particular Cr and Mn, which are known to be toxic to methanogens. The cost-benefit analysis (CBA) based on the settings of the study (cellulase concentration of 15×10(6)Utonne(-1) waste) showed that leachate bioaugmentation using cellulase is economically viable, with a net benefit of approximately €12.1million on a 5Mt mixed waste landfill.

  6. Analysis of additives in dairy products by liquid chromatography coupled to quadrupole-orbitrap mass spectrometry.

    PubMed

    Jia, Wei; Ling, Yun; Lin, Yuanhui; Chang, James; Chu, Xiaogang

    2014-04-04

    A new method combining QuEChERS with ultrahigh-performance liquid chromatography and electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC/ESI Q-Orbitrap) was developed for the highly accurate and sensitive screening of 43 antioxidants, preservatives and synthetic sweeteners in dairy products. Response surface methodology was employed to optimize a quick, easy, cheap, effective, rugged, and safe (QuEChERS) sample preparation method for the determination of 42 different analytes in dairy products for the first time. After optimization, the maximum predicted recovery was 99.33% rate for aspartame under the optimized conditions of 10 mL acetionitrile, 1.52 g sodium acetate, 410 mg PSA and 404 mgC18. For the matrices studied, the recovery rates of the other 42 compounds ranged from 89.4% to 108.2%, with coefficient of variation <6.4%. UHPLC/ESI Q-Orbitrap Mass full scan mode acquired full MS data was used to identify and quantify additives, and data-dependent scan mode obtained fragment ion spectra for confirmation. The mass accuracy typically obtained is routinely better than 1.5ppm, and only need to calibrate once a week. The 43 compounds behave dynamic in the range 0.001-1000 μg kg(-1) concentration, with correlation coefficient >0.999. The limits of detection for the analytes are in the range 0.0001-3.6 μg kg(-1). This method has been successfully applied on screening of antioxidants, preservatives and synthetic sweeteners in commercial dairy product samples, and it is very useful for fast screening of different food additives.

  7. Effect of lipase addition on hydrolysis and biomethane production of Chinese food waste.

    PubMed

    Meng, Ying; Li, Sang; Yuan, Hairong; Zou, Dexun; Liu, Yanping; Zhu, Baoning; Li, Xiujin

    2015-03-01

    The lipase obtained from Aspergillums niger was applied to promote the hydrolysis of food waste for achieving high biomethane production. Two strategies of lipase additions were investigated. One (Group A) was to pre-treat food waste to pre-decompose lipid to fatty acids before anaerobic digestion, and another one (Group B) was to add lipase to anaerobic digester directly to degrade lipid inside digester. The lipase was used at the concentrations of 0.1%, 0.5%, and 1.0% (w/v). The results showed that Group A achieved higher biomethane production, TS and VS reductions than those of Group B. At 0.5% lipase concentration, Group A obtained experimental biomethane yield of 500.1 mL/g VS(added), 4.97-26.50% higher than that of Group B. The maximum Bd of 73.8% was also achieved in Group A. Therefore, lipase pre-treatment strategy is recommended. This might provide one of alternatives for efficient biomethane production from food waste and mitigating environmental impact associated.

  8. Enhanced camptothecin production by ethanol addition in the suspension culture of the endophyte, Fusarium solani.

    PubMed

    Venugopalan, Aarthi; Srivastava, Smita

    2015-01-01

    Ethanolic extract of a non-camptothecin producing plant, Catharanthus roseus when added in the suspension culture of the endophyte Fusarium solani known to produce camptothecin, resulted in enhanced production of camptothecin by 10.6-fold in comparison to that in control (2.8 μg/L). Interestingly, addition of pure ethanol (up to 5% v/v) in the suspension culture of F. solani resulted in maximum enhancement in camptothecin production (up to 15.5-fold) from that obtained in control. In the presence of ethanol, a reduced glucose uptake (by ∼ 40%) and simultaneous ethanol consumption (up to 9.43 g/L) was observed during the cultivation period (14 days). Also, the total NAD level and the protein content in the biomass increased by 3.7- and 1.9-fold, respectively, in comparison to that in control. The study indicates a dual role of ethanol, presumably as an elicitor and also as a carbon/energy source, leading to enhanced biomass and camptothecin production.

  9. Dropwise additive manufacturing of pharmaceutical products for solvent-based dosage forms.

    PubMed

    Hirshfield, Laura; Giridhar, Arun; Taylor, Lynne S; Harris, Michael T; Reklaitis, Gintaras V

    2014-02-01

    In recent years, the US Food and Drug Administration has encouraged pharmaceutical companies to develop more innovative and efficient manufacturing methods with improved online monitoring and control. Mini-manufacturing of medicine is one such method enabling the creation of individualized product forms for each patient. This work presents dropwise additive manufacturing of pharmaceutical products (DAMPP), an automated, controlled mini-manufacturing method that deposits active pharmaceutical ingredients (APIs) directly onto edible substrates using drop-on-demand (DoD) inkjet printing technology. The use of DoD technology allows for precise control over the material properties, drug solid state form, drop size, and drop dynamics and can be beneficial in the creation of high-potency drug forms, combination drugs with multiple APIs or individualized medicine products tailored to a specific patient. In this work, DAMPP was used to create dosage forms from solvent-based formulations consisting of API, polymer, and solvent carrier. The forms were then analyzed to determine the reproducibility of creating an on-target dosage form, the morphology of the API of the final form and the dissolution behavior of the drug over time. DAMPP is found to be a viable alternative to traditional mass-manufacturing methods for solvent-based oral dosage forms.

  10. Identification and engineering of regulation-related genes toward improved kasugamycin production.

    PubMed

    Zhu, Chenchen; Kang, Qianjin; Bai, Linquan; Cheng, Lin; Deng, Zixin

    2016-02-01

    Kasugamycin, produced by Streptomyces kasugaensis and Streptomyces microaureus, is an important amino-glycoside family antibiotic and widely used for veterinary and agricultural applications. In the left flanking region of the previously reported kasugamycin gene cluster, four additional genes (two-component system kasW and kasX, MerR-family kasV, and isoprenylcysteine carboxyl methyltransferase kasS) were identified both in the low-yielding S. kasugaensis BCRC12349 and high-yielding S. microaureus XM301. Deletion of regulatory gene kasT abolished kasugamycin production, and its overexpression in BCRC12349 resulted in an increased titer by 186 %. Deletion of kasW, kasX, kasV, and kasS improved kasugamycin production by 12, 19, 194, and 22 %, respectively. qRT-PCR analysis demonstrated that the transcription of kas genes was significantly increased in all the four mutants. Similar gene inactivation was performed in the high-yielding strain S. microaureus XM301. As expected, the deletion of kasW/X resulted in a 58 % increase of the yield from 6 to 9.5 g/L. However, the deletion of kasV and over-expression of kasT had no obvious effect, and the disruption of kasS surprisingly decreased kasugamycin production. In addition, trans-complementation of the kasS mutant with a TTA codon-mutated kasS increased the kasugamycin yield by 20 %. A much higher transcription of kas genes was detected in the high-yielding XM301 than in the low-yielding BCRC12349, which may partially account for the discrepancy of gene inactivation effects between them. Our work not only generated engineered strains with improved kasugamycin yield, but also pointed out that different strategies on manipulating regulatory-related genes should be considered for low-yielding or high-yielding strains.

  11. Use of soybean oil and ammonium sulfate additions to optimize secondary metabolite production.

    PubMed

    Junker, B; Mann, Z; Gailliot, P; Byrne, K; Wilson, J

    1998-12-05

    A valine-overproducing mutant (MA7040, Streptomyces hygroscopicus) was found to produce 1.5 to 2.0 g/L of the immunoregulant, L-683,590, at the 0.6 m3 fermentation scale in a simple batch process using soybean oil and ammonium sulfate-based GYG5 medium. Levels of both lower (L-683,795) and higher (HH1 and HH2) undesirable homolog levels were controlled adequately. This batch process was utilized to produce broth economically at the 19 m3 fermentation scale. Material of acceptable purity was obtained without the multiple pure crystallizations previously required for an earlier culture, MA6678, requiring valine supplementation for impurity control. Investigations at the 0.6 m3 fermentation scale were conducted, varying agitation, pH, initial soybean oil/ammonium sulfate charges, and initial aeration rate to further improve growth and productivity. Mid-cycle ammonia levels and lipase activity appeared to have an important role. Using mid-cycle soybean oil additions, a titer of 2.3 g/L of L-683,590 was obtained, while titers reached 2.7 g/L using mid-cycle soybean oil and ammonium sulfate additions. Both higher and lower homolog levels remained acceptable during this fed-batch process. Optimal timing of mid-cycle oil and ammonium sulfate additions was considered a critical factor to further titer improvements.

  12. Production of fired construction brick from high sulfate-containing fly ash with boric acid addition.

    PubMed

    Başpinar, M Serhat; Kahraman, Erhan; Görhan, Gökhan; Demir, Ismail

    2010-01-01

    The increase of power plant capacity has led to the production of an increasing amount of fly ash that causes high environmental impact in Turkey. Some of the fly ash is utilized within the fired brick industry but high sulfate-containing fly ash creates severe problems during sintering of the fired brick. This study attempted to investigate the potential for converting high sulfate-containing fly ash into useful material for the construction industry by the addition of boric acid. The chemical and mineralogical composition of fly ash and clay were investigated. Boric acid (H(3)BO(3)) was added to fly ash-clay mixtures with up to 5 wt.%. Six different series of test samples were produced by uniaxial pressing. The samples were fired at the industrial clay-brick firing temperatures of 800, 900 and 1000 degrees C. The microstructures of the fired samples were investigated by scanning electron microscopy and some physical and mechanical properties were measured. It was concluded that the firing at conventional brick firing temperature of high sulfate fly ash without any addition of boric acid resulted in very weak strength bricks. The addition of boric acid and clay simultaneously to the high sulfate- containing fly ash brick dramatically increased the compressive strength of the samples at a firing temperature of 1000 degrees C by modifying the sintering behaviour of high sulfate fly ash.

  13. Analysis of ldh genes in Lactobacillus casei BL23: role on lactic acid production.

    PubMed

    Rico, Juan; Yebra, María Jesús; Pérez-Martínez, Gaspar; Deutscher, Josef; Monedero, Vicente

    2008-06-01

    Lactobacillus casei is a lactic acid bacterium that produces L-lactate as the main product of sugar fermentation via L-lactate dehydrogenase (Ldh1) activity. In addition, small amounts of the D-lactate isomer are produced by the activity of a D-hydroxycaproate dehydrogenase (HicD). Ldh1 is the main L-lactate producing enzyme, but mutation of its gene does not eliminate L-lactate synthesis. A survey of the L. casei BL23 draft genome sequence revealed the presence of three additional genes encoding Ldh paralogs. In order to study the contribution of these genes to the global lactate production in this organism, individual, as well as double mutants (ldh1 ldh2, ldh1 ldh3, ldh1 ldh4 and ldh1 hicD) were constructed and lactic acid production was assessed in culture supernatants. ldh2, ldh3 and ldh4 genes play a minor role in lactate production, as their single mutation or a mutation in combination with an ldh1 deletion had a low impact on L-lactate synthesis. A Deltaldh1 mutant displayed an increased production of D-lactate, which was probably synthesized via the activity of HicD, as it was abolished in a Deltaldh1 hicD double mutant. Contrarily to HicD, no Ldh1, Ldh2, Ldh3 or Ldh4 activities could be detected by zymogram assays. In addition, these assays revealed the presence of extra bands exhibiting D-/L-lactate dehydrogenase activity, which could not be attributed to any of the described genes. These results suggest that L. casei BL23 possesses a complex enzymatic system able to reduce pyruvic to lactic acid.

  14. Epigenetic engineering of ribosomal RNA genes enhances protein production.

    PubMed

    Santoro, Raffaella; Lienemann, Philipp; Fussenegger, Martin

    2009-08-14

    Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA) genes encode the major component of the ribosome but many rRNA gene copies are not transcribed due to epigenetic silencing by the nucleolar remodelling complex (NoRC) [6], which may limit the cell's full production capacity. Here we show that the knockdown of TIP5, a subunit of NoRC, decreases the number of silent rRNA genes, upregulates rRNA transcription, enhances ribosome synthesis and increases production of recombinant proteins. However, general enhancement of rRNA transcription rate did not stimulate protein synthesis. Our data demonstrates that the number of transcriptionally competent rRNA genes limits efficient ribosome synthesis. Epigenetic engineering of ribosomal RNA genes offers new possibilities for improving biopharmaceutical manufacturing and provides novel insights into the complex regulatory network which governs the translation machinery in normal cellular processes as well as in pathological conditions like cancer.

  15. Natural Products Version 2.0: Connecting Genes to Molecules

    PubMed Central

    Walsh, Christopher T.; Fischbach, Michael A.

    2009-01-01

    Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, biological probes, and targets of study for synthetic and analytical chemists. In this perspective, we explore how connecting Nature’s small molecules to the genes that encode them has sparked a renaissance in natural product research, focusing primarily on the biosynthesis of polyketides and nonribosomal peptides. We survey monomer biogenesis, coupling chemistries from templated and non-templated pathways, and the broad set of tailoring reactions and hybrid pathways that give rise to the diverse scaffolds and functionalization patterns of natural products. We conclude by considering two questions: What would it take to find all natural product scaffolds? What kind of scientists will be studying natural products in the future? PMID:20121095

  16. Id-1 gene and gene products as therapeutic targets for treatment of breast cancer and other types of carcinoma

    DOEpatents

    Desprez, Pierre-Yves; Campisi, Judith

    2014-08-19

    A method for treatment of breast cancer and other types of cancer. The method comprises targeting and modulating Id-1 gene expression, if any, for the Id-1 gene, or gene products in breast or other epithelial cancers in a patient by delivering products that modulate Id-1 gene expression. When expressed, Id-1 gene is a prognostic indicator that cancer cells are invasive and metastatic.

  17. Transcriptional activation of cloned human beta-globin genes by viral immediate-early gene products.

    PubMed

    Green, M R; Treisman, R; Maniatis, T

    1983-11-01

    When the human beta-globin gene is transfected into Hela cells, no beta-globin RNA is detected unless the gene is linked to a viral transcription enhancer. In this paper we show that trans-acting adenovirus and herpesvirus (pseudorabies) transcriptional regulatory proteins can circumvent this enhancer requirement for detectable beta-globin transcription in transient expression assays. The viral gene products can be provided by constitutively expressed, integrated viral genes in established cell lines, by viral infection of permissive cells, or by transfection of cells with bacterial plasmids carrying the viral immediate-early genes. These results demonstrate the utility of transient expression assays for studying regulatory mechanisms involving trans-acting factors. Analysis of beta-globin promoter mutants indicates that between 75 and 128 bp of sequence 5' to the mRNA cap site is required for enhancer-dependent transcription in Hela cells. In contrast, beta-globin transcription in the presence of viral immediate-early gene products requires only 36 bp of 5'-flanking sequence, which includes the TATA box. Thus both cis and trans-acting viral factors activate beta-globin gene transcription in transient expression experiments, but the mechanisms by which they act appear to be fundamentally different.

  18. Identification of a sugar beet BvM14-MADS box gene through differential gene expression analysis of monosomic addition line M14.

    PubMed

    Ma, Chunquan; Wang, Yuguang; Wang, Yuting; Wang, Lifa; Chen, Sixue; Li, Haiying

    2011-11-01

    Monosomic addition line M14 carrying an additional chromosome 9 from Beta corolliflora Zosimovic ex Buttler was obtained through hybridization between the wild species B. corolliflora and a cultivated species Beta vulgaris L. var Saccharifera Alef. The M14 line showed diplosporic reproduction and stress tolerance. To identify differentially expressed genes in M14, a subtractive cDNA library was prepared by suppression subtractive hybridization (SSH) between M14 (2n=18+1) and B. vulgaris (2n=18). A total of 190 unique sequences were identified in the library and their putative functions were analyzed using Gene Ontology (GO). One of the genes, designated as BvM14-MADS box, encodes a MADS box transcription factor. It was cloned from M14 and over-expressed in transgenic tobacco plants. Interestingly, this gene was located on chromosome 2 of B. vulgaris, not on the additional chromosome 9. Overexpression of BvM14-MADS box led to significant phenotypic changes in tobacco. The differential expression of BvM14-MADS box gene in M14 may be caused by the interaction between the additional chromosome 9 from B. corolliflora and the B. vulgaris chromosomes in M14.

  19. Nano-porous pottery using calcined waste sediment from tap water production as an additive.

    PubMed

    Sangsuk, Supin; Khunthon, Srichalai; Nilpairach, Siriphan

    2010-10-01

    A suspension of sediment from a lagoon in a tap water production plant was collected for this experiment. The suspension was spray dried and calcined at 700 °C for 1 h. After calcining, 30 wt.% of the sediment were mixed with pottery clay. Samples with and without calcined sediment were sintered at 900, 1000 and 1100 °C. The results show that calcined sediment can be used as an additive in pottery clay. The samples with calcined sediment show higher porosity, water absorption and flexural strength, especially for 900 and 1000 °C. At 900 °C, samples with calcined sediment show a porosity of 50% with an average pore size of 68 nm, water absorption of 31% and flexural strength of 12.61 MPa.

  20. The effect of addition Ni and Co on biogas production from fish innards

    NASA Astrophysics Data System (ADS)

    Hadiyarto, Agus; Hutama, Indra; Hasyim, Wahid

    2015-12-01

    Micro nutrients are needed by the microbes to help decomposition of the organic waste into simple inorganic compounds. In the anaerobic decay is one of the results of methane gas. This research was conducted by adding nickel and cobalt with various concentrations of each the same, namely 0.2 mg/l, 0.4 mg/l and 0.6 mg/l into fish innards with F / M ratio of 0.2. Anaerobic decomposition process conducted in a batch at pH 7-8, mesophilic conditions/ambient temperature. To separate CO2 from CH4 gas used NaOH solution. The volume of gas produced is measured by the fluid displaced method. Most of methane production resulting in the addition of Ni and Co with a concentration of 0.4 mg /l with a yield of 165 liters CH4/kg CODMn or 18,1 liter CH4/kg VSS substrate.

  1. CASCADES AFTER K-VACANCY PRODUCTION AND ADDITIONAL IONIZATION OR EXCITATION IN ATOMS OF LIGHT ELEMENTS

    SciTech Connect

    Kucas, S.; Momkauskaitė, A.; Karazija, R.

    2015-09-01

    The results of Auger and radiative cascades after the production of a vacancy in the K-shell and the additional ionization or excitation of the other shell are presented for the various ions of astrophysically important elements, namely, Ne, Mg, Si, S, and Ar. The detailed level-by-level calculations are performed using a single-configuration quasi-relativistic approximation. The populations of the levels of the excited configurations produced during a cascade as well as for the final ions are presented. These data enable us to take into account two-electron processes at the K-shell ionization, and thus to supplement the results of our earlier investigation of K-vacancy cascades.

  2. Effect of addition of sodium alginate on bacterial cellulose production by Acetobacter xylinum.

    PubMed

    Zhou, L L; Sun, D P; Hu, L Y; Li, Y W; Yang, J Z

    2007-07-01

    Bacterial cellulose (BC) production by Acetobacter xylinum NUST4.1 was carried out in the shake flask and in a stirred-tank reactor by means of adding sodium alginate (NaAlg) into the medium. When 0.04% (w/v) NaAlg was added in the shake flask, BC production reached 6.0 g/l and the terminal yield of the cellulose was 27% of the total sugar initially added, compared with 3.7 g/l and 24% in the control, respectively. The variation between replicates in all determinations was less than 5%. During the cultivation in the stirred-tank reactor, the addition of NaAlg changed the morphology of cellulose from the irregular clumps and fibrous masses entangled in the internals to discrete masses dispersing into the broth, which indicates that NaAlg hinders formation of large clumps of BC, and enhances cellulose yield. Because the structure of cellulose is changed depending on the culture condition such as additives, structural characteristics of BC produced in the NaAlg-free and NaAlg medium are compared using scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD). SEM photographs show some differences in reticulated structures and ribbon width and FT-IR spectra indicate that there is the hydrogen bonding interaction between BC and NaAlg, then X-ray diffraction (XRD) analysis reveals that BC produced with NaAlg-added has a lower crystallinity and a smaller crystalline size. The results show that enhanced yields and modification of cellulose structure occur in the presence of NaAlg.

  3. Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption

    PubMed Central

    Pirastu, Nicola; Kooyman, Maarten; Robino, Antonietta; van der Spek, Ashley; Navarini, Luciano; Amin, Najaf; Karssen, Lennart C.; Van Duijn, Cornelia M; Gasparini, Paolo

    2016-01-01

    Coffee is one of the most consumed beverages world-wide and one of the primary sources of caffeine intake. Given its important health and economic impact, the underlying genetics of its consumption has been widely studied. Despite these efforts, much has still to be uncovered. In particular, the use of non-additive genetic models may uncover new information about the genetic variants driving coffee consumption. We have conducted a genome-wide association study in two Italian populations using additive, recessive and dominant models for analysis. This has uncovered a significant association in the PDSS2 gene under the recessive model that has been replicated in an independent cohort from the Netherlands (ERF). The identified gene has been shown to negatively regulate the expression of the caffeine metabolism genes and can thus be linked to coffee consumption. Further bioinformatics analysis of eQTL and histone marks from Roadmap data has evidenced a possible role of the identified SNPs in regulating PDSS2 gene expression through enhancers present in its intron. Our results highlight a novel gene which regulates coffee consumption by regulating the expression of the genes linked to caffeine metabolism. Further studies will be needed to clarify the biological mechanism which links PDSS2 and coffee consumption. PMID:27561104

  4. Improvements in nanoscale zero-valent iron production by milling through the addition of alumina

    NASA Astrophysics Data System (ADS)

    Ribas, D.; Cernik, M.; Martí, V.; Benito, J. A.

    2016-07-01

    A new milling procedure for a cost-effective production of nanoscale zero-valent iron for environmental remediation is presented. Conventional ball milling of iron in an organic solvent as Mono Ethylene Glycol produces flattened iron particles that are unlikely to break even after very long milling times. With the aim of breaking down these iron flakes, in this new procedure, further milling is carried out by adding an amount of fine alumina powder to the previously milled solution. As the amount of added alumina increases from 9 to 54 g l-1, a progressive decrease of the presence of flakes is observed. In the latter case, the appearance of the particles formed by fragments of former flakes is rather homogeneous, with most of the final nanoparticles having an equivalent diameter well below 1 µm and with an average particle size in solution of around 400 nm. An additional increase of alumina content results in a highly viscous solution showing worse particle size distribution. Milled particles, in the case of alumina concentrations of 54 g l-1, have a fairly large specific surface area and high Fe(0) content. These new particles show a very good Cr(VI) removal efficiency compared with other commercial products available. This good reactivity is related to the absence of an oxide layer, the large amount of superficial irregularities generated by the repetitive fracture process during milling and the presence of a fine nanostructure within the iron nanoparticles.

  5. Qualitative Analysis of Additives in Plastic Marine Debris and Its New Products.

    PubMed

    Rani, Manviri; Shim, Won Joon; Han, Gi Myung; Jang, Mi; Al-Odaini, Najat Ahmed; Song, Young Kyong; Hong, Sang Hee

    2015-10-01

    Due to their formulation and/or processing, plastics contain additives and impurities that may leach out under conditions of use and accumulate in the environment. To evaluate their role as vectors of chemical contaminants in marine environment, plastic debris (n = 19) collected from coastal beaches along with new plastics (n = 25; same or same brand) bought from local markets were screened by gas chromatography-mass spectrometry in full scan mode. Detected peaks were identified using NIST library in different polymers (polypropylene (PP) > polyethylene (PE) > PP + PE > polyethyl terephthalate > poly(acylene:styrene) with different use (food, fishery, and general use). A database on the presence of 231 different chemicals were grouped into hydrocarbons, ultra-violet (UV)-stabilizers, antioxidants, plasticizers, lubricants, intermediates, compounds for dyes and inks, flame retardants, etc. The UV326, UV327, UV328, UV320, UvinualMC80, irganox 1076, DEHP, antioxidant no 33, di-n-octylisophthalate, diisooctyl phthalate, hexanoic acid 2-ethyl-hexadecyl ester, and hydrocarbons were most frequently detected. Finding of toxic phthalates and UV stabilizers in those products having moisture contact (like bottles with short use) raised concern to humans and indicated their irregular use. The comparison between new and debris plastics clearly indicated the leaching and absorption of chemicals and supports our assumption of plastic as media for transferring these additives in marine environment.

  6. Quality of shrimp analogue product as affected by addition of modified potato starch.

    PubMed

    Remya, S; Basu, S; Venkateshwarlu, G; Mohan, C O

    2015-07-01

    The present study was aimed to investigate the effects of addition of modified potato starch on the biochemical and textural properties of shrimp analogue/imitation shrimp, a popular value-added product prepared from surimi. Three batches of shrimp analogues were prepared with 0 % (NPS), 50 % (CPS) and 100 % (MPS) of modified starch incorporation and various quality attributes were monitored at regular intervals during frozen storage (-20 °C). Loss of myofibrillar protein was least for the shrimp analogue sample added with 100 % modified potato starch. The expressible moisture content of MPS (2.48 %) was less affected by long term storage compared to CPS (3.38 %) and NPS (3.99 %). During extended low temperature storage, the textural quality of sea food analogue was highly influenced by the type of starch added to it. The percentage of modified potato starch added to shrimp analogue significantly (p ≤ 0.05) affected its hardness and fracturability. MPS samples did not show significant changes in hardness during storage as compared to other two samples. Springiness of shrimp analogue increased 2.57, 1.5 and 1.77 times with the storage period for samples with NPS, CPS and MPS, respectively. Addition of modified potato starch improved the sensory quality and textural properties of shrimp analogue and reduced the quality degradation during frozen storage as compared to NPS which contained only native potato starch.

  7. Plasmid genes required for microcin B17 production.

    PubMed Central

    San Millán, J L; Kolter, R; Moreno, F

    1985-01-01

    The production of the antibiotic substance microcin B17 (Mcc) is determined by a 3.5-kilobase DNA fragment from plasmid pMccB17. Several Mcc- mutations on plasmid pMccB17 were obtained by both transposon insertion and nitrosoguanidine mutagenesis. Plasmids carrying these mutations were tested for their ability to complement Mcc- insertion or deletion mutations on pMM102 (pMM102 is a pBR322 derivative carrying the region encoding microcin B17). Results from these experiments indicate that at least four plasmid genes are required for microcin production. PMID:2993228

  8. Characterization of the Soluble NSF Attachment Protein gene family identifies two members involved in additive resistance to a plant pathogen

    PubMed Central

    Lakhssassi, Naoufal; Liu, Shiming; Bekal, Sadia; Zhou, Zhou; Colantonio, Vincent; Lambert, Kris; Barakat, Abdelali; Meksem, Khalid

    2017-01-01

    Proteins with Tetratricopeptide-repeat (TPR) domains are encoded by large gene families and distributed in all plant lineages. In this study, the Soluble NSF-Attachment Protein (SNAP) subfamily of TPR containing proteins is characterized. In soybean, five members constitute the SNAP gene family: GmSNAP18, GmSNAP11, GmSNAP14, GmSNAP02, and GmSNAP09. Recently, GmSNAP18 has been reported to mediate resistance to soybean cyst nematode (SCN). Using a population of recombinant inbred lines from resistant and susceptible parents, the divergence of the SNAP gene family is analysed over time. Phylogenetic analysis of SNAP genes from 22 diverse plant species showed that SNAPs were distributed in six monophyletic clades corresponding to the major plant lineages. Conservation of the four TPR motifs in all species, including ancestral lineages, supports the hypothesis that SNAPs were duplicated and derived from a common ancestor and unique gene still present in chlorophytic algae. Syntenic analysis of regions harbouring GmSNAP genes in soybean reveals that this family expanded from segmental and tandem duplications following a tetraploidization event. qRT-PCR analysis of GmSNAPs indicates a co-regulation following SCN infection. Finally, genetic analysis demonstrates that GmSNAP11 contributes to an additive resistance to SCN. Thus, GmSNAP11 is identified as a novel minor gene conferring resistance to SCN. PMID:28338077

  9. Detection of additional genes of the patulin biosynthetic pathway in Penicillium griseofulvum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genes in the patulin biosynthetic pathway are likely to be arranged in a cluster as has been found for biosynthetic pathways of other mycotoxins. The mycotoxin patulin, common in apples and apple juice, is most often associated with Penicillium expansum. However, of 15 fungal species capable of sy...

  10. Natural product proteomining, a quantitative proteomics platform, allows rapid discovery of biosynthetic gene clusters for different classes of natural products.

    PubMed

    Gubbens, Jacob; Zhu, Hua; Girard, Geneviève; Song, Lijiang; Florea, Bogdan I; Aston, Philip; Ichinose, Koji; Filippov, Dmitri V; Choi, Young H; Overkleeft, Herman S; Challis, Gregory L; van Wezel, Gilles P

    2014-06-19

    Information on gene clusters for natural product biosynthesis is accumulating rapidly because of the current boom of available genome sequencing data. However, linking a natural product to a specific gene cluster remains challenging. Here, we present a widely applicable strategy for the identification of gene clusters for specific natural products, which we name natural product proteomining. The method is based on using fluctuating growth conditions that ensure differential biosynthesis of the bioactivity of interest. Subsequent combination of metabolomics and quantitative proteomics establishes correlations between abundance of natural products and concomitant changes in the protein pool, which allows identification of the relevant biosynthetic gene cluster. We used this approach to elucidate gene clusters for different natural products in Bacillus and Streptomyces, including a novel juglomycin-type antibiotic. Natural product proteomining does not require prior knowledge of the gene cluster or secondary metabolite and therefore represents a general strategy for identification of all types of gene clusters.

  11. Modern plant metabolomics: Advanced natural product gene discoveries, improved technologies, and future prospects

    SciTech Connect

    Sumner, Lloyd W.; Lei, Zhentian; Nikolau, Basil J.; Saito, Kazuki

    2014-10-24

    Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This study highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR for metabolite identifications, and x-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.

  12. Modern plant metabolomics: Advanced natural product gene discoveries, improved technologies, and future prospects

    DOE PAGES

    Sumner, Lloyd W.; Lei, Zhentian; Nikolau, Basil J.; ...

    2014-10-24

    Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This study highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR formore » metabolite identifications, and x-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.« less

  13. Chromosomal Localization of Genes Conferring Desirable Agronomic Traits from Wheat-Agropyron cristatum Disomic Addition Line 5113.

    PubMed

    Li, Qingfeng; Lu, Yuqing; Pan, Cuili; Yao, Miaomiao; Zhang, Jinpeng; Yang, Xinming; Liu, Weihua; Li, Xiuquan; Xi, Yajun; Li, Lihui

    2016-01-01

    Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F1, BC1F1 and BC1F2 populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding.

  14. Chromosomal Localization of Genes Conferring Desirable Agronomic Traits from Wheat-Agropyron cristatum Disomic Addition Line 5113

    PubMed Central

    Pan, Cuili; Yao, Miaomiao; Zhang, Jinpeng; Yang, Xinming; Liu, Weihua; Li, Xiuquan; Xi, Yajun; Li, Lihui

    2016-01-01

    Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F1, BC1F1 and BC1F2 populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding. PMID:27824906

  15. Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes.

    PubMed

    Abdel-Ghany, Salah E; Day, Irene; Heuberger, Adam L; Broeckling, Corey D; Reddy, Anireddy S N

    2013-11-01

    1,2,4-butanetriol (butanetriol) is a useful precursor for the synthesis of the energetic material butanetriol trinitrate and several pharmaceutical compounds. Bacterial synthesis of butanetriol from xylose or arabinose takes place in a pathway that requires four enzymes. To produce butanetriol in plants by expressing bacterial enzymes, we cloned native bacterial or codon optimized synthetic genes under different promoters into a binary vector and stably transformed Arabidopsis plants. Transgenic lines expressing introduced genes were analyzed for the production of butanetriol using gas chromatography coupled to mass spectrometry (GC-MS). Soil-grown transgenic plants expressing these genes produced up to 20 µg/g of butanetriol. To test if an exogenous supply of pentose sugar precursors would enhance the butanetriol level, transgenic plants were grown in a medium supplemented with either xylose or arabinose and the amount of butanetriol was quantified. Plants expressing synthetic genes in the arabinose pathway showed up to a forty-fold increase in butanetriol levels after arabinose was added to the medium. Transgenic plants expressing either bacterial or synthetic xylose pathways, or the arabinose pathway showed toxicity symptoms when xylose or arabinose was added to the medium, suggesting that a by-product in the pathway or butanetriol affected plant growth. Furthermore, the metabolite profile of plants expressing arabinose and xylose pathways was altered. Our results demonstrate that bacterial pathways that produce butanetriol can be engineered into plants to produce this chemical. This proof-of-concept study for phytoproduction of butanetriol paves the way to further manipulate metabolic pathways in plants to enhance the level of butanetriol production.

  16. Physiological basis of tolerance to complete submergence in rice involves genetic factors in addition to the SUB1 gene

    PubMed Central

    Singh, Sudhanshu; Mackill, David J.; Ismail, Abdelbagi M.

    2014-01-01

    Recurring floods in Asia cause poor crop establishment. Yields decline drastically when plants are completely submerged for a few days. Traditional rice cultivars predominate because they have acquired moderate tolerance to flooding but they carry the penalty of inherently lower grain yields. In contrast, modern high-yielding varieties are highly susceptible to flooding. Cultivars with tolerance to complete submergence were recently developed in the background of popular varieties by transferring the submergence tolerance gene SUBMERGENCE1 (SUB1) from the highly tolerant Indian landrace FR13A. The present study evaluated three pairs of Sub1 near-isogenic lines (NILs) together with FR13A and two of its submergence-tolerant derivatives under field conditions to assess the survival and growth processes occurring during submergence and recovery that are associated with SUB1. Under control conditions, the NILs showed similar growth and biomass accumulation, indicating that SUB1 had no apparent effects. Submergence substantially decreased biomass accumulation but with greater reduction in the genotypes lacking SUB1, particularly when submergence was prolonged for 17 days. When submerged, the lines lacking SUB1 showed greater elongation and lower or negative biomass accumulation. Sub1 lines maintained higher chlorophyll concentrations during submergence and lost less non-structural carbohydrates (NSC) after submergence. This indicates that the introgression of SUB1 resulted in better regulation of NSC during submergence and that high pre-submergence NSC is not essential for the submergence tolerance conferred by SUB1. During recovery, chlorophyll degradation was faster in genotypes lacking SUB1 and any surviving plants showed poorer and delayed emergence of tillers and leaves. Sub1 lines restored new leaf and tiller production faster. During submergence, FR13A showed not only slower leaf elongation but also accumulated extra biomass and was able to recover faster than Sub

  17. Physiological basis of tolerance to complete submergence in rice involves genetic factors in addition to the SUB1 gene.

    PubMed

    Singh, Sudhanshu; Mackill, David J; Ismail, Abdelbagi M

    2014-10-03

    Recurring floods in Asia cause poor crop establishment. Yields decline drastically when plants are completely submerged for a few days. Traditional rice cultivars predominate because they have acquired moderate tolerance to flooding but they carry the penalty of inherently lower grain yields. In contrast, modern high-yielding varieties are highly susceptible to flooding. Cultivars with tolerance to complete submergence were recently developed in the background of popular varieties by transferring the submergence tolerance gene SUBMERGENCE1 (SUB1) from the highly tolerant Indian landrace FR13A. The present study evaluated three pairs of Sub1 near-isogenic lines (NILs) together with FR13A and two of its submergence-tolerant derivatives under field conditions to assess the survival and growth processes occurring during submergence and recovery that are associated with SUB1. Under control conditions, the NILs showed similar growth and biomass accumulation, indicating that SUB1 had no apparent effects. Submergence substantially decreased biomass accumulation but with greater reduction in the genotypes lacking SUB1, particularly when submergence was prolonged for 17 days. When submerged, the lines lacking SUB1 showed greater elongation and lower or negative biomass accumulation. Sub1 lines maintained higher chlorophyll concentrations during submergence and lost less non-structural carbohydrates (NSC) after submergence. This indicates that the introgression of SUB1 resulted in better regulation of NSC during submergence and that high pre-submergence NSC is not essential for the submergence tolerance conferred by SUB1. During recovery, chlorophyll degradation was faster in genotypes lacking SUB1 and any surviving plants showed poorer and delayed emergence of tillers and leaves. Sub1 lines restored new leaf and tiller production faster. During submergence, FR13A showed not only slower leaf elongation but also accumulated extra biomass and was able to recover faster than Sub

  18. Supplementing High-Density SNP Microarrays for Additional Coverage of Disease-Related Genes: Addiction as a Paradigm

    PubMed Central

    Saccone, Scott F.; Bierut, Laura J.; Chesler, Elissa J.; Kalivas, Peter W.; Lerman, Caryn; Saccone, Nancy L.; Uhl, George R.; Li, Chuan-Yun; Philip, Vivek M.; Edenberg, Howard J.; Sherry, Stephen T.; Feolo, Michael; Moyzis, Robert K.; Rutter, Joni L.

    2009-01-01

    Commercial SNP microarrays now provide comprehensive and affordable coverage of the human genome. However, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is thought to be influenced by complex interactions among many relevant genes and pathways. We have assembled a list of 486 biologically relevant genes nominated by a panel of experts on addiction. We then added 424 genes that showed evidence of association with addiction phenotypes through mouse QTL mappings and gene co-expression analysis. We demonstrate that there are a substantial number of SNPs in these genes that are not well represented by commercial SNP platforms. We address this problem by introducing a publicly available SNP database for addiction. The database is annotated using numeric prioritization scores indicating the extent of biological relevance. The scores incorporate a number of factors such as SNP/gene functional properties (including synonymy and promoter regions), data from mouse systems genetics and measures of human/mouse evolutionary conservation. We then used HapMap genotyping data to determine if a SNP is tagged by a commercial microarray through linkage disequilibrium. This combination of biological prioritization scores and LD tagging annotation will enable addiction researchers to supplement commercial SNP microarrays to ensure comprehensive coverage of biologically relevant regions. PMID:19381300

  19. Supplementing High-Density SNP Microarrays for Additional Coverage of Disease-Related Genes: Addiction as a Paradigm

    SciTech Connect

    SacconePhD, Scott F; Chesler, Elissa J; Bierut, Laura J; Kalivas, Peter J; Lerman, Caryn; Saccone, Nancy L; Uhl, George R; Li, Chuan-Yun; Philip, Vivek M; Edenberg, Howard; Sherry, Steven; Feolo, Michael; Moyzis, Robert K; Rutter, Joni L

    2009-01-01

    Commercial SNP microarrays now provide comprehensive and affordable coverage of the human genome. However, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is thought to be influenced by complex interactions among many relevant genes and pathways. We have assembled a list of 486 biologically relevant genes nominated by a panel of experts on addiction. We then added 424 genes that showed evidence of association with addiction phenotypes through mouse QTL mappings and gene co-expression analysis. We demonstrate that there are a substantial number of SNPs in these genes that are not well represented by commercial SNP platforms. We address this problem by introducing a publicly available SNP database for addiction. The database is annotated using numeric prioritization scores indicating the extent of biological relevance. The scores incorporate a number of factors such as SNP/gene functional properties (including synonymy and promoter regions), data from mouse systems genetics and measures of human/mouse evolutionary conservation. We then used HapMap genotyping data to determine if a SNP is tagged by a commercial microarray through linkage disequilibrium. This combination of biological prioritization scores and LD tagging annotation will enable addiction researchers to supplement commercial SNP microarrays to ensure comprehensive coverage of biologically relevant regions.

  20. Encapsulated whey-native yeast Kluyveromyces marxianus as a feed additive for animal production.

    PubMed

    Díaz-Vergara, Ladislao; Pereyra, Carina Maricel; Montenegro, Mariana; Pena, Gabriela Alejandra; Aminahuel, Carla Ayelen; Cavaglieri, Lilia R

    2017-03-06

    Whey is the main byproduct of the cheese industry. While the composition is variable, it retains up to 55% of milk nutrients. The beneficial features of whey indicates a promising source of new potentially probiotic strains for the development of food additives destined for animal production. The aim of this study was to identify Kluyveromyces spp. isolated from whey, to study some probiotic properties and to select the best strain to be encapsulated using derivatised chitosan. Kluyveromyces marxianus strains (VM003, VM004 and VM005) were isolated from whey and identified by phenotypic and molecular techniques. These three yeast strains were able to survive under gastrointestinal conditions. Moreover, they exhibited weak auto-aggregation and co-aggregation with pathogenic bacteria (Salmonella sp., Serratia sp., Escherichia coli and Salmonella typhimurium). In general the K. marxianus strains had a strong antimicrobial activity against pathogenic bacteria. The potential probiotic K. marxianus VM004 strain was selected for derivatised-chitosan encapsulation. Material treated with native chitosan exhibited a strong antimicrobial activity of K. marxianus, showing a total growth inhibition at 10 min exposure. However, derivatised-chitosan encapsulation showed a reduced antimicrobial activity. This is the first study to show some probiotic properties of whey-native K. marxianus, in vitro. An encapsulation strategy was applied using derivatised chitosan.

  1. Post Processing Methods used to Improve Surface Finish of Products which are Manufactured by Additive Manufacturing Technologies: A Review

    NASA Astrophysics Data System (ADS)

    Kumbhar, N. N.; Mulay, A. V.

    2016-08-01

    The Additive Manufacturing (AM) processes open the possibility to go directly from Computer-Aided Design (CAD) to a physical prototype. These prototypes are used as test models before it is finalized as well as sometimes as a final product. Additive Manufacturing has many advantages over the traditional process used to develop a product such as allowing early customer involvement in product development, complex shape generation and also save time as well as money. Additive manufacturing also possess some special challenges that are usually worth overcoming such as Poor Surface quality, Physical Properties and use of specific raw material for manufacturing. To improve the surface quality several attempts had been made by controlling various process parameters of Additive manufacturing and also applying different post processing techniques on components manufactured by Additive manufacturing. The main objective of this work is to document an extensive literature review in the general area of post processing techniques which are used in Additive manufacturing.

  2. Genetic variation at the TPH2 gene influences impulsivity in addition to eating disorders.

    PubMed

    Slof-Op't Landt, Margarita C T; Bartels, Meike; Middeldorp, Christel M; van Beijsterveldt, Catherina E M; Slagboom, P Eline; Boomsma, Dorret I; van Furth, Eric F; Meulenbelt, Ingrid

    2013-01-01

    Genes are involved in eating disorders (EDs) and self-induced vomiting (SV), a key symptom of different types of EDs. Perfectionism and impulsivity are potential risk factors for EDs. TPH2 (tryptophan hydroxylase 2) SNP rs1473473 was previously associated with anorexia nervosa and EDs characterized by SV. Could perfectionism or impulsivity be underlying the association between rs1473473 and EDs? Genetic association between TPH2 SNP rs1473473 and perfectionism or impulsivity was first evaluated in a random control group (N = 512). The associations obtained in this control group were subsequently tested in a group of patients with an ED (N = 267). The minor allele of rs1473473 (OR = 1.49) was more frequent in impulsive controls, but also in impulsive patients with an ED (OR = 1.83). The largest effect was found in the patients with an ED characterized by SV (OR = 2.51, p = 0.02). Genetic variation at the TPH2 gene appeared to affect impulsivity which, in turn, might predispose to the SV phenotype.

  3. Gene expression suggests conserved aspects of Hox gene regulation in arthropods and provides additional support for monophyletic Myriapoda.

    PubMed

    Janssen, Ralf; Budd, Graham E

    2010-07-05

    Antisense transcripts of Ultrabithorax (aUbx) in the millipede Glomeris and the centipede Lithobius are expressed in patterns complementary to that of the Ubx sense transcripts. A similar complementary expression pattern has been described for non-coding RNAs (ncRNAs) of the bithoraxoid (bxd) locus in Drosophila, in which the transcription of bxd ncRNAs represses Ubx via transcriptional interference. We discuss our findings in the context of possibly conserved mechanisms of Ubx regulation in myriapods and the fly.Bicistronic transcription of Ubx and Antennapedia (Antp) has been reported previously for a myriapod and a number of crustaceans. In this paper, we show that Ubx/Antp bicistronic transcripts also occur in Glomeris and an onychophoran, suggesting further conserved mechanisms of Hox gene regulation in arthropods.Myriapod monophyly is supported by the expression of aUbx in all investigated myriapods, whereas in other arthropod classes, including the Onychophora, aUbx is not expressed. Of the two splice variants of Ubx/Antp only one could be isolated from myriapods, representing a possible further synapomorphy of the Myriapoda.

  4. Single gene insertion drives bioalcohol production by a thermophilic archaeon

    PubMed Central

    Basen, Mirko; Schut, Gerrit J.; Nguyen, Diep M.; Lipscomb, Gina L.; Benn, Robert A.; Prybol, Cameron J.; Vaccaro, Brian J.; Poole, Farris L.; Kelly, Robert M.; Adams, Michael W. W.

    2014-01-01

    Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 °C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways. PMID:25368184

  5. Single gene insertion drives bioalcohol production by a thermophilic archaeon

    SciTech Connect

    Basen, M; Schut, GJ; Nguyen, DM; Lipscomb, GL; Benn, RA; Prybol, CJ; Vaccaro, BJ; Poole, FL; Kelly, RM; Adams, MWW

    2014-12-09

    Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 degrees C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.

  6. Single gene insertion drives bioalcohol production by a thermophilic archaeon.

    PubMed

    Basen, Mirko; Schut, Gerrit J; Nguyen, Diep M; Lipscomb, Gina L; Benn, Robert A; Prybol, Cameron J; Vaccaro, Brian J; Poole, Farris L; Kelly, Robert M; Adams, Michael W W

    2014-12-09

    Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 °C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.

  7. Additional copies of the proteolipid protein gene causing Pelizaeus-Merzbacher disease arise by separate integration into the X chromosome.

    PubMed

    Hodes, M E; Woodward, K; Spinner, N B; Emanuel, B S; Enrico-Simon, A; Kamholz, J; Stambolian, D; Zackai, E H; Pratt, V M; Thomas, I T; Crandall, K; Dlouhy, S R; Malcolm, S

    2000-07-01

    The proteolipid protein gene (PLP) is normally present at chromosome Xq22. Mutations and duplications of this gene are associated with Pelizaeus-Merzbacher disease (PMD). Here we describe two new families in which males affected with PMD were found to have a copy of PLP on the short arm of the X chromosome, in addition to a normal copy on Xq22. In the first family, the extra copy was first detected by the presence of heterozygosity of the AhaII dimorphism within the PLP gene. The results of FISH analysis showed an additional copy of PLP in Xp22.1, although no chromosomal rearrangements could be detected by standard karyotype analysis. Another three affected males from the family had similar findings. In a second unrelated family with signs of PMD, cytogenetic analysis showed a pericentric inversion of the X chromosome. In the inv(X) carried by several affected family members, FISH showed PLP signals at Xp11.4 and Xq22. A third family has previously been reported, in which affected members had an extra copy of the PLP gene detected at Xq26 in a chromosome with an otherwise normal banding pattern. The identification of three separate families in which PLP is duplicated at a noncontiguous site suggests that such duplications could be a relatively common but previously undetected cause of genetic disorders.

