Characterization of Coupled Gold Nanoparticles in a Sparsely Populated Square Lattice

Metal nanoparticles deposited in regular arrays spaced at optical wavelengths support a resonance due to a coherent coupling between localized surface plasmon mode and lattice diffraction allowing for engineering of tunable devices for use in biological sensors, nanoantennae, and enhanced spectroscopy. Techniques such as electron beam lithography, focused ion beam lithography, nanosphere lithography, and nanoimprint lithography are used for fabrication but are limited by cost, device throughput, and small deposition. Polymer soft lithography and continuous dewetting of particles is a potentially viable alternative showing promise in all of those areas. This thesis developed the fabrication of a refined hydrophilic nanoimprinted polymer substrate with a regular square lattice and characterized the optical response of sparsely deposited nanoparticles by continuous dewetting which permit a diffractive lattice coupling

Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model

AbstractStructure of Wheat streak mosaic virus (WSMV) populations derived from a common founding event and subjected to serial passage at high multiplicity of infection (MOI) was evaluated. The founding population was generated by limiting dilution inoculation. Lineages of known pedigree were sampled at passage 9 (two populations) and at passage 15, with (three populations) or without mixing (four populations) of lineages at passage 10. Polymorphism within each population was assessed by sequencing 17–21 clones containing a 1371 nt region (WSMV-Sidney 81 nts 8001–9371) encompassing the entire coat protein cistron and flanking regions. Mutation frequency averaged ∼5.0 × 10−4/nt across all populations and ranged from 2.4 to 11.6 × 10−4/nt within populations, but did not consistently increase or decrease with the number of passages removed from the founding population. Shared substitutions (19 nonsynonymous, 10 synonymous, and 3 noncoding) occurred at 32 sites among 44 haplotypes. Only four substitutions became fixed (frequency = 100%) within a population and nearly one third (10/32) never achieved a frequency of 10% or greater in any sampled population. Shared substitutions were randomly distributed with respect to genome position, with transitions outnumbering transversions 5.4:1 and a clear bias for A to G and U to C substitutions. Haplotype composition of each population was unique with complexity of each population varying unpredictably, in that the number and frequency of haplotypes within a lineage were not correlated with number of passages removed from the founding population or whether the population was derived from a single or mixed lineage. The simplest explanation is that plant virus lineages, even those propagated at high MOI, are subject to frequent, narrow genetic bottlenecks during systemic movement that result in low effective population size and stochastic changes in population structure upon serial passage

Genome sequences of \u3ci\u3eAgropyron mosaic virus\u3c/i\u3e and \u3ci\u3eHordeum mosaic virus \u3c/i\u3esupport reciprocal monophyly of the genera \u3ci\u3ePotyvirus\u3c/i\u3e and \u3ci\u3eRymovirus \u3c/i\u3e in the family \u3ci\u3ePotyviridae\u3c/i\u3e

Assignment of mite-transmitted species to the genus Rymovirus (family Potyviridae) has changed several times, and the status of the genus has been questioned. To address this issue, complete genome sequences of the rymoviruses Agropyron mosaic virus (AgMV) and Hordeum mosaic virus (HoMV) were determined. AgMV (9540 nucleotides) and HoMV (9463 nucleotides) each encode a single polyprotein with proteinase cleavage sites demarcating protein products characteristic of monopartite species of the family Potyviridae. Of the described species of Potyviridae, AgMV and HoMV are most closely related to each other (68.5% nucleotide and 71.6% amino acid sequence identity) and equidistant (about 53% nucleotide and about 49% amino acid sequence identity) from a third rymovirus, Ryegrass mosaic virus (RGMV). Phylogenetic analyses by neighbor joining, maximum parsimony, and Bayesian inference each grouped the three Rymovirus species in an exclusive clade distinct from a clade containing 34 species of the genus Potyvirus. Because AgMV, HoMV, and RGMV share a reciprocal monophyletic relationship with species of the genus Potyvirus and are divergent in sequence and type of vector, the genus Rymovirus should be retained as a taxonomic unit within the family Potyviridae

Integrating multicriteria decision analysis and scenario planning : review and extension

Scenario planning and multiple criteria decision analysis (MCDA) are two key management science tools used in strategic planning. In this paper, we explore the integration of these two approaches in a coherent manner, recognizing that each adds value to the implementation of the other. Various approaches that have been adopted for such integration are reviewed, with a primary focus on the process of constructing preferences both within and between scenarios. Biases that may be introduced by inappropriate assumptions during such processes are identified, and used to motivate a framework for integrating MCDA and scenario thinking, based on applying MCDA concepts across a range of "metacriteria" (combinations of scenarios and primary criteria). Within this framework, preferences according to each primary criterion can be expressed in the context of different scenarios. The paper concludes with a hypothetical but non-trivial example of agricultural policy planning in a developing country

United States Patent 5,500,360: RNA TRANSFORMATION VECTOR

A + strand RNA viral transformation of host organisms with foreign RNA, and expression of said foreign RNA. The foreign RNA is inserted into an infective RNA viral segment containing replication elements, and allowed to infect the host organism. The invention is exemplified utilizing brome mosaic RNA modified to contain a gene coding for chloramphenicol acetyl transferase (CAT) in the transformation of barley protoplasts

United States Patent, Number: 5,633,447: PLANT TISSUE COMPRISING A SUBGENOMIC PROMOTER

A subgenomic promoter of a positive strand RNA virus is disclosed which directs the amplified expression of a structural gene in plant tissue. The core region and an upstream activating domain of the subgenomic promoter are identified. This promoter can be utilized in a modified virus. or in an appropriate engineered recombinant DNA derivative which may be chromosomally integrated or maintained as an episome in transformed cells

Replication confers β cell immaturity.

Pancreatic β cells are highly specialized to regulate systemic glucose levels by secreting insulin. In adults, increase in β-cell mass is limited due to brakes on cell replication. In contrast, proliferation is robust in neonatal β cells that are functionally immature as defined by a lower set point for glucose-stimulated insulin secretion. Here we show that β-cell proliferation and immaturity are linked by tuning expression of physiologically relevant, non-oncogenic levels of c-Myc. Adult β cells induced to replicate adopt gene expression and metabolic profiles resembling those of immature neonatal β that proliferate readily. We directly demonstrate that priming insulin-producing cells to enter the cell cycle promotes a functionally immature phenotype. We suggest that there exists a balance between mature functionality and the ability to expand, as the phenotypic state of the β cell reverts to a less functional one in response to proliferative cues

Multiple Interactions among Proteins Encoded by the Mite-Transmitted Wheat Streak Mosaic Tritimovirus

AbstractThe genome organization of the mite-transmitted wheat streak mosaic virus (WSMV) appears to parallel that of members of the Potyviridae with monopartite genomes, but there are substantial amino acid dissimilarities with other potyviral polyproteins. To initiate studies on the functions of WSMV-encoded proteins, a protein interaction map was generated using a yeast two-hybrid system. Because the pathway of proteolytic maturation of the WSMV polyprotein has not been experimentally determined, random libraries of WSMV cDNA were made both in DNA-binding domain and activation domain plasmid vectors and introduced into yeast. Sequence analysis of multiple interacting pairs revealed that interactions largely occurred between domains within two groups of proteins. The first involved interactions among nuclear inclusion protein a, nuclear inclusion protein b, and coat protein (CP), and the second involved helper component-proteinase (HC-Pro) and cylindrical inclusion protein (CI). Further immunoblot and deletion mapping analyses of the interactions suggest that subdomains of CI, HC-Pro, and P1 interact with one another. The two-hybrid assay was then performed using full-length genes of CI, HC-Pro, P1, P3, and CP, but no heterologous interactions were detected. In vitro binding assay using glutathione-S-transferase fusion proteins and in vitro translation products, however, revealed mutual interactions among CI, HC-Pro, P1, and P3. The failure to detect interactions between full-length proteins by the two-hybrid assay might be due to adverse effects of expression of viral proteins in yeast cells. The capacity to participate in multiple homomeric and heteromeric molecular interactions is consistent with the pleiotropic nature of many potyviral gene mutants and suggests mechanisms for regulation of various viral processes via a network of viral protein complexes

The open reading frame 5A of foxtail mosaic virus is expressed in vivo and is dispensable for systemic infection

Infectious transcripts were successfully derived from full-length cDNA clones of foxtail mosaic potexvirus (FoMV). Full-length clones were constructed by RT-PCR whereby 50 and 30 genomic segments of 2.7 and 3.4 kb, respectively, were ligated into Bluescript II KS. The in vitro RNA transcripts were infectious to moncotyledonous (barley) and dicotyledonous (Chenopodium amaranticolor) plant species. Individual mutation studies on clones of each of the five major ORFs confirmed predicted gene function for the polymerase, TGB (triple gene block), and coat protein (CP) genes. Protoplast studies on expression of a unique open reading frame, ORF 5A, which initiates 143 nts upstream of the CP before it “reads through” the CP, revealed that the 5A protein was produced in vivo. Mutation analysis of the 5A ORF indicated, however, that it was not required for either replication or for productive infection of plants. However, the nucleic acid sequences encoding the extended CP segment were shown to be important for CP expression. Additional mutations in 5A had no effect on FoMV replication in protoplasts but rendered the virus noninfectious to plants. A correlation with diminished CP production from both mutant clones implies that synthesis of subgenomic CP mRNA was compromised, and this limited systemic infection

Molecular Cloning of Sugarcane Mosaic Virus Complementary-Dna: Use as a Probe for the Detection of Virus Infection and Viral-Rnas.

DNA complementary (cDNA) to the RNA genome of sugarcane mosaic virus strain H (SCMV-H) was synthesized using avian myeloblastosis virus reverse transcriptase and oligo(dT) as primer. Second strand synthesis used the same enzyme and oligo(dG) primer after tailing the first strand with oligo(dC). Double-stranded cDNA was inserted into the PstI site of plasmid pBR322 by the G-C tailing method and cloned in Esherichia coli HB101. Twenty recombinant clones containing SCMV-H sequences were obtained, but most had inserts less than 500 base pairs (0.5 kbp). Two plasmids, S47-6 and S47-20, however, had larger inserts of 1.2 kbp and 2.7 kbp, respectively and were used for further study. These two plasmids had some SCMV-H sequences in common, but did not share any BamHI, EcoRI, HindIII, PstI, or SalI restriction sites. Dot blot hybridization, which involves spotting crude plant extracts on nitrocellulose filters and hybridizing with (\u2732)P-labeled recombinant S47-6 or S47-20 plasmid DNA, proved to be a rapid and sensitive method for detecting SCMV-H infection. Sap from SCMV-infected plants diluted 1/1000 to 1/3000 gave detectable hybridization signals as did 15 to 40 pg purified viral RNA. Dot blot hybridization also revealed that SCMV strain I, but not SCMV strains A, B, D, M, and J, has sequences in common with the strain H-derived clones. Northern hybridization of single-stranded RNA from SCMV-infected tissue showed that, besides genomic RNA, a series of smaller RNAs with sizes of 7.9, 6.6, 4.7, 2.8, 1.5, 1.2, 0.9, and 0.7 kb hybridized to the probe. No discrete viral double-stranded RNA species were found. Serologically specific electron microscopy of plant extracts was used to demonstrate a series of discrete less-than-full-length virus particles, two of which correlate with the 7.9 and 6.6 kb RNAs