  8. Integrating products of Bessel functions with an additional exponential or rational factor

    NASA Astrophysics Data System (ADS)

    Van Deun, Joris; Cools, Ronald

    2008-04-01

    We provide two MATLAB programs to compute integrals of the form ex∏i=1kJν_i(ax)dxand 0∞xr+x∏i=1kJν_i(ax)dx with Jν_i(x) the Bessel function of the first kind and (real) order ν. The parameter m is a real number such that ∑ν+m>-1 (to assure integrability near zero), r is real and the numbers c and a are all strictly positive. The program can deliver accurate error estimates. Program summaryProgram title: BESSELINTR, BESSELINTC Catalogue identifier: AEAH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1601 No. of bytes in distributed program, including test data, etc.: 13 161 Distribution format: tar.gz Programming language: Matlab (version ⩾6.5), Octave (version ⩾2.1.69) Computer: All supporting Matlab or Octave Operating system: All supporting Matlab or Octave RAM: For k Bessel functions our program needs approximately ( 500+140k) double precision variables Classification: 4.11 Nature of problem: The problem consists in integrating an arbitrary product of Bessel functions with an additional rational or exponential factor over a semi-infinite interval. Difficulties arise from the irregular oscillatory behaviour and the possible slow decay of the integrand, which prevents truncation at a finite point. Solution method: The interval of integration is split into a finite and infinite part. The integral over the finite part is computed using Gauss-Legendre quadrature. The integrand on the infinite part is approximated using asymptotic expansions and this approximation is integrated exactly with the aid of the upper incomplete gamma function. In the case where a rational factor is present, this factor is first expanded in a Taylor series around infinity. Restrictions: Some (and eventually all

  9. Greenhouse gas emissions from sub-tropical agricultural soils after addition of organic by-products.

    PubMed

    Nguyen, Dai H; Biala, Johannes; Grace, Peter R; Scheer, Clemens; Rowlings, David W

    2014-01-01

    As the cost of mineral fertilisers increases globally, organic soil amendments (OAs) from agricultural sources are increasingly being used as substitutes for nitrogen. However, the impact of OAs on the production of greenhouse gases (CO2 and N2O) is not well understood. A 60-day laboratory incubation experiment was conducted to investigate the impacts of applying OAs (equivalent to 296 kg N ha(-1) on average) on N2O and CO2 emissions and soil properties of clay and sandy loam soils from sugar cane production. The experiment included 6 treatments, one being an un-amended (UN) control with addition of five OAs being raw mill mud (MM), composted mill mud (CM), high N compost (HC), rice husk biochar (RB), and raw mill mud plus rice husk biochar (MB). These OAs were incubated at 60, 75 and 90% water-filled pore space (WFPS) at 25°C with urea (equivalent to 200 kg N ha(-1)) added to the soils thirty days after the incubation commenced. Results showed WFPS did not influence CO2 emissions over the 60 days but the magnitude of emissions as a proportion of C applied was RB < CM < MB < HC < MM. Nitrous oxide emissions were significantly less in the clay soil compared to the sandy loam at all WFPS, and could be ranked RB < MB < MM < CM < UN < HC. These results led to linear models being developed to predict CO2 and N2O emissions as a function of the dry matter and C/N ratio of the OAs, WFPS, and the soil CEC. Application of RB reduced N2O emissions by as much as 42-64% depending on WFPS. The reductions in both CO2 and N2O emissions after application of RB were due to a reduced bioavailability of C and not immobilisation of N. These findings show that the effect of OAs on soil GHG emissions can vary substantially depending on their chemical properties. OAs with a high availability of labile C and N can lead to elevated emissions of CO2 and N2O, while rice husk biochar showed potential in reducing overall soil GHG emissions.

  10. Identification of an additional gene required for eukaryotic nonsense mRNA turnover.

    PubMed Central

    Lee, B S; Culbertson, M R

    1995-01-01

    Loss of function of any one of three UPF genes prevents the accelerated decay of nonsense mRNAs in Saccharomyces cerevisiae. We report the identification and DNA sequence of UPF3, which is present in one nonessential copy on chromosome VII. Upf3 contains three putative nuclear localization signal sequences, suggesting that it may be located in a different compartment than the cytoplasmic Upf1 protein. Epitope-tagged Upf3 (FLAG-Upf3) does not cofractionate with polyribosomes or 80S ribosomal particles. Double disruptions of UPF1 and UPF3 affect nonsense mRNA decay in a manner indistinguishable from single disruptions. These results suggest that the Upf proteins perform related functions in a common pathway. Images Fig. 1 Fig. 3 PMID:7479783

  11. 76 FR 9028 - Guidance for Industry: Potency Tests for Cellular and Gene Therapy Products; Availability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-16

    ... Industry: Potency Tests for Cellular and Gene Therapy Products'' dated January 2011. The guidance document provides manufacturers of cellular and gene therapy (CGT) products with recommendations for developing... document entitled ``Guidance for Industry: Potency Tests for Cellular and Gene Therapy Products''...

  12. The Gene bldA, a regulator of morphological differentiation and antibiotic production in streptomyces.

    PubMed

    Hackl, Stefanie; Bechthold, Andreas

    2015-07-01

    Streptomyces species are well known for their particular features of morphological differentiation. On solid agar, a mold-like aerial mycelium is formed and spores are produced, in which the bld genes play a crucial role. In S. coelicolor, mutations in one specific bld gene called bldA led to a "naked" phenotype lacking aerial hyphae and spores. This peculiar behavior became a major interest for scientific research in the past and it was revealed that bldA is coding for a unique tRNA able to translate a UUA codon into the amino acid leucine. UUA codons are a very rare property of G + C-rich Streptomyces genomes. The impact of bldA on morphology can in parts be attributed to the regulatory effect of bldA on the translational level, because TTA-containing genes can only be translated into their corresponding protein in the presence of a fully functioning bldA gene. In addition to the visible effect of bldA expression on the phenotype of S. coelicolor, bldA mutants were also deficient in antibiotic production. This led to the assumption that the role of bldA must exceed translational control. Many TTA-containing genes are coding for transcriptional regulators which are activating or repressing the transcription of many more genes. Proteomics and transcriptomics are two powerful methods for identifying bldA target genes and it was possible to assign also post-translational regulation to bldA. This review wants to give a short overview on the importance of bldA as a regulator of morphological differentiation and antibiotic production by switching on "silent" gene clusters in Streptomyces.

  13. 77 FR 71750 - DSM Nutritional Products; Filing of Food Additive Petition (Animal Use)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-04

    ... HUMAN SERVICES Food and Drug Administration 21 CFR Part 573 DSM Nutritional Products; Filing of Food.... SUMMARY: The Food and Drug Administration (FDA) is announcing that DSM Nutritional Products has filed a... petition (FAP 2273) has been filed by DSM Nutritional Products, 45 Waterview Blvd., Parsippany, NJ...

  14. 49 CFR 1300.5 - Additional publication requirement for agricultural products and fertilizer.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... agricultural products and fertilizer. 1300.5 Section 1300.5 Transportation Other Regulations Relating to... fertilizer. (a) With respect to transportation of agricultural products (including grain, as defined in 7 U.S.C. 75, and all products thereof) and fertilizer, a rail carrier shall publish, make available,...

  15. 49 CFR 1300.5 - Additional publication requirement for agricultural products and fertilizer.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... agricultural products and fertilizer. 1300.5 Section 1300.5 Transportation Other Regulations Relating to... fertilizer. (a) With respect to transportation of agricultural products (including grain, as defined in 7 U.S.C. 75, and all products thereof) and fertilizer, a rail carrier shall publish, make available,...

  16. 49 CFR 1300.5 - Additional publication requirement for agricultural products and fertilizer.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... agricultural products and fertilizer. 1300.5 Section 1300.5 Transportation Other Regulations Relating to... fertilizer. (a) With respect to transportation of agricultural products (including grain, as defined in 7 U.S.C. 75, and all products thereof) and fertilizer, a rail carrier shall publish, make available,...

  17. 49 CFR 1300.5 - Additional publication requirement for agricultural products and fertilizer.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... agricultural products and fertilizer. 1300.5 Section 1300.5 Transportation Other Regulations Relating to... fertilizer. (a) With respect to transportation of agricultural products (including grain, as defined in 7 U.S.C. 75, and all products thereof) and fertilizer, a rail carrier shall publish, make available,...

  18. 49 CFR 1300.5 - Additional publication requirement for agricultural products and fertilizer.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... agricultural products and fertilizer. 1300.5 Section 1300.5 Transportation Other Regulations Relating to... fertilizer. (a) With respect to transportation of agricultural products (including grain, as defined in 7 U.S.C. 75, and all products thereof) and fertilizer, a rail carrier shall publish, make available,...

  19. Infection of Mice by Salmonella enterica Serovar Enteritidis Involves Additional Genes That Are Absent in the Genome of Serovar Typhimurium

    PubMed Central

    Silva, Cecilia A.; Blondel, Carlos J.; Quezada, Carolina P.; Porwollik, Steffen; Andrews-Polymenis, Helene L.; Toro, Cecilia S.; Zaldívar, Mercedes; Contreras, Inés

    2012-01-01

    Salmonella enterica serovar Enteritidis causes a systemic, typhoid-like infection in newly hatched poultry and mice. In the present study, a library of 54,000 transposon mutants of S. Enteritidis phage type 4 (PT4) strain P125109 was screened for mutants deficient in the in vivo colonization of the BALB/c mouse model using a microarray-based negative-selection screening. Mutants in genes known to contribute to systemic infection (e.g., Salmonella pathogenicity island 2 [SPI-2], aro, rfa, rfb, phoP, and phoQ) and enteric infection (e.g., SPI-1 and SPI-5) in this and other Salmonella serovars displayed colonization defects in our assay. In addition, a strong attenuation was observed for mutants in genes and genomic islands that are not present in S. Typhimurium or in most other Salmonella serovars. These genes include a type I restriction/modification system (SEN4290 to SEN4292), the peg fimbrial operon (SEN2144A to SEN2145B), a putative pathogenicity island (SEN1970 to SEN1999), and a type VI secretion system remnant SEN1001, encoding a hypothetical protein containing a lysin motif (LysM) domain associated with peptidoglycan binding. Proliferation defects for mutants in these individual genes and in exemplar genes for each of these clusters were confirmed in competitive infections with wild-type S. Enteritidis. A ΔSEN1001 mutant was defective for survival within RAW264.7 murine macrophages in vitro. Complementation assays directly linked the SEN1001 gene to phenotypes observed in vivo and in vitro. The genes identified here may perform novel virulence functions not characterized in previous Salmonella models. PMID:22083712

  20. Diversity of Streptococcus thermophilus in bacteriocin production; inhibitory spectrum and occurrence of thermophilin genes.

    PubMed

    Rossi, Franca; Marzotto, Marta; Cremonese, Silvia; Rizzotti, Lucia; Torriani, Sandra

    2013-08-01

    The bacteriocin-producing Streptococcus thermophilus strains that can dominate in natural dairy ecosystems, may also enhance safety in products obtained from natural cultures. In this study, we sought to identify bacteriocin production and bacteriocin genes in 75 strains of dairy and plant origin. The strains were tested for antimicrobial activity against pathogens or pathogen models, spoiling bacteria, and lactic acid bacteria associated with dairy products. All strains moderately inhibited Staphylococcus aureus P310, none inhibited Listeria innocua LMG 11387(T) or Clostridium tyrobutyricum LMG 1285(T). In addition, 14 were active against one or more indicators in addition to S. aureus P310. Inhibition of other starter bacteria was more common than the inhibition of unwanted microorganisms. The involvement of a proteinaceous compound was ascertained in all cases. Results suggested that the selection of bacteriocinogenic S. thermophilus strains for use in biopreservation must take into account the effects exerted on other lactic acid bacteria. PCR detection of thermophilin genes proved unreliable in predicting antimicrobial activity. For S. thermophilus PRI36 and PRI45, with relevant inhibitory features, the identity of the bacteriocin genes present in the thermophilin 9 cluster was defined, thus revealing novel variants for this genome region.

  1. Decarboxylase gene expression and cadaverine and putrescine production by Serratia proteamaculans in vitro and in beef.

    PubMed

    De Filippis, Francesca; Pennacchia, Carmela; Di Pasqua, Rosangela; Fiore, Alberto; Fogliano, Vincenzo; Villani, Francesco; Ercolini, Danilo

    2013-08-01

    Studies of the molecular basis of microbial metabolic activities that are important for the changes in food quality are valuable in order to help in understanding the behavior of spoiling bacteria in food. The growth of a psychrotrophic Serratia proteamaculans strain was monitored in vitro and in artificially inoculated raw beef. Two growth temperatures (25°C and 4°C) were tested in vitro, while growth at 15°C and 4°C was monitored in beef. During growth, the expression of inducible lysine and ornithine-decarboxylase genes was evaluated by quantitative reverse transcription-PCR (qRT-PCR), while the presence of cadaverine and putrescine was quantified by LC-ESI-MS/MS. The expression of the decarboxylase genes, and the consequent production of cadaverine and putrescine were shown to be influenced by the temperature, as well as by the complexity of the growth medium. Generally, the maximum gene expression and amine production took place during the exponential and early stationary phase, respectively. In addition, lower temperatures caused slower growth and gene downregulation. Higher amounts of cadaverine compared to putrescine were found during growth in beef with the highest concentrations corresponding to microbial loads of ca. 9CFU/g. The differences found in gene expression evaluated in vitro and in beef suggested that such activities are more reliably investigated in situ in specific food matrices.

  2. Additive estrogenic effects of mixtures of frequently used UV filters on pS2-gene transcription in MCF-7 cells.

    PubMed

    Heneweer, Marjoke; Muusse, Martine; van den Berg, Martin; Sanderson, J Thomas

    2005-10-15

    In order to protect consumers from ultraviolet (UV) radiation and enhance light stability of the product, three to eight UV filters are usually added to consumer sunscreen products. High lipophilicity of the UV filters has been shown to cause bioaccumulation in fish and humans, leading to environmental levels of UV filters that are similar to those of PCBs and DDT. In this paper, estrogen-regulated pS2 gene transcription in the human mammary tumor cell line MCF-7 was used as a measure of estrogenicity of four individual UV filters. Since humans are exposed to more than one UV filter at a time, an equipotent binary mixture of 2-hydroxy-4-methoxy-benzophenone (BP-3) and its metabolite 2,4-dihydroxy benzophenone (BP-1), as well as an equipotent multi-component mixture of BP-1, BP-3, octyl methoxy cinnamate (OMC) and 3-(4-methylbenzylidene) camphor (4-MBC), were also evaluated for their ability to induce pS2 gene transcription in order to examine additivity. An estrogen receptor-mediated mechanism of action was expected for all UV filters. Therefore, our null-hypothesis was that combined estrogenic responses, measured as increased pS2 gene transcription in MCF-7 cells after exposure to mixtures of UV filters, are additive, according to a concentration-addition model. Not all UV filters produced a full concentration-response curve within the concentration range tested (100 nM-1 microM). Therefore, instead of using EC50 values for comparison, the concentration at which each compound caused a 50% increase of basal pS2 gene transcription was defined as the C50 value for that compound and used to calculate relative potencies. For comparison, the EC50 value of a compound is the concentration at which the compound elicits an effect that is 50% of its maximal effect. Individual UV filters increased pS2 gene transcription concentration-dependently with C50 values of 0.12 microM, 0.5 microM, 1.9 microM, and 1.0 microM for BP-1, BP-3, 4-MBC and OMC, respectively. Estradiol (E2

  3. Additive estrogenic effects of mixtures of frequently used UV filters on pS2-gene transcription in MCF-7 cells

    SciTech Connect

    Heneweer, Marjoke . E-mail: M.Heneweer@iras.uu.nl; Muusse, Martine; Berg, Martin van den; Sanderson, J. Thomas

    2005-10-15

    In order to protect consumers from ultraviolet (UV) radiation and enhance light stability of the product, three to eight UV filters are usually added to consumer sunscreen products. High lipophilicity of the UV filters has been shown to cause bioaccumulation in fish and humans, leading to environmental levels of UV filters that are similar to those of PCBs and DDT. In this paper, estrogen-regulated pS2 gene transcription in the human mammary tumor cell line MCF-7 was used as a measure of estrogenicity of four individual UV filters. Since humans are exposed to more than one UV filter at a time, an equipotent binary mixture of 2-hydroxy-4-methoxy-benzophenone (BP-3) and its metabolite 2,4-dihydroxy benzophenone (BP-1), as well as an equipotent multi-component mixture of BP-1, BP-3, octyl methoxy cinnamate (OMC) and 3-(4-methylbenzylidene) camphor (4-MBC), were also evaluated for their ability to induce pS2 gene transcription in order to examine additivity. An estrogen receptor-mediated mechanism of action was expected for all UV filters. Therefore, our null-hypothesis was that combined estrogenic responses, measured as increased pS2 gene transcription in MCF-7 cells after exposure to mixtures of UV filters, are additive, according to a concentration-addition model. Not all UV filters produced a full concentration-response curve within the concentration range tested (100 nM-1 {mu}M). Therefore, instead of using EC{sub 50} values for comparison, the concentration at which each compound caused a 50% increase of basal pS2 gene transcription was defined as the C50 value for that compound and used to calculate relative potencies. For comparison, the EC{sub 50} value of a compound is the concentration at which the compound elicits an effect that is 50% of its maximal effect. Individual UV filters increased pS2 gene transcription concentration-dependently with C50 values of 0.12 {mu}M, 0.5 {mu}M, 1.9 {mu}M, and 1.0 {mu}M for BP-1, BP-3, 4-MBC and OMC, respectively. Estradiol

  4. Regulation of photoreceptor gene expression by the retinal homeobox (Rx) gene product

    PubMed Central

    Pan, Yi; Martinez-De Luna, Reyna I.; Lou, Chih-Hong; Nekkalapudi, Srivamsi; Kelly, Lisa E.; Sater, Amy K.; El-Hodiri, Heithem M.

    2010-01-01

    The retinal homeobox (Rx) gene product is essential for eye development. However little is known about its molecular function. It has been demonstrated that Rx binds to photoreceptor conserved element (PCE-1), a highly conserved element found in the promoter region of photoreceptor-specific genes such as rhodopsin and red cone opsin. We verify that Rx is co-expressed with rhodopsin and red cone opsin in maturing photoreceptors and demonstrate that Rx binds to the rhodopsin and red cone opsin promoters in vivo. We also find that Rx can cooperate with the Xenopus analogs of Crx and Nrl, otx5b and XLMaf (respectively), to activate a Xenopus opsin promoter-dependent reporter. Finally, we demonstrate that reduction of Rx expression in tadpoles results in decreases in expression of several PCE-1 containing photoreceptor genes, abnormal photoreceptor morphology, and impaired vision. Our data suggests that Rx, in combination with other transcription factors, is necessary for normal photoreceptor gene expression, maintenance, and function. This establishes a direct role for Rx in regulation of genes expressed in a differentiated cell type. PMID:20060393

  5. 78 FR 11791 - Flavored Milk; Petition to Amend the Standard of Identity for Milk and 17 Additional Dairy Products

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-20

    ... to Amend the Standard of Identity for Milk and 17 Additional Dairy Products AGENCY: Food and Drug... Administration (FDA) is announcing that the International Dairy Foods Association (IDFA) and the National Milk... for milk and 17 other dairy products to provide for the use of any safe and suitable sweetener as...

  6. THE CARCINOGENIC RESPONSE TO A MIXTURE OF DRINKING WATER DISINFECTION BY-PRODUCTS (DBP) WAS LESS THAN ADDITIVE

    EPA Science Inventory

    THE CARCINOGENIC RESPONSE TO A MIXTURE OF DRINKING WATER DISINFECTION BY -PRODUCTS (DBP) W AS LESS THAN ADDITIVE.

    Current default risk assessments for chemical mixtures assume additivity of carcinogenic effects but this may under or over represent the actual biological res...

  7. Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils.

    PubMed

    Jung, Jaejoon; Yeom, Jinki; Kim, Jisun; Han, Jiwon; Lim, Hyoun Soo; Park, Hyun; Hyun, Seunghun; Park, Woojun

    2011-12-01

    The microbial community (bacterial, archaeal, and fungi) and eight genes involved in the nitrogen biogeochemical cycle (nifH, nitrogen fixation; bacterial and archaeal amoA, ammonia oxidation; narG, nitrate reduction; nirS, nirK, nitrite reduction; norB, nitric oxide reduction; and nosZ, nitrous oxide reduction) were quantitatively assessed in this study, via real-time PCR with DNA extracted from three Antarctic soils. Interestingly, AOB amoA was found to be more abundant than AOA amoA in Antarctic soils. The results of microcosm studies revealed that the fungal and archaeal communities were diminished in response to warming temperatures (10 °C) and that the archaeal community was less sensitive to nitrogen addition, which suggests that those two communities are well-adapted to colder temperatures. AOA amoA and norB genes were reduced with warming temperatures. The abundance of only the nifH and nirK genes increased with both warming and the addition of nitrogen. NirS-type denitrifying bacteria outnumbered NirK-type denitrifiers regardless of the treatment used. Interestingly, dramatic increases in both NirS and NirK-types denitrifiers were observed with nitrogen addition. NirK types increase with warming, but NirS-type denitrifiers tend to be less sensitive to warming. Our findings indicated that the Antarctic microbial nitrogen cycle could be dramatically altered by temperature and nitrogen, and that warming may be detrimental to the ammonia-oxidizing archaeal community. To the best of our knowledge, this is the first report to investigate genes associated with each process of the nitrogen biogeochemical cycle in an Antarctic terrestrial soil environment.

  8. Tandem oleosin genes in a cluster acquired in Brassicaceae created tapetosomes and conferred additive benefit of pollen vigor

    PubMed Central

    Huang, Chien Yu; Chen, Pei-Ying; Huang, Ming-Der; Tsou, Chih-Hua; Jane, Wann-Neng; Huang, Anthony H. C.

    2013-01-01

    During evolution, genomes expanded via whole-genome, segmental, tandem, and individual-gene duplications, and the emerged redundant paralogs would be eliminated or retained owing to selective neutrality or adaptive benefit and further functional divergence. Here we show that tandem paralogs can contribute adaptive quantitative benefit and thus have been retained in a lineage-specific manner. In Brassicaceae, a tandem oleosin gene cluster of five to nine paralogs encodes ample tapetum-specific oleosins located in abundant organelles called tapetosomes in flower anthers. Tapetosomes coordinate the storage of lipids and flavonoids and their transport to the adjacent maturing pollen as the coat to serve various functions. Transfer-DNA and siRNA mutants of Arabidopsis thaliana with knockout and knockdown of different tandem oleosin paralogs had quantitative and correlated loss of organized structures of the tapetosomes, pollen-coat materials, and pollen tolerance to dehydration. Complementation with the knockout paralog restored the losses. Cleomaceae is the family closest to Brassicaceae. Cleome species did not contain the tandem oleosin gene cluster, tapetum oleosin transcripts, tapetosomes, or pollen tolerant to dehydration. Cleome hassleriana transformed with an Arabidopsis oleosin gene for tapetum expression possessed primitive tapetosomes and pollen tolerant to dehydration. We propose that during early evolution of Brassicaceae, a duplicate oleosin gene mutated from expression in seed to the tapetum. The tapetum oleosin generated primitive tapetosomes that organized stored lipids and flavonoids for their effective transfer to the pollen surface for greater pollen vitality. The resulting adaptive benefit led to retention of tandem-duplicated oleosin genes for production of more oleosin and modern tapetosomes. PMID:23940319

  9. Regulation of gene expression by tobacco product preparations in cultured human dermal fibroblasts.

    PubMed

    Malpass, Gloria E; Arimilli, Subhashini; Prasad, G L; Howlett, Allyn C

    2014-09-01

    Skin fibroblasts comprise the first barrier of defense against wounds, and tobacco products directly contact the oral cavity. Cultured human dermal fibroblasts were exposed to smokeless tobacco extract (STE), total particulate matter (TPM) from tobacco smoke, or nicotine at concentrations comparable to those found in these extracts for 1h or 5h. Differences were identified in pathway-specific genes between treatments and vehicle using qRT-PCR. At 1h, IL1α was suppressed significantly by TPM and less significantly by STE. Neither FOS nor JUN was suppressed at 1h by tobacco products. IL8, TNFα, VCAM1, and NFκB1 were suppressed after 5h with STE, whereas only TNFα and NFκB1 were suppressed by TPM. At 1h with TPM, secreted levels of IL10 and TNFα were increased. Potentially confounding effects of nicotine were exemplified by genes such as ATF3 (5h), which was increased by nicotine but suppressed by other components of STE. Within 2h, TPM stimulated nitric oxide production, and both STE and TPM increased reactive oxygen species. The biological significance of these findings and utilization of the gene expression changes reported herein regarding effects of the tobacco product preparations on dermal fibroblasts will require additional research.

  10. Vitreoscilla hemoglobin gene ( vgb) improves lutein production in Chlorella vulgaris

    NASA Astrophysics Data System (ADS)

    Ma, Ruijuan; Lin, Xiangzhi

    2014-03-01

    Vitreoscilla hemoglobin is an oxygen-binding protein that promotes oxygen delivery and reduces oxygen consumption under low oxygen conditions to increase the efficiency of cell respiration and metabolism. In this study, we introduced a Vitreoscilla hemoglobin gene ( vgb) into Chlorella vulgaris by Agrobacterium tumefaciens -mediated transformation (ATMT). PCR analysis confirmed that the vgb gene was successfully integrated into the Chlorella vulgaris genome. Analysis of biomass obtained in shake flasks revealed transformant biomass concentrations as high as 3.28 g/L, which was 38.81% higher than that of the wild-type strain. Lutein content of transformants also increased slightly. Further experiments recovered a maximum lutein yield of 2.91 mg/L from the transformants, which was 36.77% higher than that of the wild-type strain. The above results suggest that integrated expression of the vgb gene may improve cell growth and lutein yield in Chlorella vulgaris, with applications to lutein production from Chlorella during fermentation.

  11. Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci

    PubMed Central

    2014-01-01

    Background The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data. Results For the identification of genes underlying known heterotic QTL, we made use of tight associations between gene expression pattern and the trait of interest, identified by correlation analyses. Using this approach genes strongly associated with heterosis for GY were discovered to be clustered in pericentromeric regions of the complex maize genome. This suggests that expression differences of sequences in recombination-suppressed regions are important in the establishment of heterosis for GY in F1 hybrids and also in the conservation of heterosis for GY across genotypes. Importantly functional analysis of heterosis-associated genes from these genomic regions revealed over-representation of a number of functional classes, identifying key processes contributing to heterosis for GY. Based on the finding that the majority of the analyzed heterosis-associated genes were addtitively expressed, we propose a model referring to the influence of cis-regulatory variation on heterosis for GY by the compensation of fixed detrimental expression levels in parents. Conclusions The study highlights the utility of a meta-analysis approach that integrates phenotypic and multi-level molecular data to unravel complex traits in plants. It provides prospects for the identification of genes relevant for

  12. The effects of nutrient additions on particulate and dissolved primary production in surface waters of three Mediterranean eddies

    NASA Astrophysics Data System (ADS)

    Lagaria, A.; Psarra, S.; Lefèvre, D.; van Wambeke, F.; Courties, C.; Pujo-Pay, M.; Oriol, L.; Tanaka, T.; Christaki, U.

    2010-12-01

    The effects of additions of nitrogen (+N), phosphorus (+P), alone and in combination, were assessed during three microcosm experiments performed with surface waters of three anticyclonic eddies, located in the Western, Central and Eastern Mediterranean. We examined the effects of nutrient additions on rates of dissolved and particulate primary production and on metabolic rates of the osmotrophic community (phytoplankton and heterotrophic prokaryotes). The experiments were performed in June/July 2008 during the BOUM (Biogeochemistry from the Oligotrophic to the Ultra-oligotrophic Mediterranean) cruise. In all three experiments, particulate primary production was significantly stimulated by the additions of nitrogen (+N, +NP) while no effect was observed with the addition of phosphorus alone. Percent extracellular release (PER) showed an inverse relation with total primary production (PPtotal), displaying the lowest values (4-8%) in the +NP treatment. Among the three treatments, the +NP had the strongest effect on the community metabolic rates leading to positive net community production values (NCP>0). These changes of NCP were mainly due to enhanced gross community production (GCP) rather than lower respiration rates (CR). In +NP treatments autotrophic production (whether expressed as GCP or PPtotal) was high enough to fulfil the carbon requirements of the heterotrophic prokaryotes, with phytoplankton and heterotrophic prokaryote production positively correlated. Addition of nitrogen alone (+N) had a smaller effect on community production, resulting in metabolically balanced systems (NCP≍0). Finally, heterotrophic conditions persisted in the +P treatment at the central and eastern stations, and gross production was not sufficient to supply bacterial carbon demand, evidence of a decoupling of phytoplankton production and consumption by heterotrophic prokaryotes.

  13. 40 CFR 82.18 - Availability of production in addition to baseline production allowances for class II controlled...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... under § 82.17 is also apportioned Article 5 allowances, equal to 15 percent of their baseline production..., HCFC-22, or HCFC-142b is also apportioned Article 5 allowances, equal to 10 percent of their baseline..., equal to 10 percent of their baseline production allowances, for the specified HCFC for each...

  14. 40 CFR 82.18 - Availability of production in addition to baseline production allowances for class II controlled...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... under § 82.17 is also apportioned Article 5 allowances, equal to 15 percent of their baseline production... for HCFC-141b, HCFC-22, or HCFC-142b is also apportioned Article 5 allowances, equal to 10 percent of... apportioned Article 5 allowances, equal to 10 percent of their baseline production allowances, for...

  15. 40 CFR 82.18 - Availability of production in addition to baseline production allowances for class II controlled...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... under § 82.17 is also apportioned Article 5 allowances, equal to 15 percent of their baseline production... for HCFC-141b, HCFC-22, or HCFC-142b is also apportioned Article 5 allowances, equal to 10 percent of... apportioned Article 5 allowances, equal to 10 percent of their baseline production allowances, for...

  16. Polyhydroxyalkanoate production in Rhodobacter capsulatus: genes, mutants, expression, and physiology.

    PubMed Central

    Kranz, R G; Gabbert, K K; Locke, T A; Madigan, M T

    1997-01-01

    Like many other prokaryotes, the photosynthetic bacterium Rhodobacter capsulatus produces high levels of polyhydroxyalkanoates (PHAs) when a suitable carbon source is available. The three genes that are traditionally considered to be necessary in the PHA biosynthetic pathway, phaA (beta-ketothiolase), phaB (acetoacetylcoenzyme A reductase), and phaC (PHA synthase), were cloned from Rhodobacter capsulatus. In R. capsulatus, the phaAB genes are not linked to the phaC gene. Translational beta-galactosidase fusions to phaA and phaC were constructed and recombined into the chromosome. Both phaC and phaA were constitutively expressed regardless of whether PHA production was induced, suggesting that control is posttranslational at the enzymatic level. Consistent with this conclusion, it was shown that the R. capsulatus transcriptional nitrogen-sensing circuits were not involved in PHA synthesis. The doubling times of R. capsulatus transcriptional nitrogen-sensing circuits were not involved in PHA synthesis. The doubling times of R. capsulatus grown on numerous carbon sources were determined, indicating that this bacterium grows on C2 to C12 fatty acids. Grown on acetone, caproate, or heptanoate, wild-type R. capsulatus produced high levels of PHAs. Although a phaC deletion strain was unable to synthesize PHAs on any carbon source, phaA and phaAB deletion strains were able to produce PHAs, indicating that alternative routes for the synthesis of substrates for the synthase are present. The nutritional versatility and bioenergetic versatility of R. capsulatus, coupled with its ability to produce large amounts of PHAs and its genetic tractability, make it an attractive model for the study of PHA production. PMID:9251189

  17. Addition of alfalfa (Medicago sativa L.) to lamb diets enhances production and profits in northern China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The agro-pastoral transitional zone of northern China is an ecologically fragile area with a short growing season and extensive livestock production, where feed shortage is a key constraint to ruminant production, especially in winter. This study was conducted to evaluate the effects of various rat...

  18. Effect of biochar addition on hydrogen and methane production in two-phase anaerobic digestion of aqueous carbohydrates food waste.

    PubMed

    Sunyoto, Nimas M S; Zhu, Mingming; Zhang, Zhezi; Zhang, Dongke

    2016-11-01

    Effect of biochar addition on hydrogen and methane production in two-phase anaerobic digestion of aqueous carbohydrates was studied using bench-scale bioreactors. The cultures with biochar additions were placed in 100ml reactors and incubated at 35°C and pH 5 for hydrogen production. The residual cultures were then used for methane production, incubated at 35°C and pH 7. Daily yields of hydrogen and methane and weekly yield of volatile fatty acids (VFA) were measured. The hydrogen and methane production potentials, rate and lag phases of the two phases were analysed using the Gompertz model. The results showed that biochar addition increased the maximum production rates of hydrogen by 32.5% and methane 41.6%, improved hydrogen yield by 31.0% and methane 10.0%, and shortened the lag phases in the two phases by 36.0% and 41.0%, respectively. Biochar addition also enhanced VFA generation during hydrogen production and VFA degradation in methane production.

  19. Phytoalexin detoxification genes and gene products: Implication for the evolution of host specific traits for pathogenicity. Final report

    SciTech Connect

    VanEtten, H.

    1997-06-01

    The overall objectives of this research were to determine which differences among PDA genes were associated with different levels of virulence on pea and to clone and characterize a MAK gene. The authors also proposed to characterize the pisatin detoxifying system in pea pathogens in addition to N. haematococca to assess whether pathogens of a common host had evolved similar pathogenicity genes.

  20. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

    PubMed

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-03-09

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in L-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport--NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885--were also expressed at significantly higher levels in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, L-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.

  1. Influence of temperature, mixing, and addition of microcystin-LR on microcystin gene expression in Microcystis aeruginosa.

    PubMed

    Scherer, Pia I; Raeder, Uta; Geist, Juergen; Zwirglmaier, Katrin

    2017-02-01

    Cyanobacteria, such as the toxin producer Microcystis aeruginosa, are predicted to be favored by global warming both directly, through elevated water temperatures, and indirectly, through factors such as prolonged stratification of waterbodies. M. aeruginosa is able to produce the hepatotoxin microcystin, which causes great concern in freshwater management worldwide. However, little is known about the expression of microcystin synthesis genes in response to climate change-related factors. In this study, a new RT-qPCR assay employing four reference genes (GAPDH, gltA, rpoC1, and rpoD) was developed to assess the expression of two target genes (the microcystin synthesis genes mcyB and mcyD). This assay was used to investigate changes in mcyB and mcyD expression in response to selected environmental factors associated with global warming. A 10°C rise in temperature significantly increased mcyB expression, but not mcyD expression. Neither mixing nor the addition of microcystin-LR (10 μg L(-1) or 60 μg L(-1) ) significantly altered mcyB and mcyD expression. The expression levels of mcyB and mcyD were correlated but not identical.

  2. Additional paper waste in pulping sludge for biohydrogen production by heat-shocked sludge.

    PubMed

    Chairattanamanokorn, Prapaipid; Tapananont, Supachok; Detjaroen, Siriporn; Sangkhatim, Juthatip; Anurakpongsatorn, Patana; Sirirote, Pramote

    2012-01-01

    Dark anaerobic fermentation is an interesting alternative method for producing biohydrogen (H(2)) as a renewable fuel because of its low cost and various usable organic substrates. Pulping sludge from wastewater treatment containing plentiful cellulosic substrate could be feasibly utilized for H(2) production by dark fermentation. The objective of this study was to investigate the optimal proportion of pulping sludge to paper waste, the optimal initial pH, and the optimal ratio of carbon and nitrogen (C/N) for H(2) production by anaerobic seed sludge pretreated with heat. The pulping sludge was pretreated with NaOH solution at high temperature and further hydrolyzed with crude cellulase. Pretreatment of the pulping sludge with 3% NaOH solution under autoclave at 121 °C for 2 h, hydrolysis with 5 FPU crude cellulase at 50 °C, and pH 4.8 for 24 h provided the highest reducing sugar production yield (229.68 ± 2.09 mg/g(TVS)). An initial pH of 6 and a C/N ratio of 40 were optimal conditions for H(2) production. Moreover, the supplement of paper waste in the pulping sludge enhanced the cumulative H(2) production yield. The continuous hydrogen production was further conducted in a glass reactor with nylon pieces as supporting media and the maximum hydrogen production yield was 151.70 ml/g(TVS).

  3. Regulation of the Escherichia coli glyA gene by the metR gene product and homocysteine.

    PubMed Central

    Plamann, M D; Stauffer, G V

    1989-01-01

    The methionine component of glyA gene regulation in Escherichia coli K-12 was investigated. The results indicate that the glyA gene is positively controlled by the metR gene product. Activation of glyA by the MetR protein requires homocysteine, an intermediate in methionine biosynthesis. The positive-acting metR regulatory system functions independently of a regulatory system shown previously to control glyA gene expression. PMID:2670901

  4. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    DOEpatents

    Wohlbach, Dana J.; Gasch, Audrey P.

    2014-08-05

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  5. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    SciTech Connect

    Wohlbach, Dana J.; Gasch, Audrey P.

    2015-09-29

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  6. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    DOEpatents

    Wohlbach, Dana J.; Gasch, Audrey P.

    2016-11-29

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  7. Whey fermentation by anaerobiospirillum succiniciproducens for production of a succinate-based animal feed additive

    PubMed

    Samuelov; Datta; Jain; Zeikus

    1999-05-01

    Anaerobic fermentation processes for the production of a succinate-rich animal feed supplement from raw whey were investigated with batch, continuous, and variable-volume fed-batch cultures with Anaerobiospirillum succiniciproducens. The highest succinate yield, 90%, was obtained in a variable-volume fed-batch process in comparison to 80% yield in a batch cultivation mode. In continuous culture, succinate productivity was 3 g/liter/h, and the yield was 60%. Under conditions of excess CO2, more than 90% of the whey-lactose was consumed, with an end product ratio of 4 succinate to 1 acetate. Under conditions of limited CO2, lactose was only partially consumed and lactate was the major end product, with lower levels of ethanol, succinate, and acetate. When the succinic acid in this fermentation product was added to rumen fluid, it was completely consumed by a mixed rumen population and was 90% decarboxylated to propionate on a molar basis. The whey fermentation product formed under excess CO2, which contained mainly organic acids and cells, could potentially be used as an animal feed supplement.

  8. Whey fermentation by Anaerobiospirillum succiniciproducens for production of a succinate-based animal feed additive

    SciTech Connect

    Samuelov, N.S.; Datta, R.; Jain, M.K. |; Zeikus, J.G. |

    1999-05-01

    Anaerobic fermentation processes for the production of a succinate-rich animal feed supplement from raw whey were investigated with batch, continuous, and variable-volume fed-batch cultures with Anaerobiospirillum succiniciproducens. The highest succinate yield, 90%, was obtained in a variable-volume fed-batch process in comparison to 80% yield in a batch cultivation mode. In continuous culture, succinate productivity was 3 g/liter/h, and the yield was 60%. Under conditions of excess CO{sub 2}, more than 90% of the whey-lactose was consumed, with an end product ratio of 4 succinate to 1 acetate. Under conditions of limited CO{sub 2}, lactose was only partially consumed and lactate was the major end product, with lower levels of ethanol, succinate, and acetate. When the succinic acid in this fermentation product was added to rumen fluid, it was completely consumed by a mixed rumen population and was 90% decarboxylated to propionate on a molar basis. The whey fermentation product formed under excess CO{sub 2}, which contained mainly organic acids and cells, could potentially be used as an animal feed supplement.

  9. Enhanced Production of Green Tide Algal Biomass through Additional Carbon Supply

    PubMed Central

    de Paula Silva, Pedro H.; Paul, Nicholas A.; de Nys, Rocky; Mata, Leonardo

    2013-01-01

    Intensive algal cultivation usually requires a high flux of dissolved inorganic carbon (Ci) to support productivity, particularly for high density algal cultures. Carbon dioxide (CO2) enrichment can be used to overcome Ci limitation and enhance productivity of algae in intensive culture, however, it is unclear whether algal species with the ability to utilise bicarbonate (HCO3−) as a carbon source for photosynthesis will benefit from CO2 enrichment. This study quantified the HCO3− affinity of three green tide algal species, Cladophora coelothrix, Cladophora patentiramea and Chaetomorpha linum, targeted for biomass and bioenergy production. Subsequently, we quantified productivity and carbon, nitrogen and ash content in response to CO2 enrichment. All three species had similar high pH compensation points (9.7–9.9), and grew at similar rates up to pH 9, demonstrating HCO3− utilization. Algal cultures enriched with CO2 as a carbon source had 30% more total Ci available, supplying twenty five times more CO2 than the control. This higher Ci significantly enhanced the productivity of Cladophora coelothrix (26%), Chaetomorpha linum (24%) and to a lesser extent for Cladophora patentiramea (11%), compared to controls. We demonstrated that supplying carbon as CO2 can enhance the productivity of targeted green tide algal species under intensive culture, despite their clear ability to utilise HCO3−. PMID:24324672

  10. Enhanced production of green tide algal biomass through additional carbon supply.

    PubMed

    de Paula Silva, Pedro H; Paul, Nicholas A; de Nys, Rocky; Mata, Leonardo

    2013-01-01

    Intensive algal cultivation usually requires a high flux of dissolved inorganic carbon (Ci) to support productivity, particularly for high density algal cultures. Carbon dioxide (CO2) enrichment can be used to overcome Ci limitation and enhance productivity of algae in intensive culture, however, it is unclear whether algal species with the ability to utilise bicarbonate (HCO3 (-)) as a carbon source for photosynthesis will benefit from CO2 enrichment. This study quantified the HCO3 (-) affinity of three green tide algal species, Cladophora coelothrix, Cladophora patentiramea and Chaetomorpha linum, targeted for biomass and bioenergy production. Subsequently, we quantified productivity and carbon, nitrogen and ash content in response to CO2 enrichment. All three species had similar high pH compensation points (9.7-9.9), and grew at similar rates up to pH 9, demonstrating HCO3 (-) utilization. Algal cultures enriched with CO2 as a carbon source had 30% more total Ci available, supplying twenty five times more CO2 than the control. This higher Ci significantly enhanced the productivity of Cladophora coelothrix (26%), Chaetomorpha linum (24%) and to a lesser extent for Cladophora patentiramea (11%), compared to controls. We demonstrated that supplying carbon as CO2 can enhance the productivity of targeted green tide algal species under intensive culture, despite their clear ability to utilise HCO3 (-).

  11. The Symbiotic Performance of Chickpea Rhizobia Can Be Improved by Additional Copies of the clpB Chaperone Gene.

    PubMed

    Paço, Ana; Brígido, Clarisse; Alexandre, Ana; Mateos, Pedro F; Oliveira, Solange

    2016-01-01

    The ClpB chaperone is known to be involved in bacterial stress response. Moreover, recent studies suggest that this protein has also a role in the chickpea-rhizobia symbiosis. In order to improve both stress tolerance and symbiotic performance of a chickpea microsymbiont, the Mesorhizobium mediterraneum UPM-Ca36T strain was genetically transformed with pPHU231 containing an extra-copy of the clpB gene. To investigate if the clpB-transformed strain displays an improved stress tolerance, bacterial growth was evaluated under heat and acid stress conditions. In addition, the effect of the extra-copies of the clpB gene in the symbiotic performance was evaluated using plant growth assays (hydroponic and pot trials). The clpB-transformed strain is more tolerant to heat shock than the strain transformed with pPHU231, supporting the involvement of ClpB in rhizobia heat shock tolerance. Both plant growth assays showed that ClpB has an important role in chickpea-rhizobia symbiosis. The nodulation kinetics analysis showed a higher rate of nodule appearance with the clpB-transformed strain. This strain also induced a greater number of nodules and, more notably, its symbiotic effectiveness increased ~60% at pH5 and 83% at pH7, compared to the wild-type strain. Furthermore, a higher frequency of root hair curling was also observed in plants inoculated with the clpB-transformed strain, compared to the wild-type strain. The superior root hair curling induction, nodulation ability and symbiotic effectiveness of the clpB-transformed strain may be explained by an increased expression of symbiosis genes. Indeed, higher transcript levels of the nodulation genes nodA and nodC (~3 folds) were detected in the clpB-transformed strain. The improvement of rhizobia by addition of extra-copies of the clpB gene may be a promising strategy to obtain strains with enhanced stress tolerance and symbiotic effectiveness, thus contributing to their success as crop inoculants, particularly under

  12. Gene Disruption Technologies Have the Potential to Transform Stored Product Insect Pest Control.

    PubMed

    Perkin, Lindsey C; Adrianos, Sherry L; Oppert, Brenda

    2016-09-19

    Stored product insects feed on grains and processed commodities manufactured from grain post-harvest, reducing the nutritional value and contaminating food. Currently, the main defense against stored product insect pests is the pesticide fumigant phosphine. Phosphine is highly toxic to all animals, but is the most effective and economical control method, and thus is used extensively worldwide. However, many insect populations have become resistant to phosphine, in some cases to very high levels. New, environmentally benign and more effective control strategies are needed for stored product pests. RNA interference (RNAi) may overcome pesticide resistance by targeting the expression of genes that contribute to resistance in insects. Most data on RNAi in stored product insects is from the coleopteran genetic model, Tribolium castaneum, since it has a strong RNAi response via injection of double stranded RNA (dsRNA) in any life stage. Additionally, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology has been suggested as a potential resource for new pest control strategies. In this review we discuss background information on both gene disruption technologies and summarize the advances made in terms of molecular pest management in stored product insects, mainly T. castaneum, as well as complications and future needs.

  13. Gene Disruption Technologies Have the Potential to Transform Stored Product Insect Pest Control

    PubMed Central

    Perkin, Lindsey C.; Adrianos, Sherry L.; Oppert, Brenda

    2016-01-01

    Stored product insects feed on grains and processed commodities manufactured from grain post-harvest, reducing the nutritional value and contaminating food. Currently, the main defense against stored product insect pests is the pesticide fumigant phosphine. Phosphine is highly toxic to all animals, but is the most effective and economical control method, and thus is used extensively worldwide. However, many insect populations have become resistant to phosphine, in some cases to very high levels. New, environmentally benign and more effective control strategies are needed for stored product pests. RNA interference (RNAi) may overcome pesticide resistance by targeting the expression of genes that contribute to resistance in insects. Most data on RNAi in stored product insects is from the coleopteran genetic model, Tribolium castaneum, since it has a strong RNAi response via injection of double stranded RNA (dsRNA) in any life stage. Additionally, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology has been suggested as a potential resource for new pest control strategies. In this review we discuss background information on both gene disruption technologies and summarize the advances made in terms of molecular pest management in stored product insects, mainly T. castaneum, as well as complications and future needs. PMID:27657138

  14. Identification of the dnaA and dnaN gene products of Escherichia coli.

    PubMed

    Yuasa, S; Sakakibara, Y

    1980-01-01

    A specialized transducing lambda phage carrying the dnaN genes of Escherichia coli specifies two proteins of about 41 and 48 kilodaltons (kd). The temperature-sensitive mutations, dnaN59 and dnaA167, were found to result in altered isoelectric points of the 41 and 48 kd proteins, respectively. Thus the dnaN gene product was identified as a weakly acidic 41 and 48 kd protein. The synthesis of the dnaN gene product is greatly reduced by insertion of a transposon Tn3 in the dnaA gene and by deletion in the gene at the distal end to the dnaN gene. Temperature-sensitive dnaA mutations, on the dnaN gene product. These results indicate that the synthesis of the dnaN gene product is dependent on the structural integrity of the dnaA gene.

  15. Production, sintering, and application of nanocrystalline iron-copper additions in a powder steel

    NASA Astrophysics Data System (ADS)

    Meilakh, A. G.

    2015-12-01

    A method is proposed for activated sintering of a sprayed iron powder by the coalescence of pressed particles through fine-grained layers based on iron-copper nanodispersed (ND) additions. The mechanical properties of composite materials containing 2% Fe-Cu ND addition are higher than those of the materials prepared from a mixture of standard powders by a factor of 1.5.

  16. Evidence for susceptibility genes to familial Wilms tumour in addition to WT1, FWT1 and FWT2

    PubMed Central

    Rapley, E A; Barfoot, R; Bonaïti-Pellié, C; Chompret, A; Foulkes, W; Perusinghe, N; Reeve, A; Royer-Pokora, B; Schumacher, V; Shelling, A; Skeen, J; Tourreil, S de; Weirich, A; Pritchard-Jones, K; Stratton, M R; Rahman, N

    2000-01-01

    Three loci have been implicated in familial Wilms tumour: WT1 located on chromosome 11p13, FWT1 on 17q12-q21, and FWT2 on 19q13. Two out of 19 Wilms tumour families evaluated showed strong evidence against linkage at all three loci. Both of these families contained at least three cases of Wilms tumour indicating that they were highly likely to be due to genetic susceptibility and therefore that one or more additional familial Wilms tumour susceptibility genes remain to be found. © 2000 Cancer Research Campaign PMID:10901367

  17. Microbial oils as food additives: recent approaches for improving microbial oil production and its polyunsaturated fatty acid content.

    PubMed

    Bellou, Stamatia; Triantaphyllidou, Irene-Eva; Aggeli, Dimitra; Elazzazy, Ahmed Mohammed; Baeshen, Mohammed Nabih; Aggelis, George

    2016-02-01

    In this short review, we summarize the latest research in the production of polyunsaturated microbial oils that are of interest in food technology. The current research targets the productivity of oleaginous microorganisms, as well as the biosynthesis of particular polyunsaturated fatty acids (PUFAs). The most important efforts target the efficiency of the oleaginous machinery, via overexpression of key-enzymes involved in lipid biosynthesis, as well as the minimization of lipid degradation, by repressing genes involved in the β-oxidation pathway. The production of specific PUFAs is approached by homologous or heterologous expression of specific desaturases and elongases involved in PUFA biosynthesis in oleaginous microorganisms. New perspectives, such as the production of triacylglycerols of specific structure and the employment of adaptive experimental evolution for creating robust oleaginous strains able to produce PUFAs are also discussed.

  18. Characterization of the Expression of Basigin Gene Products Within the Pineal Gland of Mice.

    PubMed

    Tokar, Derek; van Ekeris, Leslie; Linser, Paul J; Ochrietor, Judith D

    2016-11-04

    The expression of Basigin gene products and monocarboxylate transporter-1 (MCT1) has been investigated within the mammalian neural retina and suggests a role for these proteins in cellular metabolism within that tissue. The purpose of the present study was to investigate the expression of these same proteins in the pineal gland of the mouse brain. Mouse pineal gland and neural retina RNA and protein were subjected to quantitative reverse transcription-polymerase chain reaction and immunoblotting analyses. In addition, paraffin-embedded sections of each tissue were analyzed for expression of Basigin gene products and MCT1 via immunohistochemistry. The results indicate that MCT1 and Basigin variant-2, but not Basigin variant-1, are expressed within the mouse pineal gland. The expression of Basigin variant-2 and MCT1 was localized to the capsule surrounding the gland. The position and relative amounts of the gene products suggest that they play a much less prominent role within the pineal gland than in the neural retina.

  19. Associating cooking additives with sodium hydroxide to pretreat bamboo residues for improving the enzymatic saccharification and monosaccharides production.

    PubMed

    Huang, Caoxing; He, Juan; Wang, Yan; Min, Douyong; Yong, Qiang

    2015-10-01

    Cooking additive pulping technique is used in kraft mill to increase delignification degree and pulp yield. In this work, cooking additives were firstly applied in the sodium hydroxide pretreatment for improving the bioconversion of bamboo residues to monosaccharides. Meanwhile, steam explosion and sulfuric acid pretreatments were also carried out on the sample to compare their impacts on monosaccharides production. Results indicated that associating anthraquinone with sodium hydroxide pretreatment showed the best performance in improving the original carbohydrates recovery, delignification, enzymatic saccharification, and monosaccharides production. After consecutive pretreatment and enzymatic saccharification process, 347.49 g, 307.48 g, 142.93 g, and 87.15 g of monosaccharides were released from 1000 g dry bamboo residues pretreated by sodium hydroxide associating with anthraquinone, sodium hydroxide, steam explosion and sulfuric acid, respectively. The results suggested that associating cooking additive with sodium hydroxide is an effective pretreatment for bamboo residues to enhance enzymatic saccharification for monosaccharides production.

  20. The transport of antibiotic resistance genes and residues in groundwater near swine production facilities

    NASA Astrophysics Data System (ADS)

    Lin, Y. F.; Yannarell, A. C.; Mackie, R. I.; Krapac, I. G.; Chee-Sanford, J. S.; Koike, S.

    2008-12-01

    The use of antibiotics at concentrated animal feeding operations (CAFOs) for disease prevention, disease treatment, and growth promotion can contribute to the spread of antibiotic compounds, their breakdown products, and antibiotic resistant bacteria and/or the genes that confer resistance. In addition, constitutive use of antibiotics at sub-therapeutic levels can select for antibiotic resistance among the bacteria that inhabit animal intestinal tracts, onsite manure treatment facilities, and any environments receiving significant inputs of manure (e.g. through waste lagoon leakage or fertilizer amendments to farm soils). If the antibiotic resistant organisms persist in these new environments, or if they participate in genetic exchanges with the native microflora, then CAFOs may constitute a significant reservoir for the spread of antibiotic resistance to the environment at large. Our results have demonstrated that leakage from waste treatment lagoons can influence the presence and persistence of tetracycline resistance genes in the shallow aquifer adjacent to swine CAFOs, and molecular phylogeny allowed us to distinguish "native" tetracycline resistance genes in control groundwater wells from manure-associated genes introduced from the lagoon. We have also been able to detect the presence of erythromycin resistance genes in CAFO surface and groundwater even though erythromycin is strictly reserved for use in humans and thus is not utilized at any of these sites. Ongoing research, including modeling of particle transport in groundwater, will help to determine the potential spatial and temporal extent of CAFO-derived antibiotic resistance.

  1. 40 CFR 82.18 - Availability of production in addition to baseline production allowances for class II controlled...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... quantity of production that the nation is permitted under the Montreal Protocol or to receive from the... allowances, for a specified control period through trades with another Party to the Protocol as set forth in... that is also listed in Appendix C, Annex 1 of the Protocol as having ratified the Beijing...

  2. 40 CFR 82.18 - Availability of production in addition to baseline production allowances for class II controlled...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... quantity of production that the nation is permitted under the Montreal Protocol or to receive from the... allowances, for a specified control period through trades with another Party to the Protocol as set forth in... that is also listed in Appendix C, Annex 1 of the Protocol as having ratified the Beijing...

  3. A repressor-response regulator gene pair controlling jadomycin B production in Streptomyces venezuelae ISP5230.

    PubMed

    Yang, K; Han, L; He, J; Wang, L; Vining, L C

    2001-11-28

    A second regulatory gene (jadR(1)) is located immediately upstream of the putative repressor gene (jadR(2)) in the jad cluster for biosynthesis of the antibiotic jadomycin B in Streptomyces venezuelae ISP5230. It encodes a 234-amino acid polypeptide with a sequence resembling those of response regulator proteins in two-component control systems. Features in the conserved C-terminal domain of JadR(1) place the protein in the OmpR-PhoB subfamily of response regulators. In mutants where jadR(1) was deleted or disrupted, jadomycin B was not produced, implying that the gene has an essential role in biosynthesis of the antibiotic. Cloning jadR(1) from S. venezuelae in pJV73A, and introducing additional copies of the gene into the wild-type parent by plasmid transformation gave unstable strains with pJV73A integrated into the chromosome. The transformants initially showed increased production of jadomycin B but gave lower titers as excess copies of jadR(1) were lost; mature cultures stabilized with a wild-type level of antibiotic production. The mutant from which jadR(1) had been deleted could not be transformed with pJV73A. Altering the composition of jadR genes in the chromosome by integration of vectors carrying intact and disrupted copies of jadR(1) and jadR(2) provided evidence that the two genes form a regulatory pair different in function from previously reported two-component systems controlling antibiotic biosynthesis in streptomycetes.

  4. The paf gene product modulates asexual development in Penicillium chrysogenum.

    PubMed

    Hegedüs, Nikoletta; Sigl, Claudia; Zadra, Ivo; Pócsi, Istvan; Marx, Florentine

    2011-06-01

    Penicillium chrysogenum secretes a low molecular weight, cationic and cysteine-rich protein (PAF). It has growth inhibitory activity against the model organism Aspergillus nidulans and numerous zoo- and phytopathogenic fungi but shows only minimal conditional antifungal activity against the producing organism itself. In this study we provide evidence for an additional function of PAF which is distinct from the antifungal activity against putative ecologically concurrent microorganisms. Our data indicate that PAF enhances conidiation in P. chrysogenum by modulating the expression of brlA, the central regulatory gene for mitospore development. A paf deletion strain showed a significant impairment of mitospore formation which sustains our hypothesis that PAF plays an important role in balancing asexual differentiation in P. chrysogenum.

  5. Ubiquinone-10 production using Agrobacterium tumefaciens dps gene in Escherichia coli by coexpression system.

    PubMed

    Zhang, Dawei; Shrestha, Binaya; Li, Zhaopeng; Tan, Tianwei

    2007-01-01

    Ubiquinone (Coenzyme Q; abbreviation, UQ) acts as a mobile component of the respiratory chain by playing an essential role in the electron transport system, and has been widely used in pharmaceuticals. The biosynthesis of UQ involves 10 sequential reactions brought about by various enzymes. In this study we have cloned, expressed the decaprenyl diphosphate synthase, designated dps gene, from Agrobacterium tumefaciens, and succeeded in detecting UQ-10 in addition to innate UQ-8 in Escherichia coli. Furthermore, the production of UQ-10 was higher than UQ-8. To establish an efficient expression system for UQ- 10 production, we used genes, including ubiC, ubiA, and ubiG involved in UQ biosynthesis in E. coli, to construct a better co-expression system. The expression coupled by dps and ubiCA was effective for increasing UQ-10 production by five times than that by expressing single dps gene in the shake flask culture. To study for a large-scale production of UQ-10 in E. coli, fed-batch fermentations were implemented to achieve a high cell density culture. A cell concentration of 85.40 g/L and 94.58 g/L dry cell weight (DCW), and UQ-10 content of 50.29 mg/L and 45.86 mg/L was obtained after 32.5 h and 27.5 h of cultivation, subsequent to isopropyl-beta-D-thiogalactopyranoside and lactose induction, respectively. In addition, plasmid stability was maintained at high level throughout the fermentation.

  6. [Impact on human health of hormonal additives used in animal production].

    PubMed

    Larrea, Fernando; Chirinos, Mayel

    2007-01-01

    The establishment of the impact of environmental compounds or additives with hormone-like activity on human health still requires further investigation, as well as a reexamination of biologic models and experimental methodology employed so far. In 1988, the FAO/WHO Expert Committee on Food Additives Joint with the Federal Drug Administration (FDA) considered that sexual hormone residues usually present in meat do not represent a risk for human consumption. Nevertheless, this resolution seems to be uncertain since the scientific elements employed for this statement may not be adequate. In this review the principal objections to the evidence used to establish the innocuousness of growth promoter hormones are considered.

  7. Enhanced production of triterpenoid in submerged cultures of Antrodia cinnamomea with the addition of citrus peel extract.

    PubMed

    Ma, Te-Wei; Lai, Yueting; Yang, Fan-Chiang

    2014-11-01

    In recent years, Antrodia cinnamomea has become a well-known medicinal mushroom in Taiwan. Triterpenoids are considered one of the most biologically active components found in A. cinnamomea. The aim of this research is to investigate the feasibility of enhancing triterpenoid production in shake flask cultures of A. cinnamomea by adding citrus peel extract. As a result of its containing essential oils, citrus peel extract is inhibitory to mycelial growth. In the experiments, the appropriate adding time is determined to be on day 7. Of the various citrus peel extracts tested, tangerine proves to be the most effective in enhancing polyphenol and triterpenoid production. With an addition of 2% (v/v), the content and production of total polyphenols rises from 5.95 mg/g DW of the control and 56.73 mg/L to 23.52 mg/g DW and 224.39 mg/L, respectively, on day 28. The production of triterpenoids also increases from 99.93 to 1,028.02 mg/L, for more than a tenfold increase. An optimal level of tangerine peel additive is determined to be around 4%. Furthermore, when compared with the mycelia of the control culture, the profiles of the HPLC analysis show that the mycelia cultured with the tangerine-peel addition contain more kinds of triterpenoids. This study demonstrates that the addition of citrus peel extract effectively enhances the production of bioactive metabolites in the submerged cultures of A. cinnamomea.

  8. The effects of high pressure treatments on C. jejuni in ground poultry products containing polyphosphate additives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Marinades containing polyphosphates have been previously implicated in the enhanced survival of Campylobacter spp. in poultry product exudates. The enhanced Campylobacter survival was attributed primarily to the ability of some polyphosphates to change the pH of the exudate to one more amenable to ...

  9. Teachers' Misconceptions about the Effects of Addition of More Reactants or Products on Chemical Equilibrium

    ERIC Educational Resources Information Center

    Cheung, Derek; Ma, Hong-jia; Yang, Jie

    2009-01-01

    The importance of research on misconceptions about chemical equilibrium is well recognized by educators, but in the past, researchers' interest has centered on student misconceptions and has neglected teacher misconceptions. Focusing on the effects of adding more reactants or products on chemical equilibrium, this article discusses the various…

  10. Oregano Essential Oil as an Antimicrobial and Antioxidant Additive in Food Products.

    PubMed

    Rodriguez-Garcia, I; Silva-Espinoza, B A; Ortega-Ramirez, L A; Leyva, J M; Siddiqui, M W; Cruz-Valenzuela, M R; Gonzalez-Aguilar, G A; Ayala-Zavala, J F

    2016-07-26

    Food consumers and industries urged the need of natural alternatives to assure food safety and quality. As a response, the use of natural compounds from herbs and spices is an alternative to synthetic additives associated with toxic problems. This review discusses the antimicrobial and antioxidant activity of oregano essential oil (OEO) and its potential as a food additive. Oregano is a plant that has been used as a food seasoning since ancient times. The common name of oregano is given to several species: Origanum (family: Lamiaceae) and Lippia (family: Verbenaceae), amongst others. The main compounds identified in the different OEOs are carvacrol and thymol, which are responsible for the characteristic odor, antimicrobial, and antioxidant activity; however, their content may vary according to the species, harvesting season, and geographical sources. These substances as antibacterial agents make the cell membrane permeable due to its impregnation in the hydrophobic domains, this effect is higher against gram positive bacteria. In addition, the OEO has antioxidant properties effective in retarding the process of lipid peroxidation in fatty foods, and scavenging free radicals. In this perspective, the present review analyzes and discusses the state of the art about the actual and potential uses of OEO as an antimicrobial and antioxidant food additives.

  11. A macrocyclic approach to tetracycline natural products. Investigation of transannular alkylations and Michael additions.

    PubMed

    Wzorek, Joseph S; Knöpfel, Thomas F; Sapountzis, Ioannis; Evans, David A

    2012-12-07

    A new approach to the tetracycline core structure is presented. The pivotal intermediate is identified as macrocycle III. The two interior bonds (C4a-C12a and C5a-C11a) are to be constructed through sequential transannular Michael additions (III-II) and compression-promoted transannular isoxazole alkylations from intermediate II.

  12. Grassland productivity in response to nutrient additions and herbivory is scale-dependent.

    PubMed

    Smithwick, Erica A H; Baldwin, Douglas C; Naithani, Kusum J

    2016-01-01

    Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m). The remaining plots either received no additions or were fertilized evenly across the entire area. Three of the six plots were fenced to exclude herbivory. We calculated empirical semivariograms for all plots one year following nutrient additions to determine whether the scale of grass response (biomass and nutrient concentrations) corresponded to the scale of the sub-plot additions and compared these results to reference plots (unfertilized or unscaled) and to plots with and without herbivory. We compared empirical semivariogram parameters to parameters from semivariograms derived from a set of simulated landscapes (neutral models). Empirical semivariograms showed spatial structure in plots that received multi-scaled nutrient additions, particularly at the 2 × 2 m grain. The level of biomass response was predicted by foliar P concentration and, to a lesser extent, N, with the treatment effect of herbivory having a minimal influence. Neutral models confirmed the length scale of the biomass response and indicated few differences due to herbivory. Overall, we conclude that interpretation of nutrient limitation in grasslands is dependent on the grain used to measure grass response and that herbivory had a secondary effect.

  13. Grassland productivity in response to nutrient additions and herbivory is scale-dependent

    PubMed Central

    Baldwin, Douglas C.; Naithani, Kusum J.

    2016-01-01

    Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m). The remaining plots either received no additions or were fertilized evenly across the entire area. Three of the six plots were fenced to exclude herbivory. We calculated empirical semivariograms for all plots one year following nutrient additions to determine whether the scale of grass response (biomass and nutrient concentrations) corresponded to the scale of the sub-plot additions and compared these results to reference plots (unfertilized or unscaled) and to plots with and without herbivory. We compared empirical semivariogram parameters to parameters from semivariograms derived from a set of simulated landscapes (neutral models). Empirical semivariograms showed spatial structure in plots that received multi-scaled nutrient additions, particularly at the 2 × 2 m grain. The level of biomass response was predicted by foliar P concentration and, to a lesser extent, N, with the treatment effect of herbivory having a minimal influence. Neutral models confirmed the length scale of the biomass response and indicated few differences due to herbivory. Overall, we conclude that interpretation of nutrient limitation in grasslands is dependent on the grain used to measure grass response and that herbivory had a secondary effect. PMID:27920956

  14. Gene Delivery into Plant Cells for Recombinant Protein Production

    PubMed Central

    Chen, Qiang

    2015-01-01

    Recombinant proteins are primarily produced from cultures of mammalian, insect, and bacteria cells. In recent years, the development of deconstructed virus-based vectors has allowed plants to become a viable platform for recombinant protein production, with advantages in versatility, speed, cost, scalability, and safety over the current production paradigms. In this paper, we review the recent progress in the methodology of agroinfiltration, a solution to overcome the challenge of transgene delivery into plant cells for large-scale manufacturing of recombinant proteins. General gene delivery methodologies in plants are first summarized, followed by extensive discussion on the application and scalability of each agroinfiltration method. New development of a spray-based agroinfiltration and its application on field-grown plants is highlighted. The discussion of agroinfiltration vectors focuses on their applications for producing complex and heteromultimeric proteins and is updated with the development of bridge vectors. Progress on agroinfiltration in Nicotiana and non-Nicotiana plant hosts is subsequently showcased in context of their applications for producing high-value human biologics and low-cost and high-volume industrial enzymes. These new advancements in agroinfiltration greatly enhance the robustness and scalability of transgene delivery in plants, facilitating the adoption of plant transient expression systems for manufacturing recombinant proteins with a broad range of applications. PMID:26075275

  15. Hyperexpression of two Aspergillus Niger Xylanase Genes in Escherichia Coli and Characterization of the Gene Products

    PubMed Central

    Yi, Xiuli; Shi, Yan; Xu, Hui; Li, Wei; Xie, Jie; Yu, Rongqing; Zhu, Jun; Cao, Yi; Qiao, Dairong

    2010-01-01

    The analysis of individual gene product should enable to clarify the role of a particular enzyme in a complex xylanase system of A. niger. The two genes encoding precursors of co-produced endo-1,4-β-D-xylanases, xynA1 and xynB, were isolated from Aspergillus niger SCTCC 400264 (SCTCC, China) by using RT-PCR technique and then successfully expressed in Escherichia coli BL21. The nucleotide sequences of the xynA1 and xynB genes revealed that they were only 52.5% homology to each other. Characterization of the recombinant enzymes revealed the different properties: the specific activity of recombinant XYNA1 was 16.58 U/mg compared to 1201.7 U/mg for recombinant XYNB; The optimum temperature and pH of the recombinant XYNA1 were 35 °C and 3.0, respectively, whereas the corresponding values for the recombinant XYNB were 55 °C and 5.0, respectively; The recombinant XYNB showed much more thermostability than recombinant XYNA1; The recombinant XYNB showed 94% of maximal activity after incubating in water for 60 min at 60 °C compared to no activity for recombinant XYNA1. Various metal ions had different effects on activity between the two recombinant xylanases. PMID:24031555

  16. Additives to Prevent Deleterious Effects Associated with Long-Term Storage of Petroleum Products,

    DTIC Science & Technology

    1980-09-01

    source of carbon for bacteria than the fuel itself. When the material is used it must be protected by a bactericide . 50. Sulfate-reducing bacteria... Bactericides have been widely used to control microbial effects in petroleum storage. Most of these compounds dissolve in the petroleum product but, move into...the bactericides . Generally these materials would be deactivated by absorp- tion on particulates or oxidation. Testing of bactericides for use in long

  17. Production and clinical development of nanoparticles for gene delivery

    PubMed Central

    Chen, Jie; Guo, Zhaopei; Tian, Huayu; Chen, Xuesi

    2016-01-01

    Gene therapy is a promising strategy for specific treatment of numerous gene-associated human diseases by intentionally altering the gene expression in pathological cells. A successful clinical application of gene-based therapy depends on an efficient gene delivery system. Many efforts have been attempted to improve the safety and efficiency of gene-based therapies. Nanoparticles have been proved to be the most promising vehicles for clinical gene therapy due to their tunable size, shape, surface, and biological behaviors. In this review, the clinical development of nanoparticles for gene delivery will be particularly highlighted. Several promising candidates, which are closest to clinical applications, will be briefly reviewed. Then, the recent developments of nanoparticles for clinical gene therapy will be identified and summarized. Finally, the development of nanoparticles for clinical gene delivery in future will be prospected. PMID:27088105

  18. Enhanced production of Monacolin K by addition of precursors and surfactants in submerged fermentation of Monascus purpureus 9901.

    PubMed

    Zhang, Jun; Wang, Yuan-Long; Lu, Li-Ping; Zhang, Bo-Bo; Xu, Gan-Rong

    2014-01-01

    The main problem in Monacolin K (MK) production by submerged fermentation of Monascus purpureus is low productivity. In this study, on one hand, addition of precursors was used to activate the biosynthesis of MK. When 4.0 g/L of sodium citrate was supplemented at the 48th H of the fermentation, the final MK production reached to 1,658.9 ± 28.5 mg/L after 20 day of fermentation, which was improved by 52.6% compared with that of the control. On the other hand, addition of surfactants could increase the permeability of cell membrane, thus driving more intracellular metabolites secreted into the fermentation broth and alleviating the product inhibition. When 40.0 g/L of Triton X-100 was added at the beginning of the fermentation, the final MK production reached to 2,026.0 ± 30.4 mg/L after 20 day of fermentation, which was improved by 84.9% compared with that of the control. These results are helpful to provide some new insights into the biosynthetic regulation on MK production; the approach can be applied to other fungal fermentation processes for enhancing production of useful metabolites.

  19. Production of cellobionate from cellulose using an engineered Neurospora crassa strain with laccase and redox mediator addition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report a novel production process for cellobionic acid from cellulose using an engineered fungal strain with the exogenous addition of laccase and a redox mediator. A previously engineered strain of Neurospora crassa (F5'ace-1'cre-1'ndvB) was shown to produce cellobionate directly from cellulose ...

  20. THE COMBINED CARCINOGENIC RISK FOR EXPOSURE TO MIXTURES OF DRINKING WATER DISINFECTION BY-PRODUCTS MAY BE LESS THAN ADDITIVE

    EPA Science Inventory

    The Combined Carcinogenic Risk for Exposure to Mixtures of Drinking Water Disinfection By-Products May be Less Than Additive

    Risk assessment methods for chemical mixtures in drinking water are not well defined. Current default risk assessments for chemical mixtures assume...

  1. PILOT-SCALE STUDIES ON THE EFFECT OF BROMINE ADDITION ON THE EMISSIONS OF CHLORINATED ORGANIC COMBUSTION BY-PRODUCTS

    EPA Science Inventory

    The addition of brominated organic compounds to the feed of a pilot-scale incinerator burning chlorinated waste has been found previously, under some circumstances, to enhance emissions of volatile and semivolatile organic chlorinated products of incomplete combustion (PiCs) incl...

  2. Search for anomalous production of events with two photons and additional energetic objects at CDF

    NASA Astrophysics Data System (ADS)

    Aaltonen, T.; Adelman, J.; Álvarez González, B.; Amerio, S.; Amidei, D.; Anastassov, A.; Annovi, A.; Antos, J.; Apollinari, G.; Apresyan, A.; Arisawa, T.; Artikov, A.; Asaadi, J.; Ashmanskas, W.; Attal, A.; Aurisano, A.; Azfar, F.; Badgett, W.; Barbaro-Galtieri, A.; Barnes, V. E.; Barnett, B. A.; Barria, P.; Bartos, P.; Bauer, G.; Beauchemin, P.-H.; Bedeschi, F.; Beecher, D.; Behari, S.; Bellettini, G.; Bellinger, J.; Benjamin, D.; Beretvas, A.; Bhatti, A.; Binkley, M.; Bisello, D.; Bizjak, I.; Blair, R. E.; Blocker, C.; Blumenfeld, B.; Bocci, A.; Bodek, A.; Boisvert, V.; Bortoletto, D.; Boudreau, J.; Boveia, A.; Brau, B.; Bridgeman, A.; Brigliadori, L.; Bromberg, C.; Brubaker, E.; Budagov, J.; Budd, H. S.; Budd, S.; Burkett, K.; Busetto, G.; Bussey, P.; Buzatu, A.; Byrum, K. L.; Cabrera, S.; Calancha, C.; Camarda, S.; Campanelli, M.; Campbell, M.; Canelli, F.; Canepa, A.; Carls, B.; Carlsmith, D.; Carosi, R.; Carrillo, S.; Carron, S.; Casal, B.; Casarsa, M.; Castro, A.; Catastini, P.; Cauz, D.; Cavaliere, V.; Cavalli-Sforza, M.; Cerri, A.; Cerrito, L.; Chang, S. H.; Chen, Y. C.; Chertok, M.; Chiarelli, G.; Chlachidze, G.; Chlebana, F.; Cho, K.; Chokheli, D.; Chou, J. P.; Chung, K.; Chung, W. H.; Chung, Y. S.; Chwalek, T.; Ciobanu, C. I.; Ciocci, M. A.; Clark, A.; Clark, D.; Compostella, G.; Convery, M. E.; Conway, J.; Corbo, M.; Cordelli, M.; Cox, C. A.; Cox, D. J.; Crescioli, F.; Cuenca Almenar, C.; Cuevas, J.; Culbertson, R.; Cully, J. C.; Dagenhart, D.; Datta, M.; Davies, T.; de Barbaro, P.; de Cecco, S.; Deisher, A.; de Lorenzo, G.; Dell'Orso, M.; Deluca, C.; Demortier, L.; Deng, J.; Deninno, M.; D'Errico, M.; di Canto, A.; di Giovanni, G. P.; di Ruzza, B.; Dittmann, J. R.; D'Onofrio, M.; Donati, S.; Dong, P.; Dorigo, T.; Dube, S.; Ebina, K.; Elagin, A.; Erbacher, R.; Errede, D.; Errede, S.; Ershaidat, N.; Eusebi, R.; Fang, H. C.; Farrington, S.; Fedorko, W. T.; Feild, R. G.; Feindt, M.; Fernandez, J. P.; Ferrazza, C.; Field, R.; Flanagan, G.; Forrest, R.; Frank, M. J.; Franklin, M.; Freeman, J. C.; Furic, I.; Gallinaro, M.; Galyardt, J.; Garberson, F.; Garcia, J. E.; Garfinkel, A. F.; Garosi, P.; Gerberich, H.; Gerdes, D.; Gessler, A.; Giagu, S.; Giakoumopoulou, V.; Giannetti, P.; Gibson, K.; Gimmell, J. L.; Ginsburg, C. M.; Giokaris, N.; Giordani, M.; Giromini, P.; Giunta, M.; Giurgiu, G.; Glagolev, V.; Glenzinski, D.; Gold, M.; Goldschmidt, N.; Golossanov, A.; Gomez, G.; Gomez-Ceballos, G.; Goncharov, M.; González, O.; Gorelov, I.; Goshaw, A. T.; Goulianos, K.; Gresele, A.; Grinstein, S.; Grosso-Pilcher, C.; Group, R. C.; Grundler, U.; Guimaraes da Costa, J.; Gunay-Unalan, Z.; Haber, C.; Hahn, S. R.; Halkiadakis, E.; Han, B.-Y.; Han, J. Y.; Happacher, F.; Hara, K.; Hare, D.; Hare, M.; Harr, R. F.; Hartz, M.; Hatakeyama, K.; Hays, C.; Heck, M.; Heinrich, J.; Herndon, M.; Heuser, J.; Hewamanage, S.; Hidas, D.; Hill, C. S.; Hirschbuehl, D.; Hocker, A.; Hou, S.; Houlden, M.; Hsu, S.-C.; Hughes, R. E.; Hurwitz, M.; Husemann, U.; Hussein, M.; Huston, J.; Incandela, J.; Introzzi, G.; Iori, M.; Ivanov, A.; James, E.; Jang, D.; Jayatilaka, B.; Jeon, E. J.; Jha, M. K.; Jindariani, S.; Johnson, W.; Jones, M.; Joo, K. K.; Jun, S. Y.; Jung, J. E.; Junk, T. R.; Kamon, T.; Kar, D.; Karchin, P. E.; Kato, Y.; Kephart, R.; Ketchum, W.; Keung, J.; Khotilovich, V.; Kilminster, B.; Kim, D. H.; Kim, H. S.; Kim, H. W.; Kim, J. E.; Kim, M. J.; Kim, S. B.; Kim, S. H.; Kim, Y. K.; Kimura, N.; Kirsch, L.; Klimenko, S.; Kondo, K.; Kong, D. J.; Konigsberg, J.; Korytov, A.; Kotwal, A. V.; Kreps, M.; Kroll, J.; Krop, D.; Krumnack, N.; Kruse, M.; Krutelyov, V.; Kuhr, T.; Kulkarni, N. P.; Kurata, M.; Kwang, S.; Laasanen, A. T.; Lami, S.; Lammel, S.; Lancaster, M.; Lander, R. L.; Lannon, K.; Lath, A.; Latino, G.; Lazzizzera, I.; Lecompte, T.; Lee, E.; Lee, H. S.; Lee, J. S.; Lee, S. W.; Leone, S.; Lewis, J. D.; Lin, C.-J.; Linacre, J.; Lindgren, M.; Lipeles, E.; Lister, A.; Litvintsev, D. O.; Liu, C.; Liu, T.; Lockyer, N. S.; Loginov, A.; Lovas, L.; Lucchesi, D.; Lueck, J.; Lujan, P.; Lukens, P.; Lungu, G.; Lys, J.; Lysak, R.; MacQueen, D.; Madrak, R.; Maeshima, K.; Makhoul, K.; Maksimovic, P.; Malde, S.; Malik, S.; Manca, G.; Manousakis-Katsikakis, A.; Margaroli, F.; Marino, C.; Marino, C. P.; Martin, A.; Martin, V.; Martínez, M.; Martínez-Ballarín, R.; Mastrandrea, P.; Mathis, M.; Mattson, M. E.; Mazzanti, P.; McFarland, K. S.; McIntyre, P.; McNulty, R.; Mehta, A.; Mehtala, P.; Menzione, A.; Mesropian, C.; Miao, T.; Mietlicki, D.; Miladinovic, N.; Miller, R.; Mills, C.; Milnik, M.; Mitra, A.; Mitselmakher, G.; Miyake, H.; Moed, S.; Moggi, N.; Mondragon, M. N.; Moon, C. S.; Moore, R.; Morello, M. J.; Morlock, J.; Movilla Fernandez, P.; Mülmenstädt, J.; Mukherjee, A.; Muller, Th.; Murat, P.; Mussini, M.; Nachtman, J.; Nagai, Y.; Naganoma, J.; Nakamura, K.; Nakano, I.; Napier, A.; Nett, J.; Neu, C.; Neubauer, M. S.; Neubauer, S.; Nielsen, J.; Nodulman, L.; Norman, M.; Norniella, O.; Nurse, E.; Oakes, L.; Oh, S. H.; Oh, Y. D.; Oksuzian, I.; Okusawa, T.; Orava, R.; Osterberg, K.; Pagan Griso, S.; Pagliarone, C.; Palencia, E.; Papadimitriou, V.; Papaikonomou, A.; Paramanov, A. A.; Parks, B.; Pashapour, S.; Patrick, J.; Pauletta, G.; Paulini, M.; Paus, C.; Peiffer, T.; Pellett, D. E.; Penzo, A.; Phillips, T. I.; Piacentino, G.; Pianori, E.; Pinera, L.; Pitts, K.; Plager, C.; Pondrom, L.; Potamianos, K.; Poukhov, O.; Prokoshin, F.; Pronko, A.; Ptohos, F.; Pueschel, E.; Punzi, G.; Pursley, J.; Rademacker, J.; Rahaman, A.; Ramakrishnan, V.; Ranjan, N.; Redondo, I.; Renton, P.; Renz, M.; Rescigno, M.; Richter, S.; Rimondi, F.; Ristori, L.; Robson, A.; Rodrigo, T.; Rodriguez, T.; Rogers, E.; Rolli, S.; Roser, R.; Rossi, M.; Rossin, R.; Roy, P.; Ruiz, A.; Russ, J.; Rusu, V.; Rutherford, B.; Saarikko, H.; Safonov, A.; Sakumoto, W. K.; Santi, L.; Sartori, L.; Sato, K.; Savoy-Navarro, A.; Schlabach, P.; Schmidt, A.; Schmidt, E. E.; Schmidt, M. A.; Schmidt, M. P.; Schmitt, M.; Schwarz, T.; Scodellaro, L.; Scribano, A.; Scuri, F.; Sedov, A.; Seidel, S.; Seiya, Y.; Semenov, A.; Sexton-Kennedy, L.; Sforza, F.; Sfyrla, A.; Shalhout, S. Z.; Shears, T.; Shepard, P. F.; Shimojima, M.; Shiraishi, S.; Shochet, M.; Shon, Y.; Shreyber, I.; Simonenko, A.; Sinervo, P.; Sisakyan, A.; Slaughter, A. J.; Slaunwhite, J.; Sliwa, K.; Smith, J. R.; Snider, F. D.; Snihur, R.; Soha, A.; Somalwar, S.; Sorin, V.; Squillacioti, P.; Stanitzki, M.; St. Denis, R.; Stelzer, B.; Stelzer-Chilton, O.; Stentz, D.; Strologas, J.; Strycker, G. L.; Suh, J. S.; Sukhanov, A.; Suslov, I.; Taffard, A.; Takashima, R.; Takeuchi, Y.; Tanaka, R.; Tang, J.; Tecchio, M.; Teng, P. K.; Thom, J.; Thome, J.; Thompson, G. A.; Thomson, E.; Tipton, P.; Ttito-Guzmán, P.; Tkaczyk, S.; Toback, D.; Tokar, S.; Tollefson, K.; Tomura, T.; Tonelli, D.; Torre, S.; Torretta, D.; Totaro, P.; Tourneur, S.; Trovato, M.; Tsai, S.-Y.; Tu, Y.; Turini, N.; Ukegawa, F.; Uozumi, S.; van Remortel, N.; Varganov, A.; Vataga, E.; Vázquez, F.; Velev, G.; Vellidis, C.; Vidal, M.; Vila, I.; Vilar, R.; Vogel, M.; Volobouev, I.; Volpi, G.; Wagner, P.; Wagner, R. G.; Wagner, R. L.; Wagner, W.; Wagner-Kuhr, J.; Wakisaka, T.; Wallny, R.; Wang, S. M.; Warburton, A.; Waters, D.; Weinberger, M.; Weinelt, J.; Wester, W. C., III; Whitehouse, B.; Whiteson, D.; Wicklund, A. B.; Wicklund, E.; Wilbur, S.; Williams, G.; Williams, H. H.; Wilson, P.; Winer, B. L.; Wittich, P.; Wolbers, S.; Wolfe, C.; Wolfe, H.; Wright, T.; Wu, X.; Würthwein, F.; Yagil, A.; Yamamoto, K.; Yamaoka, J.; Yang, U. K.; Yang, Y. C.; Yao, W. M.; Yeh, G. P.; Yi, K.; Yoh, J.; Yorita, K.; Yoshida, T.; Yu, G. B.; Yu, I.; Yu, S. S.; Yun, J. C.; Zanetti, A.; Zeng, Y.; Zhang, X.; Zheng, Y.; Zucchelli, S.; CDF Collaboration

    2010-09-01

    We present results of a search for anomalous production of two photons together with an electron, muon, τ lepton, missing transverse energy, or jets using pp¯ collision data from 1.1-2.0fb-1 of integrated luminosity collected by the Collider Detector at Fermilab (CDF). The event yields and kinematic distributions are examined for signs of new physics without favoring a specific model of new physics. The results are consistent with the standard model expectations. The search employs several new analysis techniques that significantly reduce instrumental backgrounds in channels with an electron and missing transverse energy.

  3. Search for Anomalous Production of Events with Two Photons and Additional Energetic Objects at CDF

    SciTech Connect

    Aaltonen, T.; Adelman, J.; Alvarez Gonzalez, B.; Amerio, S.; Amidei, D.; Anastassov, A.; Annovi, A.; Antos, J.; Apollinari, G.; Apresyan, A.; Arisawa, T.; /Waseda U. /Dubna, JINR

    2009-10-01

    The authors present results of a search for anomalous production of two photons together with an electron, muon, {tau} lepton, missing transverse energy, or jets using p{bar p} collision data from 1.1-2.0 fb{sup -1} of integrated luminosity collected by the Collider Detector at Fermilab (CDF). The event yields and kinematic distributions are examined for signs for new physics without favoring a specific model of new physics. The results are consistent with the standard model expectations. The search employs several new analysis techniques that significantly reduce instrumental backgrounds in channels with an electron and missing transverse energy.

  4. Exopolysaccharide Production and Ropy Phenotype Are Determined by Two Gene Clusters in Putative Probiotic Strain Lactobacillus paraplantarum BGCG11

    PubMed Central

    Zivkovic, Milica; Miljkovic, Marija; Ruas-Madiedo, Patricia; Strahinic, Ivana; Tolinacki, Maja; Golic, Natasa

    2014-01-01

    Lactobacillus paraplantarum BGCG11, a putative probiotic strain isolated from a soft, white, artisanal cheese, produces a high-molecular-weight heteropolysaccharide, exopolysaccharide (EPS)-CG11, responsible for the ropy phenotype and immunomodulatory activity of the strain. In this study, a 26.4-kb region originating from the pCG1 plasmid, previously shown to be responsible for the production of EPS-CG11 and a ropy phenotype, was cloned, sequenced, and functionally characterized. In this region 16 putative open reading frames (ORFs), encoding enzymes for the production of EPS-CG11, were organized in specific loci involved in the biosynthesis of the repeat unit, polymerization, export, regulation, and chain length determination. Interestingly, downstream of the eps gene cluster, a putative transposase gene was identified, followed by an additional rfb gene cluster containing the rfbACBD genes, the ones most probably responsible for dTDP-l-rhamnose biosynthesis. The functional analysis showed that the production of the high-molecular-weight fraction of EPS-CG11 was absent in two knockout mutants, one in the eps and the other in the rfb gene cluster, as confirmed by size exclusion chromatography analysis. Therefore, both eps and rfb genes clusters are prerequisites for the production of high-molecular-weight EPS-CG11 and for the ropy phenotype of strain L. paraplantarum BGCG11. PMID:25527533

  5. Additive Manufacturing for Cost Efficient Production of Compact Ceramic Heat Exchangers and Recuperators

    SciTech Connect

    Shulman, Holly; Ross, Nicole

    2015-10-30

    An additive manufacture technique known as laminated object manufacturing (LOM) was used to fabricate compact ceramic heat exchanger prototypes. LOM uses precision CO2 laser cutting of ceramic green tapes, which are then precision stacked to build a 3D object with fine internal features. Modeling was used to develop prototype designs and predict the thermal response, stress, and efficiency in the ceramic heat exchangers. Build testing and materials analyses were used to provide feedback for the design selection. During this development process, laminated object manufacturing protocols were established. This included laser optimization, strategies for fine feature integrity, lamination fluid control, green handling, and firing profile. Three full size prototypes were fabricated using two different designs. One prototype was selected for performance testing. During testing, cross talk leakage prevented the application of a high pressure differential, however, the prototype was successful at withstanding the high temperature operating conditions (1300 °F). In addition, analysis showed that the bulk of the part did not have cracks or leakage issues. This led to the development of a module method for next generation LOM heat exchangers. A scale-up cost analysis showed that given a purpose built LOM system, these ceramic heat exchangers would be affordable for the applications.

  6. Production of Synthetic Rutile from Molten Titanium Slag with the Addition of B2O3

    NASA Astrophysics Data System (ADS)

    Fan, Helin; Duan, Huamei; Tan, Kai; Li, Yuankun; Chen, Dengfu; Long, Mujun; Liu, Tao

    2017-02-01

    A new process of producing synthetic rutile from molten titanium slag with the addition B2O3 is proposed. The process includes a molten modification process and a leaching process. The molten modification process was conducted by adding B2O3 into molten slag. The leaching process was conducted by adding hydrochloric acid and subsequent NaOH. The results show that CaO and MgO are leached out by hydrochloric acid and that synthetic rutile is further improved by NaOH. The optimized conditions are 2% B2O3 amount, 5% hydrochloric concentration, 80°C leaching temperature, and 30 min leaching time. The synthetic rutile with 86.77% TiO2 and 1.23% (CaO + MgO) was prepared. From x-ray diffraction results, thermodynamic calculation and the theory of bond parameter function, with the addition of B2O3, calcium silicate is transformed into calcium borate and anosovite is transformed into magnesium borate. Calcium borate and magnesium borate are leached out by hydrochloric acid, leading to the enrichment of rutile.

  7. Nutrient additions by waterfowl to lakes and reservoirs: predicting their effects on productivity and water quality

    USGS Publications Warehouse

    Manny, Bruce A.; Johnson, W.C.; Wetzel, R.G.

    1994-01-01

    Lakes and reservoirs provide water for human needs and habitat for aquatic birds. Managers of such waters may ask whether nutrients added by waterfowl degrade water quality. For lakes and reservoirs where primary productivity is limited by phosphorus (P), we developed a procedure that integrates annual P loads from waterfowl and other external sources, applies a nutrient load-response model, and determines whether waterfowl that used the lake or reservoir degraded water quality. Annual P loading by waterfowl can be derived from a figure in this report, using the days per year that each kind spent on any lake or reservoir. In our example, over 6500 Canada geese (Branta canadensis) and 4200 ducks (mostly mallards, Anas platyrhynchos) added 4462 kg of carbon (C), 280 kg of nitrogen (N), and 88 kg of P y-1 to Wintergreen Lake in southwestern Michigan, mostly during their migration. These amounts were 69% of all C, 27% of all N, and 70% of all P that entered the lake from external sources. Loads from all external sources totaled 840 mg P m-2 y-1. Application of a nutrient load-response model to this concentration, the hydraulic load (0.25 m y-1), and the water residence time (9.7 y) of Wintergreen Lake yielded an average annual concentration of total P in the lake of 818 mg m-3 that classified the lake as hypertrophic. This trophic classification agreed with independent measures of primary productivity, chlorophyll-a, total P, total N, and Secchi disk transparency made in Wintergreen Lake. Our procedure showed that waterfowl caused low water quality in Wintergreen Lake.

  8. Enhanced L-lactic acid production in Lactobacillus paracasei by exogenous proline addition based on comparative metabolite profiling analysis.

    PubMed

    Tian, Xiwei; Wang, Yonghong; Chu, Ju; Zhuang, Yingping; Zhang, Siliang

    2016-03-01

    This study investigated cell physiological and metabolic responses of Lactobacillus paracasei to osmotic stresses. Both cellular fatty acid composition and metabolite profiling were responded by increasing unsaturated and epoxy-fatty acid proportions, as well as accumulating some specific intracellular metabolites. Simultaneously, metabolite profiling was adopted to rationally and systematically discover potential osmoprotectants. Consequently, exogenous addition of proline or aspartate was validated to be a feasible and efficacious approach to improve cell growth under hyperosmotic stress in shake flasks. Particularly, with 5-L cultivation system, L-lactic acid concentration increased from 108 to 150 g/L during the following 16-h fermentation in 2 g/L proline addition group, while it only increased from 110 to 140 g/L in no proline addition group. Moreover, glucose consumption rate with proline addition reached 3.49 g/L/h during this phase, 35.8 % higher than that with no proline addition. However, extreme high osmotic pressure would significantly limit the osmoprotection of proline, and the osmolality threshold for L. paracasei was approximately 3600 mOsm/kg. It was suggested that proline principally played a role as a compatible solute accumulated in the cell for hyperosmotic preservation. The strategies of exploiting osmotic protectant with metabolite profiling and enhancing L-lactic acid production by osmoprotectant addition would be potential to provide a new insight for other microorganisms and organic acids production.

  9. Anaerobic Codigestion of Sludge: Addition of Butcher's Fat Waste as a Cosubstrate for Increasing Biogas Production.

    PubMed

    Martínez, E J; Gil, M V; Fernandez, C; Rosas, J G; Gómez, X

    2016-01-01

    Fat waste discarded from butcheries was used as a cosubstrate in the anaerobic codigestion of sewage sludge (SS). The process was evaluated under mesophilic and thermophilic conditions. The codigestion was successfully attained despite some inhibitory stages initially present that had their origin in the accumulation of volatile fatty acids (VFA) and adsorption of long-chain fatty acids (LCFA). The addition of a fat waste improved digestion stability and increased biogas yields thanks to the higher organic loading rate (OLR) applied to the reactors. However, thermophilic digestion was characterized by an effluent of poor quality and high VFA content. Results from spectroscopic analysis suggested the adsorption of lipid components onto the anaerobic biomass, thus disturbing the complete degradation of substrate during the treatment. The formation of fatty aggregates in the thermophilic reactor prevented process failure by avoiding the exposure of biomass to the toxic effect of high LCFA concentrations.

  10. SSF of steam-pretreated wheat straw with the addition of saccharified or fermented wheat meal in integrated bioethanol production

    PubMed Central

    2013-01-01

    Background Integration of second-generation (2G) bioethanol production with existing first-generation (1G) production may facilitate commercial production of ethanol from cellulosic material. Since 2G hydrolysates have a low sugar concentration and 1G streams often have to be diluted prior to fermentation, mixing of streams is beneficial. Improved ethanol concentrations in the 2G production process lowers energy demand in distillation, improves overall energy efficiency and thus lower production cost. There is also a potential to reach higher ethanol yields, which is required in economically feasible ethanol production. Integrated process scenarios with addition of saccharified wheat meal (SWM) or fermented wheat meal (FWM) were investigated in simultaneous saccharification and (co-)fermentation (SSF or SSCF) of steam-pretreated wheat straw, while the possibility of recovering the valuable protein-rich fibre residue from the wheat was also studied. Results The addition of SWM to SSF of steam-pretreated wheat straw, using commercially used dried baker’s yeast, S. cerevisiae, resulted in ethanol concentrations of about 60 g/L, equivalent to ethanol yields of about 90% of the theoretical. The addition of FWM in batch mode SSF was toxic to baker’s yeast, due to the ethanol content of FWM, resulting in a very low yield and high accumulation of glucose. The addition of FWM in fed-batch mode still caused a slight accumulation of glucose, but the ethanol concentration was fairly high, 51.2 g/L, corresponding to an ethanol yield of 90%, based on the amount of glucose added. In batch mode of SSCF using the xylose-fermenting, genetically modified S. cerevisiae strain KE6-12, no improvement was observed in ethanol yield or concentration, compared with baker’s yeast, despite the increased xylose utilization, probably due to the considerable increase in glycerol production. A slight increase in xylose consumption was seen when glucose from SWM was fed at a low feed rate

  11. Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association

    PubMed Central

    Wilson, Larissa M.; Whitt, Sherry R.; Ibáñez, Ana M.; Rocheford, Torbert R.; Goodman, Major M.; Buckler, Edward S.

    2004-01-01

    Cereal starch production forms the basis of subsistence for much of the world's human and domesticated animal populations. Starch concentration and composition in the maize (Zea mays ssp mays) kernel are complex traits controlled by many genes. In this study, an association approach was used to evaluate six maize candidate genes involved in kernel starch biosynthesis: amylose extender1 (ae1), brittle endosperm2 (bt2), shrunken1 (sh1), sh2, sugary1, and waxy1. Major kernel composition traits, such as protein, oil, and starch concentration, were assessed as well as important starch composition quality traits, including pasting properties and amylose levels. Overall, bt2, sh1, and sh2 showed significant associations for kernel composition traits, whereas ae1 and sh2 showed significant associations for starch pasting properties. ae1 and sh1 both associated with amylose levels. Additionally, haplotype analysis of sh2 suggested this gene is involved in starch viscosity properties and amylose content. Despite starch concentration being only moderately heritable for this particular panel of diverse maize inbreds, high resolution was achieved when evaluating these starch candidate genes, and diverse alleles for breeding and further molecular analysis were identified. PMID:15377761

  12. Novel glycol chitosan-based polymeric gene carrier synthesized by a Michael addition reaction with low molecular weight polyethylenimine.

    PubMed

    Lee, Young Hwa; Park, Hae In; Choi, Joon Sig

    2016-02-10

    A glycol chitosan-based polymer that spontaneously assembles with plasmid DNA into nanorods was evaluated as a non-viral vector for gene delivery. Glycol chitosan-methyl acrylate-polyethylenimine (GMP) was synthesized by grafting polyethylenimine onto glycol chitosan via amidation after Michael addition using methyl acrylate. Gel retardation and PicoGreen assay experiments showed complete complex formation with plasmid DNA. GMP/pDNA complexes were characterized using biophysical techniques and were found to be positively charged rod-shape structures with widths in the nanometer scale and lengths in the micrometer scale. Transfection efficiency and cytotoxicity of GMP polymer was evaluated in human epithelial ovary carcinoma (HeLa) cells, human embryonic kidney 293 (HEK293) cells, and human hepatocellular liver carcinoma (HepG2) cells, in comparison to high molecular weight polyethylenimine, a commonly used transfection reagent. Intracellular polymer uptake was compared and confirmed by confocal microscopy. The results demonstrate that GMP, a hybrid polymer of glycol chitosan grafted with branched polyethylenimine, may serve as a promising vehicle for efficient gene delivery.

  13. Clustered Genes Involved in Cyclopiazonic Acid Production are Next to the Aflatoxin Biosynthesis Gene Cluster in Aspergillus flavus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cyclopiazonic acid (CPA), an indole-tetramic acid toxin, is produced by many species of Aspergillus and Penicillium. In addition to CPA Aspergillus flavus produces polyketide-derived carcinogenic aflatoxins (AFs). AF biosynthesis genes form a gene cluster in a subtelomeric region. Isolates of A. fla...

  14. Exogenous N addition enhances the responses of gross primary productivity to individual precipitation events in a temperate grassland

    PubMed Central

    Guo, Qun; Hu, Zhong-min; Li, Sheng-gong; Yu, Gui-rui; Sun, Xiao-min; Li, Ling-hao; Liang, Nai-shen; Bai, Wen-ming

    2016-01-01

    Predicted future shifts in the magnitude and frequency (larger but fewer) of precipitation events and enhanced nitrogen (N) deposition may interact to affect grassland productivity, but the effects of N enrichment on the productivity response to individual precipitation events remain unclear. In this study, we quantified the effects of N addition on the response patterns of gross primary productivity (GPP) to individual precipitation events of different sizes (Psize) in a temperate grassland in China. The results showed that N enrichment significantly increased the time-integrated amount of GPP in response to an individual precipitation event (GPPtotal), and the N-induced stimulation of GPP increased with increasing Psize. N enrichment rarely affected the duration of the GPP response, but it significantly stimulated the maximum absolute GPP response. Higher foliar N content might play an important role in the N-induced stimulation of GPP. GPPtotal in both the N-addition and control treatments increased linearly with Psize with similar Psize intercepts (approximately 5 mm, indicating a similar lower Psize threshold to stimulate the GPP response) but had a steeper slope under N addition. Our work indicates that the projected larger precipitation events will stimulate grassland productivity, and this stimulation might be amplified by increasing N deposition. PMID:27264386

  15. Jatropha oil derived sophorolipids: production and characterization as laundry detergent additive.

    PubMed

    Joshi-Navare, Kasturi; Khanvilkar, Poonam; Prabhune, Asmita

    2013-01-01

    Sophorolipids (SLs) are glycolipidic biosurfactants suitable for various biological and physicochemical applications. The nonedible Jatropha oil has been checked as the alternative raw material for SL synthesis using C. bombicola (ATCC22214). This is useful towards lowering the SL production cost. Through optimization of fermentation parameters and use of resting cell method, the yield 15.25 g/L could be achieved for Jatropha oil derived SL (SLJO) with 1% v/v oil feeding. The synthesized SL displayed good surfactant property. It reduced the surface tension of distilled water from 70.7 mN/m to 33.5 mN/m with the Critical Micelle Concentration (CMC) value of 9.5 mg/L. Keeping the prospective use of the SL in mind, the physicochemical properties were checked along with emulsion stability under temperature, pH stress, and in hard water. Also antibacterial action and stain removal capability in comparison with commercial detergent was demonstrated. SLJO enhanced the detergent performance. Based on the results, it can be said that SLs have utility as fabric cleaner with advantageous properties such as skin friendly nature, antibacterial action, and biodegradability. Therefore SLs are potential green molecules to replace synthetic surfactants in detergents so as to reduce harm caused to environment through detergent usage.

  16. Jatropha Oil Derived Sophorolipids: Production and Characterization as Laundry Detergent Additive

    PubMed Central

    Joshi-Navare, Kasturi; Khanvilkar, Poonam; Prabhune, Asmita

    2013-01-01

    Sophorolipids (SLs) are glycolipidic biosurfactants suitable for various biological and physicochemical applications. The nonedible Jatropha oil has been checked as the alternative raw material for SL synthesis using C. bombicola (ATCC22214). This is useful towards lowering the SL production cost. Through optimization of fermentation parameters and use of resting cell method, the yield 15.25 g/L could be achieved for Jatropha oil derived SL (SLJO) with 1% v/v oil feeding. The synthesized SL displayed good surfactant property. It reduced the surface tension of distilled water from 70.7 mN/m to 33.5 mN/m with the Critical Micelle Concentration (CMC) value of 9.5 mg/L. Keeping the prospective use of the SL in mind, the physicochemical properties were checked along with emulsion stability under temperature, pH stress, and in hard water. Also antibacterial action and stain removal capability in comparison with commercial detergent was demonstrated. SLJO enhanced the detergent performance. Based on the results, it can be said that SLs have utility as fabric cleaner with advantageous properties such as skin friendly nature, antibacterial action, and biodegradability. Therefore SLs are potential green molecules to replace synthetic surfactants in detergents so as to reduce harm caused to environment through detergent usage. PMID:24455261

  17. Hydrogen production from water decomposition by redox of Fe 2O 3 modified with single- or double-metal additives

    NASA Astrophysics Data System (ADS)

    Liu, Xiaojie; Wang, Hui

    2010-05-01

    Iron oxide modified with single- or double-metal additives (Cr, Ni, Zr, Ag, Mo, Mo-Cr, Mo-Ni, Mo-Zr and Mo-Ag), which can store and supply pure hydrogen by reduction of iron oxide with hydrogen and subsequent oxidation of reduced iron oxide with steam (Fe 3O 4 (initial Fe 2O 3)+4H 2↔3Fe+4H 2O), were prepared by impregnation. Effects of various metal additives in the samples on hydrogen production were investigated by the above-repeated redox. All the samples with Mo additive exhibited a better redox performance than those without Mo, and the Mo-Zr additive in iron oxide was the best effective one enhancing hydrogen production from water decomposition. For Fe 2O 3-Mo-Zr, the average H 2 production temperature could be significantly decreased to 276 °C, the average H 2 formation rate could be increased to 360.9-461.1 μmol min -1 Fe-g -1 at operating temperature of 300 °C and the average storage capacity was up to 4.73 wt% in four cycles, an amount close to the IEA target.

  18. Effect of modifying additions on the physicomechanical properties of composites based on polyethylene and wastes from linen yarn production

    NASA Astrophysics Data System (ADS)

    Kayaks, Ya. A.; Bulmanis, V. N.; Reikhmane, S. A.; Tsiprin, M. G.

    1997-07-01

    This article examines the feasibility of using coupling agents to alleviate the shortcomings characteristics of materials that contain natural fibers: low water resistance and a high degree of heterogeneity. A determination is made of the effect of additions of polyisocyanate and stearic acid on the fluidity of the melts and the strainstrength properties and water resistance of polyethylene composites containing mixtures of wastes from linen yarn production. It is shown that an addition of stearic acid significantly improves the dispersion of fibers in the composites, which in turn leads to a reduction in melt fluidity and an increase in elastic modulus in the high-filler-content region compared to composites that do not have additions of stearic acid. Additions of polyisocyanate appreciably increase the strength and water resistance of the given composites.

  19. Addition of Vital Wheat Gluten to Enhance the Quality Characteristics of Frozen Dough Products.

    PubMed

    Giannou, Virginia; Tzia, Constantina

    2016-01-06

    The aim of this study was to enhance the quality and sensory characteristics of bread made from frozen dough. Both white and whole-wheat flour were used. In order to improve dough strength and stability during frozen storage, samples were supplemented with vital wheat gluten at the levels of 2%, 4%, 5%, and 6% of flour weight. The characteristics of baked samples were determined through weight loss, specific volume, crust, and crumb color, texture, and sensory evaluation. Dough behavior at sub-zero temperatures was further examined for control samples and samples with 6% gluten using Differential Scanning Calorimetry (DSC), while their low molecular sugar content (fructose, glucose, sucrose) was measured using High Pressure Liquid Chromatography (HPLC), as it can be associated with yeast viability and dough freezing point depression. The most stable samples were those with 4% and 6% gluten (for white flour) and those with 4% and 5% gluten (for whole-wheat flour). Gluten addition raised the freezing point of dough samples and preserved low molecular sugar generation after prolonged storage.

  20. Utilization of municipal sewage sludge as additives for the production of eco-cement.

    PubMed

    Lin, Yiming; Zhou, Shaoqi; Li, Fuzhen; Lin, Yixiao

    2012-04-30

    The effects of using dried sewage sludge as additive on cement property in the process of clinker burning were investigated in this paper. The eco-cement samples were prepared by adding 0.50-15.0% of dried sewage sludge to unit raw meal, and then the mixtures were burned at 1450 °C for 2 h. The results indicated that the major components in the eco-cement clinkers were similar to those in ordinary Portland cement. Although the C(2)S phase formation increased with the increase of sewage sludge content, it was also found that the microstructure of the mixture containing 15.0% sewage sludge in raw meal was significantly different and that a larger amount of pores were distributed in the clinker. Moreover, all the eco-cement pastes had a longer initial setting time and final setting time than those of plain cement paste, which increased as the sewage sludge content in the raw meal increased. All the eco-cement pastes had lower early flexural strengths, which increased as the sewage sludge content increased, while the compressive strengths decreased slightly. However, this had no significant effect on all the strengths at later stages. Furthermore, the leaching concentrations of all the types of eco-cement clinkers met the standard of Chinese current regulatory thresholds.

  1. Extended gene expression by medium exchange and repeated transient transfection for recombinant protein production enhancement.

    PubMed

    Cervera, Laura; Gutiérrez-Granados, Sonia; Berrow, Nicholas Simon; Segura, Maria Mercedes; Gòdia, Francesc

    2015-05-01

    Production of recombinant products in mammalian cell cultures can be achieved by stable gene expression (SGE) or transient gene expression (TGE). The former is based on the integration of a plasmid DNA into the host cell genome allowing continuous gene expression. The latter is based on episomal plasmid DNA expression. Conventional TGE is limited to a short production period of usually about 96 h, therefore limiting productivity. A novel gene expression approach termed extended gene expression (EGE) is explored in this study. The aim of EGE is to prolong the production period by the combination of medium exchange and repeated transfection of cell cultures with plasmid DNA to improve overall protein production. The benefit of this methodology was evaluated for the production of three model recombinant products: intracellular GFP, secreted GFP, and a Gag-GFP virus-like particles (VLPs). Productions were carried out in HEK 293 cell suspension cultures grown in animal-derived component free media using polyethylenimine (PEI) as transfection reagent. Transfections were repeated throughout the production process using different plasmid DNA concentrations, intervals of time, and culture feeding conditions in order to identify the best approach to achieve sustained high-level gene expression. Using this novel EGE strategy, the production period was prolonged between 192 and 240 h with a 4-12-fold increase in production levels, depending on the product type considered.

  2. [Collaborative study on regulatory science for facilitating clinical development of gene therapy products for genetic diseases].

    PubMed

    Uchida, Eriko; Igarashi, Yuka; Sato, Yoji

    2014-01-01

    Gene therapy products are expected as innovative medicinal products for intractable diseases such as life-threatening genetic diseases and cancer. Recently, clinical developments by pharmaceutical companies are accelerated in Europe and the United States, and the first gene therapy product in advanced countries was approved for marketing authorization by the European Commission in 2012. On the other hand, more than 40 clinical studies for gene therapy have been completed or ongoing in Japan, most of them are conducted as clinical researches by academic institutes, and few clinical trials have been conducted for approval of gene therapy products. In order to promote the development of gene therapy products, revision of the current guideline and/or preparation of concept paper to address the evaluation of the quality and safety of gene therapy products are necessary and desired to clearly show what data should be submitted before First-in-Human clinical trials of novel gene therapy products. We started collaborative study with academia and regulatory agency to promote regulatory science toward clinical development of gene therapy products for genetic diseases based on lentivirus and adeno-associated virus vectors; National Center for Child Health and Development (NCCHD), Nippon Medical School and PMDA have been joined in the task force. At first, we are preparing pre-draft of the revision of the current gene therapy guidelines in this project.

  3. Genetic association between SNPs in the DGAT1 gene and milk production traits in Murrah buffaloes.

    PubMed

    de Freitas, Ana Cláudia; de Camargo, Gregório Miguel Ferreira; Stafuzza, Nedenia Bonvino; Aspilcueta-Borquis, Rusbel Raul; Venturini, Guilherme Costa; Dias, Marina Mortati; Cardoso, Diercles Francisco; Tonhati, Humberto

    2016-10-01

    This study identified polymorphisms in the DGAT1 gene in Murrah buffaloes and investigated the associations to milk production and quality traits (milk, fat and protein yields and percentages, somatic cell count). Genomic DNA was extracted from hair follicles collected from the tail of 196 females. Three SNPs were identified in DGAT1 gene by sequencing. Statistical analyses were performed to verify the linkage and the association between polymorphisms and traits. The estimated value of r (2) between two SNPs in exon 17 (g.11,783G > A and g.11,785 T > C) was 0.029. SNP g.11,785 T > C was significantly associated (P < 0.05) to fat and protein percentage. Dominance effect was significant for milk and fat yields and protein percentage (P < 0.05). The additive effect of the SNP g.11,785 T > C was significant for protein production and somatic cell count (P < 0.05). It indicates that assisted marker selection might be done with considerations to balance production and udder health.

  4. Expression of Clostridium acetobutylicum ATCC 824 Genes in Escherichia coli for Acetone Production and Acetate Detoxification

    PubMed Central

    Bermejo, Lourdes L.; Welker, Neil E.; Papoutsakis, Eleftherios T.

    1998-01-01

    A synthetic acetone operon (ace4) composed of four Clostridium acetobutylicum ATCC 824 genes (adc, ctfAB, and thl, coding for the acetoacetate decarboxylase, coenzyme A transferase, and thiolase, respectively) under the control of the thl promoter was constructed and was introduced into Escherichia coli on vector pACT. Acetone production demonstrated that ace4 is expressed in E. coli and resulted in the reduction of acetic acid levels in the fermentation broth. Since different E. coli strains vary significantly in their growth characteristics and acetate metabolism, ace4 was expressed in three E. coli strains: ER2275, ATCC 11303, and MC1060. Shake flask cultures of MC1060(pACT) produced ca. 2 mM acetone, while both strains ER2275(pACT) and ATCC 11303(pACT) produced ca. 40 mM acetone. Glucose-fed cultures of strain ATCC 11303(pACT) resulted in a 150% increase in acetone titers compared to those of batch shake flask cultures. External addition of sodium acetate to glucose-fed cultures of ATCC 11303(pACT) resulted in further increased acetone titers. In bioreactor studies, acidic conditions (pH 5.5 versus 6.5) improved acetone production. Despite the substantial acetone evaporation due to aeration and agitation in the bioreactor, 125 to 154 mM acetone accumulated in ATCC 11303(pACT) fermentations. These acetone titers are equal to or higher than those produced by wild-type C. acetobutylicum. This is the first study to demonstrate the ability to use clostridial genes in nonclostridial hosts for solvent production. In addition, acetone-producing E. coli strains may be useful hosts for recombinant protein production in that detrimental acetate accumulation can be avoided. PMID:9501448

  5. Production of complex organic molecules:H-atom addition versus UV irradiation

    NASA Astrophysics Data System (ADS)

    Chuang, K.-J.; Fedoseev, G.; Qasim, D.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

    2017-01-01

    Complex organic molecules (COMs) have been identified in different environments in star-forming regions. Laboratory studies show that COMs form in the solid state, on icy grains, typically following a `non-energetic' (atom-addition) or `energetic' (UV photon absorption) trigger. So far, such studies have been largely performed for single processes. Here we present the first work that quantitatively investigates both the relative importance and the cumulative effect of `(non)energetic' processing. We focus on astronomically relevant CO:CH3OH = 4:1 ice analogues exposed to doses relevant for the collapse stage of dense clouds. Hydrogenation experiments result in the formation of methyl formate (MF; HC(O)OCH3), glycolaldehyde (GA; HC(O)CH2OH) and ethylene glycol (EG; H2C(OH)CH2OH) at 14 K. The absolute abundances and the abundance fractions are found to be dependent on the H-atom/CO:CH3OH-molecule ratios and on the overall deposition rate. In the case that ices are exposed to UV photons only, several different COMs are found. Typically, the abundance fractions are 0.2 for MF, 0.3 for GA, and 0.5 for EG as opposed to the values found in pure hydrogenation experiments without UV in which MF is largely absent: 0.0, 0.2-0.6 and 0.8-0.4, respectively. In experiments where both are applied, overall COM abundances drop to about half of those found in the pure UV irradiation experiments, but the composition fractions are very similar. This implies COM ratios can be used as a diagnostic tool to derive the processing history of an ice. Solid-state branching ratios derived here for GA and EG compare well with observations, while the MF case cannot be explained by solid state conditions investigated here.

  6. Effect of uracil addition on proteomic profiles and 1,3-β-glucan production in Agrobacterium sp.

    PubMed

    Jin, Li-Hua; Lee, Jung-Heon

    2014-01-01

    Uridine diphosphate (UDP)-glucose is a precursor of 1,3-β-glucan and is synthesized from glucose-1-phosphate and uridine triphosphate (UTP). Uracil was used as a precursor for UTP, which resulted in an increase in both the UDP-glucose level and the rate of 1,3-β-glucan synthesis. 1,3-β-Glucan production metabolism was reactivated after uracil addition during fermentation. 2D-PAGE was used to examine the changes in the expression level of the key metabolic enzymes in the production of 1,3-β-glucan after uracil addition. The results showed that the expression levels of UTP-glucose-1-phosphate uridylytransferase, phosphoglucomutase, and 1,3-β-glucan synthase catalytic subunit, key metabolic enzymes in the curdlan biosynthesis pathway, were increased after uracil addition by 3.5%, 30%, and 35%, respectively. Uracil phosphoribosyltransferase, which converts uracil to uridine monophosphate (UMP), was also upregulated 79% more than that without uracil addition. However, the expression levels of orotidine 5-phosphate decarboxylase, glucose-1-phosphate adenylyltransferase, and glucose-6-phosphate isomerase were decreased after uracil addition. This proteomic information is useful for predicting changes in the pathway of uracil utilization. This work provides proteomic information for the integrative analysis of bioinformatic databases, which can be used to predict and understand the metabolism of glucan synthesis at the cellular level.

  7. Improvement of exopolysaccharide production in Lactobacillus casei LC2W by overexpression of NADH oxidase gene.

    PubMed

    Li, Nan; Wang, Yuanlong; Zhu, Ping; Liu, Zhenmin; Guo, Benheng; Ren, Jing

    2015-02-01

    Lactobacillus casei LC2W is an exopolysaccharide (EPS)-producing strain with probiotic effects. To investigate the regulation mechanism of EPS biosynthesis and to improve EPS production through cofactor engineering, a H₂O-forming NADH oxidase gene was cloned from Streptococcus mutans and overexpressed in L. casei LC2W under the control of constitutive promoter P₂₃. The recombinant strain LC-nox exhibited 0.854 U/mL of NADH oxidase activity, which was elevated by almost 20-fold in comparison with that of wild-type strain. As a result, overexpression of NADH oxidase resulted in a reduction in growth rate. In addition, lactate production was decreased by 22% in recombinant strain. It was proposed that more carbon source was saved and used for the biosynthesis of EPS, the production of which was reached at 219.4 mg/L, increased by 46% compared to that of wild-type strain. This work provided a novel and convenient genetic approach to manipulate metabolic flux and to increase EPS production. To the best of our knowledge, this is the first report which correlates cofactor engineering with EPS production.

  8. Pro-inflammatory NF-κB and early growth response gene 1 regulate epithelial barrier disruption by food additive carrageenan in human intestinal epithelial cells.

    PubMed

    Choi, Hye Jin; Kim, Juil; Park, Seong-Hwan; Do, Kee Hun; Yang, Hyun; Moon, Yuseok

    2012-06-20

    The widely used food additive carrageenan (CGN) has been shown to induce intestinal inflammation, ulcerative colitis-like symptoms, or neoplasm in the gut epithelia in animal models, which are also clinical features of human inflammatory bowel disease. In this study, the effects of CGN on pro-inflammatory transcription factors NF-κB and early growth response gene 1 product (EGR-1) were evaluated in terms of human intestinal epithelial barrier integrity. Both pro-inflammatory transcription factors were elevated by CGN and only NF-κB activation was shown to be involved in the induction of pro-inflammatory cytokine interleukin-8. Moreover, the integrity of the in vitro epithelial monolayer under the CGN insult was maintained by both activated pro-inflammatory transcription factors NF-κB and EGR-1. Suppression of NF-κB or EGR-1 aggravated barrier disruption by CGN, which was associated with the reduced gene expression of tight junction component zonula occludens 1 and its irregular localization in the epithelial monolayer.

  9. Effect of the Food Additives Sodium Citrate and Disodium Phosphate on Shiga Toxin-Producing Escherichia coli and Production of stx-Phages and Shiga toxin

    PubMed Central

    Lenzi, Lucas J.; Lucchesi, Paula M. A.; Medico, Lucía; Burgán, Julia; Krüger, Alejandra

    2016-01-01

    Induction and propagation of bacteriophages along the food production chain can represent a significant risk when bacteriophages carry genes for potent toxins. The aim of this study was to evaluate the effect of different compounds used in the food industry on the growth of Shiga toxin-producing Escherichia coli (STEC) and the production of stx-phage particles and Shiga toxin. We tested the in vitro effect of lactic acid, acetic acid, citric acid, disodium phosphate, and sodium citrate on STEC growth. A bacteriostatic effect was observed in most of treated cultures. The exceptions were those treated with sodium citrate and disodium phosphate in which similar growth curves to the untreated control were observed, but with reduced OD600 values. Evaluation of phage production by plaque-based assays showed that cultures treated with sodium citrate and disodium phosphate released phages in similar o lower levels than untreated cultures. However, semi-quantification of Stx revealed higher levels of extracellular Stx in STEC cultures treated with 2.5% sodium citrate than in untreated cultures. Our results reinforce the importance to evaluate if additives and other treatments used to decrease bacterial contamination in food induce stx-phage and Stx production. PMID:27446032

  10. Effect of the Food Additives Sodium Citrate and Disodium Phosphate on Shiga Toxin-Producing Escherichia coli and Production of stx-Phages and Shiga toxin.

    PubMed

    Lenzi, Lucas J; Lucchesi, Paula M A; Medico, Lucía; Burgán, Julia; Krüger, Alejandra

    2016-01-01

    Induction and propagation of bacteriophages along the food production chain can represent a significant risk when bacteriophages carry genes for potent toxins. The aim of this study was to evaluate the effect of different compounds used in the food industry on the growth of Shiga toxin-producing Escherichia coli (STEC) and the production of stx-phage particles and Shiga toxin. We tested the in vitro effect of lactic acid, acetic acid, citric acid, disodium phosphate, and sodium citrate on STEC growth. A bacteriostatic effect was observed in most of treated cultures. The exceptions were those treated with sodium citrate and disodium phosphate in which similar growth curves to the untreated control were observed, but with reduced OD600 values. Evaluation of phage production by plaque-based assays showed that cultures treated with sodium citrate and disodium phosphate released phages in similar o lower levels than untreated cultures. However, semi-quantification of Stx revealed higher levels of extracellular Stx in STEC cultures treated with 2.5% sodium citrate than in untreated cultures. Our results reinforce the importance to evaluate if additives and other treatments used to decrease bacterial contamination in food induce stx-phage and Stx production.

  11. Increased biomass production of industrial bakers' yeasts by overexpression of Hap4 gene.

    PubMed

    Dueñas-Sánchez, Rafael; Codón, Antonio C; Rincón, Ana M; Benítez, Tahía

    2010-10-15

    HAP4 encodes a transcriptional activator of respiration-related genes and so, redirection from fermentation to respiration flux should give rise to an increase in biomass production in Saccharomyces cerevisiae transformants that overexpress HAP4. With this aim, three bakers' yeasts, that is, V1 used for lean doughs, its 2-deoxy-D-glucose resistant derivative DOG21, and V3 employed for sweet doughs, were transformed with integrative cassettes that carried HAP4 gene under the control of constitutive promoter pTEF2; in addition VTH, DTH and 3TH transformants were selected and characterized. Transformants showed increased expression of HAP4 and respiration-related genes such as QCR7 and QCR8 with regard to parental, and similar expression of SUC2 and MAL12; these genes are relevant in bakers' industry. Invertase (Suc2p) and maltase (Mal12p) activities, growth and sugar consumption rates in laboratory (YPD) or industrial media (MAB) were also comparable in bakers' strains and their transformants, but VTH, DTH and 3TH increased their final biomass production by 9.5, 5.0 and 5.0% respectively as compared to their parentals in MAB. Furthermore, V1 and its transformant VTH had comparable capacity to ferment lean doughs (volume increase rate and final volume) while V3 and its transformant 3TH fermented sweet doughs in a similar manner. Therefore transformants possessed increased biomass yield and appropriate characteristics to be employed in bakers' industry because they lacked drug resistant markers and bacterial DNA, and were genetically stable.

  12. Further improvement in ganoderic acid production in static liquid culture of Ganoderma lucidum by integrating nitrogen limitation and calcium ion addition.

    PubMed

    Li, Huan-Jun; Zhang, De-Huai; Han, Li-Liang; Yu, Xuya; Zhao, Peng; Li, Tao; Zhong, Jian-Jiang; Xu, Jun-Wei

    2016-01-01

    To further improve the ganoderic acid (GA) production, a novel integrated strategy by combining nitrogen limitation and calcium ion addition was developed. The effects of the integrated combination on the content of GA-T (one powerful anticancer compound), their intermediates (squalene and lanosterol) and on the transcription levels of GA biosynthetic genes in G. lucidum fermentation were investigated. The maximum GA-T content with the integrated strategy were 1.87 mg/ 100 mg dry cell weight, which was 2.1-4.2 fold higher than that obtained with either calcium ion addition or nitrogen limitation alone, and it is also the highest record as ever reported in submerged fermentation of G. lucidum. The squalene content was increased by 3.9- and 2.2-fold in this case compared with either individual strategy alone. Moreover, the transcription levels of the GA biosynthetic genes encoding 3-hydroxy-3-methyglutaryl coenzyme A reductase and lanosterol synthase were also up-regulated by 3.3-7.5 and 1.3-2.3 fold, respectively.

  13. Form gene clustering method about pan-ethnic-group products based on emotional semantic

    NASA Astrophysics Data System (ADS)

    Chen, Dengkai; Ding, Jingjing; Gao, Minzhuo; Ma, Danping; Liu, Donghui

    2016-09-01

    The use of pan-ethnic-group products form knowledge primarily depends on a designer's subjective experience without user participation. The majority of studies primarily focus on the detection of the perceptual demands of consumers from the target product category. A pan-ethnic-group products form gene clustering method based on emotional semantic is constructed. Consumers' perceptual images of the pan-ethnic-group products are obtained by means of product form gene extraction and coding and computer aided product form clustering technology. A case of form gene clustering about the typical pan-ethnic-group products is investigated which indicates that the method is feasible. This paper opens up a new direction for the future development of product form design which improves the agility of product design process in the era of Industry 4.0.

  14. Regulatory Oversight of Gene Therapy and Cell Therapy Products in Korea.

    PubMed

    Choi, Minjoung; Han, Euiri; Lee, Sunmi; Kim, Taegyun; Shin, Won

    2015-01-01

    The Ministry of Food and Drug Safety regulates gene therapy and cell therapy products as biological products under the authority of the Pharmaceutical Affairs Act. As with other medicinal products, gene therapy and cell therapy products are subject to approval for use in clinical trials and for a subsequent marketing authorization and to post-market surveillance. Research and development of gene therapy and cell therapy products have been progressing rapidly in Korea with extensive investment, offering great potential for the treatment of various serious diseases. To facilitate development of safe and effective products and provide more opportunities to patients suffering from severe diseases, several regulatory programs, such as the use of investigational products for emergency situations, fast-track approval, prereview of application packages, and intensive regulatory consultation, can be applied to these products. The regulatory approach for these innovative products is case by case and founded on science-based review that is flexible and balances the risks and benefits.

  15. Requirements for Clinical Trials with Gene Therapy and Transplant Products in Switzerland.

    PubMed

    Marti, Andreas

    2015-01-01

    This chapter aims to describe and summarize the regulation of gene and cell therapy products in Switzerland and its legal basis. Product types are briefly described, as are Swiss-specific terminologies such as the term "transplant product," which means products manufactured from cells, tissues, or even whole organs. Although some parts of this chapter may show a guideline character, they are not legally binding, but represent the current thinking of Swissmedic, the Swiss Agency for Therapeutic Products. As so far the experience with marketing approval of gene therapy and cell therapy products in Switzerland is limited, this chapter focuses on the regulation of clinical trials conducted with these products. Quality, nonclinical, and clinical aspects are summarized separately for gene therapy products and transplant products.

  16. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect l-Lysine Production in Corynebacterium glutamicum

    PubMed Central

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-01-01

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in l-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport—NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885—were also expressed at significantly higher levels in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, l-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production. PMID:27005618

  17. Impact of milling, enzyme addition, and steam explosion on the solid waste biomethanation of an olive oil production plant.

    PubMed

    Donoso-Bravo, Andres; Ortega-Martinez, E; Ruiz-Filippi, G

    2016-02-01

    Anaerobic digestion is a consolidated bioprocess which can be further enhanced by incorporating an upstream pretreatment unit. The olive oil production produces a large amount of solid waste which needs to be properly managed and disposed. Three different pretreatment techniques were evaluated in regard to their impact on the anaerobic biodegradability: manual milling of olive pomace (OP), enzyme maceration, direct enzyme addition, and thermal hydrolysis of two-phase olive mill waste. The Gompertz equation was used to obtain parameters for comparison purposes. A substrate/inoculum ratio 0.5 was found to be the best to be used in anaerobic batch test with olive pomace as substrate. Mechanical pretreatment of OP by milling increases the methane production rate while keeping the maximum methane yield. The enzymatic pretreatment showed different results depending on the chosen pretreatment strategies. After the enzymatic maceration pretreatment, a methane production of 274 ml CH4 g VS added (-1) was achieved, which represents an improvement of 32 and 71 % compared to the blank and control, respectively. The direct enzyme addition pretreatment showed no improvement in both the rate and the maximum methane production. Steam explosion showed no improvement on the anaerobic degradability of two-phase olive mill waste; however, thermal hydrolysis with no rapid depressurization enhanced notoriously both the maximum rate (50 %) and methane yield (70 %).

  18. A second common mutation in the methylenetetrahydrofolate reductase gene: an additional risk factor for neural-tube defects?

    PubMed Central

    van der Put, N M; Gabreëls, F; Stevens, E M; Smeitink, J A; Trijbels, F J; Eskes, T K; van den Heuvel, L P; Blom, H J

    1998-01-01

    Recently, we showed that homozygosity for the common 677(C-->T) mutation in the methylenetetrahydrofolate reductase (MTHFR) gene, causing thermolability of the enzyme, is a risk factor for neural-tube defects (NTDs). We now report on another mutation in the same gene, the 1298(A-->C) mutation, which changes a glutamate into an alanine residue. This mutation destroys an MboII recognition site and has an allele frequency of .33. This 1298(A-->C) mutation results in decreased MTHFR activity (one-way analysis of variance [ANOVA] P < .0001), which is more pronounced in the homozygous than heterozygous state. Neither the homozygous nor the heterozygous state is associated with higher plasma homocysteine (Hcy) or a lower plasma folate concentration-phenomena that are evident with homozygosity for the 677(C-->T) mutation. However, there appears to be an interaction between these two common mutations. When compared with heterozygosity for either the 677(C-->T) or 1298(A-->C) mutations, the combined heterozygosity for the 1298(A-->C) and 677(C-->T) mutations was associated with reduced MTHFR specific activity (ANOVA P < .0001), higher Hcy, and decreased plasma folate levels (ANOVA P <.03). Thus, combined heterozygosity for both MTHFR mutations results in similar features as observed in homozygotes for the 677(C-->T) mutation. This combined heterozygosity was observed in 28% (n =86) of the NTD patients compared with 20% (n =403) among controls, resulting in an odds ratio of 2.04 (95% confidence interval: .9-4.7). These data suggest that the combined heterozygosity for the two MTHFR common mutations accounts for a proportion of folate-related NTDs, which is not explained by homozygosity for the 677(C-->T) mutation, and can be an additional genetic risk factor for NTDs. PMID:9545395

  19. Influences of nitrogen, phosphorus and silicon addition on plant productivity and species richness in an alpine meadow.

    PubMed

    Xu, Danghui; Fang, Xiangwen; Zhang, Renyi; Gao, Tianpeng; Bu, Haiyan; Du, Guozhen

    2015-11-15

    Fertilization, especially with nitrogen (N), increases aboveground primary productivity (APP), but reduces plant species richness at some level. Silicon (Si) fertilization alone, or with addition of N or phosphorus (P), has multiple direct and indirect beneficial effects on plant growth and development, both for individuals and the whole community. This study aimed to examine the effects of Si, N, P, NSi and PSi combinations on APP and species richness of the community and of four functional groups in an alpine meadow. The results showed that plots fertilized with Si in combination with either N or P had higher APP than when fertilized with N or P alone. Addition of N or P increased APP, and the higher APP occurred when the highest level of N was added, indicating co-limitation of N and P, with N being most limiting. Silicon fertilization alone or with addition of N increased the APP of grasses and forbs. Nitrogen addition decreased the community species richness; Si with addition of N alleviated the loss of species richness of the whole community and the forbs group. For the four functional groups, N or P addition increased the species richness of grasses and decreased that of forbs. Our findings highlight the importance of Si in improving APP and alleviating N fertilization-induced biodiversity loss in grasslands, and will help improve our ability to predict community composition and biomass dynamics in alpine meadow ecosystems subject to changing nutrient availability.

  20. Linking gene regulation to mRNA production and export.

    PubMed

    Rodríguez-Navarro, Susana; Hurt, Ed

    2011-06-01

    Regulation of gene expression can occur at many different levels. One important step in the gene expression process is the transport of mRNA from the nucleus to the cytoplasm. In recent years, studies have described how nuclear mRNA export depends on the steps preceding and following transport through nuclear pore complexes. These include gene activation, transcription, mRNA processing and mRNP assembly and disassembly. In this review, we summarise recent insights into the links between these steps in the gene expression cascade.

  1. The Spinal Muscular Atrophy Disease Gene Product, Smn

    PubMed Central

    Carvalho, Teresa; Almeida, Fátima; Calapez, Alexandre; Lafarga, Miguel; Berciano, Maria T.; Carmo-Fonseca, Maria

    1999-01-01

    The spliceosomal snRNAs U1, U2, U4, and U5 are synthesized in the nucleus, exported to the cytoplasm to assemble with Sm proteins, and reimported to the nucleus as ribonucleoprotein particles. Recently, two novel proteins involved in biogenesis of small nuclear ribonucleoproteins (snRNPs) were identified, the Spinal muscular atrophy disease gene product (SMN) and its associated protein SIP1. It was previously reported that in HeLa cells, SMN and SIP1 form discrete foci located next to Cajal (coiled) bodies, the so-called “gemini of coiled bodies” or “gems.” An intriguing feature of gems is that they do not appear to contain snRNPs. Here we show that gems are present in a variable but small proportion of rapidly proliferating cells in culture. In the vast majority of cultured cells and in all primary neurons analyzed, SMN and SIP1 colocalize precisely with snRNPs in the Cajal body. The presence of SMN and SIP1 in Cajal bodies is confirmed by immunoelectron microscopy and by microinjection of antibodies that interfere with the integrity of the structure. The association of SMN with snRNPs and coilin persists during cell division, but at the end of mitosis there is a lag period between assembly of new Cajal bodies in the nucleus and detection of SMN in these structures, suggesting that SMN is targeted to preformed Cajal bodies. Finally, treatment of cells with leptomycin B (a drug that blocks export of U snRNAs to the cytoplasm and consequently import of new snRNPs into the nucleus) is shown to deplete snRNPs (but not SMN or SIP1) from the Cajal body. This suggests that snRNPs flow through the Cajal body during their biogenesis pathway. PMID:10562276

  2. Indirect additive manufacturing as an elegant tool for the production of self-supporting low density gelatin scaffolds.

    PubMed

    Van Hoorick, Jasper; Declercq, Heidi; De Muynck, Amelie; Houben, Annemie; Van Hoorebeke, Luc; Cornelissen, Ria; Van Erps, Jürgen; Thienpont, Hugo; Dubruel, Peter; Van Vlierberghe, Sandra

    2015-10-01

    The present work describes for the first time the production of self-supporting low gelatin density (<10 w/v%) porous scaffolds using methacrylamide-modified gelatin as an extracellular matrix mimicking component. As porous scaffolds starting from low gelatin concentrations cannot be realized with the conventional additive manufacturing techniques in the abscence of additives, we applied an indirect fused deposition modelling approach. To realize this, we have printed a sacrificial polyester scaffold which supported the hydrogel material during UV crosslinking, thereby preventing hydrogel structure collapse. After complete curing, the polyester scaffold was selectively dissolved leaving behind a porous, interconnective low density gelatin scaffold. Scaffold structural analysis indicated the success of the selected indirect additive manufacturing approach. Physico-chemical testing revealed scaffold properties (mechanical, degradation, swelling) to depend on the applied gelatin concentration and methacrylamide content. Preliminary biocompatibility studies revealed the cell-interactive and biocompatible properties of the materials developed.

  3. Providencia stuartii genes activated by cell-to-cell signaling and identification of a gene required for production or activity of an extracellular factor.

    PubMed

    Rather, P N; Ding, X; Baca-DeLancey, R R; Siddiqui, S

    1999-12-01

    By utilizing reporter transposons, five Providencia stuartii genes that are activated by the accumulation of self-produced extracellular signals have been identified. These genes have been designated cma for conditioned medium activated. The presence of conditioned medium from stationary-phase cultures grown in rich media resulted in the premature activation of each gene in cells at early log phase, with activation values ranging from 6- to 26-fold. Preparation of conditioned medium from an M9 salts medium and fractionation by gel filtration chromatography resulted in fractions within the included volume which activated three of the cma fusions. In addition, depending on the reporter fusion, peak activity was found in different fractions. The partially purified factors activated in a dose-dependent manner. Characterization of the factors activating the cma fusions indicated that they were stable to heat, alkali, and acid. Furthermore, for each cma fusion, factor activity was not reproduced by the addition of homoserine lactone, homocysteine thiolactone, pyruvate, Casamino Acids, or alpha-ketoglutarate. The identities of three cma genes have been determined and revealed physiological roles in amino acid biosynthesis and nutrient import. To begin to address the pathways for production of or response to the extracellular factors, we have identified a locus, aarA, that is required for the activation of four cma fusions. The AarA product was required for factor activity in extracellular supernatants, indicating a possible role in biosynthesis or export.

  4. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism

    PubMed Central

    2011-01-01

    Background Isobutanol can be a better biofuel than ethanol due to its higher energy density and lower hygroscopicity. Furthermore, the branched-chain structure of isobutanol gives a higher octane number than the isomeric n-butanol. Saccharomyces cerevisiae was chosen as the production host because of its relative tolerance to alcohols, robustness in industrial fermentations, and the possibility for future combination of isobutanol production with fermentation of lignocellulosic materials. Results The yield of isobutanol was improved from 0.16 to 0.97 mg per g glucose by simultaneous overexpression of biosynthetic genes ILV2, ILV3, and ILV5 in valine metabolism in anaerobic fermentation of glucose in mineral medium in S. cerevisiae. Isobutanol yield was further improved by twofold by the additional overexpression of BAT2, encoding the cytoplasmic branched-chain amino-acid aminotransferase. Overexpression of ILV6, encoding the regulatory subunit of Ilv2, in the ILV2 ILV3 ILV5 overexpression strain decreased isobutanol production yield by threefold. In aerobic cultivations in shake flasks in mineral medium, the isobutanol yield of the ILV2 ILV3 ILV5 overexpression strain and the reference strain were 3.86 and 0.28 mg per g glucose, respectively. They increased to 4.12 and 2.4 mg per g glucose in yeast extract/peptone/dextrose (YPD) complex medium under aerobic conditions, respectively. Conclusions Overexpression of genes ILV2, ILV3, ILV5, and BAT2 in valine metabolism led to an increase in isobutanol production in S. cerevisiae. Additional overexpression of ILV6 in the ILV2 ILV3 ILV5 overexpression strain had a negative effect, presumably by increasing the sensitivity of Ilv2 to valine inhibition, thus weakening the positive impact of overexpression of ILV2, ILV3, and ILV5 on isobutanol production. Aerobic cultivations of the ILV2 ILV3 ILV5 overexpression strain and the reference strain showed that supplying amino acids in cultivation media gave a substantial

  5. Addition of ammonia or amino acids to a nitrogen-depleted medium affects gene expression patterns in yeast cells during alcoholic fermentation.

    PubMed

    Jiménez-Martí, Elena; del Olmo, Marcel Lí

    2008-03-01

    Yeast cells require nitrogen and are capable of selectively using good nitrogen sources in preference to poor ones by means of the regulatory mechanism known as nitrogen catabolite repression (NCR). Herein, the effect of ammonia or amino acid addition to nitrogen-depleted medium on global yeast expression patterns in yeast cells was studied using alcoholic fermentation as a system. The results indicate that there is a differential reprogramming of the gene expression depending on the nitrogen source added. Ammonia addition resulted in a higher expression of genes involved in amino acids biosynthesis while amino acid addition prepares the cells for protein biosynthesis. Therefore, a high percentage of the genes regulated by the transcription factors involved in the regulation of amino acid biosynthesis are more expressed during the first hours after ammonia addition compared with amino acid addition. The opposite occurs for those genes regulated by the transcription factor Sfp1p, related to ribosome biosynthesis. Although both additions include rich nitrogen sources, most NCR-regulated genes are more expressed after adding ammonia than amino acids. One of the differentially expressed genes, YBR174W, is required for optimal growth in synthetic medium.

  6. Transcriptome analysis of genes related to resistance against powdery mildew in wheat-Thinopyrum alien addition disomic line germplasm SN6306.

    PubMed

    Li, Quanquan; Niu, Zubiao; Bao, Yinguang; Tian, Qiuju; Wang, Honggang; Kong, Lingrang; Feng, Deshun

    2016-09-15

    Wheat powdery mildew, which is mainly caused by Blumeria graminis f. sp. tritici (Bgt), seriously damages wheat production. The wheat-Thinopyrum intermedium alien addition disomic line germplasm SN6306, being one of the important sources of genes for wheat resistance, is highly resistant to Bgt E09 and to many other powdery mildew physiological races. However, knowledge on the resistance mechanism of SN6306 remains limited. Our study employed high-throughput RNA sequencing based on next-generation sequencing technology (Illumina) to obtain an overview of the transcriptome characteristics of SN6306 and its parent wheat Yannong 15 (YN15) during Bgt infection. The sequencing generated 104,773 unigenes, 9909 of which showed varied expression levels. Among the 9909 unigenes, 1678 unigenes showed 0 reads in YN15. The expression levels in Bgt-inoculated SN6306 and YN15 of exactly 39 unigenes that showed 0 or considerably low reads in YN15 were validated to identify the genes involved in Bgt resistance. Among the 39 unigenes, 12 unigenes were upregulated in SN6306 by 3-45 times. These unigenes mainly encoded kinase, synthase, proteases, and signal transduction proteins, which may play an important role in the resistance against Bgt. To confirm whether the unigenes that showed 0 reads in YN15 are really unique to SN6306, 8 unigenes were cloned and sequenced. Results showed that the selected unigenes are more similar to SN6306 and Th. intermedium than to the wheat cultivar YN15. The sequencing results further confirmed that the unigenes showing 0 reads in YN15 are unique to SN6306 and are most likely derived from Th. intermedium (Host) Nevski. Thus, the genes from Th. intermedium most probably conferred the resistance of SN6306 to Bgt.

  7. The effects of leachate recirculation with supplemental water addition on methane production and waste decomposition in a simulated tropical landfill.

    PubMed

    Sanphoti, N; Towprayoon, S; Chaiprasert, P; Nopharatana, A

    2006-10-01

    In order to increase methane production efficiency, leachate recirculation is applied in landfills to increase moisture content and circulate organic matter back into the landfill cell. In the case of tropical landfills, where high temperature and evaporation occurs, leachate recirculation may not be enough to maintain the moisture content, therefore supplemental water addition into the cell is an option that could help stabilize moisture levels as well as stimulate biological activity. The objectives of this study were to determine the effects of leachate recirculation and supplemental water addition on municipal solid waste decomposition and methane production in three anaerobic digestion reactors. Anaerobic digestion with leachate recirculation and supplemental water addition showed the highest performance in terms of cumulative methane production and the stabilization period time required. It produced an accumulated methane production of 54.87 l/kg dry weight of MSW at an average rate of 0.58 l/kg dry weight/d and reached the stabilization phase on day 180. The leachate recirculation reactor provided 17.04 l/kg dry weight at a rate of 0.14l/kg dry weight/d and reached the stabilization phase on day 290. The control reactor provided 9.02 l/kg dry weight at a rate of 0.10 l/kg dry weight/d, and reached the stabilization phase on day 270. Increasing the organic loading rate (OLR) after the waste had reached the stabilization phase made it possible to increase the methane content of the gas, the methane production rate, and the COD removal. Comparison of the reactors' efficiencies at maximum OLR (5 kgCOD/m(3)/d) in terms of the methane production rate showed that the reactor using leachate recirculation with supplemental water addition still gave the highest performance (1.56 l/kg dry weight/d), whereas the leachate recirculation reactor and the control reactor provided 0.69 l/kg dry weight/d and 0.43 l/kg dry weight/d, respectively. However, when considering

  8. Identification of potentially hazardous human gene products in GMO risk assessment.

    PubMed

    Bergmans, Hans; Logie, Colin; Van Maanen, Kees; Hermsen, Harm; Meredyth, Michelle; Van Der Vlugt, Cécile

    2008-01-01

    Genetically modified organisms (GMOs), e.g. viral vectors, could threaten the environment if by their release they spread hazardous gene products. Even in contained use, to prevent adverse consequences, viral vectors carrying genes from mammals or humans should be especially scrutinized as to whether gene products that they synthesize could be hazardous in their new context. Examples of such potentially hazardous gene products (PHGPs) are: protein toxins, products of dominant alleles that have a role in hereditary diseases, gene products and sequences involved in genome rearrangements, gene products involved in immunomodulation or with an endocrine function, gene products involved in apoptosis, activated proto-oncogenes. For contained use of a GMO that carries a construct encoding a PHGP, the precautionary principle dictates that safety measures should be applied on a "worst case" basis, until the risks of the specific case have been assessed. The potential hazard of cloned genes can be estimated before empirical data on the actual GMO become available. Preliminary data may be used to focus hazard identification and risk assessment. Both predictive and empirical data may also help to identify what further information is needed to assess the risk of the GMO. A two-step approach, whereby a PHGP is evaluated for its conceptual dangers, then checked by data bank searches, is delineated here.

  9. Effects of a combination of feed additives on methane production, diet digestibility, and animal performance in lactating dairy cows.

    PubMed

    van Zijderveld, S M; Fonken, B; Dijkstra, J; Gerrits, W J J; Perdok, H B; Fokkink, W; Newbold, J R

    2011-03-01

    Two experiments were conducted to assess the effects of a mixture of dietary additives on enteric methane production, rumen fermentation, diet digestibility, energy balance, and animal performance in lactating dairy cows. Identical diets were fed in both experiments. The mixture of feed additives investigated contained lauric acid, myristic acid, linseed oil, and calcium fumarate. These additives were included at 0.4, 1.2, 1.5, and 0.7% of dietary dry matter, respectively (treatment ADD). Experimental fat sources were exchanged for a rumen inert source of fat in the control diet (treatment CON) to maintain isolipidic rations. Cows (experiment 1, n=20; experiment 2, n=12) were fed restricted amounts of feed to avoid confounding effects of dry matter intake on methane production. In experiment 1, methane production and energy balance were studied using open-circuit indirect calorimetry. In experiment 2, 10 rumen-fistulated animals were used to measure rumen fermentation characteristics. In both experiments animal performance was monitored. The inclusion of dietary additives decreased methane emissions (g/d) by 10%. Milk yield and milk fat content tended to be lower for ADD in experiment 1. In experiment 2, milk production was not affected by ADD, but milk fat content was lower. Fat- and protein-corrected milk was lower for ADD in both experiments. Milk urea nitrogen content was lowered by ADD in experiment 1 and tended to be lower in experiment 2. Apparent total tract digestibility of fat, but not that of starch or neutral detergent fiber, was higher for ADD. Energy retention did not differ between treatments. The decrease in methane production (g/d) was not evident when methane emission was expressed per kilogram of milk produced. Feeding ADD resulted in increases of C12:0 and C14:0 and the intermediates of linseed oil biohydrogenation in milk in both experiments. In experiment 2, ADD-fed cows tended to have a decreased number of protozoa in rumen fluid when

  10. Analysis of the effects of section 29 tax credits on reserve additions and production of gas from unconventional resources

    SciTech Connect

    Not Available

    1990-09-01

    Federal tax credits for production of natural gas from unconventional resources can stimulate drilling and reserves additions at a relatively low cost to the Treasury. This report presents the results of an analysis of the effects of a proposed extension of the Section 29 alternative fuels production credit specifically for unconventional gas. ICF Resources estimated the net effect of the extension of the credit (the difference between development activity expected with the extension of the credit and that expected if the credit expires in December 1990 as scheduled). The analysis addressed the effect of tax credits on project economics and capital formation, drilling and reserve additions, production, impact on the US and regional economies, and the net public sector costs and incremental revenues. The analysis was based on explicit modeling of the three dominant unconventional gas resources: Tight sands, coalbed methane, and Devonian shales. It incorporated the most current data on resource size, typical well recoveries and economics, and anticipated activity of the major producers. Each resource was further disaggregated for analysis based on distinct resource characteristics, development practices, regional economics, and historical development patterns.

  11. Effect of catalyst additives on the production of biofuels from palm oil cracking in a transport riser reactor.

    PubMed

    Chew, Thiam Leng; Bhatia, Subhash

    2009-05-01

    Catalytic cracking of crude palm oil (CPO) and used palm oil (UPO) were studied in a transport riser reactor for the production of biofuels at a reaction temperature of 450 degrees C, with residence time of 20s and catalyst-to-oil ratio (CTO) of 5 gg(-1). The effect of HZSM-5 (different Si/Al ratios), beta zeolite, SBA-15 and AlSBA-15 were studied as physically mixed additives with cracking catalyst Rare earth-Y (REY). REY catalyst alone gave 75.8 wt% conversion with 34.5 wt% of gasoline fraction yield using CPO, whereas with UPO, the conversion was 70.9 wt% with gasoline fraction yield of 33.0 wt%. HZSM-5, beta zeolite, SBA-15 and AlSBA-15 as additives with REY increased the conversion and the yield of organic liquid product. The transport riser reactor can be used for the continuous production of biofuels from cracking of CPO and UPO over REY catalyst.

  12. Rapid detection of the addition of soybean proteins to cheese and other dairy products by reversed-phase perfusion chromatography.

    PubMed

    García, M C; Marina, M L

    2006-04-01

    The undeclared addition of soybean proteins to milk products is forbidden and a method is needed for food control and enforcement. This paper reports the development of a chromatographic method for routine analysis enabling the detection of the addition of soybean proteins to dairy products. A perfusion chromatography column and a linear binary gradient of acetonitrile-water-0.1% (v/v) trifluoroacetic acid at a temperature of 60 degrees C were used. A very simple sample treatment consisting of mixing the sample with a suitable solvent (Milli-Q water or bicarbonate buffer (pH=11)) and centrifuging was used. The method enabled the separation of soybean proteins from milk proteins in less than 4 min (at a flow-rate of 3 ml/min). The method has been successfully applied to the detection of soybean proteins in milk, cheese, yogurt, and enteral formula. The correct quantitation of these vegetable proteins has also been possible in milk adulterated at origin with known sources of soybean proteins. The application of the method to samples adulterated at origin also leads to interesting conclusions as to the effect of the processing conditions used for the preparation of each dairy product on the determination of soybean proteins.

  13. The product of the adenovirus intermediate gene IX is a transcriptional activator.

    PubMed Central

    Lutz, P; Rosa-Calatrava, M; Kedinger, C

    1997-01-01

    We have investigated the functional properties of the product of the adenovirus type 5 gene IX. This gene, which is expressed at intermediate times postinfection, encodes a small polypeptide (pIX) of 140 residues that has previously been shown to be incorporated into the viral capsid. Here, we show that pIX, in addition to its structural contribution, exhibits transcriptional properties. In transient transfection experiments, expression of pIX stimulated adenovirus major late promoter activity. The effect was independent of other viral proteins, but the level of promoter activation appeared strongly pIX dose dependent; similar levels of induction were observed with other cellular or viral TATA-containing (but not with TATA-less) promoters. This promoter specificity could be reproduced in a cell-free transcription system by the addition of purified recombinant pIX, further stressing the transcriptional nature of the phenomenon. A preliminary structural analysis of pIX indicated that the integrity of a putative leucine zipper at the carboxy-terminal end of the molecule, as well as elements within the amino-terminal half, was critical for pIX transcriptional activity. The relevance of these findings in adenovirus infection is discussed. PMID:9188576

  14. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid.

  15. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  16. Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

    NASA Astrophysics Data System (ADS)

    Aravindran, S.; Sahilah, A. M.; Aminah, A.

    2014-09-01

    Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

  17. Possibilities of the Technology of Additive Production for Making Complex-Shape Parts and Depositing Functional Coatings from Metallic Powders

    NASA Astrophysics Data System (ADS)

    Grigor'ev, S. N.; Tarasova, T. V.

    2016-01-01

    The aspects of terminology, definitions and classification in the technology of additive production are considered. The principal possibility of fabrication of complex-shape parts from a refractory cobalt alloy by the method of selective laser melting and deposition of hard and wear-resistant coatings from Ti and SiC powders by coaxial laser surfacing is shown. The technological possibility of microlaser surfacing with lateral resolution about 100 μm in the production of parts from aluminum alloys is considered. The mechanisms of formation of structure in the studied alloys typical for selective laser melting, laser surfacing and microlaser surfacing are determined. The physical and mechanical properties of the alloys are investigated.

  18. Significantly enhanced production of acarbose in fed-batch fermentation with the addition of S-adenosylmethionine.

    PubMed

    Sun, Li-Hui; Li, Ming-Gang; Wang, Yuan-Shan; Zheng, Yu-Guo

    2012-06-01

    Acarbose, a pseudo-oligosaccharide, is widely used clinically in therapies for non-insulin-dependent diabetes. In the present study, S-adenosylmethionine (SAM) was added to selected media in order to investigate its effect on acarbose fermentation by Actinoplanes utahensis ZJB- 08196. Acarbose titer was seen to increase markedly when concentrations of SAM were added over a period of time. The effects of glucose and maltose on the production of acarbose were investigated in both batch and fed-batch fermentation. Optimal acarbose production was observed at relatively low glucose levels and high maltose levels. Based on these results, a further fed-batch experiment was designed so as to enhance the production of acarbose. Fed-batch fermentation was carried out at an initial glucose level of 10 g/l and an initial maltose level of 60 g/l. Then, 12 h post inoculation, 100 micromol/l SAM was added. In addition, 8 g/l of glucose was added every 24 h, and 20 g/l of maltose was added at 96 h. By way of this novel feeding strategy, the maximum titer of acarbose achieved was 6,113 mg/l at 192 h. To our knowledge, the production level of acarbose achieved in this study is the highest ever reported.

  19. Additional safeguards for children in clinical investigations of food and drug administration-regulated products. Final rule.

    PubMed

    2013-02-26

    The Food and Drug Administration (FDA) is amending its regulations to provide additional safeguards for children enrolled in clinical investigations of FDA-regulated products. This rule finalizes the interim rule published in 2001 to bring FDA regulations into compliance with provisions of the Children's Health Act of 2000 (the Children's Health Act). The Children's Health Act requires that all research involving children that is conducted, supported, or regulated by the Department of Health and Human Services (HHS) be in compliance with HHS regulations providing additional protections for children involved as subjects in research. FDA is taking this action both to comply with the congressional mandate and because of increases in the enrollment of children in clinical investigations as a result of ongoing pediatric initiatives.

  20. Variation in lipid extractability by solvent in microalgae. Additional criterion for selecting species and strains for biofuel production from microalgae.

    PubMed

    Mendoza, Héctor; Carmona, Laura; Assunção, Patricia; Freijanes, Karen; de la Jara, Adelina; Portillo, Eduardo; Torres, Alicia

    2015-12-01

    The lipid extractability of 14 microalgae species and strains was assessed using organic solvents (methanol and chloroform). The high variability detected indicated the potential for applying this parameter as an additional criterion for microalgae screening in industrial processes such as biofuel production from microalgae. Species without cell walls presented higher extractability than species with cell walls. Analysis of cell integrity by flow cytometry and staining with propidium iodide showed a significant correlation between higher resistance to the physical treatments of cell rupture by sonication and the lipid extractability of the microalgae. The results highlight the cell wall as a determining factor in the inter- and intraspecific variability in lipid extraction treatments.

  1. Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery(F).

    PubMed

    Ono, Nadia Nicole; Britton, Monica Therese; Fass, Joseph Nathaniel; Nicolet, Charles Meyer; Lin, Dawei; Tian, Li

    2011-10-01

    Pomegranate fruit peel is rich in bioactive plant natural products, such as hydrolyzable tannins and anthocyanins. Despite their documented roles in human nutrition and fruit quality, genes involved in natural product biosynthesis have not been cloned from pomegranate and very little sequence information is available on pomegranate in the public domain. Shotgun transcriptome sequencing of pomegranate fruit peel cDNA was performed using RNA-Seq on the Illumina Genome Analyzer platform. Over 100 million raw sequence reads were obtained and assembled into 9,839 transcriptome assemblies (TAs) (>200 bp). Candidate genes for hydrolyzable tannin, anthocyanin, flavonoid, terpenoid and fatty acid biosynthesis and/or regulation were identified. Three lipid transfer proteins were obtained that may contribute to the previously reported IgE reactivity of pomegranate fruit extracts. In addition, 115 SSR markers were identified from the pomegranate fruit peel transcriptome and primers were designed for 77 SSR markers. The pomegranate fruit peel transcriptome set provides a valuable platform for natural product biosynthetic gene and SSR marker discovery in pomegranate. This work also demonstrates that next-generation transcriptome sequencing is an economical and effective approach for investigating natural product biosynthesis, identifying genes controlling important agronomic traits, and discovering molecular markers in non-model specialty crop species.

  2. The Effect of Additional Dead Space on Respiratory Exchange Ratio and Carbon Dioxide Production Due to Training

    PubMed Central

    Smolka, Lukasz; Borkowski, Jacek; Zaton, Marek

    2014-01-01

    The purpose of the study was to investigate the effects of implementing additional respiratory dead space during cycloergometry-based aerobic training. The primary outcome measures were respiratory exchange ratio (RER) and carbon dioxide production (VCO2). Two groups of young healthy males: Experimental (Exp, n = 15) and Control (Con, n = 15), participated in this study. The training consisted of 12 sessions, performed twice a week for 6 weeks. A single training session consisted of continuous, constant-rate exercise on a cycle ergometer at 60% of VO2max which was maintained for 30 minutes. Subjects in Exp group were breathing through additional respiratory dead space (1200ml), while subjects in Con group were breathing without additional dead space. Pre-test and two post-training incremental exercise tests were performed for the detection of gas exchange variables. In all training sessions, pCO2 was higher and blood pH was lower in the Exp group (p < 0.001) ensuring respiratory acidosis. A 12-session training program resulted in significant increase in performance time in both groups (from 17”29 ± 1”31 to 18”47 ± 1”37 in Exp; p=0.02 and from 17”20 ± 1”18 to 18”45 ± 1”44 in Con; p = 0.02), but has not revealed a significant difference in RER and VCO2 in both post-training tests, performed at rest and during submaximal workload. We interpret the lack of difference in post-training values of RER and VCO2 between groups as an absence of inhibition in glycolysis and glycogenolysis during exercise with additional dead space. Key Points The purpose of the study was to investigate the effects of implementing additional respiratory dead space during cycloergometry-based aerobic training on respiratory exchange ratio and carbon dioxide production. In all training sessions, respiratory acidosis was gained by experimental group only. No significant difference in RER and VCO2 between experimental and control group due to the trainings. The lack of

  3. The effect of additional dead space on respiratory exchange ratio and carbon dioxide production due to training.

    PubMed

    Smolka, Lukasz; Borkowski, Jacek; Zaton, Marek

    2014-01-01

    The purpose of the study was to investigate the effects of implementing additional respiratory dead space during cycloergometry-based aerobic training. The primary outcome measures were respiratory exchange ratio (RER) and carbon dioxide production (VCO2). Two groups of young healthy males: Experimental (Exp, n = 15) and Control (Con, n = 15), participated in this study. The training consisted of 12 sessions, performed twice a week for 6 weeks. A single training session consisted of continuous, constant-rate exercise on a cycle ergometer at 60% of VO2max which was maintained for 30 minutes. Subjects in Exp group were breathing through additional respiratory dead space (1200ml), while subjects in Con group were breathing without additional dead space. Pre-test and two post-training incremental exercise tests were performed for the detection of gas exchange variables. In all training sessions, pCO2 was higher and blood pH was lower in the Exp group (p < 0.001) ensuring respiratory acidosis. A 12-session training program resulted in significant increase in performance time in both groups (from 17"29 ± 1"31 to 18"47 ± 1"37 in Exp; p=0.02 and from 17"20 ± 1"18 to 18"45 ± 1"44 in Con; p = 0.02), but has not revealed a significant difference in RER and VCO2 in both post-training tests, performed at rest and during submaximal workload. We interpret the lack of difference in post-training values of RER and VCO2 between groups as an absence of inhibition in glycolysis and glycogenolysis during exercise with additional dead space. Key PointsThe purpose of the study was to investigate the effects of implementing additional respiratory dead space during cycloergometry-based aerobic training on respiratory exchange ratio and carbon dioxide production.In all training sessions, respiratory acidosis was gained by experimental group only.No significant difference in RER and VCO2 between experimental and control group due to the trainings.The lack of difference in post

  4. Components of yeast (Sacchromyces cervisiae) extract as defined media additives that support the growth and productivity of CHO cells.

    PubMed

    Spearman, Maureen; Chan, Sarah; Jung, Vince; Kowbel, Vanessa; Mendoza, Meg; Miranda, Vivian; Butler, Michael

    2016-09-10

    Yeast and plant hydrolysates are used as media supplements to support the growth and productivity of CHO cultures for biopharmaceutical production. Through fractionation of a yeast lysate and metabolic analysis of a fraction that had bioactivity equivalent to commercial yeast extract (YE), bioactive components were identified that promoted growth and productivity of two recombinant CHO cell lines (CHO-Luc and CHO-hFcEG2) equivalent to or greater than YE-supplemented media. Autolysis of the yeast lysate was not necessary for full activity, suggesting that the active components are present in untreated yeast cells. A bioactive fraction (3KF) of the yeast lysate was isolated from the permeate using a 3kDa molecular weight cut-off (MWCO) filter. Supplementation of this 3KF fraction into the base media supported growth of CHO-Luc cells over eight passages equivalent to YE-supplemented media. The 3KF fraction was fractionated further by a cation exchange spin column using a stepwise pH elution. Metabolomic analysis of a bioactive fraction isolated at high pH identified several arginine and lysine-containing peptides as well as two polyamines, spermine and spermidine, with 3.5× and 4.5× higher levels compared to a fraction showing no bioactivity. The addition of a mixture of polyamines and their precursors (putrescine, spermine, spermidine, ornithine and citrulline) as well as increasing the concentration of some of the components of the original base medium resulted in a chemically-defined (CD) formulation that produced an equivalent viable cell density (VCD) and productivity of the CHO-Luc cells as the YE-supplemented medium. The VCD of the CHO-hFcEG2 culture in the CD medium was 1.9× greater and with equivalent productivity to the YE-supplemented media.

  5. Vector systems for prenatal gene therapy: principles of non-viral vector design and production.

    PubMed

    Wong, Suet Ping; Argyros, Orestis; Harbottle, Richard P

    2012-01-01

    Gene therapy vectors based on viruses are the most effective gene delivery systems in use today and although efficient at gene transfer their potential toxicity (Hacein-Bey-Abina et al., Science 302:415-419, 2003) provides impetus for the development of safer non-viral alternatives. An ideal vector for human gene therapy should deliver sustainable therapeutic levels of gene expression without affecting the viability of the host at either the cellular or somatic level. Vectors, which comprise entirely human elements, may provide the most suitable method of achieving this. Non-viral vectors are attractive alternatives to viral gene delivery systems because of their low toxicity, relatively easy production, and great versatility. The development of more efficient, economically prepared, and safer gene delivery vectors is a crucial prerequisite for their successful clinical application and remains a primary strategic task of gene therapy research.

  6. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.

    PubMed

    Guigo, Roderic; Dermitzakis, Emmanouil T; Agarwal, Pankaj; Ponting, Chris P; Parra, Genis; Reymond, Alexandre; Abril, Josep F; Keibler, Evan; Lyle, Robert; Ucla, Catherine; Antonarakis, Stylianos E; Brent, Michael R

    2003-02-04

    A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this goal proved challenging because of the large proportion of the mouse and human genomes that is apparently conserved but apparently does not code for protein. We developed a two-stage procedure that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods. RT-PCR amplification and direct sequencing applied to an initial sample of mouse predictions that do not overlap previously known genes verified the regions flanking one intron in 139 predictions, with verification rates reaching 76%. On average, the confirmed predictions show more restricted expression patterns than the mouse orthologs of known human genes, and two-thirds lack homologs in fish genomes, demonstrating the sensitivity of this dual-genome approach to hard-to-find genes. We verified 112 previously unknown homologs of known proteins, including two homeobox proteins relevant to developmental biology, an aquaporin, and a homolog of dystrophin. We estimate that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes. This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes.

  7. Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida

    PubMed Central

    Mwinyi, Adina; Meyer, Achim; Bleidorn, Christoph; Lieb, Bernhard; Bartolomaeus, Thomas; Podsiadlowski, Lars

    2009-01-01

    Background Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula. PMID:19149868

  8. Introduction, stable integration, and controlled expression of a chimeric adenovirus gene whose product is toxic to the recipient human cell.

    PubMed Central

    Klessig, D F; Brough, D E; Cleghon, V

    1984-01-01

    The DNA-binding protein (DBP) encoded by human adenoviruses is a multifunctional polypeptide which plays a central role in regulating the expression of the viral genes. To gain a better understanding of the relationships between the various functions provided by DBP, an extensive collection of DBP mutants is essential. To this end we have constructed several permissive human cell lines which contain and express the DBP gene at high levels to allow propagation of otherwise lethal, nonrecoverable mutants of DBP. Because DBP is toxic to human cells, cell lines were constructed by using a vector in which the DBP gene is under the control of the dexamethasone-inducible promoter of the mouse mammary tumor virus. The low basal levels of DBP synthesis in the absence of dexamethasone allows isolation and propagation of these cells. Addition of dexamethasone enhances DBP production 50- to 200-fold, and within 8 h its synthesis from the single integrated copy of the chimeric gene is 5 to 15% of that observed during peak DBP synthesis in infected human cells in which hundreds of copies of the DBP gene serve as templates. At the nonpermissive temperature, adenovirus mutants with ts lesions in the DBP gene replicate their DNAs, express their late genes, and form infectious viral particles in these DBP+ cell lines but not in the parental HeLa cells. Images PMID:6542172

  9. Sustained reduction in methane production from long-term addition of 3-nitrooxypropanol to a beef cattle diet.

    PubMed

    Romero-Perez, A; Okine, E K; McGinn, S M; Guan, L L; Oba, M; Duval, S M; Kindermann, M; Beauchemin, K A

    2015-04-01

    The objective was to evaluate whether long-term addition of 3-nitrooxypropanol (NOP) to a beef cattle diet results in a sustained reduction in enteric CH4 emissions in beef cattle. Eight ruminally cannulated heifers (637 ± 16.2 kg BW) were used in a completely randomized design with 2 treatments: Control (0 g/d of NOP) and NOP (2 g/d of NOP). Treatments were mixed by hand into the total mixed ration (60% forage, DM basis) at feeding time. Feed offered was restricted to 65% of ad libitum DMI (slightly over maintenance energy intake) and provided once per day. The duration of the experiment was 146 d, including an initial 18-d covariate period without NOP use; a 112-d treatment period with NOP addition to the diet, divided into four 28-d time intervals (d 1 to 28, 29 to 56, 57 to 84, and 85 to 112); and a final 16-d recovery period without NOP use. During the covariate period and at the end of each interval and the end of the recovery period, CH4 was measured for 3 d using whole animal metabolic chambers. The concentration of VFA was measured in rumen fluid samples collected 0, 3, and 6 h after feeding, and the microbial population was evaluated using rumen samples collected 3 h after feeding on d 12 of the covariate period, d 22 of each interval within the treatment period, and d 8 of the recovery period. Average DMI for the experiment was 7.04 ± 0.27 kg. Methane emissions were reduced by 59.2% when NOP was used (9.16 vs. 22.46 g/kg DMI; P < 0.01). Total VFA concentrations were not affected (P = 0.12); however, molar proportion of acetate was reduced and that for propionate increased when NOP was added (P < 0.01), which reduced the acetate to propionate ratio (3.0 vs. 4.0; P < 0.01). The total copy number of the 16S rRNA gene of total bacteria was not affected (P = 0.50) by NOP, but the copy number of the 16S rRNA gene of methanogens was reduced (P < 0.01) and the copy number of the 18S rRNA gene of protozoa was increased (P = 0.03). The residual effect of NOP for

  10. Nitric oxide production and NO synthase gene expression contribute to vascular regulation during exercise.

    PubMed

    Shen, W; Zhang, X; Zhao, G; Wolin, M S; Sessa, W; Hintze, T H

    1995-08-01

    Nitric oxide (NO) is a vasodilator produced under normal physiologic conditions primarily by the vascular endothelium lining all blood vessels. The primary stimulus for the production of nitric oxide by the constitutive endothelial nitric oxide synthase (ECNOS, Type II) found in blood vessels is most likely the shear stress, the frictional force, caused by blood flowing through blood vessels. During exercise there is an increase in cardiac output and redistribution of blood flow to increase blood flow in skeletal muscle and in the coronary circulation. These adjustments provide increased oxygen delivery to support aerobic energy production and to sustain the exercise response. NO may be involved in the regulation of vascular tone in exercising skeletal and cardiac muscle by promoting, enhancing the metabolic vasodilation. In addition, the production of NO by capillary endothelium may regulate oxygen consumption by mitochondria through chemical interactions between NO and the iron-sulfur center of these enzymes. Finally, brief exercise training may alter the gene expression for the enzyme, the constitutive endothelial NO synthase, which forms NO and may be part of the vascular adaptation seen after aerobic exercise training. Furthermore, if there is a genetic predisposition to produce NO, as in world class athletes or animals bred to race, NO may contribute to spectacular exercise performance. These three potential roles of NO will be discussed and data presented to support each of these in our review.

  11. Characterization of Clostridium perfringens TpeL Toxin Gene Carriage, Production, Cytotoxic Contributions, and Trypsin Sensitivity

    PubMed Central

    Chen, Jianming

    2015-01-01

    Large clostridial toxins (LCTs) are produced by at least four pathogenic clostridial species, and several LCTs are proven pivotal virulence factors for both human and veterinary diseases. TpeL is a recently identified LCT produced by Clostridium perfringens that has received relatively limited study. In response, the current study surveyed carriage of the tpeL gene among different C. perfringens strains, detecting this toxin gene in some type A, B, and C strains but not in any type D or E strains. This study also determined that all tested strains maximally produce, and extracellularly release, TpeL at the late-log or early-stationary growth stage during in vitro culture, which is different from the maximal late-stationary-phase production reported previously for other LCTs and for TpeL production by C. perfringens strain JIR12688. In addition, the present study found that TpeL levels in culture supernatants can be repressed by either glucose or sucrose. It was also shown that, at natural production levels, TpeL is a significant contributor to the cytotoxic activity of supernatants from cultures of tpeL-positive strain CN3685. Lastly, this study identified TpeL, which presumably is produced in the intestines during diseases caused by TpeL-positive type B and C strains, as a toxin whose cytotoxicity decreases after treatment with trypsin; this finding may have pathophysiologic relevance by suggesting that, like beta toxin, TpeL contributes to type B and C infections in hosts with decreased trypsin levels due to disease, diet, or age. PMID:25824828

  12. Immunological characterization of the gag gene products of bovine immunodeficiency virus.

    PubMed Central

    Battles, J K; Hu, M Y; Rasmussen, L; Tobin, G J; Gonda, M A

    1992-01-01

    The bovine immunodeficiency virus (BIV) gag gene encodes a 53-kDa precursor (Pr53gag) that is involved in virus particle assembly and is further processed into the putative matrix (MA), capsid (CA), and nucleocapsid (NC) functional domains in the mature virus. Gag determinants are also found in the Gag-Pol polyprotein precursor. To immunologically identify the major precursors and processed products of the BIV gag gene, monospecific rabbit sera to recombinant BIV MA protein and Pr53gag and peptides predicted to correspond to the CA and NC proteins and the MA-CA cleavage site were developed and used in immunoprecipitations and immunoblots of BIV antigens. Monospecific antisera to native and recombinant human immunodeficiency virus type 1 proteins were also used to identify analogous BIV Gag proteins and to determine whether cross-reactive epitopes were present in the BIV Gag precursors or processed products. The BIV MA, CA, and NC Gag proteins were identified as p16, p26, and p13, respectively. In addition to BIV Pr53gag, the major Gag precursor, two other Gag-related precursors of 170 and 49 kDa were identified that have been designated pPr170gag-pol and Pr49gag, respectively; pPr170gag-pol is the Gag-Pol polyprotein precursor, and Pr49gag is the transframe Gag precursor present in pPr170gag-pol. Several alternative Gag cleavage products were also observed, including p23, which contains CA and NC determinants, and p10, which contains a peptide sequence conserved in the CA proteins of most lentiviruses. The monospecific antisera to human immunodeficiency virus type 1 CA (p24) and NC (p7) proteins showed cross-reactivity to and aided in the identification of analogous BIV proteins. Based on the present data, a scheme for the processing of BIV Gag precursors is proposed. Images PMID:1331499

  13. Immunological characterization of the gag gene products of bovine immunodeficiency virus.

    PubMed

    Battles, J K; Hu, M Y; Rasmussen, L; Tobin, G J; Gonda, M A

    1992-12-01

    The bovine immunodeficiency virus (BIV) gag gene encodes a 53-kDa precursor (Pr53gag) that is involved in virus particle assembly and is further processed into the putative matrix (MA), capsid (CA), and nucleocapsid (NC) functional domains in the mature virus. Gag determinants are also found in the Gag-Pol polyprotein precursor. To immunologically identify the major precursors and processed products of the BIV gag gene, monospecific rabbit sera to recombinant BIV MA protein and Pr53gag and peptides predicted to correspond to the CA and NC proteins and the MA-CA cleavage site were developed and used in immunoprecipitations and immunoblots of BIV antigens. Monospecific antisera to native and recombinant human immunodeficiency virus type 1 proteins were also used to identify analogous BIV Gag proteins and to determine whether cross-reactive epitopes were present in the BIV Gag precursors or processed products. The BIV MA, CA, and NC Gag proteins were identified as p16, p26, and p13, respectively. In addition to BIV Pr53gag, the major Gag precursor, two other Gag-related precursors of 170 and 49 kDa were identified that have been designated pPr170gag-pol and Pr49gag, respectively; pPr170gag-pol is the Gag-Pol polyprotein precursor, and Pr49gag is the transframe Gag precursor present in pPr170gag-pol. Several alternative Gag cleavage products were also observed, including p23, which contains CA and NC determinants, and p10, which contains a peptide sequence conserved in the CA proteins of most lentiviruses. The monospecific antisera to human immunodeficiency virus type 1 CA (p24) and NC (p7) proteins showed cross-reactivity to and aided in the identification of analogous BIV proteins. Based on the present data, a scheme for the processing of BIV Gag precursors is proposed.

  14. A Gene Optimization Strategy that Enhances Production of Fully Functional P-Glycoprotein in Pichia pastoris

    PubMed Central

    Protasevich, Irina I.; Brouillette, Christie G.; Harrell, Patina M.; Hildebrandt, Ellen; Gasser, Brigitte; Mattanovich, Diethard; Ward, Andrew; Chang, Geoffrey; Urbatsch, Ina L.

    2011-01-01

    Background Structural and biochemical studies of mammalian membrane proteins remain hampered by inefficient production of pure protein. We explored codon optimization based on highly expressed Pichia pastoris genes to enhance co-translational folding and production of P-glycoprotein (Pgp), an ATP-dependent drug efflux pump involved in multidrug resistance of cancers. Methodology/Principal Findings Codon-optimized “Opti-Pgp” and wild-type Pgp, identical in primary protein sequence, were rigorously analyzed for differences in function or solution structure. Yeast expression levels and yield of purified protein from P. pastoris (∼130 mg per kg cells) were about three-fold higher for Opti-Pgp than for wild-type protein. Opti-Pgp conveyed full in vivo drug resistance against multiple anticancer and fungicidal drugs. ATP hydrolysis by purified Opti-Pgp was strongly stimulated ∼15-fold by verapamil and inhibited by cyclosporine A with binding constants of 4.2±2.2 µM and 1.1±0.26 µM, indistinguishable from wild-type Pgp. Maximum turnover number was 2.1±0.28 µmol/min/mg and was enhanced by 1.2-fold over wild-type Pgp, likely due to higher purity of Opti-Pgp preparations. Analysis of purified wild-type and Opti-Pgp by CD, DSC and limited proteolysis suggested similar secondary and ternary structure. Addition of lipid increased the thermal stability from Tm ∼40°C to 49°C, and the total unfolding enthalpy. The increase in folded state may account for the increase in drug-stimulated ATPase activity seen in presence of lipids. Conclusion The significantly higher yields of protein in the native folded state, higher purity and improved function establish the value of our gene optimization approach, and provide a basis to improve production of other membrane proteins. PMID:21826197

  15. Energy budgeting and carbon footprint of transgenic cotton-wheat production system through peanut intercropping and FYM addition.

    PubMed

    Singh, Raman Jeet; Ahlawat, I P S

    2015-05-01

    Two of the most pressing sustainability issues are the depletion of fossil energy resources and the emission of atmospheric green house gases like carbon dioxide to the atmosphere. The aim of this study was to assess energy budgeting and carbon footprint in transgenic cotton-wheat cropping system through peanut intercropping with using 25-50% substitution of recommended dose of nitrogen (RDN) of cotton through farmyard manure (FYM) along with 100% RDN through urea and control (0 N). To quantify the residual effects of previous crops and their fertility levels, a succeeding crop of wheat was grown with varying rates of nitrogen, viz. 0, 50, 100, and 150 kg ha(-1). Cotton + peanut-wheat cropping system recorded 21% higher system productivity which ultimately helped to maintain higher net energy return (22%), energy use efficiency (12%), human energy profitability (3%), energy productivity (7%), carbon outputs (20%), carbon efficiency (17%), and 11% lower carbon footprint over sole cotton-wheat cropping system. Peanut addition in cotton-wheat system increased the share of renewable energy inputs from 18 to 21%. With substitution of 25% RDN of cotton through FYM, share of renewable energy resources increased in the range of 21% which resulted into higher system productivity (4%), net energy return (5%), energy ratio (6%), human energy profitability (74%), energy productivity (6%), energy profitability (5%), and 5% lower carbon footprint over no substitution. The highest carbon footprint (0.201) was recorded under control followed by 50 % substitution of RDN through FYM (0.189). With each successive increase in N dose up to 150 kg N ha(-1) to wheat, energy productivity significantly reduced and share of renewable energy inputs decreased from 25 to 13%. Application of 100 kg N ha(-1) to wheat maintained the highest grain yield (3.71 t ha(-1)), net energy return (105,516 MJ ha(-1)), and human energy profitability (223.4) over other N doses applied to wheat

  16. Influence of Anthropogenic Nutrient Additions on Greenhouse Gas Production Rates at Water-soil Interfaces in an Urban Dominated Estuary

    NASA Astrophysics Data System (ADS)

    Brigham, B. A.; O'Mullan, G. D.; Bird, J. A.

    2014-12-01

    The tidal Hudson River Estuary (HRE) receives significant inputs of readily dissolvable carbon (C) and nitrogen (N) from incomplete wastewater treatment and sewer overflow during storm events associated with NYC and other urban centers. Nutrient deposition may alter C utilization in the estuarine water column, associated sediments and surrounding wetlands. In these anaerobic systems, we hypothesize that microbial activity is limited by the availability of easily-degradable C (not electron acceptors), which acts as a co-metabolite and provides energy for organic matter decomposition. Sporadic transport of highly C enriched storm derived runoff may substantially enhance greenhouse gas (GHG) production rates through the utilization of stored C pools. To test our hypothesis carbon dioxide (CO2) and methane (CH4) process rates (1) were evaluated from soil cores removed from three distinct HRE wetland sites (Saw Mill Creek, Piermont, and Iona Island Marsh(s)) across a salinity gradient and incubated under varying nutrient treatments. Further, CO2 and CH4 surface water effluxes (2) were quantified from multiple river cruises spanning two years at varying distance from nutrient sources associated with NYC. Incubation experiments from wetland soil core experiments demonstrated that readily degradable C but not inorganic N additions stimulated GHG production (200 - 350 ug C g-1 of dry soil day-1) threefold compared to negative controls. The HRE was found to be both a CO2 and CH4 source under all conditions. The greatest GHG efflux (300 - 3000 nmoles C m-2 day-1) was quantified in mid-channel, tributary, and near shore sites in close proximity to NYC which following precipitation events demonstrated 2-20X increased GHG efflux. These results demonstrate that anthropogenic C additions associated with dense urban centers have the potential to enhance anaerobic microbial degradation of organic matter and subsequent GHG production.

  17. Two additional human serum proteins structurally related to complement factor H: Evidence for a family of factor H-related genes

    SciTech Connect

    Skerka, C.; Timmann, C.; Horstmann, R.D. ); Zipfel, P.F.

    1992-05-15

    The authors identify and characterize two human serum proteins with an apparent molecular mass of 24 and 29 kDa, which are antigenically related to complement factor H. These proteins represent differently glycosylated forms and are encoded by the same mRNA. The corresponding cDNA clone is 1051 bp in size and hybridized to a 1.4-kb mRNA derived from human liver. The predicted translation product represents a protein of 270 amino acids, which displays a hydrophobic leader sequence, indicative of a secreted protein. The secreted part is organized in four short consensus repeats (SCR) and has a single putative N-linked glycosylation site. The predicted sequence is closely related to that of the previously described factor H-related proteins h37 and h42, which are also derived from a 1.4-kb mRNA. Amino acid comparison of these factor H-related proteins showed identical leader sequences, an exchange of three amino acids in SCR1, identical sequences of SCR2, and a lower degree of homology between SCR3-4 (h24 and h29) and SCR4-5 (h37 and h42). In addition, SCR3-4 of h24 and h29 display homology to SCR19-20 of human complement factor H. The relatedness of structural elements of the factor H-related proteins h24, h29, h37, and h42 and of factor H, suggests a function common to these proteins and indicates the existence of a gene family consisting of factor H and at least two factor H-related genes. 28 refs., 7 figs., 1 tab.

  18. Examination of the jarosite-alunite precipitate addition in the raw meal for the production of sulfoaluminate cement clinker.

    PubMed

    Katsioti, M; Tsakiridis, P E; Leonardou-Agatzini, S; Oustadakis, P

    2006-04-17

    The aim of the present research work was to investigate the possibility of adding a jarosite-alunite chemical precipitate, a waste product of a new hydrometallurgical process developed to treat economically low-grade nickel oxides ores, in the raw meal for the production of sulfoaluminate cement clinker. For that reason, two samples of raw meals were prepared, one contained 20% gypsum, as a reference sample ((SAC)Ref) and another with 11.31% jarosite-alunite precipitate ((SAC)J/A). Both raw meals were sintered at 1300 degrees C. The results of chemical and mineralogical analyses as well as the microscopic examination showed that the use of the jarosite-alunite precipitate did not affect the mineralogical characteristics of the so produced sulfoaluminate cement clinker and there was confirmed the formation of the sulfoaluminate phase (C4A3S), the most typical phase of this cement type. Furthermore, both clinkers were tested by determining the grindability, setting time, compressive strength and expansibility. The hydration products were examined by XRD analysis at 2, 7, 28 and 90 days. The results of the physico-mechanical tests showed that the addition of jarosite-alunite precipitate did not negatively affect the quality of the produced cement.

  19. Effect of caries in mentally handicapped children of addition of fluoride and bicarbonate-phosphate to dietary sugar products.

    PubMed

    Luoma, H; Nyman, A; Toivonen, A; Söderholm, S; Nuuja, T; Kantero, R L; Hassinen, M L; Jokela, M; Nummikoski, P; Ranta, H; Thesleff, I

    1979-06-01

    Mentally handicapped children, aged 5--15 years and living in institutions, received fluoride supplement in several sugar products of their diet; in candies, marmalades, jams, fruit juices and in sweet desserts corresponding to 10 mg F as NaF per kg of the sugar (sucrose or glucose) of each product. To two of the four daily candies was also added a NaHCO3 + KH2PO4 mixture (mole ratio 9.8/l, resp.) to substitute for 2.5% of the sugar of the candy. The control children received the respective products without the additives. After stepwise exclusions of subjects for various reasons, e.g. for the absence of permanent teeth, low initial caries activity, strong medication, Down's syndrome, etc., the mean DMFS-increment in the remaining 43 control subjects was 4.5 and in the 41 test subjects 2.6 lesions/100 surfaces at risk, i.e. 42% reduction. Caries arrestment had occurred in these test subjects after the first year, while in the respective controls it was continuously increasing. Among numerous oral and body parameters studied, only surface enamel fluoride in primary teeth was increased by the fluoride supplements and urinary phosphate and calcium excretion decreased.

  20. Effects of CMC addition on bacterial cellulose production in a biofilm reactor and its paper sheets analysis.

    PubMed

    Cheng, Kuan-Chen; Catchmark, Jeffrey M; Demirci, Ali

    2011-03-14

    Bacterial cellulose (BC) can be grown into any desired shape such as pellicles, pellets, and spherelike balls, depending on the cultivation method, additives, and cell population. In this study, Acetobacter xylinum (ATCC 700178) was grown in the production medium with different concentrations of carboxylmethylcellulose (CMC) and were evaluated for BC production by using a PCS biofilm reactor. The results demonstrated that BC production was enhanced to its maximum (∼13 g/L) when 1.5% of CMC was applied, which was 1.7-fold higher than the result obtained from control culture. The major type of the produced BC was also switched from BC pellicle to small pellets. The ratio of BC pellets in suspension increased from 0 to 93%. Fourier transform infrared (FTIR) spectroscopy demonstrated that CMC was incorporated into BC during fermentation and resulted in the decreased crystallinity and crystal size. The X-ray diffraction (XRD) patterns indicated that CMC-BC exhibited both lower crystallinity (80%) and crystal size (4.2 nm) when compared with control samples (86% and 5.3 nm). The harvested BC was subjected to paper formation and its mechanical strength was determined. Dynamic mechanical analysis (DMA) results demonstrated that BC paper sheets exhibited higher tensile strength and Young's modulus when compared with regular paper.

  1. Improvement of gougerotin and nikkomycin production by engineering their biosynthetic gene clusters.

    PubMed

    Du, Deyao; Zhu, Yu; Wei, Junhong; Tian, Yuqing; Niu, Guoqing; Tan, Huarong

    2013-07-01

    Nikkomycins and gougerotin are peptidyl nucleoside antibiotics with broad biological activities. The nikkomycin biosynthetic gene cluster comprises one pathway-specific regulatory gene (sanG) and 21 structural genes, whereas the gene cluster for gougerotin biosynthesis includes one putative regulatory gene, one major facilitator superfamily transporter gene, and 13 structural genes. In the present study, we introduced sanG driven by six different promoters into Streptomyces ansochromogenes TH322. Nikkomycin production was increased significantly with the highest increase in engineered strain harboring hrdB promoter-driven sanG. In the meantime, we replaced the native promoter of key structural genes in the gougerotin (gou) gene cluster with the hrdB promoters. The heterologous producer Streptomyces coelicolor M1146 harboring the modified gene cluster produced gougerotin up to 10-fold more than strains carrying the unmodified cluster. Therefore, genetic manipulations of genes involved in antibiotics biosynthesis with the constitutive hrdB promoter present a robust, easy-to-use system generally useful for the improvement of antibiotics production in Streptomyces.

  2. Inducible Amplification of Gene Copy Number and Heterologous Protein Production in the Yeast Kluyveromyces lactis

    PubMed Central

    Morlino, Giovanni B.; Tizzani, Lorenza; Fleer, Reinhard; Frontali, Laura; Bianchi, Michele M.

    1999-01-01

    Heterologous protein production can be doubled by increasing the copy number of the corresponding heterologous gene. We constructed a host-vector system in the yeast Kluyveromyces lactis that was able to induce copy number amplification of pKD1 plasmid-based vectors upon expression of an integrated copy of the plasmid recombinase gene. We increased the production and secretion of two heterologous proteins, glucoamylase from the yeast Arxula adeninivorans and mammalian interleukin-1β, following gene dosage amplification when the heterologous genes were carried by pKD1-based vectors. The choice of the promoters for expression of the integrated recombinase gene and of the episomal heterologous genes are critical for the mitotic stability of the host-vector system. PMID:10543790

  3. Inducible amplification of gene copy number and heterologous protein production in the yeast Kluyveromyces lactis.

    PubMed

    Morlino, G B; Tizzani, L; Fleer, R; Frontali, L; Bianchi, M M

    1999-11-01

    Heterologous protein production can be doubled by increasing the copy number of the corresponding heterologous gene. We constructed a host-vector system in the yeast Kluyveromyces lactis that was able to induce copy number amplification of pKD1 plasmid-based vectors upon expression of an integrated copy of the plasmid recombinase gene. We increased the production and secretion of two heterologous proteins, glucoamylase from the yeast Arxula adeninivorans and mammalian interleukin-1beta, following gene dosage amplification when the heterologous genes were carried by pKD1-based vectors. The choice of the promoters for expression of the integrated recombinase gene and of the episomal heterologous genes are critical for the mitotic stability of the host-vector system.

  4. DNA sequence, products, and transcriptional pattern of the genes involved in production of the DNA replication inhibitor microcin B17.

    PubMed Central

    Genilloud, O; Moreno, F; Kolter, R

    1989-01-01

    The 3.8-kilobase segment of plasmid DNA that contains the genes required for production of the DNA replication inhibitor microcin B17 was sequenced. The sequence contains four open reading frames which were shown to be translated in vivo by the construction of fusions to lacZ. The location of these open reading frames fits well with the location of the four microcin B17 production genes, mcbABCD, identified previously through genetic complementation. The products of the four genes have been identified, and the observed molecular weights of the proteins agree with those predicted from the nucleotide sequence. The transcription of these genes was studied by using fusions to lacZ and physical mapping of mRNA start sites. Three promoters were identified in this region. The major promoter for all the genes is a growth phase-regulated OmpR-dependent promoter located upstream of mcbA. A second promoter is located within mcbC and is responsible for a low-level basal expression of mcbD. A third promoter, located within mcbD, promotes transcription in the reverse direction starting within mcbD and extending through mcbC. The resulting mRNA appears to be an untranslated antisense transcript that could play a regulatory role in the expression of these genes. Images PMID:2644225

  5. Identification of Gene Expression Signatures in the Chicken Intestinal Intraepithelial Lymphocytes in Response to Herb Additive Supplementations

    PubMed Central

    Won, Kyeong-Hye; Song, Ki-Duk; Park, Jong-Eun; Kim, Duk-Kyung; Na, Chong-Sam

    2016-01-01

    Anethole and garlic have an immune modulatory effects on avian coccidiosis, and these effects are correlated with gene expression changes in intestinal epithelial lymphocytes (IELs). In this study, we integrated gene expression datasets from two independent experiments and investigated gene expression profile changes by anethole and garlic respectively, and identified gene expression signatures, which are common targets of these herbs as they might be used for the evaluation of the effect of plant herbs on immunity toward avian coccidiosis. We identified 4,382 and 371 genes, which were differentially expressed in IELs of chickens supplemented with garlic and anethole respectively. The gene ontology (GO) term of differentially expressed genes (DEGs) from garlic treatment resulted in the biological processes (BPs) related to proteolysis, e.g., “modification-dependent protein catabolic process”, “proteolysis involved in cellular protein catabolic process”, “cellular protein catabolic process”, “protein catabolic process”, and “ubiquitin-dependent protein catabolic process”. In GO analysis, one BP term, “Proteolysis”, was obtained. Among DEGs, 300 genes were differentially regulated in response to both garlic and anethole, and 234 and 59 genes were either up- or down-regulated in supplementation with both herbs. Pathway analysis resulted in enrichment of the pathways related to digestion such as “Starch and sucrose metabolism” and “Insulin signaling pathway”. Taken together, the results obtained in the present study could contribute to the effective development of evaluation system of plant herbs based on molecular signatures related with their immunological functions in chicken IELs. PMID:26954117

  6. Microarray Analysis of Gene Expression in Saccharomyces cerevisiae kap108Δ Mutants upon Addition of Oxidative Stress.

    PubMed

    Belanger, Kenneth D; Larson, Nathaniel; Kahn, Jonathan; Tkachev, Dmitry; Ay, Ahmet

    2016-04-07

    Protein transport between the nucleus and cytoplasm of eukaryotic cells is tightly regulated, providing a mechanism for controlling intracellular localization of proteins, and regulating gene expression. In this study, we have investigated the importance of nucleocytoplasmic transport mediated by the karyopherin Kap108 in regulating cellular responses to oxidative stress in Saccharomyces cerevisiae We carried out microarray analyses on wild-type and kap108 mutant cells grown under normal conditions, shortly after introduction of oxidative stress, after 1 hr of oxidative stress, and 1 hr after oxidative stress was removed. We observe more than 500 genes that undergo a 40% or greater change in differential expression between wild-type and kap108Δ cells under at least one of these conditions. Genes undergoing changes in expression can be categorized in two general groups: 1) those that are differentially expressed between wild-type and kap108Δ cells, no matter the oxidative stress conditions; and 2) those that have patterns of response dependent upon both the absence of Kap108, and introduction or removal of oxidative stress. Gene ontology analysis reveals that, among the genes whose expression is reduced in the absence of Kap108 are those involved in stress response and intracellular transport, while those overexpressed are largely involved in mating and pheromone response. We also identified 25 clusters of genes that undergo similar patterns of change in gene expression when oxidative stresses are added and subsequently removed, including genes involved in stress response, oxidation-reduction processing, iron homeostasis, ascospore wall assembly, transmembrane transport, and cell fusion during mating. These data suggest that Kap108 is important for regulating expression of genes involved in a variety of specific cell functions.

  7. Effects of whey or maltodextrin addition during production on physical quality of white cheese powder during storage.

    PubMed

    Erbay, Zafer; Koca, Nurcan

    2015-12-01

    There is an increasing demand for cheese as a food ingredient, especially as a flavoring agent. One of the most important cheese flavoring agents is cheese powder. To obtain an intense cheese flavor, ripened cheese is used as a raw material in cheese powder but this increases production costs. Moreover, use of natural cheese decreases the physical quality of powder because of its high fat content. In this study, we evaluated opportunities to use whey or maltodextrin for improving the physical quality of powders in production of white cheese powder. We produced cheese powders with 3 different formulations-control (CON), whey-added (WACP), and maltodextrin-added (MACP)-and determined the effects of formulation on cheese powder quality. Physical quality parameters such as color, densities, reconstitution properties, free fat content, particle morphology, and sensory characteristics were investigated. The different cheese powders were stored for 12 mo at 20°C and we evaluated the effect of storage on powder quality. Addition of maltodextrin to cheese powder formulations significantly improved their physical quality. The densities and reconstitution properties of cheese powder were increased and free fat content was decreased by use of maltodextrin. The MACP particles were spherical with a uniform distribution and larger particle sizes, whereas CON and WACP particles were wrinkled, irregular shaped with deep surface dents, and variable in size. Although caking was observed in scanning electron micrographs after 12 mo of storage, it was not detected by sensory panelists. The color of cheese powders changed very slowly during storage but browning was detected. The results of this study show that it is possible to use maltodextrin or whey in production of white cheese powder to reduce production costs and improve the physical quality of powders.

  8. Molecular characterization of tocopherol biosynthetic genes in sweetpotato that respond to stress and activate the tocopherol production in tobacco.

    PubMed

    Ji, Chang Yoon; Kim, Yun-Hee; Kim, Ho Soo; Ke, Qingbo; Kim, Gun-Woo; Park, Sung-Chul; Lee, Haeng-Soon; Jeong, Jae Cheol; Kwak, Sang-Soo

    2016-09-01

    Tocopherol (vitamin E) is a chloroplast lipid that is presumed to be involved in the plant response to oxidative stress. In this study, we isolated and characterized five tocopherol biosynthetic genes from sweetpotato (Ipomoea batatas [L.] Lam) plants, including genes encoding 4-hydroxyphenylpyruvate dioxygenase (IbHPPD), homogentisate phytyltransferase (IbHPT), 2-methyl-6-phytylbenzoquinol methyltransferase (IbMPBQ MT), tocopherol cyclase (IbTC) and γ-tocopherol methyltransferase (IbTMT). Fluorescence microscope analysis indicated that four proteins localized into the chloroplast, whereas IbHPPD observed in the nuclear. Quantitative RT-PCR analysis revealed that the expression patterns of the five tocopherol biosynthetic genes varied in different plant tissues and under different stress conditions. All five genes were highly expressed in leaf tissues, whereas IbHPPD and IbHPT were highly expressed in the thick roots. The expression patterns of these five genes significantly differed in response to PEG, NaCl and H2O2-mediated oxidative stress. IbHPPD was strongly induced following PEG and H2O2 treatment and IbHPT was strongly induced following PEG treatment, whereas IbMPBQ MT and IbTC were highly expressed following NaCl treatment. Upon infection of the bacterial pathogen Pectobacterium chrysanthemi, the expression of IbHPPD increased sharply in sweetpotato leaves, whereas the expression of the other genes was reduced or unchanged. Additionally, transient expression of the five tocopherol biosynthetic genes in tobacco (Nicotiana bentamiana) leaves resulted in increased transcript levels of the transgenes expressions and tocopherol production. Therefore, our results suggested that the five tocopherol biosynthetic genes of sweetpotato play roles in the stress defense response as transcriptional regulators of the tocopherol production.

  9. WWOX gene and gene product: tumor suppression through specific protein interactions.

    PubMed

    Salah, Zaidoun; Aqeilan, Rami; Huebner, Kay

    2010-02-01

    The WWOX gene, an archetypal fragile gene, encompasses a chromosomal fragile site at 16q23.2, and encodes the approximately 46-kDa Wwox protein, with WW domains that interact with a growing list of interesting proteins. If the function of a protein is defined by the company it keeps, then Wwox is involved in numerous important signal pathways for bone and germ-cell development, cellular and animal growth and death, transcriptional control and suppression of cancer development. Because alterations to genes at fragile sites are exquisitely sensitive to replication stress-induced DNA damage, there has been an ongoing scientific discussion questioning whether such gene expression alterations provide a selective advantage for clonal expansion of neoplastic cells, and a parallel discussion on why important genes would be present at sites that are susceptible to inactivation. We offer some answers through a description of known WWOX functions.

  10. Database of cattle candidate genes and genetic markers for milk production and mastitis

    PubMed Central

    Ogorevc, J; Kunej, T; Razpet, A; Dovc, P

    2009-01-01

    A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3′UTRs of candidate genes. PMID:19508288

  11. Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes

    PubMed Central

    2013-01-01

    Background Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The genomes of actinomycetes revealed that these bacteria have a large number of natural product gene clusters, although many of these are difficult to tie to products in the laboratory. Large scale comparisons of these clusters are difficult to perform due to the presence of highly similar repeated domains in the most common biosynthetic machinery: polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). Results We have used comparative genomics to provide an overview of the genomic features of a set of 102 closed genomes from this important group of bacteria with a focus on natural product biosynthetic genes. We have focused on well-represented genera and determine the occurrence of gene cluster families therein. Conservation of natural product gene clusters within Mycobacterium, Streptomyces and Frankia suggest crucial roles for natural products in the biology of each genus. The abundance of natural product classes is also found to vary greatly between genera, revealing underlying patterns that are not yet understood. Conclusions A large-scale analysis of natural product gene clusters presents a useful foundation for hypothesis formulation that is currently underutilized in the field. Such studies will be increasingly necessary to study the diversity and ecology of natural products as the number of genome sequences available continues to grow. PMID:24020438

  12. Double replacement gene targeting for the production of a series of mouse strains with different prion protein gene alterations

    SciTech Connect

    Moore, R.C.; Redhead, N.J.; Selfridge, J.

    1995-09-01

    We have developed a double replacement gene targeting strategy which enables the production of a series of mouse strains bearing different subtle alterations to endogenous genes. This is a two-step process in which a region of the gene of interest is first replaced with a selectable marker to produce an inactivated allele, which is then re-targeted with a second vector to reconstruct the inactivated allele, concomitantly introducing an engineered mutation. Five independent embryonic stem cell lines have been produced bearing different targeted alterations to the prion protein gene, including one which raises the level of expression. We have constructed mice bearing the codon 101 proline to leucine substitution linked to the human familial prion disease, Gerstmann-Straussler-Scheinker syndrome. We anticipate that this procedure will have applications to the study of human inherited diseases and the development of therapies. 43 refs., 6 figs., 1 tab.

  13. Enhanced heterologous production of desosaminyl macrolides and their hydroxylated derivatives by overexpression of the pikD regulatory gene in Streptomyces venezuelae.

    PubMed

    Jung, Won Seok; Jeong, Soon Jeong; Park, Sung Ryeol; Choi, Cha Yong; Park, Byoung Chul; Park, Je Won; Yoon, Yeo Joon

    2008-04-01

    To elevate the production level of heterologous polyketide in Streptomyces venezuelae, an additional copy of the positive regulatory gene pikD was introduced into the pikromycin (Pik) polyketide synthase (PKS) deletion mutant of S. venezuelae ATCC 15439 expressing tylosin PKS genes. The resulting mutant strain showed enhanced production of both tylactone (TL) and desosaminyl tylactone (DesTL) of 2.7- and 17.1-fold, respectively. The notable increase in DesTL production strongly suggested that PikD upregulates the expression of the desosamine (des) biosynthetic gene cluster. In addition, two hydroxylated forms of DesTL were newly detected from the extract of this mutant. These hydroxylated forms presumably resulted from a PikD-dependent increase in expression of the pikC gene that encodes P450 hydroxylase. Gene expression analysis by reverse transcriptase PCR and bioconversion experiments of 10-deoxymethynolide, narbonolide, and TL into the corresponding desosaminyl macrolides indicated that PikD is a positive regulator of the des and pikC genes, as well as the Pik PKS genes. These results demonstrate the role of PikD as a pathway-specific positive regulator of the entire Pik biosynthetic pathway and its usefulness in the development of a host-vector system for efficient heterologous production of desosaminyl macrolides and novel hydroxylated compounds.

  14. The Effect of a Newly Developed Oat-Banana Fermented Beverage with a Beta-glucan Additive on ldhL Gene Expression in Streptococcus thermophilus TKM3 KKP 2030p.

    PubMed

    Goncerzewicz, Anna; Misiewicz, Anna; Owczarek, Lubomiła; Jasińska, Urszula; Skąpska, Sylwia

    2016-12-01

    The number of people who cannot consume dairy products due to intolerance or allergies to food components is increasing. Consumers are increasingly searching for alternative, nondairy beverages which have an advantageous effect on the body and which stimulate gut microflora. Previous studies have shown that Streptococcus thermophilus TKM3 KKP 2030p can be an efficient starter culture for the fermentation of plant material and can also ensure an acceptable sensory profile and a high number of lactic acid bacteria during 4 week cold storage. The aim of this study was to determine the relative gene expression of the L-lactate dehydrogenase gene (ldhL) in selected strain using the RT qPCR technique at particular time points. The gene expression experiments were conducted in laboratory broth (LABm) and fruit-cereal (OBPromOat) matrix with a beta-glucan additive. Levels of gene relative expression in the selected strain in these two media were correlated with the amount of L-lactate produced. The results showed that the plant matrix stimulated stronger ldhL gene expression in the first 4 h of the experiment (although the synthesis of L-lactate was less than in laboratory broth). This study broadens existing knowledge of the transcriptional mechanisms which arise from the adaptation of the analyzed strain to different habitats during L-lactate synthesis. This could contribute to the development of new alternative food products for people who show intolerance to milk proteins or lactose.

  15. Mobile antibiotic resistance - the spread of genes determining the resistance of bacteria through food products.

    PubMed

    Godziszewska, Jolanta; Guzek, Dominika; Głąbski, Krzysztof; Wierzbicka, Agnieszka

    2016-07-07

    In recent years, more and more antibiotics have become ineffective in the treatment of bacterial nfections. The acquisition of antibiotic resistance by bacteria is associated with circulation of genes in the environment. Determinants of antibiotic resistance may be transferred to pathogenic bacteria. It has been shown that conjugation is one of the key mechanisms responsible for spread of antibiotic resistance genes, which is highly efficient and allows the barrier to restrictions and modifications to be avoided. Some conjugative modules enable the transfer of plasmids even between phylogenetically distant bacterial species. Many scientific reports indicate that food is one of the main reservoirs of these genes. Antibiotic resistance genes have been identified in meat products, milk, fruits and vegetables. The reason for such a wide spread of antibiotic resistance genes is the overuse of antibiotics by breeders of plants and animals, as well as by horizontal gene transfer. It was shown, that resistance determinants located on mobile genetic elements, which are isolated from food products, can easily be transferred to another niche. The antibiotic resistance genes have been in the environment for 30 000 years. Their removal from food products is not possible, but the risks associated with the emergence of multiresistant pathogenic strains are very large. The only option is to control the emergence, selection and spread of these genes. Therefore measures are sought to prevent horizontal transfer of genes. Promising concepts involve the combination of developmental biology, evolution and ecology in the fight against the spread of antibiotic resistance.

  16. Comparative Genomic Analysis of Delftia tsuruhatensis MTQ3 and the Identification of Functional NRPS Genes for Siderophore Production

    PubMed Central

    Guo, Haimeng; Yang, Yanan; Liu, Kai; Xu, Wenfeng; Gao, Jianyong; Duan, Hairong; Du, Binghai

    2016-01-01

    Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production. PMID:27847812

  17. Comparative Genomic Analysis of Delftia tsuruhatensis MTQ3 and the Identification of Functional NRPS Genes for Siderophore Production.

    PubMed

    Guo, Haimeng; Yang, Yanan; Liu, Kai; Xu, Wenfeng; Gao, Jianyong; Duan, Hairong; Du, Binghai; Ding, Yanqin; Wang, Chengqiang

    2016-01-01

    Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.

  18. Use of Staby(®) technology for development and production of DNA vaccines free of antibiotic resistance gene.

    PubMed

    Reschner, Anca; Scohy, Sophie; Vandermeulen, Gaëlle; Daukandt, Marc; Jacques, Céline; Michel, Benjamin; Nauwynck, Hans; Xhonneux, Florence; Préat, Véronique; Vanderplasschen, Alain; Szpirer, Cédric

    2013-10-01

    The appearance of new viruses and the cost of developing certain vaccines require that new vaccination strategies now have to be developed. DNA vaccination seems to be a particularly promising method. For this application, plasmid DNA is injected into the subject (man or animal). This plasmid DNA encodes an antigen that will be expressed by the cells of the subject. In addition to the antigen, the plasmid also encodes a resistance to an antibiotic, which is used during the construction and production steps of the plasmid. However, regulatory agencies (FDA, USDA and EMA) recommend to avoid the use of antibiotics resistance genes. Delphi Genetics developed the Staby(®) technology to replace the antibiotic-resistance gene by a selection system that relies on two bacterial genes. These genes are small in size (approximately 200 to 300 bases each) and consequently encode two small proteins. They are naturally present in the genomes of bacteria and on plasmids. The technology is already used successfully for production of recombinant proteins to achieve higher yields and without the need of antibiotics. In the field of DNA vaccines, we have now the first data validating the innocuousness of this Staby(®) technology for eukaryotic cells and the feasibility of an industrial production of an antibiotic-free DNA vaccine. Moreover, as a proof of concept, mice have been successfully vaccinated with our antibiotic-free DNA vaccine against a deadly disease, pseudorabies (induced by Suid herpesvirus-1).

  19. The sps Gene Products Affect the Germination, Hydrophobicity, and Protein Adsorption of Bacillus subtilis Spores

    PubMed Central

    Cangiano, Giuseppina; Sirec, Teja; Panarella, Cristina; Isticato, Rachele; Baccigalupi, Loredana; De Felice, Maurilio

    2014-01-01

    The multilayered surface of the Bacillus subtilis spore is composed of proteins and glycans. While over 70 different proteins have been identified as surface components, carbohydrates associated with the spore surface have not been characterized in detail yet. Bioinformatic data suggest that the 11 products of the sps operon are involved in the synthesis of polysaccharides present on the spore surface, but an experimental validation is available only for the four distal genes of the operon. Here, we report a transcriptional analysis of the sps operon and a functional study performed by constructing and analyzing two null mutants lacking either all or only the promoter-proximal gene of the operon. Our results show that both sps mutant spores apparently have normal coat and crust but have a small germination defect and are more hydrophobic than wild-type spores. We also show that spores lacking all Sps proteins are highly adhesive and form extensive clumps. In addition, sps mutant spores have an increased efficiency in adsorbing a heterologous enzyme, suggesting that hydrophobic force is a major determinant of spore adsorption and indicating that a deep understanding of the surface properties of the spore is essential for its full development as a surface display platform. PMID:25239894

  20. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle

    PubMed Central

    2013-01-01

    Background Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ −2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed. Results A total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion SNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be

  1. High frequency of additional gene mutations in acute myeloid leukemia with MLL partial tandem duplication: DNMT3A mutation is associated with poor prognosis.

    PubMed

    Kao, Hsiao-Wen; Liang, D Cherng; Kuo, Ming-Chung; Wu, Jin-Hou; Dunn, Po; Wang, Po-Nan; Lin, Tung-Liang; Shih, Yu-Shu; Liang, Sung-Tzu; Lin, Tung-Huei; Lai, Chen-Yu; Lin, Chun-Hui; Shih, Lee-Yung

    2015-10-20

    The mutational profiles of acute myeloid leukemia (AML) with partial tandem duplication of mixed-lineage leukemia gene (MLL-PTD) have not been comprehensively studied. We studied 19 gene mutations for 98 patients with MLL-PTD AML to determine the mutation frequency and clinical correlations. MLL-PTD was screened by reverse-transcriptase PCR and confirmed by real-time quantitative PCR. The mutational analyses were performed with PCR-based assays followed by direct sequencing. Gene mutations of signaling pathways occurred in 63.3% of patients, with FLT3-ITD (44.9%) and FLT3-TKD (13.3%) being the most frequent. 66% of patients had gene mutations involving epigenetic regulation, and DNMT3A (32.7%), IDH2 (18.4%), TET2 (18.4%), and IDH1 (10.2%) mutations were most common. Genes of transcription pathways and tumor suppressors accounted for 23.5% and 10.2% of patients. RUNX1 mutation occurred in 23.5% of patients, while none had NPM1 or double CEBPA mutation. 90.8% of MLL-PTD AML patients had at least one additional gene mutation. Of 55 MLL-PTD AML patients who received standard chemotherapy, age older than 50 years and DNMT3A mutation were associated with inferior outcome. In conclusion, gene mutations involving DNA methylation and activated signaling pathway were common co-existed gene mutations. DNMT3A mutation was a poor prognostic factor in MLL-PTD AML.

  2. A chimeric mouse histone H4 gene containing either an intron or poly(A) addition signal behaves like a basal histone.

    PubMed Central

    Seiler-Tuyns, A; Paterson, B M

    1986-01-01

    We have modified the basic structure of the mouse H4 histone gene by introducing, in one case, the IVS-II of the human beta globin gene in the middle of the H4 coding region and, in the second case, the poly(A) addition signal from either the chicken vimentin gene or the alpha globin gene, displacing the hairpin loop structure in the 3' direction. Constructs were placed into the vector, PSV2gpt, and stably transformed into L cells. Pools of 100-500 independent transformants were analyzed for H4 expression. Even though the intron is processed correctly, the growth regulated expression of the modified gene is lost and the gene is now expressed at a constant basal level. Furthermore, unprocessed transcripts accumulate in the nucleus of Go cells when compared to exponentially growing cultures. Polyadenylated H4 RNA is correctly processed but expressed at reduced levels (30 fold) in a constitutive manner, independent of the growth state of the cell. The altered expression of these chimeric H4 genes compared to the endogenous copy or the transfected wild type gene suggests a structural model to explain the cell cycle independent expression of the basal histones. Images PMID:3024121

  3. Natural and engineered hydroxyectoine production based on the Pseudomonas stutzeri ectABCD-ask gene cluster.

    PubMed

    Seip, Britta; Galinski, Erwin A; Kurz, Matthias

    2011-02-01

    We report on the presence of a functional hydroxyectoine biosynthesis gene cluster, ectABCD-ask, in Pseudomonas stutzeri DSM5190(T) and evaluate the suitability of P. stutzeri DSM5190(T) for hydroxyectoine production. Furthermore, we present information on heterologous de novo production of the compatible solute hydroxyectoine in Escherichia coli. In this host, the P. stutzeri gene cluster remained under the control of its salt-induced native promoters. We also noted the absence of trehalose when hydroxyectoine genes were expressed, as well as a remarkable inhibitory effect of externally applied betaine on hydroxyectoine synthesis. The specific heterologous production rate in E. coli under the conditions employed exceeded that of the natural producer Pseudomonas stutzeri and, for the first time, enabled effective hydroxyectoine production at low salinity (2%), with the added advantage of simple product processing due to the absence of other cosolutes.

  4. Polymorphism of the ovocalyxin-32 gene and its association with egg production traits in the chicken.

    PubMed

    Uemoto, Y; Suzuki, C; Sato, S; Sato, S; Ohtake, T; Sasaki, O; Takahashi, H; Kobayashi, E

    2009-12-01

    We performed candidate gene analysis to identify SNP in the chicken ovocalyxin-32 (OCX-32) gene in the F(2) resource population, to develop a PCR-RFLP method for genotyping and to evaluate the associations of the gene polymorphism with egg production traits. The F(2) resource population-comprising 272 chickens-was obtained by crossing White Leghorn (WL) males and Rhode Island Red (RIR) females. They were measured for egg production traits and used for candidate gene analysis. Among parental individuals of the F(2) population, 2 novel nonsynonymous polymorphisms (c.267T>G and c.494A>C) and 1 known nonsynonymous polymorphism (c.381G>C) in the coding sequences of the chicken OCX-32 gene were detected. The PCR-RFLP method was used for screening the chickens of the F(2) population. In parental populations, genotype c.267T>G and c.494A>C were segregated within WL and RIR breeds, respectively, but genotype c.381G>C was breed-specific SNP between WL and RIR breeds. A total of 4 haplotypes were constructed based on the 3 SNP in parental populations, and there was no recombination between c.267T>G and c.494A>C. There was a significant association (P < 0.05) between the OCX-32 gene SNP and egg production traits, but there was no significant association between the haplotypes of the OCX-32 gene and egg production traits in the F(2) population. In the present study, there was the most significant association between c.381G>C of the OCX-32 gene and rate of egg production. The current study is the first step to confirm the relationship between OCX-32 gene polymorphisms and egg production traits.

  5. Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics

    SciTech Connect

    Hess, Becky M.; Xue, Junfeng; Markillie, Lye Meng; Taylor, Ronald C.; Wiley, H. S.; Ahring, Birgitte K.; Linggi, Bryan E.

    2013-06-19

    The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding the system level regulation and control of the pathway. To address this limitation, we examined Bacillus subtilis grown under multiple conditions and then determined the relationship between altered isoprene production and the pattern of gene expression. We found that terpenoid genes appeared to fall into two distinct subsets with opposing correlations with respect to the amount of isoprene produced. The group whose expression levels positively correlated with isoprene production included dxs, the gene responsible for the commitment step in the pathway, as well as ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. This analysis showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model which accurately predicts production of this secondary metabolite across many simulated environmental conditions.

  6. Significant Change in Marine Plankton Structure and Carbon Production After the Addition of River Water in a Mesocosm Experiment.

    PubMed

    Fouilland, E; Trottet, A; Alves-de-Souza, C; Bonnet, D; Bouvier, T; Bouvy, M; Boyer, S; Guillou, L; Hatey, E; Jing, H; Leboulanger, C; Le Floc'h, E; Liu, H; Mas, S; Mostajir, B; Nouguier, J; Pecqueur, D; Rochelle-Newall, E; Roques, C; Salles, C; Tournoud, M-G; Vasseur, C; Vidussi, F

    2017-03-16

    Rivers are known to be major contributors to eutrophication in marine coastal waters, but little is known on the short-term impact of freshwater surges on the structure and functioning of the marine plankton community. The effect of adding river water, reducing the salinity by 15 and 30%, on an autumn plankton community in a Mediterranean coastal lagoon (Thau Lagoon, France) was determined during a 6-day mesocosm experiment. Adding river water brought not only nutrients but also chlorophyceans that did not survive in the brackish mesocosm waters. The addition of water led to initial increases (days 1-2) in bacterial production as well as increases in the abundances of bacterioplankton and picoeukaryotes. After day 3, the increases were more significant for diatoms and dinoflagellates that were already present in the Thau Lagoon water (mainly Pseudo-nitzschia spp. group delicatissima and Prorocentrum triestinum) and other larger organisms (tintinnids, rotifers). At the same time, the abundances of bacterioplankton, cyanobacteria, and picoeukaryote fell, some nutrients (NH4(+), SiO4(3-)) returned to pre-input levels, and the plankton structure moved from a trophic food web based on secondary production to the accumulation of primary producers in the mesocosms with added river water. Our results also show that, after freshwater inputs, there is rapid emergence of plankton species that are potentially harmful to living organisms. This suggests that flash flood events may lead to sanitary issues, other than pathogens, in exploited marine areas.

  7. Photo-oxidation of 6-thioguanine by UVA: the formation of addition products with low molecular weight thiol compounds.

    PubMed

    Ren, Xiaolin; Xu, Yao-Zhong; Karran, Peter

    2010-01-01

    The thiopurine, 6-thioguanine (6-TG) is present in the DNA of patients treated with the immunosuppressant and anticancer drugs azathioprine or mercaptopurine. The skin of these patients is selectively sensitive to UVA radiation-which comprises >90% of the UV light in incident sunlight-and they suffer high rates of skin cancer. UVA irradiation of DNA 6-TG produces DNA lesions that may contribute to the development of cancer. Antioxidants can protect 6-TG against UVA but 6-TG oxidation products may undergo further reactions. We characterize some of these reactions and show that addition products are formed between UVA-irradiated 6-TG and N-acetylcysteine and other low molecular weight thiol compounds including β-mercaptoethanol, cysteine and the cysteine-containing tripeptide glutathione (GSH). GSH is also adducted to 6-TG-containing oligodeoxynucleotides in an oxygen- and UVA-dependent nucleophilic displacement reaction that involves an intermediate oxidized 6-TG, guanine sulfonate (G(SO3) ). These photochemical reactions of 6-TG, particularly the formation of a covalent oligodeoxynucleotide-GSH complex, suggest that crosslinking of proteins or low molecular weight thiol compounds to DNA may be a previously unrecognized hazard in sunlight-exposed cells of thiopurine-treated patients.

  8. Tribological performance of Mg/Al/Ce layered double hydroxides nanoparticles and intercalated products as lubricant additives

    NASA Astrophysics Data System (ADS)

    Li, Shuo; Qin, Haojing; Zuo, Ranfang; Bai, Zhimin

    2015-10-01

    Mg/Al/Ce ternary layered double hydroxides (LDHs) were synthesized via coprecipitation and intercalated by succinic acid and lauric acid through ion exchange method respectively. The LDHs products were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM) and Fourier transform infrared (FT-IR). Tribological properties of LDHs as lubricant additives were evaluated by four-ball friction and air compressor test. The results indicated that Mg/Al/Ce LDHs were prepared successfully with Ce/Al molar ratio of 0.05 and crystallization temperature of 140 °C. The interlayer spacing of LDHs precursor was expanded by succinic acid and lauric acid to 8.838 and 17.519 Å respectively. All the three LDHs products can reduce friction and wear of engine lubricating oil in the tests. LDHs intercalated with lauric acid showed best tribological performance among them which was attributed to sliding each other between laminates, good dispersibility in oil medium and a protective tribofilm formed on the worn surface.

  9. Effect of nutrient supplements addition on ethanol production from cheese whey using Candida psuedotropicalis under batch condition

    SciTech Connect

    Ghaly, A.E.; El-Taweel, A.A.

    1995-05-01

    Candida psuedotropicalis ATCC 8619 was selected among nine strains of lactose fermenting yeast for the production of ethanol from cheese whey. The effects of three nutrients (ammonium sulfate (NH{sub 4}){sub 2}SO{sub 4}, dipotassium hydrogen phosphate K{sub 2}HPO{sub 4}, yeast extract, and combination of them) on the ethanol yield from cheese whey were investigated. The results indicated that no addition of nutrient supplement is necessary to achieve complete lactose utilization during the cheese whey ethanol fermentation. However, addition of a small concentration (0.005% w/v) of these supplements reduced the lag period and the total fermentation time and increased the specific growth rate of the yeast. Higher concentrations (0.01 and 0.015% w/v) of ammonium sulfate and dipotassium hydrogen phosphate inhibited the cell growth rate of the yeast. The highest ethanol (21.7% g/L) was achieved using yeast extract at a concentration of 0.01% w/v, given a conversion efficiency of 98.3%. No indication of alcohol inhibition was observed in this study. 60 refs., 9 figs., 3 tabs.

  10. Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans

    PubMed Central

    Alink, Gerrit M.; Scherjon, Fulco; MacDonald, Katharine; Smith, Alison C.; Nijveen, Harm; Roebroeks, Wil

    2016-01-01

    Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions. PMID:27655273

  11. Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans.

    PubMed

    Aarts, Jac M M J G; Alink, Gerrit M; Scherjon, Fulco; MacDonald, Katharine; Smith, Alison C; Nijveen, Harm; Roebroeks, Wil

    Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions.

  12. Knockout targeting of the Drosophila nap1 gene and examination of DNA repair tracts in the recombination products.

    PubMed Central

    Lankenau, Susanne; Barnickel, Thorsten; Marhold, Joachim; Lyko, Frank; Mechler, Bernard M; Lankenau, Dirk-Henner

    2003-01-01

    We used ends-in gene targeting to generate knockout mutations of the nucleosome assembly protein 1 (Nap1) gene in Drosophila melanogaster. Three independent targeted null-knockout mutations were produced. No wild-type NAP1 protein could be detected in protein extracts. Homozygous Nap1(KO) knockout flies were either embryonic lethal or poorly viable adult escapers. Three additional targeted recombination products were viable. To gain insight into the underlying molecular processes we examined conversion tracts in the recombination products. In nearly all cases the I-SceI endonuclease site of the donor vector was replaced by the wild-type Nap1 sequence. This indicated exonuclease processing at the site of the double-strand break (DSB), followed by replicative repair at donor-target junctions. The targeting products are best interpreted either by the classical DSB repair model or by the break-induced recombination (BIR) model. Synthesis-dependent strand annealing (SDSA), which is another important recombinational repair pathway in the germline, does not explain ends-in targeting products. We conclude that this example of gene targeting at the Nap1 locus provides added support for the efficiency of this method and its usefulness in targeting any arbitrary locus in the Drosophila genome. PMID:12618400

  13. Antibacterial Discovery and Development: From Gene to Product and Back

    PubMed Central

    Fedorenko, Victor; Genilloud, Olga; Horbal, Liliya; Marcone, Giorgia Letizia; Marinelli, Flavia; Paitan, Yossi; Ron, Eliora Z.

    2015-01-01

    Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement. PMID:26339625

  14. Association of single nucleotide polymorphism in melatonin receptor 1A gene with egg production traits in Yangzhou geese.

    PubMed

    Alsiddig, M A; Yu, S G; Pan, Z X; Widaa, H; Badri, T M; Chen, J; Liu, H L

    2017-04-01

    In the present study the melatonin receptor 1A gene (MTNR1A) was proposed to be a candidate gene for egg production in Yangzhou geese. A total of 210 goose blood samples were collected to investigate the association of the MTNR1A gene with the number of eggs produced. Using a direct sequencing method, a single nucleotide polymorphism (SNP; g.177G>C) was detected in the 5' regulatory region of the MTNR1A gene (Genbank ss1985399687). Two alleles (G and C) and three genotypes were identified. Association analysis results showed that the g.177G>C SNP significantly affected the level of egg production within a 34-week egg-laying period (P < 0.05). Furthermore, the geese with the GG genotype produced significantly more eggs compared to the geese with the CC genotype. Quantitative real-time PCR analysis showed that the MTNR1A gene was highly expressed in small intestine, granulosa cell and ovary compared to other examined tissues. In addition, the mRNA expression level of MTNR1A in ovary indicated that significantly higher expression levels were recorded for geese with the GG genotype compared to those with the CC genotype. Moreover, a luciferase reporter assay showed that the CC genotype had significantly lower promoter activity than did GG. These results suggest that the identified SNP in the MTNR1A gene may influence the number of eggs produced and mRNA expression levels in Yangzhou geese and could be considered as a useful molecular marker in goose selection and improvement, especially for egg production.

  15. Exploring the role of sigma factor gene expression on production by Corynebacterium glutamicum: sigma factor H and FMN as example

    PubMed Central

    Taniguchi, Hironori; Wendisch, Volker F.

    2015-01-01

    Bacteria are known to cope with environmental changes by using alternative sigma factors binding to RNA polymerase core enzyme. Sigma factor is one of the targets to modify transcription regulation in bacteria and to influence production capacities. In this study, the effect of overexpressing each annotated sigma factor gene in Corynebacterium glutamicum WT was assayed using an IPTG inducible plasmid system and different IPTG concentrations. It was revealed that growth was severely decreased when sigD or sigH were overexpressed with IPTG concentrations higher than 50 μM. Overexpression of sigH led to an obvious phenotypic change, a yellow-colored supernatant. High performance liquid chromatography analysis revealed that riboflavin was excreted to the medium when sigH was overexpressed and DNA microarray analysis confirmed increased expression of riboflavin biosynthesis genes. In addition, genes for enzymes related to the pentose phosphate pathway and for enzymes dependent on flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), or NADPH as cofactor were upregulated when sigH was overexpressed. To test if sigH overexpression can be exploited for production of riboflavin-derived FMN or FAD, the endogenous gene for bifunctional riboflavin kinase/FMN adenyltransferase was co-expressed with sigH from a plasmid. Balanced expression of sigH and ribF improved accumulation of riboflavin (19.8 ± 0.3 μM) and allowed for its conversion to FMN (33.1 ± 1.8 μM) in the supernatant. While a proof-of-concept was reached, conversion was not complete and titers were not high. This study revealed that inducible and gradable overexpression of sigma factor genes is an interesting approach to switch gene expression profiles and to discover untapped potential of bacteria for chemical production. PMID:26257719

  16. Exploring the role of sigma factor gene expression on production by Corynebacterium glutamicum: sigma factor H and FMN as example.

    PubMed

    Taniguchi, Hironori; Wendisch, Volker F

    2015-01-01

    Bacteria are known to cope with environmental changes by using alternative sigma factors binding to RNA polymerase core enzyme. Sigma factor is one of the targets to modify transcription regulation in bacteria and to influence production capacities. In this study, the effect of overexpressing each annotated sigma factor gene in Corynebacterium glutamicum WT was assayed using an IPTG inducible plasmid system and different IPTG concentrations. It was revealed that growth was severely decreased when sigD or sigH were overexpressed with IPTG concentrations higher than 50 μM. Overexpression of sigH led to an obvious phenotypic change, a yellow-colored supernatant. High performance liquid chromatography analysis revealed that riboflavin was excreted to the medium when sigH was overexpressed and DNA microarray analysis confirmed increased expression of riboflavin biosynthesis genes. In addition, genes for enzymes related to the pentose phosphate pathway and for enzymes dependent on flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), or NADPH as cofactor were upregulated when sigH was overexpressed. To test if sigH overexpression can be exploited for production of riboflavin-derived FMN or FAD, the endogenous gene for bifunctional riboflavin kinase/FMN adenyltransferase was co-expressed with sigH from a plasmid. Balanced expression of sigH and ribF improved accumulation of riboflavin (19.8 ± 0.3 μM) and allowed for its conversion to FMN (33.1 ± 1.8 μM) in the supernatant. While a proof-of-concept was reached, conversion was not complete and titers were not high. This study revealed that inducible and gradable overexpression of sigma factor genes is an interesting approach to switch gene expression profiles and to discover untapped potential of bacteria for chemical production.

  17. Nonlinear biosynthetic gene cluster dose effect on penicillin production by Penicillium chrysogenum.

    PubMed

    Nijland, Jeroen G; Ebbendorf, Bjorg; Woszczynska, Marta; Boer, Rémon; Bovenberg, Roel A L; Driessen, Arnold J M

    2010-11-01

    Industrial penicillin production levels by the filamentous fungus Penicillium chrysogenum increased dramatically by classical strain improvement. High-yielding strains contain multiple copies of the penicillin biosynthetic gene cluster that encodes three key enzymes of the β-lactam biosynthetic pathway. We have analyzed the gene cluster dose effect on penicillin production using the high-yielding P. chrysogenum strain DS17690 that was cured from its native clusters. The amount of penicillin V produced increased with the penicillin biosynthetic gene cluster number but was saturated at high copy numbers. Likewise, transcript levels of the biosynthetic genes pcbAB [δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase], pcbC (isopenicillin N synthase), and penDE (acyltransferase) correlated with the cluster copy number. Remarkably, the protein level of acyltransferase, which localizes to peroxisomes, was saturated already at low cluster copy numbers. At higher copy numbers, intracellular levels of isopenicillin N increased, suggesting that the acyltransferase reaction presents a limiting step at a high gene dose. Since the number and appearance of the peroxisomes did not change significantly with the gene cluster copy number, we conclude that the acyltransferase activity is limiting for penicillin biosynthesis at high biosynthetic gene cluster copy numbers. These results suggest that at a high penicillin production level, productivity is limited by the peroxisomal acyltransferase import activity and/or the availability of coenzyme A (CoA)-activated side chains.

  18. Id-1 and Id-2 genes and products as markers of epithelial cancer

    DOEpatents

    Desprez, Pierre-Yves; Campisi, Judith

    2008-09-30

    A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

  19. Id-1 and Id-2 genes and products as markers of epithelial cancer

    DOEpatents

    Desprez, Pierre-Yves [El Cerrito, CA; Campisi, Judith [Berkeley, CA

    2011-10-04

    A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

  20. B-cell translocation gene 2 promotes hepatic hepcidin production via induction of Yin Yang 1.

    PubMed

    Lee, Sung-Eun; Hwang, Seung-Lark; Jang, Won-Gu; Chang, Hyeun Wook; Kim, Yong Deuk

    2015-05-15

    Hepcidin is a peptide hormone secreted in the liver and plays a key role in maintaining iron homeostasis. Here, we demonstrate that B-cell translocation gene 2 (BTG2) is a key player in hepatic hepcidin regulation via induction of Yin Yang 1 (YY1). Hepatic hepcidin gene expression significantly enhanced by fasting states and glucagon exposure led to induction of gluconeogenic gene expression, and elevated serum hepcidin production in mice. Notably, overexpression of BTG2 using adenoviral system (Ad-BTG2) significantly elevated serum hepcidin levels via a significant induction of YY1 gene transcription. Immunoprecipitation studies demonstrated that BTG2 physically interacted with YY1 and recruited on the hepcidin gene promoter. Finally, ablation of hepatic BTG2 gene by gene silencing markedly attenuated the elevation of serum hepcidin production along with YY1 and hepcidin mRNA expression in fasting state. Likewise, forskolin (FSK)-stimulated hepcidin promoter activity was dramatically disrupted by endogenous BTG2 knockdown. Overall, our current study provides a novel molecular mechanism of BTG2-mediated induction of hepcidin gene expression, thereby contributing to a better understanding of the hepatic hepcidin production involved in iron homeostasis.

  1. Dynamics and modeling of temperature-regulated gene product expression in recombinant yeast fermentation.

    PubMed

    Cheng, C; Yang, S T

    1996-06-20

    The dynamic response of temperature-regulated gene expression in the recombinant yeast Saccharomyces cerevisiae, strain XK1-C2 carrying plasmid pSXR125, to temperature changes during fed-batch and continuous (chemostat) cultures was studied. The production of the gene product, beta-galactosidase, in the yeast cell is sensitive to the growth temperature. Gene expression of this product was fully turned on or off by temperature shifts between 24 and 30 degrees C. However, the response for gene turn-on and turn-off in this recombinant yeast was slow, requiring from several hours to over 10 h to fully appear. The continuous reactor took 30-60 h after the temperature shift to reach a new steady state. A dynamic process model was developed to simulate the reactor and cell responses to temperature shift. A first-order model was used to account for the effect of dilution rate on the change of protein concentration in the chemostat. It was found that cell response in gene expression to temperature shift followed first-order plus dead-time dynamics. Also, the response time for gene expression to temperature shift varied with specific growth rate or dilution rate of the continuous reactor. In general, the response was slower at a higher dilution rate and for gene turn-on than for gene turn-off.

  2. Lovastatin in Aspergillus terreus: Fermented Rice Straw Extracts Interferes with Methane Production and Gene Expression in Methanobrevibacter smithii

    PubMed Central

    Liang, Juan Boo; Ho, Yin Wan; Mohamad, Rosfarizan; Goh, Yong Meng; Shokryazdan, Parisa; Chin, James

    2013-01-01

    Lovastatin, a natural byproduct of some fungi, is able to inhibit HMG-CoA (3-hydroxy-3methyl glutaryl CoA) reductase. This is a key enzyme involved in isoprenoid synthesis and essential for cell membrane formation in methanogenic Archaea. In this paper, experiments were designed to test the hypothesis that lovastatin secreted by Aspergillus terreus in fermented rice straw extracts (FRSE) can inhibit growth and CH4 production in Methanobrevibacter smithii (a test methanogen). By HPLC analysis, 75% of the total lovastatin in FRSE was in the active hydroxyacid form, and in vitro studies confirmed that this had a stronger effect in reducing both growth and CH4 production in M. smithii compared to commercial lovastatin. Transmission electron micrographs revealed distorted morphological divisions of lovastatin- and FRSE-treated M. smithii cells, supporting its role in blocking normal cell membrane synthesis. Real-time PCR confirmed that both commercial lovastatin and FRSE increased (P < 0.01) the expression of HMG-CoA reductase gene (hmg). In addition, expressions of other gene transcripts in M. smithii. with a key involvement in methanogenesis were also affected. Experimental confirmation that CH4 production is inhibited by lovastatin in A. terreus-fermented rice straw paves the way for its evaluation as a feed additive for mitigating CH4 production in ruminants. PMID:23710454

  3. Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

    NASA Astrophysics Data System (ADS)

    Bailey, Andy M.; Alberti, Fabrizio; Kilaru, Sreedhar; Collins, Catherine M.; de Mattos-Shipley, Kate; Hartley, Amanda J.; Hayes, Patrick; Griffin, Alison; Lazarus, Colin M.; Cox, Russell J.; Willis, Christine L.; O’Dwyer, Karen; Spence, David W.; Foster, Gary D.

    2016-05-01

    Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi.

  4. Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

    PubMed Central

    Bailey, Andy M.; Alberti, Fabrizio; Kilaru, Sreedhar; Collins, Catherine M.; de Mattos-Shipley, Kate; Hartley, Amanda J.; Hayes, Patrick; Griffin, Alison; Lazarus, Colin M.; Cox, Russell J.; Willis, Christine L.; O’Dwyer, Karen; Spence, David W.; Foster, Gary D.

    2016-01-01

    Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi. PMID:27143514

  5. High Polyhydroxybutyrate Production in Pseudomonas extremaustralis Is Associated with Differential Expression of Horizontally Acquired and Core Genome Polyhydroxyalkanoate Synthase Genes

    PubMed Central

    Catone, Mariela V.; Ruiz, Jimena A.; Castellanos, Mildred; Segura, Daniel; Espin, Guadalupe; López, Nancy I.

    2014-01-01

    Pseudomonas extremaustralis produces mainly polyhydroxybutyrate (PHB), a short chain length polyhydroxyalkanoate (sclPHA) infrequently found in Pseudomonas species. Previous studies with this strain demonstrated that PHB genes are located in a genomic island. In this work, the analysis of the genome of P. extremaustralis revealed the presence of another PHB cluster phbFPX, with high similarity to genes belonging to Burkholderiales, and also a cluster, phaC1ZC2D, coding for medium chain length PHA production (mclPHA). All mclPHA genes showed high similarity to genes from Pseudomonas species and interestingly, this cluster also showed a natural insertion of seven ORFs not related to mclPHA metabolism. Besides PHB, P. extremaustralis is able to produce mclPHA although in minor amounts. Complementation analysis demonstrated that both mclPHA synthases, PhaC1 and PhaC2, were functional. RT-qPCR analysis showed different levels of expression for the PHB synthase, phbC, and the mclPHA synthases. The expression level of phbC, was significantly higher than the obtained for phaC1 and phaC2, in late exponential phase cultures. The analysis of the proteins bound to the PHA granules showed the presence of PhbC and PhaC1, whilst PhaC2 could not be detected. In addition, two phasin like proteins (PhbP and PhaI) associated with the production of scl and mcl PHAs, respectively, were detected. The results of this work show the high efficiency of a foreign gene (phbC) in comparison with the mclPHA core genome genes (phaC1 and phaC2) indicating that the ability of P. extremaustralis to produce high amounts of PHB could be explained by the different expression levels of the genes encoding the scl and mcl PHA synthases. PMID:24887088

  6. [Quality control of gene therapy products: approach of the French Agency for the Safety of Health Products].

    PubMed

    Chenivesse, Xavier; Ridoux, Valérie; Tissier, Marie-Hélène

    2003-04-01

    Gene therapy is a new therapeutic strategy which can constitute in some diseases a true alternative or a complement to the "classical treatments". Regarding the innovative features, the complexity and the extreme diversity of the gene therapy products (naked DNA, synthetic vectors, viral vectors, genetically modified cells), these new products presently in clinical trials have to be precisely evaluated and controlled for their medicine quality as well as their biological origin and/or their specific characteristics of genetically modified organisms. The French Agency for the Safety of Health Products engaged an in-depth scientific review concerning the control of this very heterogeneous class of potential therapeutics through the creation of a working group. The objectives of this group were to determine the testings to be performed by a national authority for each type of gene therapy products and to select the appropriate techniques or methods to be developed. Controls considered as essential are listed and include the verification of the identity, the purity, the transfer and expression efficiency as well as the microbiological and viral safety of the products. This implies the development of diverse techniques of molecular biology, cellular biology, physico-chemistry, animal testing, histology and microbiology. Finally, in order to define the basis of testings of these emerging products, the marketing of which should be effective for some of them in the next years, it appears extremely important to harmonize the quality, efficiency and safety criteria, to develop specific references and standards and to create specific guidelines for the control of gene therapy products.

  7. Characterization of a beta-tubulin gene and a beta-tubulin gene products of Brugia pahangi.

    PubMed

    Guénette, S; Prichard, R K; Klein, R D; Matlashewski, G

    1991-02-01

    A genomic clone containing a beta-tubulin gene from the parasitic nematode Brugia pahangi was isolated. This gene was sequenced to determine its size, structural organization, and corresponding primary amino acid sequence. The coding sequence of the beta-tubulin gene spans 3.8 kb, is organized into 9 exons and expresses an mNRA of 1.8 kb which codes for a protein of 448 amino acids. The predicted beta-tubulin amino acid sequence is 89%, 94%, 90% and 88% identical to the chicken beta 2, and the Caenorhabditis elegans ben-1, tub-1 and mec-7 gene products, respectively. Southern hybridization analyses demonstrated that there is only one copy of this gene isotype but that other distinct beta-tubulin genes may exist in the Brugia pahangi genome. A nematode specific antipeptide rabbit antiserum raised against the predicted amino acid sequence of the extreme carboxy-terminal region of the B. pahangi beta-tubulin was used to identify beta-tubulin isoforms in adult nematodes and microfilariae. Isoforms detected by this nematode-specific antipeptide antiserum were identical in both adult worms and microfilariae and did not differ from the isoform patterns detected by a monoclonal antibody recognizing a conserved beta-tubulin epitope. This suggests that this carboxy-terminal peptide is highly represented in the beta-tubulin isoforms of B. pahangi.

  8. Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16

    SciTech Connect

    Brigham, CJ; Speth, DR; Rha, C; Sinskey, AJ

    2012-10-22

    Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but in only a few instances has PHB production been explored in relation to other cellular processes. We examined the global gene expression of wild-type R. eutropha throughout the PHB cycle: growth on fructose, PHB production using fructose following ammonium depletion, and PHB utilization in the absence of exogenous carbon after ammonium was resupplied. Our results confirm or lend support to previously reported results regarding the expression of PHB-related genes and enzymes. Additionally, genes for many different cellular processes, such as DNA replication, cell division, and translation, are selectively repressed during PHB production. In contrast, the expression levels of genes under the control of the alternative sigma factor sigma(54) increase sharply during PHB production and are repressed again during PHB utilization. Global gene regulation during PHB production is strongly reminiscent of the gene expression pattern observed during the stringent response in other species. Furthermore, a ppGpp synthase deletion mutant did not show an accumulation of PHB, and the chemical induction of the stringent response with DL-norvaline caused an increased accumulation of PHB in the presence of ammonium. These results indicate that the stringent response is required for PHB accumulation in R. eutropha, helping to elucidate a thus-far-unknown physiological basis for this process.

  9. Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics

    PubMed Central

    Hess, Becky M.; Xue, Junfeng; Markillie, Lye Meng; Taylor, Ronald C.; Wiley, H. Steven; Ahring, Birgitte K.; Linggi, Bryan

    2013-01-01

    The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes, as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding system level regulation and control of the pathway. To address these limitations, we examined Bacillus subtilis grown under multiple conditions and determined the relationship between altered isoprene production and gene expression patterns. We found that with respect to the amount of isoprene produced, terpenoid genes fall into two distinct subsets with opposing correlations. The group whose expression levels positively correlated with isoprene production included dxs, which is responsible for the commitment step in the pathway, ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome-wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. These analyses showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model that accurately predicts production of this secondary metabolite across many simulated environmental conditions. PMID:23840410

  10. Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics.

    PubMed

    Hess, Becky M; Xue, Junfeng; Markillie, Lye Meng; Taylor, Ronald C; Wiley, H Steven; Ahring, Birgitte K; Linggi, Bryan

    2013-01-01

    The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes, as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding system level regulation and control of the pathway. To address these limitations, we examined Bacillus subtilis grown under multiple conditions and determined the relationship between altered isoprene production and gene expression patterns. We found that with respect to the amount of isoprene produced, terpenoid genes fall into two distinct subsets with opposing correlations. The group whose expression levels positively correlated with isoprene production included dxs, which is responsible for the commitment step in the pathway, ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome-wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. These analyses showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model that accurately predicts production of this secondary metabolite across many simulated environmental conditions.

  11. Effects of Lupenone, Lupeol, and Taraxerol Derived from Adenophora triphylla on the Gene Expression and Production of Airway MUC5AC Mucin

    PubMed Central

    Yoon, Yong Pill; Lee, Hyun Jae; Lee, Dong-Ung; Lee, Sang Kook; Hong, Jang-Hee

    2015-01-01

    Background Adenophora triphylla var. japonica is empirically used for controlling airway inflammatory diseases in folk medicine. We evaluated the gene expression and production of mucin from airway epithelial cells in response to lupenone, lupeol and taraxerol derived from Adenophora triphylla var. japonica. Methods Confluent NCI-H292 cells were pretreated with lupenone, lupeol or taraxerol for 30 minutes and then stimulated with tumor necrosis factor α (TNF-α) for 24 hours. The MUC5AC mucin gene expression and production were measured by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Additionally, we examined whether lupenone, lupeol or taraxerol affects MUC5AC mucin production induced by epidermal growth factor (EGF) and phorbol 12-myristate 13-acetate (PMA), the other 2 stimulators of airway mucin production. Results Lupenone, lupeol, and taraxerol inhibited the gene expression and production of MUC5AC mucin induced by TNF-α from NCI-H292 cells, respectively. The 3 compounds inhibited the EGF or PMA-induced production of MUC5AC mucin in NCI-H292 cells. Conclusion These results indicated that lupenone, lupeol and taraxerol derived from Adenophora triphylla var. japonica regulates the production and gene expression of mucin, by directly acting on airway epithelial cells. In addition, the results partly explain the mechanism of of Adenophora triphylla var. japonica as a traditional remedy for diverse inflammatory pulmonary diseases. PMID:26175774

  12. Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes.

    PubMed

    Fang, J; Cai, C; Wang, Q; Lin, P; Zhao, Z; Cheng, F

    2017-03-01

    Massive cancer genomics data have facilitated the rapid revolution of a novel oncology drug discovery paradigm through targeting clinically relevant driver genes or mutations for the development of precision oncology. Natural products with polypharmacological profiles have been demonstrated as promising agents for the development of novel cancer therapies. In this study, we developed an integrated systems pharmacology framework that facilitated identifying potential natural products that target mutated genes across 15 cancer types or subtypes in the realm of precision medicine. High performance was achieved for our systems pharmacology framework. In case studies, we computationally identified novel anticancer indications for several US Food and Drug Administration-approved or clinically investigational natural products (e.g., resveratrol, quercetin, genistein, and fisetin) through targeting significantly mutated genes in multiple cancer types. In summary, this study provides a powerful tool for the development of molecularly targeted cancer therapies through targeting the clinically actionable alterations by exploiting the systems pharmacology of natural products.

  13. Systems Pharmacology‐Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes

    PubMed Central

    Fang, J; Cai, C; Wang, Q; Lin, P

    2017-01-01

    Massive cancer genomics data have facilitated the rapid revolution of a novel oncology drug discovery paradigm through targeting clinically relevant driver genes or mutations for the development of precision oncology. Natural products with polypharmacological profiles have been demonstrated as promising agents for the development of novel cancer therapies. In this study, we developed an integrated systems pharmacology framework that facilitated identifying potential natural products that target mutated genes across 15 cancer types or subtypes in the realm of precision medicine. High performance was achieved for our systems pharmacology framework. In case studies, we computationally identified novel anticancer indications for several US Food and Drug Administration‐approved or clinically investigational natural products (e.g., resveratrol, quercetin, genistein, and fisetin) through targeting significantly mutated genes in multiple cancer types. In summary, this study provides a powerful tool for the development of molecularly targeted cancer therapies through targeting the clinically actionable alterations by exploiting the systems pharmacology of natural products. PMID:28294568

  14. Alphavirus vectors for vaccine production and gene therapy.

    PubMed

    Lundstrom, Kenneth

    2003-06-01

    Alphavirus vectors demonstrate high expression of heterologous proteins in a broad range of host cells. Replication-deficient as well as replication-competent variants exist. Systemic delivery of many viral antigens has elicited strong antibody responses in immunized mice and primates, and protection against challenges with lethal viruses was obtained. Similarly, prophylactic vaccination was established against tumor challenges. Attention has been paid to the engineering of improved targeting to immunologically active cells, such as dendritic cells. In the area of gene therapy, intratumoral injections of alphavirus vectors have resulted in potentially promising tumor rejection. Moreover, encapsulation of alphavirus particles into liposomes demonstrated efficient tumor targeting in mice with severe combined immunodeficiency, which permitted the initiation of clinical trials for patients with advanced kidney carcinoma and melanoma.

  15. CONVECTION-ENHANCED DELIVERY AND SYSTEMIC MANNITOL INCREASE GENE PRODUCT DISTRIBUTION OF AAV VECTORS 5, 8, AND 9 AND INCREASE GENE PRODUCT IN THE ADULT MOUSE BRAIN

    PubMed Central

    Carty, Nikisha; Lee, Daniel; Dickey, Chad; Ceballos-Diaz, Carolina; Jansen-West, Karen; Golde, Todd E.; Gordon, Marcia N.; Morgan, Dave; Nash, Kevin

    2010-01-01

    The use of recombinant adeno-associated viral (rAAV) vectors as a means of gene delivery to the central nervous system has emerged as a potentially viable method for the treatment of several types of degenerative brain diseases. However, a limitation of typical intracranial injections into the adult brain parenchyma is the relatively restricted distribution of the delivered gene to large brain regions such as the cortex, presumably due to confined dispersion of the injected particles. Optimizing the administration techniques to maximize gene distribution and gene expression is an important step in developing gene therapy studies. Here, we have found additive increases in distribution when 3 methods to increase brain distribution of rAAV were combined. The convection enhanced delivery (CED) method with the step-design cannula was used to deliver rAAV vector serotypes 5, 8 and 9 encoding GFP into the hippocampus of the mouse brain. While the CED method improved distribution of all 3 serotypes, the combination of rAAV9 and CED was particularly effective. Systemic mannitol administration, which reduces intracranial pressure, also further expanded distribution of GFP expression, in particular, increased expression on the contralateral hippocampi. These data suggest that combining advanced injection techniques with newer rAAV serotypes greatly improves viral vector distribution, which could have significant benefits for implementation of gene therapy strategies. PMID:20951738

  16. Detection of rice tungro bacilliform virus gene products in vivo.

    PubMed

    Hay, J; Grieco, F; Druka, A; Pinner, M; Lee, S C; Hull, R

    1994-12-01

    To study the products of the open reading frames (ORFs) of rice tungro bacilliform virus in rice plants the sequences containing ORFs I (encoding a 24-kDa protein, P24) and IV (P46) and the protease and polymerase (reverse transcriptase+RNaseH) domains of ORF III were cloned into a pGEX expression vector. The proteins, which were C-terminal fusions to glutathione S-transferase, were expressed in Escherichia coli and antisera were raised against them which, together with an antiserum against virus particles, was used to probe blots of proteins from infected and uninoculated plants and from virus preparations. The P24 antiserum detected virus-specific proteins of 74, 60, and 52 kDa, which are much bigger than expected. These proteins were found in virus preparations and immunogold labeling suggested that they might be internal in the particles. Virus-specific proteins of 33, 37, 62, and > 150 kDa were revealed by antiserum to virus particles. The antiserum to the protease revealed proteins of 13.5, 37, and 68 kDa both in extracts from infected plants and in purified virus preparations. This antiserum decorated intact virus particles as did the particle antiserum. The polymerase domain antiserum reacted with products of 56, 65, and 68 kDa in extracts from infected plants but not in virus particles. The antiserum to the ORF IV product did not detect any bands in either infected plant extracts or virus preparations. The significance of these products is discussed.

  17. Direct comparison between genomic constitution and flavonoid contents in Allium multiple alien addition lines reveals chromosomal locations of genes related to biosynthesis from dihydrokaempferol to quercetin glucosides in scaly leaf of shallot (Allium cepa L.).

    PubMed

    Masuzaki, S; Shigyo, M; Yamauchi, N

    2006-02-01

    The extrachromosome 5A of shallot (Allium cepa L., genomes AA) has an important role in flavonoid biosynthesis in the scaly leaf of Allium fistulosum-shallot monosomic addition lines (FF+nA). This study deals with the production and biochemical characterisation of A. fistulosum-shallot multiple alien addition lines carrying at least 5A to determine the chromosomal locations of genes for quercetin formation. The multiple alien additions were selected from the crossing between allotriploid FFA (female symbol) and A. fistulosum (male symbol). The 113 plants obtained from this cross were analysed by a chromosome 5A-specific PGI isozyme marker of shallot. Thirty plants were preliminarily selected for an alien addition carrying 5A. The chromosome numbers of the 30 plants varied from 18 to 23. The other extrachromosomes in 19 plants were completely identified by using seven other chromosome markers of shallot. High-performance liquid chromatography analyses of the 19 multiple additions were conducted to identify the flavonoid compounds produced in the scaly leaves. Direct comparisons between the chromosomal constitution and the flavonoid contents of the multiple alien additions revealed that a flavonoid 3'-hydroxylase (F3'H) gene for the synthesis of quercetin from kaempferol was located on 7A and that an anonymous gene involved in the glucosidation of quercetin was on 3A or 4A. As a result of supplemental SCAR analyses by using genomic DNAs from two complete sets of A. fistulosum-shallot monosomic additions, we have assigned F3'H to 7A and flavonol synthase to 4A.

  18. Effects of dust additions on phytoplankton growth and DMS production in high CO2 northeast Pacific HNLC waters

    NASA Astrophysics Data System (ADS)

    Mélançon, J.; Levasseur, M.; Lizotte, M.; Scarratt, M.; Tremblay, J.-É.; Tortell, P.; Yang, G.-P.; Shi, G.-Y.; Gao, H.-W.; Semeniuk, D. M.; Robert, M.; Arychuk, M.; Johnson, K.; Sutherland, N.; Davelaar, M.; Nemcek, N.; Peña, A.; Richardson, W.

    2015-08-01

    Ocean acidification (OA) is likely to have an effect on the fertilizing potential of desert dust in high-nutrient, low-chlorophyll oceanic regions, either by modifying Fe speciation and bioavailability, or by altering phytoplankton Fe requirements and acquisition. To address this issue, short incubations (4 days) of northeast subarctic Pacific waters enriched with either FeSO4 or dust, and set at pH 8.0 (in situ) and 7.8 were conducted in August 2010. We assessed the impact of a decrease in pH on dissolved Fe concentration, phytoplankton biomass, taxonomy and productivity, and the production of dimethylsulfide (DMS) and its algal precursor dimethylsulfoniopropionate (DMSP). Chlorophyll a (chl a) remained unchanged in the controls and doubled in both the FeSO4-enriched and dust-enriched incubations, confirming the Fe-limited status of the plankton assemblage during the experiment. In the acidified treatments, a significant reduction (by 16-38 %) of the final concentration of chl a was measured compared to their non-acidified counterparts, and a 15 % reduction in particulate organic carbon (POC) concentration was measured in the dust-enriched acidified treatment compared to the dust-enriched non-acidified treatment. FeSO4 and dust additions had a fertilizing effect mainly on diatoms and cyanobacteria. Lowering the pH affected mostly the haptophytes, but pelagophyte concentrations were also reduced in some acidified treatments. Acidification did not significantly alter DMSP and DMS concentrations. These results show that dust deposition events in a low-pH iron-limited Northeast subarctic Pacific are likely to stimulate phytoplankton growth to a lesser extent than in today's ocean during the few days following fertilization and point to a low initial sensitivity of the DMSP and DMS dynamics to OA.

  19. Effect of red mud addition on tetracycline and copper resistance genes and microbial community during the full scale swine manure composting.

    PubMed

    Wang, Rui; Zhang, Junya; Sui, Qianwen; Wan, Hefeng; Tong, Juan; Chen, Meixue; Wei, Yuansong; Wei, Dongbin

    2016-09-01

    Swine manure has been considered as the reservoir of antibiotic resistance genes (ARGs). Composting is one of the most suitable technologies for treating livestock manures, and red mud was proved to have a positive effect on nitrogen conservation during composting. This study investigated the abundance of eight tetracycline and three copper resistance genes, the bacterial community during the full scale swine manure composting with or without addition of red mud. The results showed that ARGs in swine manure could be effectively removed through composting (reduced by 2.4log copies/g TS), especially during the thermophilic phase (reduced by 1.5log copies/g TS), which the main contributor might be temperature. Additionally, evolution of bacterial community could also have a great influence on ARGs. Although addition of red mud could enhance nitrogen conservation, it obviously hindered removal of ARGs (reduced by 1.7log copies/g TS) and affected shaping of bacterial community during composting.

  20. Variation in Siderophore Biosynthetic Gene Distribution and Production across Environmental and Faecal Populations of Escherichia coli

    PubMed Central

    Porcelli, Ida; Sheppard, Samuel K.; Lucchini, Sacha

    2015-01-01

    Iron is essential for Escherichia coli growth and survival in the host and the external environment, but its availability is generally low due to the poor solubility of its ferric form in aqueous environments and the presence of iron-withholding proteins in the host. Most E. coli can increase access to iron by excreting siderophores such as enterobactin, which have a very strong affinity for Fe3+. A smaller proportion of isolates can generate up to 3 additional siderophores linked with pathogenesis; aerobactin, salmochelin, and yersiniabactin. However, non-pathogenic E. coli are also able to synthesise these virulence-associated siderophores. This raises questions about their role in the ecology of E. coli, beyond virulence, and whether specific siderophores might be linked with persistence in the external environment. Under the assumption that selection favours phenotypes that confer a fitness advantage, we compared siderophore production and gene distribution in E. coli isolated either from agricultural plants or the faeces of healthy mammals. This population-level comparison has revealed that under iron limiting growth conditions plant-associated isolates produced lower amounts of siderophores than faecal isolates. Additionally, multiplex PCR showed that environmental isolates were less likely to contain loci associated with aerobactin and yersiniabactin synthesis. Although aerobactin was linked with strong siderophore excretion, a significant difference in production was still observed between plant and faecal isolates when the analysis was restricted to strains only able to synthesise enterobactin. This finding suggests that the regulatory response to iron limitation may be an important trait associated with adaptation to the non-host environment. Our findings are consistent with the hypothesis that the ability to produce multiple siderophores facilitates E. coli gut colonisation and plays an important role in E. coli commensalism. PMID:25756870

  1. Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli.

    PubMed

    Searle, Laura J; Méric, Guillaume; Porcelli, Ida; Sheppard, Samuel K; Lucchini, Sacha

    2015-01-01

    Iron is essential for Escherichia coli growth and survival in the host and the external environment, but its availability is generally low due to the poor solubility of its ferric form in aqueous environments and the presence of iron-withholding proteins in the host. Most E. coli can increase access to iron by excreting siderophores such as enterobactin, which have a very strong affinity for Fe3+. A smaller proportion of isolates can generate up to 3 additional siderophores linked with pathogenesis; aerobactin, salmochelin, and yersiniabactin. However, non-pathogenic E. coli are also able to synthesise these virulence-associated siderophores. This raises questions about their role in the ecology of E. coli, beyond virulence, and whether specific siderophores might be linked with persistence in the external environment. Under the assumption that selection favours phenotypes that confer a fitness advantage, we compared siderophore production and gene distribution in E. coli isolated either from agricultural plants or the faeces of healthy mammals. This population-level comparison has revealed that under iron limiting growth conditions plant-associated isolates produced lower amounts of siderophores than faecal isolates. Additionally, multiplex PCR showed that environmental isolates were less likely to contain loci associated with aerobactin and yersiniabactin synthesis. Although aerobactin was linked with strong siderophore excretion, a significant difference in production was still observed between plant and faecal isolates when the analysis was restricted to strains only able to synthesise enterobactin. This finding suggests that the regulatory response to iron limitation may be an important trait associated with adaptation to the non-host environment. Our findings are consistent with the hypothesis that the ability to produce multiple siderophores facilitates E. coli gut colonisation and plays an important role in E. coli commensalism.

  2. Identification of an additional ferric-siderophore uptake gene clustered with receptor, biosynthesis, and fur-like regulatory genes in fluorescent Pseudomonas sp. strain M114.

    PubMed Central

    O'Sullivan, D J; Morris, J; O'Gara, F

    1990-01-01

    Five cosmid clones with insert sizes averaging 22.6 kilobases (kb) were isolated after complementation of 22 Tn5-induced Sid- mutants of Pseudomonas sp. strain M114. One of these plasmids (pMS639) was also shown to encode ferric-siderophore receptor and dissociation functions. The receptor gene was located on this plasmid since introduction of the plasmid into three wild-type fluorescent pseudomonads enabled them to utilize the ferric-siderophore from strain M114. The presence of an extra iron-regulated protein in the outer membrane profile of one of these strains was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A ferric-siderophore dissociation gene was attributed to pMS639 since it complemented the ferric-siderophore uptake mutation in strain M114FR2. This mutant was not defective in the outer membrane receptor for ferric-siderophore but apparently accumulated ferric-siderophore internally. Since ferric-citrate alleviated the iron stress of the mutant, there was no defect in iron metabolism subsequent to release of iron from the ferric-siderophore complex. Consequently, this mutant was defective in ferric-siderophore dissociation. A fur-like regulatory gene also present on pMS639 was subcloned to a 7.0-kb BglII insert of pCUP5 and was located approximately 7.3 kb from the receptor region. These results established that the 27.2-kb insert of pMS639 encoded at least two siderophore biosynthesis genes, ferric-siderophore receptor and dissociation genes, and a fur-like regulatory gene from the biocontrol fluorescent Pseudomonas sp. strain M114. Images PMID:2143887

  3. De Novo Assembly, Gene Annotation, and Marker Discovery in Stored-Product Pest Liposcelis entomophila (Enderlein) Using Transcriptome Sequences

    PubMed Central

    Wei, Dan-Dan; Chen, Er-Hu; Ding, Tian-Bo; Chen, Shi-Chun; Dou, Wei; Wang, Jin-Jun

    2013-01-01

    Background As a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels. Methodology/Principal Findings We applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of genes potentially involved in insecticide resistance were manually curated, including 68 putative cytochrome P450 genes, 37 putative glutathione S-transferase (GST) genes, 19 putative carboxyl/cholinesterase (CCE) genes, and other 126 transcripts to contain target site sequences or encoding detoxification genes representing eight types of resistance enzymes. Furthermore, to gain insight into the molecular basis of the L. entomophila toward thermal stresses, 25 heat shock protein (Hsp) genes were identified. In addition, 1,100 SSRs and 57,757 SNPs were detected and 231 pairs of SSR primes were designed for investigating the genetic diversity in future. Conclusions/Significance We developed a comprehensive transcriptomic database for L. entomophila. These sequences and putative molecular markers would further promote our understanding of the molecular mechanisms underlying insecticide resistance

  4. Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis

    PubMed Central

    Rautio, Jari J; Bailey, Michael; Kivioja, Teemu; Söderlund, Hans; Penttilä, Merja; Saloheimo, Markku

    2007-01-01

    Background Biologically relevant molecular markers can be used in evaluation of the physiological state of an organism in biotechnical processes. We monitored at high frequency the expression of 34 marker genes in batch, fed-batch and continuous cultures of the filamentous fungus Trichoderma reesei by the transcriptional analysis method TRAC (TRanscript analysis with the aid of Affinity Capture). Expression of specific genes was normalised either with respect to biomass or to overall polyA RNA concentration. Expressional variation of the genes involved in various process relevant cellular functions, such as protein production, growth and stress responses, was related to process parameters such as specific growth and production rates and substrate and dissolved oxygen concentrations. Results Gene expression of secreted cellulases and recombinant Melanocarpus albomyces laccase predicted the trends in the corresponding extracellular enzyme production rates and was highest in a narrow "physiological window" in the specific growth rate (μ) range of 0.03 – 0.05 h-1. Expression of ribosomal protein mRNAs was consistent with the changes in μ. Nine starvation-related genes were found as potential markers for detection of insufficient substrate feed for maintaining optimal protein production. For two genes induced in anaerobic conditions, increasing transcript levels were measured as dissolved oxygen decreased. Conclusion The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes. PMID:17537269

  5. Regulation of a novel gene cluster involved in secondary metabolite production in Streptomyces coelicolor.

    PubMed

    Hindra; Pak, Patricia; Elliot, Marie A

    2010-10-01

    Antibiotic biosynthesis in the streptomycetes is a complex and highly regulated process. Here, we provide evidence for the contribution of a novel genetic locus to antibiotic production in Streptomyces coelicolor. The overexpression of a gene cluster comprising four protein-encoding genes (abeABCD) and an antisense RNA-encoding gene (α-abeA) stimulated the production of the blue-pigmented metabolite actinorhodin on solid medium. Actinorhodin production also was enhanced by the overexpression of an adjacent gene (abeR) encoding a predicted Streptomyces antibiotic regulatory protein (SARP), while the deletion of this gene impaired actinorhodin production. We found the abe genes to be differentially regulated and controlled at multiple levels. Upstream of abeA was a promoter that directed the transcription of abeABCD at a low but constitutive level. The expression of abeBCD was, however, significantly upregulated at a time that coincided with the initiation of aerial development and the onset of secondary metabolism; this expression was activated by the binding of AbeR to four heptameric repeats upstream of a promoter within abeA. Expressed divergently to the abeBCD promoter was α-abeA, whose expression mirrored that of abeBCD but did not require activation by AbeR. Instead, α-abeA transcript levels were subject to negative control by the double-strand-specific RNase, RNase III.

  6. Involvement of the Haemophilus ducreyi gmhA Gene Product in Lipooligosaccharide Expression and Virulence

    PubMed Central

    Bauer, Beth A.; Stevens, Marla K.; Hansen, Eric J.

    1998-01-01

    The lipooligosaccharide (LOS) present in the outer membrane of Haemophilus ducreyi is likely a virulence factor for this sexually transmitted pathogen. An open reading frame in H. ducreyi 35000 was found to encode a predicted protein that had 87% identity with the protein product of the gmhA (isn) gene of Haemophilus influenzae. In H. influenzae type b, inactivation of the gmhA gene caused the synthesis of a significantly truncated LOS which possessed only lipid A and a single 2-keto-3-deoxyoctulosonic acid molecule (A. Preston, D. J. Maskell, A. Johnson, and E. R. Moxon, J. Bacteriol. 178:396–402, 1996). The H. ducreyi gmhA gene was able to complement a gmhA-deficient Escherichia coli strain, a result which confirmed the identity of this gene. When the gmhA gene of H. ducreyi was inactivated by insertion of a cat cartridge, the resultant H. ducreyi gmhA mutant, 35000.252, expressed a LOS that migrated much faster than wild-type LOS in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. When the wild-type H. ducreyi strain and its isogenic gmhA mutant were used in the temperature-dependent rabbit model for dermal lesion production by H. ducreyi, the gmhA mutant was found to be substantially less virulent than the wild-type parent strain. The H. ducreyi gmhA gene was amplified by PCR from the H. ducreyi chromosome and cloned into the pLS88 vector. When the H. ducreyi gmhA gene was present in trans in gmhA mutant 35000.252, expression of the gmhA gene product restored the virulence of this mutant to wild-type levels. These results indicate that the gmhA gene product of H. ducreyi is essential for the expression of wild-type LOS by this pathogen. PMID:9712780

  7. Effects of Copper Addition on Copper Resistance, Antibiotic Resistance Genes, and intl1 during Swine Manure Composting

    PubMed Central

    Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Song, Wen; Zhang, Kaiyu; Sun, Wei; Zhang, Xin; Zhang, Yajun; Li, Haichao

    2017-01-01

    Copper is one of the most abundant heavy metals present in swine manure. In this study, a laboratory-scale aerobic composting system was amended with Cu at three levels (0, 200, and 2000 mg kg-1, i.e., control, Cu200, and Cu2000 treatments, respectively) to determine its effect on the fate of copper resistance genes [copper resistance genes (CRGs): pcoA, cusA, copA, and tcrB], antibiotic resistance genes [antibiotic resistance genes (ARGs): erm(A) and erm(B)], and intl1. The results showed that the absolute abundances of pcoA, tcrB, erm(A), erm(B), and intl1 were reduced, whereas those of copA and cusA increased after swine manure composting. Redundancy analysis showed that temperature significantly affected the variations in CRGs, ARGs, and intl1. The decreases in CRGs, ARGs, and intI1 were positively correlated with the exchangeable Cu levels. The bacterial community could be grouped according to the composting time under different treatments, where the high concentration of copper had a more persistent effect on the bacterial community. Network analysis determined that the co-occurrence of CRGs, ARGs, and intI1, and the bacterial community were the main contributors to the changes in CRGs, ARG, and intl1. Thus, temperature, copper, and changes in the bacterial community composition had important effects on the variations in CRGs, ARGs, and intl1 during manure composting in the presence of added copper. PMID:28316595

  8. Effects of Copper Addition on Copper Resistance, Antibiotic Resistance Genes, and intl1 during Swine Manure Composting.

    PubMed

    Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Song, Wen; Zhang, Kaiyu; Sun, Wei; Zhang, Xin; Zhang, Yajun; Li, Haichao

    2017-01-01

    Copper is one of the most abundant heavy metals present in swine manure. In this study, a laboratory-scale aerobic composting system was amended with Cu at three levels (0, 200, and 2000 mg kg(-1), i.e., control, Cu200, and Cu2000 treatments, respectively) to determine its effect on the fate of copper resistance genes [copper resistance genes (CRGs): pcoA, cusA, copA, and tcrB], antibiotic resistance genes [antibiotic resistance genes (ARGs): erm(A) and erm(B)], and intl1. The results showed that the absolute abundances of pcoA, tcrB, erm(A), erm(B), and intl1 were reduced, whereas those of copA and cusA increased after swine manure composting. Redundancy analysis showed that temperature significantly affected the variations in CRGs, ARGs, and intl1. The decreases in CRGs, ARGs, and intI1 were positively correlated with the exchangeable Cu levels. The bacterial community could be grouped according to the composting time under different treatments, where the high concentration of copper had a more persistent effect on the bacterial community. Network analysis determined that the co-occurrence of CRGs, ARGs, and intI1, and the bacterial community were the main contributors to the changes in CRGs, ARG, and intl1. Thus, temperature, copper, and changes in the bacterial community composition had important effects on the variations in CRGs, ARGs, and intl1 during manure composting in the presence of added copper.

  9. Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the EcoCyc Database

    PubMed Central

    Mackie, Amanda; Paley, Suzanne; Keseler, Ingrid M.; Shearer, Alexander; Paulsen, Ian T.

    2014-01-01

    The sets of compounds that can support growth of an organism are defined by the presence of transporters and metabolic pathways that convert nutrient sources into cellular components and energy for growth. A collection of known nutrient sources can therefore serve both as an impetus for investigating new metabolic pathways and transporters and as a reference for computational modeling of known metabolic pathways. To establish such a collection for Escherichia coli K-12, we have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database. The assembled collection revealed a substantial number of discrepancies between the high-throughput data sets, which we investigated where possible using low-throughput growth assays on soft agar and in liquid culture. We also integrated six data sets describing 16,119 observations of the growth of single-gene knockout mutants of E. coli K-12 into EcoCyc, which are relevant to antimicrobial drug design, provide clues regarding the roles of genes of unknown function, and are useful for validating metabolic models. To make this information easily accessible to EcoCyc users, we developed software for capturing, querying, and visualizing cellular growth assays and gene essentiality data. PMID:24363340

  10. Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production

    PubMed Central

    Tufail, Soban; Ismat, Fouzia; Imran, Muhammad; Iqbal, Mazhar; Mirza, Osman; Rhaman, Moazur

    2016-01-01

    Proteases are widely used to remove affinity and solubility tags from recombinant proteins to avoid potential interference of these tags with the structure and function of the fusion partner. In recent years, great interest has been seen in use of the human rhinovirus 3C protease owing to its stringent sequence specificity and enhanced activity. Like other proteases, activity of the human rhinovirus 3C protease can be affected in part by the buffer components and additives that are generally employed for purification and stabilization of proteins, hence, necessitate their removal by tedious and time-consuming procedures before proteolysis can occur. To address this issue, we examined the effect of elution buffers used for common affinity based purifications, salt ions, stability/solubility and reducing agents, and detergents on the activity of the human rhinovirus 3C protease using three different fusion proteins at 4°C, a temperature of choice for purification of many proteins. The results show that the human rhinovirus 3C protease performs better at 4°C than the frequently used tobacco etch virus protease and its activity was insensitive to most of the experimental conditions tested. Though number of fusion proteins tested is limited, we expect that these finding will facilitate the use of the human rhinovirus 3C protease in recombinant protein production for pharmaceutical and biotechnological applications. PMID:27093053

  11. Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production.

    PubMed

    Ullah, Raheem; Shah, Majid Ali; Tufail, Soban; Ismat, Fouzia; Imran, Muhammad; Iqbal, Mazhar; Mirza, Osman; Rhaman, Moazur

    2016-01-01

    Proteases are widely used to remove affinity and solubility tags from recombinant proteins to avoid potential interference of these tags with the structure and function of the fusion partner. In recent years, great interest has been seen in use of the human rhinovirus 3C protease owing to its stringent sequence specificity and enhanced activity. Like other proteases, activity of the human rhinovirus 3C protease can be affected in part by the buffer components and additives that are generally employed for purification and stabilization of proteins, hence, necessitate their removal by tedious and time-consuming procedures before proteolysis can occur. To address this issue, we examined the effect of elution buffers used for common affinity based purifications, salt ions, stability/solubility and reducing agents, and detergents on the activity of the human rhinovirus 3C protease using three different fusion proteins at 4°C, a temperature of choice for purification of many proteins. The results show that the human rhinovirus 3C protease performs better at 4°C than the frequently used tobacco etch virus protease and its activity was insensitive to most of the experimental conditions tested. Though number of fusion proteins tested is limited, we expect that these finding will facilitate the use of the human rhinovirus 3C protease in recombinant protein production for pharmaceutical and biotechnological applications.

  12. HSP70 and modified HPV 16 E7 fusion gene without the addition of a signal peptide gene sequence as a candidate therapeutic tumor vaccine.

    PubMed

    Zong, Jinbao; Wang, Changyuan; Wang, Qingyong; Peng, Qinglin; Xu, Yufei; Xie, Xixiu; Xu, Xuemei

    2013-12-01

    Millions of women are currently infected with high-risk human papillomavirus (HPV), which is considered to be a major risk factor for cervical cancer. Thus, it is urgent to develop therapeutic vaccines to eliminate the established infections or HPV-related diseases. In the present study, using the mycobacterium tuberculosis heat shock protein 70 (MtHSP70) gene linked to the modified HPV 16 E7 (mE7) gene, we generated two potential therapeutic HPV DNA vaccines, mE7/MtHSP70 and SigmE7/MtHSP70, the latter was linked to the signal peptide gene sequence of human CD33 at the upstream of the fusion gene. We found that vaccination with the mE7/MtHSP70 DNA vaccine induced a stronger E7-specific CD8+ T cell response and resulted in a more significant therapeutic effect against E7-expressing tumor cells in mice. Our results demonstrated that HSP70 can play a more important role in mE7 and MtHSP70 fusion DNA vaccine without the help of a signal peptide. This may facilitate the use of HSP70 and serve as a significant reference for future study.

  13. FlhA influences Bacillus thuringiensis PlcR-regulated gene transcription, protein production, and virulence.

    PubMed

    Bouillaut, Laurent; Ramarao, Nalini; Buisson, Christophe; Gilois, Nathalie; Gohar, Michel; Lereclus, Didier; Nielsen-Leroux, Christina

    2005-12-01

    Bacillus thuringiensis and Bacillus cereus are closely related. B. thuringiensis is well known for its entomopathogenic properties, principally due to the synthesis of plasmid-encoded crystal toxins. B. cereus appears to be an emerging opportunistic human pathogen. B. thuringiensis and B. cereus produce many putative virulence factors which are positively controlled by the pleiotropic transcriptional regulator PlcR. The inactivation of plcR decreases but does not abolish virulence, indicating that additional factors like flagella may contribute to pathogenicity. Therefore, we further analyzed a mutant (B. thuringiensis 407 Cry(-) DeltaflhA) previously described as being defective in flagellar apparatus assembly and in motility as well as in the production of hemolysin BL and phospholipases. A large picture of secreted proteins was obtained by two-dimensional electrophoresis analysis, which revealed that flagellar proteins are not secreted and that production of several virulence-associated factors is reduced in the flhA mutant. Moreover, we quantified the effect of FlhA on plcA and hblC gene transcription. The results show that the flhA mutation results in a significant reduction of plcA and hblC transcription. These results indicate that the transcription of several PlcR-regulated virulence factors is coordinated with the flagellar apparatus. Consistently, the flhA mutant also shows a strong decrease in cytotoxicity towards HeLa cells and in virulence against Galleria mellonella larvae following oral and intrahemocoelic inoculation. The decrease in virulence may be due to both a lack of flagella and a lower production of secreted factors. Hence, FlhA appears to be an essential virulence factor with a pleiotropic role.

  14. Coordinate expression of multiple bacterial carotenoid genes in canola leading to altered carotenoid production.

    PubMed

    Ravanello, Monica P; Ke, Dangyang; Alvarez, Julie; Huang, Bihua; Shewmaker, Christine K

    2003-10-01

    Carotenoids have drawn much attention recently because of their potentially positive benefits to human health as well as their utility in both food and animal feed. Previous work in canola (Brassica napus) seed over-expressing the bacterial phytoene synthase gene (crtB) demonstrated a change in carotenoid content, such that the total levels of carotenoids, including phytoene and downstream metabolites like beta-carotene, were elevated 50-fold, with the ratio of beta- to alpha-carotene being 2:1. This result raised the possibility that the composition of metabolites in this pathway could be modified further in conjunction with the increased flux obtained with crtB. Here we report on the expression of additional bacterial genes for the enzymes geranylgeranyl diphosphate synthase (crtE), phytoene desaturase (crtI) and lycopene cyclase (crtY and the plant B. napus lycopene beta-cyclase) engineered in conjunction with phytoene synthase (crtB) in transgenic canola seed. Analysis of the carotenoid levels by HPLC revealed a 90% decrease in phytoene levels for the double construct expressing crtB in conjunction with crtI. The transgenic seed from all the double constructs, including the one expressing the bacterial crtB and the plant lycopene beta-cyclase showed an increase in the levels of total carotenoid similar to that previously observed by expressing crtB alone but minimal effects were observed with respect to the ratio of beta- to alpha-carotene compared to the original construct. However, the beta- to alpha-carotene ratio was increased from 2:1 to 3:1 when a triple construct consisting of the bacterial phytoene synthase, phytoene desaturase and lycopene cyclase genes were expressed together. This result suggests that the bacterial genes may form an aggregate complex that allows in vivo activity of all three proteins through substrate channeling. This finding should allow further manipulation of the carotenoid biosynthetic pathway for downstream products with

  15. Phylogenomic study of lipid genes involved in microalgal biofuel production-candidate gene mining and metabolic pathway analyses.

    PubMed

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

    2012-01-01

    Optimizing microalgal biofuel production using metabolic engineering tools requires an in-depth understanding of the structure-function relationship of genes involved in lipid biosynthetic pathway. In the present study, genome-wide identification and characterization of 398 putative genes involved in lipid biosynthesis in Arabidopsis thaliana Chlamydomonas reinhardtii, Volvox carteri, Ostreococcus lucimarinus, Ostreococcus tauri and Cyanidioschyzon merolae was undertaken on the basis of their conserved motif/domain organization and phylogenetic profile. The results indicated that the core lipid metabolic pathways in all the species are carried out by a comparable number of orthologous proteins. Although the fundamental gene organizations were observed to be invariantly conserved between microalgae and Arabidopsis genome, with increased order of genome complexity there seems to be an association with more number of genes involved in triacylglycerol (TAG) biosynthesis and catabolism. Further, phylogenomic analysis of the genes provided insights into the molecular evolution of lipid biosynthetic pathway in microalgae and confirm the close evolutionary proximity between the Streptophyte and Chlorophyte lineages. Together, these studies will improve our understanding of the global lipid metabolic pathway and contribute to the engineering of regulatory networks of algal strains for higher accumulation of oil.

  16. 40 CFR 80.591 - What are the product transfer document requirements for additives to be used in diesel fuel?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... package contains a static dissipater additive and/or red dye having a sulfur content greater than 15 ppm... additive having a sulfur content greater than 15 ppm.” (ii) “This diesel fuel additive contains red dye... dissipater additive and red dye having a sulfur content greater than 15 ppm.” (4) Include the...

  17. 40 CFR 80.591 - What are the product transfer document requirements for additives to be used in diesel fuel?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... package contains a static dissipater additive and/or red dye having a sulfur content greater than 15 ppm... additive having a sulfur content greater than 15 ppm.” (ii) “This diesel fuel additive contains red dye... dissipater additive and red dye having a sulfur content greater than 15 ppm.” (4) Include the...

  18. 40 CFR 80.591 - What are the product transfer document requirements for additives to be used in diesel fuel?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... package contains a static dissipater additive and/or red dye having a sulfur content greater than 15 ppm... additive having a sulfur content greater than 15 ppm.” (ii) “This diesel fuel additive contains red dye... dissipater additive and red dye having a sulfur content greater than 15 ppm.” (4) Include the...

  19. 40 CFR 80.591 - What are the product transfer document requirements for additives to be used in diesel fuel?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... package contains a static dissipater additive and/or red dye having a sulfur content greater than 15 ppm... additive having a sulfur content greater than 15 ppm.” (ii) “This diesel fuel additive contains red dye... dissipater additive and red dye having a sulfur content greater than 15 ppm.” (4) Include the...

  20. 40 CFR 80.591 - What are the product transfer document requirements for additives to be used in diesel fuel?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... package contains a static dissipater additive and/or red dye having a sulfur content greater than 15 ppm... additive having a sulfur content greater than 15 ppm.” (ii) “This diesel fuel additive contains red dye... dissipater additive and red dye having a sulfur content greater than 15 ppm.” (4) Include the...

  1. Mutations of the Corynebacterium glutamicum NCgl1221 gene, encoding a mechanosensitive channel homolog, induce L-glutamic acid production.

    PubMed

    Nakamura, Jun; Hirano, Seiko; Ito, Hisao; Wachi, Masaaki

    2007-07-01

    Corynebacterium glutamicum is a biotin auxotroph that secretes L-glutamic acid in response to biotin limitation; this process is employed in industrial L-glutamic acid production. Fatty acid ester surfactants and penicillin also induce L-glutamic acid secretion, even in the presence of biotin. However, the mechanism of L-glutamic acid secretion remains unclear. It was recently reported that disruption of odhA, encoding a subunit of the 2-oxoglutarate dehydrogenase complex, resulted in L-glutamic acid secretion without induction. In this study, we analyzed odhA disruptants and found that those which exhibited constitutive L-glutamic acid secretion carried additional mutations in the NCgl1221 gene, which encodes a mechanosensitive channel homolog. These NCgl1221 gene mutations lead to constitutive L-glutamic acid secretion even in the absence of odhA disruption and also render cells resistant to an L-glutamic acid analog, 4-fluoroglutamic acid. Disruption of the NCgl1221 gene essentially abolishes L-glutamic acid secretion, causing an increase in the intracellular L-glutamic acid pool under biotin-limiting conditions, while amplification of the wild-type NCgl1221 gene increased L-glutamate secretion, although only in response to induction. These results suggest that the NCgl1221 gene encodes an L-glutamic acid exporter. We propose that treatments that induce L-glutamic acid secretion alter membrane tension and trigger a structural transformation of the NCgl1221 protein, enabling it to export L-glutamic acid.

  2. Unraveling Antimicrobial Resistance Genes and Phenotype Patterns among Enterococcus faecalis Isolated from Retail Chicken Products in Japan

    PubMed Central

    Hidano, Arata; Yamamoto, Takehisa; Hayama, Yoko; Muroga, Norihiko; Kobayashi, Sota; Nishida, Takeshi; Tsutsui, Toshiyuki

    2015-01-01

    Multidrug-resistant enterococci are considered crucial drivers for the dissemination of antimicrobial resistance determinants within and beyond a genus. These organisms may pass numerous resistance determinants to other harmful pathogens, whose multiple resistances would cause adverse consequences. Therefore, an understanding of the coexistence epidemiology of resistance genes is critical, but such information remains limited. In this study, our first objective was to determine the prevalence of principal resistance phenotypes and genes among Enterococcus faecalis isolated from retail chicken domestic products collected throughout Japan. Subsequent analysis of these data by using an additive Bayesian network (ABN) model revealed the co-appearance patterns of resistance genes and identified the associations between resistance genes and phenotypes. The common phenotypes observed among E. faecalis isolated from the domestic products were the resistances to oxytetracycline (58.4%), dihydrostreptomycin (50.4%), and erythromycin (37.2%), and the gene tet(L) was detected in 46.0% of the isolates. The ABN model identified statistically significant associations between tet(L) and erm(B), tet(L) and ant(6)-Ia, ant(6)-Ia and aph(3’)-IIIa, and aph(3’)-IIIa and erm(B), which indicated that a multiple-resistance profile of tetracycline, erythromycin, streptomycin, and kanamycin is systematic rather than random. Conversely, the presence of tet(O) was only negatively associated with that of erm(B) and tet(M), which suggested that in the presence of tet(O), the aforementioned multiple resistance is unlikely to be observed. Such heterogeneity in linkages among genes that confer the same phenotypic resistance highlights the importance of incorporating genetic information when investigating the risk factors for the spread of resistance. The epidemiological factors that underlie the persistence of systematic multiple-resistance patterns warrant further investigations with

  3. Split-gene system for hybrid wheat seed production

    PubMed Central

    Kempe, Katja; Rubtsova, Myroslava; Gils, Mario

    2014-01-01

    Hybrid wheat plants are superior in yield and growth characteristics compared with their homozygous parents. The commercial production of wheat hybrids is difficult because of the inbreeding nature of wheat and the lack of a practical fertility control that enforces outcrossing. We describe a hybrid wheat system that relies on the expression of a phytotoxic barnase and provides for male sterility. The barnase coding information is divided and distributed at two loci that are located on allelic positions of the host chromosome and are therefore “linked in repulsion.” Functional complementation of the loci is achieved through coexpression of the barnase fragments and intein-mediated ligation of the barnase protein fragments. This system allows for growth and maintenance of male-sterile female crossing partners, whereas the hybrids are fertile. The technology does not require fertility restorers and is based solely on the genetic modification of the female crossing partner. PMID:24821800

  4. Split-gene system for hybrid wheat seed production.

    PubMed

    Kempe, Katja; Rubtsova, Myroslava; Gils, Mario

    2014-06-24

    Hybrid wheat plants are superior in yield and growth characteristics compared with their homozygous parents. The commercial production of wheat hybrids is difficult because of the inbreeding nature of wheat and the lack of a practical fertility control that enforces outcrossing. We describe a hybrid wheat system that relies on the expression of a phytotoxic barnase and provides for male sterility. The barnase coding information is divided and distributed at two loci that are located on allelic positions of the host chromosome and are therefore "linked in repulsion." Functional complementation of the loci is achieved through coexpression of the barnase fragments and intein-mediated ligation of the barnase protein fragments. This system allows for growth and maintenance of male-sterile female crossing partners, whereas the hybrids are fertile. The technology does not require fertility restorers and is based solely on the genetic modification of the female crossing partner.

  5. A mutant gene that increases gibberellin production in Brassica

    SciTech Connect

    Rood, S.B. ); Williams, P.H. ); Pearce, D.; Pharis, R.P. ); Murofushi, Noboru ); Mander, L.N. )

    1990-07-01

    A single gene mutant (elongated internode (ein/ein)) with accelerated shoot elongation was identified from a rapid cycling line of Brassica rapa. Relative to normal plants, mutant plants had slightly accelerated floral development, greater stem dry weights, and particularly, increased internode and inflorescence elongation. The application of the triazole plant growth retardant, paclobutrazol, inhibited shoot elongation, returning ein to a more normal phenotype. Conversely, exogenous gibberellin A{sub 3} (GA{sub 3}) can convert normal genotypes to a phenotype resembling ein. The content of endogenous GA{sub 1} and GA{sub 3} were estimated by gas chromatography-selected ion monitoring using ({sup 2}H)GA{sub 1} as a quantitative internal standard and at day 14 were 1.5- and 12.1-fold higher per stem, respectively, in ein than in normal plants, although GA concentrations were more similar. The endogenous levels of GA{sub 20} and GA{sub 1}, and the rate of GA{sub 19} metabolism were simultaneously analyzed. Levels of GA{sub 1} and GA{sub 20} were 4.6- and 12.9-fold higher, respectively, and conversions to GA{sub 20} and GA{sub 1} were 8.3 and 1.3 times faster in ein than normal plants. Confirming the enhanced rate of GA{sub 1} biosynthesis in ein, the conversion of ({sup 3}H)GA{sub 20} to ({sup 3}H) GA{sub 1} was also faster in ein than in the normal genotype. Thus, the ein allele results in accelerated GA{sub 1} biosynthesis and an elevated content of endogenous GAs, including the dihydroxylated GAs A{sub 1} and A{sub 3}.

  6. Smoking and polymorphisms in xenobiotic metabolism and DNA repair genes are additive risk factors affecting bladder cancer in Northern Tunisia.

    PubMed

    Rouissi, Kamel; Ouerhani, Slah; Hamrita, Bechr; Bougatef, Karim; Marrakchi, Raja; Cherif, Mohamed; Ben Slama, Mohamed Riadh; Bouzouita, Mohamed; Chebil, Mohamed; Ben Ammar Elgaaied, Amel

    2011-12-01

    Cancer epidemiology has undergone marked development since the nineteen-fifties. One of the most spectacular and specific contributions was the demonstration of the massive effect of smoking and genetic polymorphisms on the occurrence of bladder cancer. The tobacco carcinogens are metabolized by various xenobiotic metabolizing enzymes, such as the super-families of N-acetyltransferases (NAT) and glutathione S-transferases (GST). DNA repair is essential to an individual's ability to respond to damage caused by tobacco carcinogens. Alterations in DNA repair genes may affect cancer risk by influencing individual susceptibility to this environmental exposure. Polymorphisms in NAT2, GST and DNA repair genes alter the ability of these enzymes to metabolize carcinogens or to repair alterations caused by this process. We have conducted a case-control study to assess the role of smoking, slow NAT2 variants, GSTM1 and GSTT1 null, and XPC, XPD, XPG nucleotide excision-repair (NER) genotypes in bladder cancer development in North Tunisia. Taken alone, each gene unless NAT2 did not appear to be a factor affecting bladder cancer susceptibility. For the NAT2 slow acetylator genotypes, the NAT2*5/*7 diplotype was found to have a 7-fold increased risk to develop bladder cancer (OR = 7.14; 95% CI: 1.30-51.41). However, in tobacco consumers, we have shown that Null GSTM1, Wild GSTT1, Slow NAT2, XPC (CC) and XPG (CC) are genetic risk factors for the disease. When combined together in susceptible individuals compared to protected individuals these risk factors give an elevated OR (OR = 61). So, we have shown a strong cumulative effect of tobacco and different combinations of studied genetic risk factors which lead to a great susceptibility to bladder cancer.

  7. High frequency of additional gene mutations in acute myeloid leukemia with MLL partial tandem duplication: DNMT3A mutation is associated with poor prognosis

    PubMed Central

    Kao, Hsiao-Wen; Liang, Der-Cherng; Kuo, Ming-Chung; Wu, Jin-Hou; Dunn, Po; Wang, Po-Nan; Lin, Tung-Liang; Shih, Yu-Shu; Liang, Sung-Tzu; Lin, Tung-Huei; Lai, Chen-Yu; Lin, Chun-Hui; Shih, Lee-Yung

    2015-01-01

    The mutational profiles of acute myeloid leukemia (AML) with partial tandem duplication of mixed-lineage leukemia gene (MLL-PTD) have not been comprehensively studied. We studied 19 gene mutations for 98 patients with MLL-PTD AML to determine the mutation frequency and clinical correlations. MLL-PTD was screened by reverse-transcriptase PCR and confirmed by real-time quantitative PCR. The mutational analyses were performed with PCR-based assays followed by direct sequencing. Gene mutations of signaling pathways occurred in 63.3% of patients, with FLT3-ITD (44.9%) and FLT3-TKD (13.3%) being the most frequent. 66% of patients had gene mutations involving epigenetic regulation, and DNMT3A (32.7%), IDH2 (18.4%), TET2 (18.4%), and IDH1 (10.2%) mutations were most common. Genes of transcription pathways and tumor suppressors accounted for 23.5% and 10.2% of patients. RUNX1 mutation occurred in 23.5% of patients, while none had NPM1 or double CEBPA mutation. 90.8% of MLL-PTD AML patients had at least one additional gene mutation. Of 55 MLL-PTD AML patients who received standard chemotherapy, age older than 50 years and DNMT3A mutation were associated with inferior outcome. In conclusion, gene mutations involving DNA methylation and activated signaling pathway were common co-existed gene mutations. DNMT3A mutation was a poor prognostic factor in MLL-PTD AML. PMID:26375248

  8. Reference Gene Selection for qPCR Analysis in Tomato-Bipartite Begomovirus Interaction and Validation in Additional Tomato-Virus Pathosystems

    PubMed Central

    Lacerda, Ana L. M.; Fonseca, Leonardo N.; Blawid, Rosana; Boiteux, Leonardo S.; Ribeiro, Simone G.; Brasileiro, Ana C. M.

    2015-01-01

    Quantitative Polymerase Chain Reaction (qPCR) is currently the most sensitive technique used for absolute and relative quantification of a target gene transcript, requiring the use of appropriated reference genes for data normalization. To accurately estimate the relative expression of target tomato (Solanum lycopersicum L.) genes responsive to several virus species in reverse transcription qPCR analysis, the identification of reliable reference genes is mandatory. In the present study, ten reference genes were analyzed across a set of eight samples: two tomato contrasting genotypes (‘Santa Clara’, susceptible, and its near-isogenic line ‘LAM 157’, resistant); subjected to two treatments (inoculation with Tomato chlorotic mottle virus (ToCMoV) and its mock-inoculated control) and in two distinct times after inoculation (early and late). Reference genes stability was estimated by three statistical programs (geNorm, NormFinder and BestKeeper). To validate the results over broader experimental conditions, a set of ten samples, corresponding to additional three tomato-virus pathosystems that included tospovirus, crinivirus and tymovirus + tobamovirus, was analyzed together with the tomato-ToCMoV pathosystem dataset, using the same algorithms. Taking into account the combined analyses of the ranking order outputs from the three algorithms, TIP41 and EF1 were identified as the most stable genes for tomato-ToCMoV pathosystem, and TIP41 and EXP for the four pathosystems together, and selected to be used as reference in the forthcoming expression qPCR analysis of target genes in experimental conditions involving the aforementioned tomato-virus pathosystems. PMID:26317870

  9. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  10. Expression of MAGE-1 and -3 genes and gene products in human hepatocellular carcinoma

    PubMed Central

    Kariyama, K; Higashi, T; Kobayashi, Y; Nouso, K; Nakatsukasa, H; Yamano, T; Ishizaki, M; Kaneyoshi, T; Toshikuni, N; Ohnishi, T; Fujiwara, K; Nakayama, E; Terracciano, L; Spagnoli, G C; Tsuji, T

    1999-01-01

    MAGE gene family encodes peptides recognized by autologous cytotoxic T lymphocytes in a major histocompatibility complex (MHC) class-I restricted fashion. In the present study, we have performed reverse-transcription polymerase chain reaction (RT-PCR) for the genes, as well as immunohistochemical analysis and Western blotting of MAGE-1 and -3 proteins in 33 surgically resected hepatocellular carcinomas (HCCs). MAGE-1 and -3 mRNAs were constitutively expressed exclusively in 78 and 42% of HCCs respectively. On immunohistochemistry with monoclonal antibodies, 77B for MAGE-1 and 57B for MAGE-3, MAGE-1 and -3 proteins were recognized in cytoplasm of only six among 33 (18%) and two of 29 HCCs (7%) respectively. The distribution pattern was mostly focal in HCC nodules. By contrast, the Western blot analysis revealed that the MAGE-1 (46 kDa) and -3 proteins (48 kDa) were expressed in 80 and 60% of 15 HCCs examined respectively. The proteins of MAGE-1 and -3 were also expressed exclusively in HCCs regardless of the histological grading and clinical staging. Our results indicate that the detection of the genes by RT-PCR or the proteins by Western blotting is useful for differentiating early HCCs from non-cancerous lesions, and that the peptides derived from MAGE-1 and -3 proteins might be suitable targets for immunotherapy of human HCC. © 1999 Cancer Research Campaign PMID:10576668

  11. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    SciTech Connect

    Tennyson, C.N.; Worton, R.G.

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  12. Skin epidermis lacking the c-myc gene is resistant to Ras-driven tumorigenesis but can reacquire sensitivity upon additional lossof the p21Cip1 gene

    PubMed Central

    Oskarsson, Thordur; Essers, Marieke Alida Gertruda; Dubois, Nicole; Offner, Sandra; Dubey, Christelle; Roger, Catherine; Metzger, Daniel; Chambon, Pierre; Hummler, Edith; Beard, Peter; Trumpp, Andreas

    2006-01-01

    The target gene(s) required for Myc-mediated tumorigenesis are still elusive. Here we show that while endogenous c-Myc is surprisingly dispensable for skin homeostasis and TPA-induced hyperplasia, c-Myc-deficient epidermis is resistant to Ras-mediated DMBA/TPAinduced tumorigenesis. This is mechanistically linked to p21Cip1, which is induced in tumors by the activated Ras–ERK pathway but repressed by c-Myc. Acute elimination of c-Myc in established tumors leads to the up-regulation of p21Cip1, and epidermis lacking both p21Cip1 and c-Myc reacquires normal sensitivity to DMBA/TPA-induced tumorigenesis. This identifies c-Myc-mediated repression of p21Cip1 as a key step for Ras-driven epidermal tumorigenesis. PMID:16882980

  13. Exploring the Relationship Between Wetland Methane Emissions and Net Ecosystem Productivity Using Experimental Shading and Labile Carbon Additions.

    NASA Astrophysics Data System (ADS)

    Owens, S.; von Fischer, J. C.

    2007-12-01

    Methane (CH4) emissions from wetlands are positively correlated with net ecosystem productivity (NEP); however the relative importance of proposed controlling mechanisms remains poorly understood. The carbon supply hypothesis suggests that recent photosynthesis contributes labile carbon substrate to methanogenic habitats, resulting in higher CH4 emissions with increases in NEP. Plant gas transport is also hypothesized to be important for conducting gases between the soil and the atmosphere. High CH4 production rates often occur in saturated wetland soils where gas diffusion is extremely slow. The aerenchymous tissues of vascular wetland plants can serve as the primary pathway for CH4 emissions from the soil to the atmosphere, while also allowing CH4 to bypass more aerobic soil regions where CH4 oxidation could occur. Using a hypothesis-driven experimental approach, we established shading treatments in a Juncus- dominated wetland in the northern Colorado Front Range, and measured CH4 and CO2 fluxes with a static chamber technique. In the summer of 2007, the shading manipulations (45% and 65% shade) significantly reduced net ecosystem exchange (NEE; an approximation of NEP) and mean CH4 fluxes compared to control plots (p=0.02 and p=0.01, respectively). To test the carbon supply hypothesis, we injected a solution containing acetate (a primary methanogenic carbon source) to a depth of 20cm below the soil surface. Acetate additions stimulated CH4 emission rates across all plots by an average of 29.3% (p=0.01). However the strength of the CH4 emission response was not significantly related to plot treatment or NEE, indicating that reduced carbon supply could not explain the response to shading. We hypothesize that reduced plant gas transport was more important than labile carbon supply for driving the lower CH4 emission rates in shaded plots. The dry weight of above-ground biomass was lower in shaded plots (p=0.04), suggesting a possible link between plant gas transport

  14. Genetic resources for advanced biofuel production described with the Gene Ontology

    PubMed Central

    Torto-Alalibo, Trudy; Purwantini, Endang; Lomax, Jane; Setubal, João C.; Mukhopadhyay, Biswarup; Tyler, Brett M.

    2014-01-01

    Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way. PMID:25346727

  15. Genetic resources for advanced biofuel production described with the Gene Ontology

    SciTech Connect

    Torto-Alalibo, Trudy; Purwantini, Endang; Lomax, Jane; Setubal, Joao C.; Mukhopadhyay, Biswarup; Tyler, Brett M.

    2014-10-10

    Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary.The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology (http://www.mengo.biochem.vt.edu) project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. We review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.

  16. Genetic resources for advanced biofuel production described with the Gene Ontology

    DOE PAGES

    Torto-Alalibo, Trudy; Purwantini, Endang; Lomax, Jane; ...

    2014-10-10

    Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary.The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology (http://www.mengo.biochem.vt.edu) project is extending the GO to include new terms to describe microbial processes of interest to bioenergymore » production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. We review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.« less

  17. Products of lipid, protein and RNA oxidation as signals and regulators of gene expression in plants

    PubMed Central

    Chmielowska-Bąk, Jagna; Izbiańska, Karolina; Deckert, Joanna

    2015-01-01

    Reactive oxygen species (ROS) are engaged in several processes essential for normal cell functioning, such as differentiation, anti-microbial defense, stimulus sensing and signaling. Interestingly, recent studies imply that cellular signal transduction and gene regulation are mediated not only directly by ROS but also by the molecules derived from ROS-mediated oxidation. Lipid peroxidation leads to non-enzymatic formation of oxylipins. These molecules were shown to modulate expression of signaling associated genes including genes encoding phosphatases, kinases and transcription factors. Oxidized peptides derived from protein oxidation might be engaged in organelle-specific ROS signaling. In turn, oxidation of particular mRNAs leads to decrease in the level of encoded proteins and thus, contributes to the post-transcriptional regulation of gene expression. Present mini review summarizes latest findings concerning involvement of products of lipid, protein and RNA oxidation in signal transduction and gene regulation. PMID:26082792

  18. Cloning and expression analyses of interferon regulatory factor (IRF) 3 and 7 genes in European eel, Anguilla anguilla with the identification of genes involved in IFN production.

    PubMed

    Huang, Bei; Huang, Wen Shu; Nie, P

    2014-04-01

    Interferon regulatory factor (IRF) 3 and IRF7 have been identified as regulators of type I interferon (IFN) gene expression in mammals. In the present study, the two genes were cloned and characterized in the European eel, Anguilla anguilla. The full-length cDNA sequence of IRF3 and IRF7 in the European eel, named as AaIRF3 and AaIRF7 consists of 2879 and 2419 bp respectively. Multiple alignments showed that the two IRFs have a highly conserved DNA binding domain (DBD) in the N terminus, with the characteristic motif containing five tryptophan residues, which is a feature present in their mammalian homologues. But, IRF7 has only four of the five residues in other species of fish. The expression of AaIRF3 and AaIRF7 both displayed an obvious dose-dependent manner following polyinosinic:polycytidylic acid (PolyI:C) challenge. In vivo expression analysis showed that the mRNA level of AaIRF3 and AaIRF7 was significantly up-regulated in response to PolyI:C stimulation in all examined tissues/organs except in muscle, with a lower level of increase observed in response to lipopolysaccharide (LPS) challenge and Edwardsiella tarda infection, indicating that AaIRF3 and AaIRF7 may be more likely involved in antiviral immune response. In addition, some pattern recognition receptors genes related with the production of type I IFNs and those genes in response to type I IFNs were identified in the European eel genome database, indicating a relatively conserved system in the production of type I IFN and its signalling in the European eel.

  19. [The possibility of using the mycelial wastes from the production of antifungal antibiotics as additives to lubricating oils].

    PubMed

    Belakhov, V V; Shenin, Iu D

    1997-01-01

    Antiwear and antitear properties of mycelial waste from production of antifungal antibiotics i.e. levorin, nystatin, mycoheptin, amphotericin B and griseofulvin were studied. It was shown that the waste mycelium from griseofulvin production had the best antiwear and antitear characteristics due to a higher percentage of phosphorus and sulphur in it as compared to the mycelial waste from production of the other antibiotics.

  20. Reducing metal alloy powder costs for use in powder bed fusion additive manufacturing: Improving the economics for production

    NASA Astrophysics Data System (ADS)

    Medina, Fransisco

    Titanium and its associated alloys have been used in industry for over 50 years and have become more popular in the recent decades. Titanium has been most successful in areas where the high strength to weight ratio provides an advantage over aluminum and steels. Other advantages of titanium include biocompatibility and corrosion resistance. Electron Beam Melting (EBM) is an additive manufacturing (AM) technology that has been successfully applied in the manufacturing of titanium components for the aerospace and medical industry with equivalent or better mechanical properties as parts fabricated via more traditional casting and machining methods. As the demand for titanium powder continues to increase, the price also increases. Titanium spheroidized powder from different vendors has a price range from 260/kg-450/kg, other spheroidized alloys such as Niobium can cost as high as $1,200/kg. Alternative titanium powders produced from methods such as the Titanium Hydride-Dehydride (HDH) process and the Armstrong Commercially Pure Titanium (CPTi) process can be fabricated at a fraction of the cost of powders fabricated via gas atomization. The alternative powders can be spheroidized and blended. Current sectors in additive manufacturing such as the medical industry are concerned that there will not be enough spherical powder for production and are seeking other powder options. It is believed the EBM technology can use a blend of spherical and angular powder to build fully dense parts with equal mechanical properties to those produced using traditional powders. Some of the challenges with angular and irregular powders are overcoming the poor flow characteristics and the attainment of the same or better packing densities as spherical powders. The goal of this research is to demonstrate the feasibility of utilizing alternative and lower cost powders in the EBM process. As a result, reducing the cost of the raw material to reduce the overall cost of the product produced with

  1. Associations between polymorphisms of the gene and milk production traits in water buffaloes.

    PubMed

    Deng, T X; Pang, C Y; Lu, X R; Zhu, P; Duan, A Q; Liang, X W

    2016-03-01

    Signal transducer and activator of transcription 1 () is an important regulator of mammary gland differentiation and cell survival that has been regarded as a candidate gene affecting milk production traits in mammals. Therefore, this study was conducted to evaluate significant associations between SNP of the gene and milk production traits in buffaloes. Here, 18 SNP were identified in the buffalo gene, including 15 intronic mutations and 3 exon mutations. All the identified SNP were then genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry methods from 192 buffaloes. All the SNP were in Hardy-Weinberg equilibrium, and 2 haplotype blocks were successfully constructed based on these SNP data, which formed 5 and 3 major haplotypes in the population (>5%), respectively. The results of association analysis showed that only SNP13 located in exon 10 was significantly associated with the milk production traits in the population ( < 0.05). Single nucleotide polymorphism 2, SNP5, SNP8, and SNP9 were associated with protein percentage, and SNP4 and SNP10 were associated with 305-d milk yield ( < 0.05). Our results provide evidence that polymorphisms of the buffalo gene are associated with milk production traits and can be used as a candidate gene for marker-assisted selection in buffalo breeding.

  2. Engineering validamycin production by tandem deletion of γ-butyrolactone receptor genes in Streptomyces hygroscopicus 5008.

    PubMed

    Tan, Gao-Yi; Peng, Yao; Lu, Chenyang; Bai, Linquan; Zhong, Jian-Jiang

    2015-03-01

    Paired homologs of γ-butyrolactone (GBL) biosynthesis gene afsA and GBL receptor gene arpA are located at different positions in genome of Streptomyces hygroscopicus 5008. Inactivation of afsA homologs dramatically decreased biosynthesis of validamycin, an important anti-fungal antibiotic and a critical substrate for antidiabetic drug synthesis, and the deletion of arpA homologs increased validamycin production by 26% (ΔshbR1) and 20% (ΔshbR3). By double deletion, the ΔshbR1/R3 mutant showed higher transcriptional levels of adpA-H (the S. hygroscopicus ortholog of the global regulatory gene adpA) and validamycin biosynthetic genes, and validamycin production increased by 55%. Furthermore, by engineering a high-producing industrial strain via tandem deletion of GBL receptor genes, validamycin production and productivity were enhanced from 19 to 24 g/L (by 26%) and from 6.7 to 9.7 g/L(-1) d(-1) (by 45%), respectively, which was the highest ever reported. The strategy demonstrated here may be useful to engineering other Streptomyces spp. with multiple pairs of afsA-arpA homologs.

  3. The product of the imprinted H19 gene is an oncofetal RNA.

    PubMed Central

    Ariel, I.; Ayesh, S.; Perlman, E. J.; Pizov, G.; Tanos, V.; Schneider, T.; Erdmann, V. A.; Podeh, D.; Komitowski, D.; Quasem, A. S.; de Groot, N.; Hochberg, A.

    1997-01-01

    AIMS/BACKGROUND: The H19 gene is an imprinted, maternally expressed gene in humans. It is tightly linked and coregulated with the imprinted, paternally expressed gene of insulin-like growth factor 2. The H19 gene product is not translated into protein and functions as an RNA molecule. Although its role has been investigated for more than a decade, its biological function is still not understood fully. H19 is abundantly expressed in many tissues from early stages of embryogenesis through fetal life, and is down regulated postnatally. It is also expressed in certain childhood and adult tumours. This study was designed to screen the expression of H19 in human cancer and its relation to the expression of H19 in the fetus. METHODS: Using in situ hybridisation with a [35S] labelled probe, H19 mRNA was detected in paraffin wax sections of fetal tissues from the first and second trimesters of pregnancy and of a large array of human adult and childhood tumours arising from these tissues. RESULTS: The H19 gene is expressed in tumours arising from tissues which express this gene in fetal life. Its expression in the fetus and in cancer is closely linked with tissue differentiation. CONCLUSIONS: Based on these and previous data, H19 is neither a tumour suppressor gene nor an oncogene. Its product is an oncofetal RNA. The potential use of this RNA as a tumour marker should be evaluated. Images PMID:9208812

  4. Investigation of genes involved in nisin production in Enterococcus spp. strains isolated from raw goat milk.

    PubMed

    Perin, Luana Martins; Todorov, Svetoslav Dimitrov; Nero, Luís Augusto

    2016-09-01

    Different strains of Lactococcus lactis are capable of producing the bacteriocin nisin. However, genetic transfer mechanisms allow the natural occurrence of genes involved in nisin production in members of other bacterial genera, such as Enterococcus spp. In a previous study, nisA was identified in eight enterococci capable of producing antimicrobial substances. The aim of this study was to verify the presence of genes involved in nisin production in Enterococcus spp. strains, as well as nisin expression. The nisA genes from eight Enterococcus spp. strains were sequenced and the translated amino acid sequences were compared to nisin amino-acid sequences previously described in databases. Although containing nisin structural and maturation related genes, the enterococci strains tested in the present study did not present the immunity related genes (nisFEG and nisI). The translated sequences of nisA showed some point mutations, identical to those presented by Lactococcus strains isolated from goat milk. All enterococci were inhibited by nisin, indicating the absence of immunity and thus that nisin cannot be expressed. This study demonstrated for the first time the natural occurrence of nisin structural genes in Enterococcus strains and highlights the importance of providing evidence of a link between the presence of bacteriocin genes and their expression.

  5. Overexpression of bacterial ethylene-forming enzyme gene in Trichoderma reesei enhanced the production of ethylene

    PubMed Central

    Chen, Xi; Liang, Yong; Hua, Jing; Tao, Li; Qin, Wensheng; Chen, Sanfeng

    2010-01-01

    In order to efficiently utilize natural cellulose materials to produce ethylene, three expression vectors containing the ethylene-forming enzyme (efe) gene from Pseudomonas syringae pv. glycinea were constructed. The target gene was respectively controlled by different promoters: cbh I promoter from Trichoderma reesei cellobiohydrolases I gene, gpd promoter from Aspergillus nidulans glyceraldehyde-3-phosphate dehydrogenase gene and pgk I promoter from T. reesei 3-phosphoglycerate kinase I gene. After transforming into T. reesei QM9414, 43 stable transformants were obtained by PCR amplification and ethylene determination. Southern blot analysis of 14 transformants demonstrated that the efe gene was integrated into chromosomal DNA with copy numbers from 1 to 4. Reverse transcription polymerase chain reaction (RT-PCR) analysis of 6 transformants showed that the heterologous gene was transcribed. By using wheat straw as a carbon source, the ethylene production rates of aforementioned 14 transformants were measured. Transformant C30-3 with pgk I promoter had the highest ethylene production (4,012 nl h-1 l-1). This indicates that agricultural wastes could be used to produce ethylene in recombinant filamentous fungus T. reesei. PMID:20150979

  6. New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

    PubMed Central

    Luo, Yunzi; Enghiad, Behnam; Zhao, Huimin

    2015-01-01

    Natural product scaffolds remain a major source and inspiration for human therapeutics. However, generation of a natural product in the post-genomic era often requires reconstruction of the corresponding biosynthetic gene cluster in a heterologous host. In the burgeoning fields of synthetic biology and metabolic engineering, a significant amount of efforts has been devoted to develop DNA assembly techniques with higher efficiency, fidelity, and modularity, and heterologous expression systems with higher productivity and yield. Here we describe recent advances in DNA assembly and host engineering and highlight their applications in natural product discovery and engineering. PMID:26647833

  7. New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters.

    PubMed

    Luo, Yunzi; Enghiad, Behnam; Zhao, Huimin

    2016-02-01

    Natural product scaffolds remain a major source and inspiration for human therapeutics. However, generation of a natural product in the post-genomic era often requires reconstruction of the corresponding biosynthetic gene cluster in a heterologous host. In the burgeoning fields of synthetic biology and metabolic engineering, a significant amount of efforts has been devoted to develop DNA assembly techniques with higher efficiency, fidelity, and modularity, and heterologous expression systems with higher productivity and yield. Here we describe recent advances in DNA assembly and host engineering and highlight their applications in natural product discovery and engineering.

  8. Production of indole antibiotics induced by exogenous gene derived from sponge metagenomes.

    PubMed

    Takeshige, Yuya; Egami, Yoko; Wakimoto, Toshiyuki; Abe, Ikuro

    2015-05-01

    Sponge metagenomes are accessible genetic sources containing genes and gene clusters responsible for the biosynthesis of sponge-derived bioactive natural products. In this study, we obtained the clone pDC112, producing turbomycin A and 2,2-di(3-indolyl)-3-indolone, based on the functional screening of the metagenome library derived from the marine sponge Discodermia calyx. The subcloning experiment identified ORF 25, which is homologous to inosine 5'-monophosphate dehydrogenase and required for the production of 2,2-di(3-indolyl)-3-indolone in Escherichia coli.

  9. Simvastatin and Dipentyl Phthalate Display Different Mechanisms of Action but Exhibit Dose Additive Effects on Fetal Testicular Testosterone Production in Sprague Dawley Rats

    EPA Science Inventory

    Sex differentiation of the male reproductive tract in mammals is driven, in part, by fetal androgen production. In utero exposure to some phthalate esters (PEs) alters fetal Leydig cell differentiation, reducing the expression of several genes associated with steroid synthesis/tr...

  10. Analysis of the genetic effects of prolactin gene polymorphisms on chicken egg production.

    PubMed

    Li, Hui-Fang; Shu, Jing-Ting; Du, Yu-Feng; Shan, Yan-Ju; Chen, Kuan-Wei; Zhang, Xue-Yu; Han, Wei; Xu, Wen-Juan

    2013-01-01

    Chicken prolactin (PRL) is a physiological candidate gene for egg production. Variations of T8052C and G8113C in exon 5 of PRL gene may associate with chicken egg production. The objective of the study was to investigate the association of these two single nucleotide polymorphisms in PRL gene with egg production of Recessive White chickens and Qingyuan Partridge chickens. Genotyping was performed by polymerase chain reaction-ligase detection reaction (PCR-LDR) method. The T8052C and G8113C of PRL were significantly associated with age at first egg (AFE) and total egg number at 300 days of age (EN 300). A significant association was also found between T8052C-G8113C haplotypes and AFE as well as EN300, the H2H3 was the most advantageous diplotype for egg production. We putatively drew the conclusion that these two SNPs in PRL gene as well as their haplotypes could be used as the potential molecular markers for egg production traits in chicken.

  11. Biofilm formation, phenotypic production of cellulose and gene expression in Salmonella enterica decrease under anaerobic conditions.

    PubMed

    Lamas, A; Miranda, J M; Vázquez, B; Cepeda, A; Franco, C M

    2016-12-05

    Salmonella enterica subsp. enterica is one of the main food-borne pathogens. This microorganism combines an aerobic life outside the host with an anaerobic life within the host. One of the main concerns related to S. enterica is biofilm formation and cellulose production. In this study, biofilm formation, morphotype, cellulose production and transcription of biofilm and quorum sensing-related genes of 11 S. enterica strains were tested under three different conditions: aerobiosis, microaerobiosis, and anaerobiosis. The results showed an influence of oxygen levels on biofilm production. Biofilm formation was significantly higher (P<0.05) in aerobiosis than in microaerobiosis and anaerobiosis. Cellulose production and RDAR (red, dry, and rough) were expressed only in aerobiosis. In microaerobiosis, the strains expressed the SAW (smooth and white) morphotype, while in anaerobiosis the colonies appeared small and red. The expression of genes involved in cellulose synthesis (csgD and adrA) and quorum sensing (sdiA and luxS) was reduced in microaerobiosis and anaerobiosis in all S. enterica strains tested. This gene expression levels were less reduced in S. Typhimurium and S. Enteritidis compared to the tested serotypes. There was a relationship between the expression of biofilm and quorum sensing-related genes. Thus, the results from this study indicate that biofilm formation and cellulose production are highly influenced by atmospheric conditions. This must be taken into account as contamination with these bacteria can occur during food processing under vacuum or modified atmospheres.

  12. Regulation of transcription of the adenovirus EII promoter by gene products: Absence of sequence specificity

    SciTech Connect

    Kingston, R.E.; Kaufman, R.J.; Sharp, P.A.

    1984-10-01

    During adenovirus infection, the EII promoter is positively regulated by products of the EIa region. The authors have studied this regulation by fusing a DNA segment containing the adenovirus EII promoter to a dihydrofolate reductase cDNA segment. Expression of this hybrid gene is stimulated in trans when cell lines containing an integrated copy are either transfected with plasmids carrying the EIa region or infected with adenovirus. This suggests that EIa activity regulates transcription of the EII promoter in the absence of other viral proteins and that this stimulation can occur when the EII promoter is organized in cellular chromatin. Transcription from the EII promoter is initiated at two sites in cell lines lacking EIa activity. Introduction of the EIa region preferentially stimulated transcription from one of these two sites. A sensitive, stable cotransfection assay was used to test for specific EII sequences required for stimulation. EIa activity stimulates all mutaant promoters; the most extensive deletion retained only 18 base pairs of sequences upstream of the initiation site. They suggest that regulation of a promoter by the EIa region does not depend on the presence of a set of specific sequences, but instead reflects a characteristic of promoters that have been exogenously introduced into cells. Insertion of the 72-base-pair repeat of simian-virus 40 in cis enhances transcription from the EII promoter. The stimulatory effects of EIa activity and of the simian virus 40 sequence are additive and appear to differ mechanistically.

  13. Evolution of the CD4 family: teleost fish possess two divergent forms of CD4 in addition to lymphocyte activation gene-3

    USGS Publications Warehouse

    Laing, K.J.; Zou, J.J.; Purcell, M.K.; Phillips, R.; Secombes, C.J.; Hansen, J.D.

    2006-01-01

    The T cell coreceptor CD4 is a transmembrane glycoprotein belonging to the Ig superfamily and is essential for cell-mediated immunity. Two different genes were identified in rainbow trout that resemble mammalian CD4. One (trout CD4) encodes four extracellular Ig domains reminiscent off mammalian CD4, whereas the other (CD4REL) codes for two Ig domains. Structural motifs within the amino acid sequences suggest that the two Ig domains of CD4REL duplicated to generate the four-domain molecule of CD4 and the related gene, lymphocyte activation gene-3. Here we present evidence that both of these molecules in trout are homologous to mammalian CD4 and that teleosts encode an additional CD4 family member, lymphocyte activation gene-3, which is a marker for activated T cells. The syntenic relationships of similar genes in other teleost and non-fish genomes provide evidence for the likely evolution of CD4-related molecules in vertebrates, with CD4REL likely representing the primordial form in fish. Expression of both CD4 genes is highest in the thymus and spleen, and mRNA expression of these genes is limited to surface IgM- lymphocytes, consistent with a role for T cell functionality. Finally, the intracellular regions of both CD4 and CD4REL possess the canonical CXC motif involved in the interaction off CD4 with p56LCK, implying that similar mechanisms for CD4 + T cell activation are present in all vertebrates. Our results therefore raise new questions about T cell development and functionality in lower vertebrates that cannot be answered by current mammalian models and, thus, is of fundamental importance for understanding the evolution of cell-mediated immunity in gnathosomes. Copyright ?? 2006 by The American Association of Immunologists, Inc.

  14. 1,3-Propanediol production by Escherichia coli using genes from Citrobacter freundii atcc 8090.

    PubMed

    Przystałowska, Hanna; Zeyland, Joanna; Kośmider, Alicja; Szalata, Marlena; Słomski, Ryszard; Lipiński, Daniel

    2015-01-01

    Compared with chemical synthesis, fermentation has the advantage of mass production at low cost, and has been used in the production of various industrial chemicals. As a valuable organic compound, 1,3-propanediol (1,3-PDO) has numerous applications in the production of polymers, lubricants, cosmetics and medicines. Here, conversion of glycerol (a renewable substrate and waste from biodiesel production) to 1,3-PDO by E. coli bacterial strain carrying altered glycerol metabolic pathway was investigated. Two gene constructs containing the 1,3-PDO operon from Citrobacter freundii (pCF1 and pCF2) were used to transform the bacteria. The pCF1 gene expression construct contained dhaBCE genes encoding the three subunits of glycerol dehydratase, dhaF encoding the large subunit of the glycerol dehydratase reactivation factor and dhaG encoding the small subunit of the glycerol dehydratase reactivating factor. The pCF2 gene expression construct contained the dhaT gene encoding the 1,3-propanediol dehydrogenase. Expression of the genes cloned in the above constructs was under regulation of the T7lac promoter. RT-PCR, SDS-PAGE analyses and functional tests confirmed that 1,3-PDO synthesis pathway genes were expressed at the RNA and protein levels, and worked flawlessly in the heterologous host. In a batch flask culture, in a short time applied just to identify the 1,3-PDO in a preliminary study, the recombinant E. coli bacteria produced 1.53 g/L of 1,3-PDO, using 21.2 g/L of glycerol in 72 h. In the Sartorius Biostat B Plus reactor, they produced 11.7 g/L of 1,3-PDO using 24.2 g/L of glycerol, attaining an efficiency of 0.58 [mol1,3-PDO/molglycerol].

  15. Diversity of Antibiotic Resistance Genes in Enterococcus Strains Isolated from Ready-to-Eat Meat Products.

    PubMed

    Chajęcka-Wierzchowska, Wioleta; Zadernowska, Anna; Łaniewska-Trokenheim, Łucja

    2016-10-25

    The objective of the study was to answer the question of whether the ready-to-eat meat products can pose indirect hazard for consumer health serving as reservoir of Enterococcus strains harboring tetracyclines, aminoglycosides, and macrolides resistance genes. A total of 390 samples of ready-to-eat meat products were investigated. Enterococcus strains were found in 74.1% of the samples. A total of 302 strains were classified as: Enterococcus faecalis (48.7%), Enterococcus faecium (39.7%), Enterococcus casseliflavus (4.3%), Enterococcus durans (3.0%), Enterococcus hirae (2.6%), and other Enterococcus spp. (1.7%). A high percentage of isolates were resistant to streptomycin high level (45%) followed by erythromycin (42.7%), fosfomycin (27.2%), rifampicin (19.2%), tetracycline (36.4%), tigecycline (19.9%). The ant(6')-Ia gene was the most frequently found gene (79.6%). Among the other genes that encode aminoglycosides-modifying enzymes, the highest portion of the strains had the aac(6')-Ie-aph(2'')-Ia (18.5%) and aph(3'')-IIIa (16.6%), but resistance of isolates from food is also an effect of the presence of aph(2'')-Ib, aph(2'')-Ic, aph(2'')-Id genes. Resistance to tetracyclines was associated with the presence of tetM (43.7%), tetL (32.1%), tetK (14.6%), tetW (0.7%), and tetO (0.3%) genes. The ermB and ermA genes were found in 33.8% and 18.9% of isolates, respectively. Nearly half of the isolates contained a conjugative transposon of the Tn916/Tn1545 family. Enterococci are widely present in retail ready-to-eat meat products. Many isolated strains (including such species as E. casseliflavus, E. durans, E. hirae, and Enterococcus gallinarum) are antibiotic resistant and carry transferable resistance genes.

  16. The effect of nitrate addition on abundance of nirK, nirS and gln genes in acidified Norway spruce forest soil

    NASA Astrophysics Data System (ADS)

    Bárta, Jiří; Tahovská, Karolina; Kaåa, Jiří; Antrå¯Čková, Hana Å.

    2010-05-01

    The denitrification is the main biotic process leading to loses of fixed nitrogen as well as removal of excess of nitrate (NO3-) from the soil environment. The reduction of NO2- to nitric oxide (NO) distinguishes the 'true' denitrifiers from other nitrate-respiring bacteria. This reaction is catalyzed by two different types of nitrite reductases, either a cytochrome cd1 encoded by nirS gene (nirS denitrifiers) or a Cu-containing enzyme encoded by nirK gene (nirK denitrifiers). The nirS denitrifiers are located mostly in rhizosphere, while the nirK denitrifiers are more abundant in bulk soil. These two groups can be also classified as markers of denitrification. Glutamine synthetase is one of the main bacterial NH4+ assimilating enzymes; it is coded by glnI gene. Glutamine synthetase is mostly active when N is the limiting factor for bacterial growth. There is recent evidence that the activity may be affected by the presence of alternative N source (i.e. NO3-). However, in anaerobic condition NO3- can be used also by the denitrifying bacteria so there may be strong competition for this nutrient. The laboratory experiment was performed to evaluate the effect of nitrates (NO3-) on abundance of nirK, nirS and gln gene copy numbers. The amount of NO3- corresponded to the actual atmospheric depositions on experimental sites in the Bohemian Forest. Litter organic layer (0-5cm of soil) was used for laboratory incubation experiment. Four replicates of control (no addition of NO3-), and NO3-addition were incubated anaerobically for one month. After the incubation DNA was extracted and the number of nirK, nirS and gln gene copies was determined using qPCR (SYBRGreen methodology). Results showed that the addition of NO3- significantly increased the number of nirK and nirS denitrifiers from 5.9x106 to 1.1x107 and from not detectable amount to 1.4x106, respectively. The gln gene copy number was also higher after NO3-addition. However, the difference was not statistically

  17. Isolated fungal promoters and gene transcription terminators and methods of protein and chemical production in a fungus

    DOEpatents

    Dai, Ziyu; Lasure, Linda L.; Magnuson, Jon K.

    2008-11-11

    The present invention encompasses isolated gene regulatory elements and gene transcription terminators that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention also encompasses a method of utilizing a fungus for protein or chemical production. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to another molecule comprising a coding region of a gene of interest. The gene regulatory element and gene transcription terminator may temporally and spatially regulate expression of particular genes for optimum production of compounds of interest in a transgenic fungus.

  18. Isolated fungal promoters and gene transcription terminators and methods of protein and chemical production in a fungus

    DOEpatents

    Dai, Ziyu; Lasure, Linda L; Magnuson, Jon K

    2014-05-27

    The present invention encompasses isolated gene regulatory elements and gene transcription terminators that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention also encompasses a method of utilizing a fungus for protein or chemical production. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to another molecule comprising a coding region of a gene of interest. The gene regulatory element and gene transcription terminator may temporally and spatially regulate expression of particular genes for optimum production of compounds of interest in a transgenic fungus.

  19. Isolated Fungal Promoters and Gene Transcription Terminators and Methods of Protein and Chemical Production in a Fungus

    DOEpatents

    Dai, Ziyu; Lasure, Linda L.; Magnuson, Jon K.

    2008-11-11

    The present invention encompasses isolated gene regulatory elements and gene transcription terminators that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention also encompasses a method of utilizing a fungus for protein or chemical production. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to another molecule comprising a coding region of a gene of interest. The gene regulatory element and gene transcription terminator may temporally and spatially regulate expression of particular genes for optimum production of compounds of interest in a transgenic fungus.

  20. Make or Buy: Cost Impacts of Additive Manufacturing, 3D Laser Scanning Technology, and Collaborative Product Lifecycle Management on Ship Maintenance and Modernization

    DTIC Science & Technology

    2015-05-01

    1 Make or Buy: Cost Impacts of Additive Manufacturing , 3D Laser Scanning Technology, and Collaborative Product Lifecycle Management on Ship...DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Make or Buy: Cost Impacts of Additive Manufacturing , 3D Laser Scanning Technology...management during operations 4 Potential Technology 3: Additive Manufacturing (“3D Printing”) 5 • 3D design/image (e.g. from 3D LS) of final part

  1. Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product

    PubMed Central

    Omelyanchuk, Leonid V.; Pertseva, Julia A.; Burns, Sarah S.; Chang, Long-Sheng

    2009-01-01

    Hepatocyte growth factor receptor tyrosine kinase substrate (HRS) is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2) gene product, and this interaction may be important for Merlin’s tumor suppressor activity. Understanding the evolution, origin, and structure of HRS may provide new insight into Merlin function. We show that HRS homologs are present across a wide range of Metazoa with the yeast Vps27 protein as their most distant ancestor. The phylogenetic tree of the HRS family coincides with species evolution and divergence, suggesting a unique function for HRS. Sequence alignment shows that various protein domains of HRS, including the VHS domain, the FYVE domain, the UIM domain, and the clathrin-binding domain, are conserved from yeast to multicellular organisms. The evolutionary transition from unicellular to multicellular organisms was accompanied by the appearance of a binding site for Merlin, which emerges in the early Metazoa after its separation from flatworms. In addition to the region responsible for growth suppression, the Merlin-binding and STAM-binding domains of HRS are conserved among multicellular organisms. The residue equivalent to tyrosine-377, which is phosphorylated in the human HRS protein, is highly conserved throughout the HRS family. Three additional conserved boxes lacking assigned functions are found in the HRS proteins of Metazoa. While boxes 1 and 3 may constitute the Eps-15-and Snx1-binding sites, respectively, box 2, containing the residue equivalent to tyrosine-377, is likely to be important for HRS phosphorylation. While several functional domains are conserved throughout the HRS family, the STAM-binding, Merlin-binding, and growth suppression domains evolved in the early Metazoa around the time the Merlin protein emerged. As these domains appear during the transition to multicellularity, their functional

  2. Regulatory structures for gene therapy medicinal products in the European Union.

    PubMed

    Klug, Bettina; Celis, Patrick; Carr, Melanie; Reinhardt, Jens

    2012-01-01

    Taking into account the complexity and technical specificity of advanced therapy medicinal products: (gene and cell therapy medicinal products and tissue engineered products), a dedicated European regulatory framework was needed. Regulation (EC) No. 1394/2007, the "ATMP Regulation" provides tailored regulatory principles for the evaluation and authorization of these innovative medicines. The majority of gene or cell therapy product development is carried out by academia, hospitals, and small- and medium-sized enterprises (SMEs). Thus, acknowledging the particular needs of these types of sponsors, the legislation also provides incentives for product development tailored to them. The European Medicines Agency (EMA) and, in particular, its Committee for Advanced Therapies (CAT) provide a variety of opportunities for early interaction with developers of ATMPs to enable them to have early regulatory and scientific input. An important tool to promote innovation and the development of new medicinal products by micro-, small-, and medium-sized enterprises is the EMA's SME initiative launched in December 2005 to offer financial and administrative assistance to smaller companies. The European legislation also foresees the involvement of stakeholders, such as patient organizations, in the development of new medicines. Considering that gene therapy medicinal products are developed in many cases for treatment of rare diseases often of monogenic origin, the involvement of patient organizations, which focus on rare diseases and genetic and congenital disorders, is fruitful. Two such organizations are represented in the CAT. Research networks play another important role in the development of gene therapy medicinal products. The European Commission is funding such networks through the EU Sixth Framework Program.

  3. High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products.

    PubMed

    Scripture, J B; Voelker, C; Miller, S; O'Donnell, R T; Polgar, L; Rade, J; Horazdovsky, B F; Hogg, R W

    1987-09-05

    The nucleotide sequence of the "high-affinity" L-arabinose transport operon has been determined 3' from the regulatory region and found to contain three open reading frames designated araF, araG and araH. The first gene 3' to the regulatory region, araF, encodes the 23-residue signal peptide and the 306-residue mature form of the L-arabinose binding protein (33,200 Mr). The binding protein, which has been described elsewhere, is hydrophilic, soluble and found in the periplasm of Escherichia coli. This gene is followed by an intragenic space of 72 nucleotides, which contains a region of dyad symmetry 23 nucleotides long capable of forming an 11-member stem-loop. The second gene, designated araG, contains an open reading frame capable of encoding an equally hydrophilic protein containing 504 residues (55,000 Mr). Following a 14-nucleotide spacer, which does not appear to have any secondary structure, the third open reading frame, herein designated araH, is capable of encoding a hydrophobic protein containing 329 residues (34,000 Mr) that can only be envisioned as having an integral membrane location. 3' to araH there is a T-rich region containing a 24-nucleotide area of dyad symmetry centered 55 nucleotides from the termination codon. Analysis of the derived primary sequences of the araG and araH products indicates the nature and potential features of these components. The araG protein was found to possess internal homology between its amino and carboxyl-terminal halves, suggesting a common origin. The araG gene product has been shown to be homologous to the rbsA gene product, the hisP product, the ptsB product and the malK product, all of which presumably play similar roles in their respective transport systems. Putative ATP binding sites are observed within the regions of homology. The araH gene product has been shown to be homologous to the rbsC gene product, which is the first observed homology between two purported membrane proteins.

  4. Development of Ecogenomic Sensors for Remote Detection of Marine Microbes, Their Genes and Gene Products

    NASA Astrophysics Data System (ADS)

    Scholin, C.; Preston, C.; Harris, A.; Birch, J.; Marin, R.; Jensen, S.; Roman, B.; Everlove, C.; Makarewicz, A.; Riot, V.; Hadley, D.; Benett, W.; Dzenitis, J.

    2008-12-01

    An internet search using the phrase "ecogenomic sensor" will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context. However, a strict and unified definition of "ecogenomic sensor" is lacking and the phrase may be used for laboratory-based tools and techniques as well as semi or fully autonomous systems that can be deployed outside of laboratory. We are exploring development of an ecogenomic sensor from the perspective of a field-portable device applied towards oceanographic research and water quality monitoring. The device is known as the Environmental Sample Processor, or ESP. The ESP employs wet chemistry molecular analytical techniques to autonomously assess the presence and abundance of specific organisms, their genes and/or metabolites in near real-time. Current detection chemistries rely on low- density DNA probe and protein arrays. This presentation will emphasize results from 2007-8 field trials when the ESP was moored in Monterey Bay, CA, as well as current engineering activities for improving analytical capacity of the instrument. Changes in microbial community structure at the rRNA level were observed remotely in accordance with changing chemical and physical oceanographic conditions. Current developments include incorporation of a reusable solid phase extraction column for purifying nucleic acids and a 4-channel real-time PCR module. Users can configure this system to support a variety of PCR master mixes, primer/probe combinations and control templates. An update on progress towards fielding a PCR- enabled ESP will be given along with an outline of plans for its use in coastal and oligotrophic oceanic regimes.

  5. Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease.

    PubMed

    De Ravin, Suk See; Reik, Andreas; Liu, Pei-Qi; Li, Linhong; Wu, Xiaolin; Su, Ling; Raley, Castle; Theobald, Narda; Choi, Uimook; Song, Alexander H; Chan, Andy; Pearl, Jocelynn R; Paschon, David E; Lee, Janet; Newcombe, Hannah; Koontz, Sherry; Sweeney, Colin; Shivak, David A; Zarember, Kol A; Peshwa, Madhusudan V; Gregory, Philip D; Urnov, Fyodor D; Malech, Harry L

    2016-04-01

    Gene therapy with genetically modified human CD34(+) hematopoietic stem and progenitor cells (HSPCs) may be safer using targeted integration (TI) of transgenes into a genomic 'safe harbor' site rather than random viral integration. We demonstrate that temporally optimized delivery of zinc finger nuclease mRNA via electroporation and adeno-associated virus (AAV) 6 delivery of donor constructs in human HSPCs approaches clinically relevant levels of TI into the AAVS1 safe harbor locus. Up to 58% Venus(+) HSPCs with 6-16% human cell marking were observed following engraftment into mice. In HSPCs from patients with X-linked chronic granulomatous disease (X-CGD), caused by mutations in the gp91phox subunit of the NADPH oxidase, TI of a gp91phox transgene into AAVS1 resulted in ∼15% gp91phox expression and increased NADPH oxidase activity in ex vivo-derived neutrophils. In mice transplanted with corrected HSPCs, 4-11% of human cells in the bone marrow expressed gp91phox. This method for TI into AAVS1 may be broadly applicable to correction of other monogenic diseases.

  6. Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error.

    PubMed

    Fan, Qiao; Verhoeven, Virginie J M; Wojciechowski, Robert; Barathi, Veluchamy A; Hysi, Pirro G; Guggenheim, Jeremy A; Höhn, René; Vitart, Veronique; Khawaja, Anthony P; Yamashiro, Kenji; Hosseini, S Mohsen; Lehtimäki, Terho; Lu, Yi; Haller, Toomas; Xie, Jing; Delcourt, Cécile; Pirastu, Mario; Wedenoja, Juho; Gharahkhani, Puya; Venturini, Cristina; Miyake, Masahiro; Hewitt, Alex W; Guo, Xiaobo; Mazur, Johanna; Huffman, Jenifer E; Williams, Katie M; Polasek, Ozren; Campbell, Harry; Rudan, Igor; Vatavuk, Zoran; Wilson, James F; Joshi, Peter K; McMahon, George; St Pourcain, Beate; Evans, David M; Simpson, Claire L; Schwantes-An, Tae-Hwi; Igo, Robert P; Mirshahi, Alireza; Cougnard-Gregoire, Audrey; Bellenguez, Céline; Blettner, Maria; Raitakari, Olli; Kähönen, Mika; Seppala, Ilkka; Zeller, Tanja; Meitinger, Thomas; Ried, Janina S; Gieger, Christian; Portas, Laura; van Leeuwen, Elisabeth M; Amin, Najaf; Uitterlinden, André G; Rivadeneira, Fernando; Hofman, Albert; Vingerling, Johannes R; Wang, Ya Xing; Wang, Xu; Tai-Hui Boh, Eileen; Ikram, M Kamran; Sabanayagam, Charumathi; Gupta, Preeti; Tan, Vincent; Zhou, Lei; Ho, Candice E H; Lim, Wan'e; Beuerman, Roger W; Siantar, Rosalynn; Tai, E-Shyong; Vithana, Eranga; Mihailov, Evelin; Khor, Chiea-Chuen; Hayward, Caroline; Luben, Robert N; Foster, Paul J; Klein, Barbara E K; Klein, Ronald; Wong, Hoi-Suen; Mitchell, Paul; Metspalu, Andres; Aung, Tin; Young, Terri L; He, Mingguang; Pärssinen, Olavi; van Duijn, Cornelia M; Jin Wang, Jie; Williams, Cathy; Jonas, Jost B; Teo, Yik-Ying; Mackey, David A; Oexle, Konrad; Yoshimura, Nagahisa; Paterson, Andrew D; Pfeiffer, Norbert; Wong, Tien-Yin; Baird, Paul N; Stambolian, Dwight; Wilson, Joan E Bailey; Cheng, Ching-Yu; Hammond, Christopher J; Klaver, Caroline C W; Saw, Seang-Mei; Rahi, Jugnoo S; Korobelnik, Jean-François; Kemp, John P; Timpson, Nicholas J; Smith, George Davey; Craig, Jamie E; Burdon, Kathryn P; Fogarty, Rhys D; Iyengar, Sudha K; Chew, Emily; Janmahasatian, Sarayut; Martin, Nicholas G; MacGregor, Stuart; Xu, Liang; Schache, Maria; Nangia, Vinay; Panda-Jonas, Songhomitra; Wright, Alan F; Fondran, Jeremy R; Lass, Jonathan H; Feng, Sheng; Zhao, Jing Hua; Khaw, Kay-Tee; Wareham, Nick J; Rantanen, Taina; Kaprio, Jaakko; Pang, Chi Pui; Chen, Li Jia; Tam, Pancy O; Jhanji, Vishal; Young, Alvin L; Döring, Angela; Raffel, Leslie J; Cotch, Mary-Frances; Li, Xiaohui; Yip, Shea Ping; Yap, Maurice K H; Biino, Ginevra; Vaccargiu, Simona; Fossarello, Maurizio; Fleck, Brian; Yazar, Seyhan; Tideman, Jan Willem L; Tedja, Milly; Deangelis, Margaret M; Morrison, Margaux; Farrer, Lindsay; Zhou, Xiangtian; Chen, Wei; Mizuki, Nobuhisa; Meguro, Akira; Mäkelä, Kari Matti

    2016-03-29

    Myopia is the most common human eye disorder and it results from complex genetic and environmental causes. The rapidly increasing prevalence of myopia poses a major public health challenge. Here, the CREAM consortium performs a joint meta-analysis to test single-nucleotide polymorphism (SNP) main effects and SNP × education interaction effects on refractive error in 40,036 adults from 25 studies of European ancestry and 10,315 adults from 9 studies of Asian ancestry. In European ancestry individuals, we identify six novel loci (FAM150B-ACP1, LINC00340, FBN1, DIS3L-MAP2K1, ARID2-SNAT1 and SLC14A2) associated with refractive error. In Asian populations, three genome-wide significant loci AREG, GABRR1 and PDE10A also exhibit strong interactions with education (P<8.5 × 10(-5)), whereas the interactions are less evident in Europeans. The discovery of these loci represents an important advance in understanding how gene and environment interactions contribute to the heterogeneity of myopia.

  7. Control of hydrogen sulfide production in oil fields by managing microbial communities through nitrate or nitrite addition

    NASA Astrophysics Data System (ADS)

    Hubert, Casey R. J.

    Nitrate or nitrite injection into oil reservoirs during water flooding has the potential to control biological souring, the production of hydrogen sulfide (H2S) by sulfate-reducing bacteria (SRB). Souring control is essential because sulfide is toxic, sulfide precipitates can plug reservoir formations, souring lowers crude oil value, and SRB induce corrosion. Nitrate and nitrite can stimulate heterotrophic nitrate- or nitrite-reducing bacteria (hNRB) and nitrate- or nitrite-reducing, sulfide oxidizing bacteria (NRSOB). Nitrite also inhibits SRB activity by blocking the sulfate reduction pathway. Continuous up-flow packed-bed bioreactors were inoculated with produced water from the Coleville oil field to establish sulfide-producing biofilms similar to those found in sour reservoirs. Nitrate or nitrite addition to bioreactors indicated that the dose required for hNRB or NR-SOB to control souring depended on the concentration of oil organics. Either mechanism mediates the net removal of oil organics (lactate) with nitrate or nitrite, with low