Implementation of garlic cryopreservation techniques in the national plant germplasm system

The USDA-ARS National Plant Germplasm System (NPGS) maintains more than 200 Allium sativum (garlic) accessions at the Western Regional Plant Introduction Station in Pullman, WA. All accessions must be grown out in the field annually since garlic plants from these accessions do not reliably produce seeds and bulbs do not store well. Shoot tips excised from garlic cloves can be successfully cryopreserved using either Plant Vitrification Solution 2 (PVS2; 15 percent v/v DMSO, 15 percent v/v ethylene glycol, 30 percent v/w glycerol, 0.4 M sucrose) or Plant Vitrification Solution 3 (PVS3; 50 percent v/w sucrose, 50 percent v/w glycerol). We compared regrowth of shoot tips representing diverse garlic germplasm after exposure to either PVS2 or PVS3 during the cryopreservation procedure. At the USDA-ARS National Center for Genetic Resources Preservation, a component of the NPGS, we consider accessions successfully preserved if a minimum of 40 percent of explants exhibit regrowth after liquid nitrogen exposure and at least 60 viable shoot tips remain in long-term storage. Ten of twelve diverse garlic accessions were successfully cryopreserved using either PVS2 or PVS3 as cryoprotectants. Five genotypes had the best post liquid nitrogen regrowth after exposure to PVS2, four genotypes had the best regrowth after exposure to PVS3, and three genotypes performed equally well using either cryoprotectant solution. This project is part of an ongoing program to cryopreserve accessions of NPGS clonal crop collections.     

Extending the GGobi pipeline from R

This paper describes progress towards developing a platform for rapid prototyping of interactive data visualizations, using R, GGobi, rggobi and RGtk2. GGobi is a software tool for multivariate interactive graphics. At the core of GGobi is a data pipeline that incrementally transforms data through a series of stages into a plot and maps user interaction with the plot back to the data. The GGobi pipeline is extensible and mutable at runtime. The rggobi package, an interface from the R language to GGobi, has been augmented with a low-level interface that supports the customization of interactive data visualizations through the extension and manipulation of the GGobi pipeline. The large size of the GGobi API has motivated the use of the RGtk2 code generation system to create the low-level interface between R and GGobi. The software is demonstrated through an application to interactive network visualization.     

On sensitivity of Gauss–Christoffel quadrature

In numerical computations the question how much does a function change under perturbations of its arguments is of central importance. In this work, we investigate sensitivity of Gauss–Christoffel quadrature with respect to small perturbations of the distribution function. In numerical quadrature, a definite integral is approximated by a finite sum of functional values evaluated at given quadrature nodes and multiplied by given weights. Consider a sufficiently smooth integrated function uncorrelated with the perturbation of the distribution function. Then it seems natural that given the same number of function evaluations, the difference between the quadrature approximations is of the same order as the difference between the (original and perturbed) approximated integrals. That is perhaps one of the reasons why, to our knowledge, the sensitivity question has not been formulated and addressed in the literature, though several other sensitivity problems, motivated, in particular, by computation of the quadrature nodes and weights from moments, have been thoroughly studied by many authors. We survey existing particular results and show that even a small perturbation of a distribution function can cause large differences in Gauss–Christoffel quadrature estimates. We then discuss conditions under which the Gauss–Christoffel quadrature is insensitive under perturbation of the distribution function, present illustrative examples, and relate our observations to known conjectures on some sensitivity problems. The work of the first author was supported by the National Science Foundation under Grants CCR-0204084 and CCF-0514213. The work of the other two authors was supported by the Program Information Society under project 1ET400300415 and by the Institutional Research Plan AV0Z100300504. P. Tichy in the years 2003–2006 on leave at the Institute of Mathematics, TU Berlin, Germany.     

SPECTRAL DEPENDENCE OF UV-INDUCED IMMEDIATE AND DELAYED APOPTOSIS: THE ROLE OF MEMBRANE AND DNA DAMAGE

Abstract— The phototoxicity of each waveband region of UV radiation (UVR), i.e., UVA (32CM100 nm), UVB (290–320 nm) and UVC (200–290 nm), was correlated with an apoptotic mechanism using equilethal doses (10% survival) on murine lymphoma L5178Y-R cells. Apoptosis was qualitatively monitored for DNA "ladder" formation (multiples of 200 base pair units) using agarose gel electrophoresis, while the percentages of apoptotic and membrane-permeabilized cells were quantified over a postexposure time course using flow cytometry. The UVA1 radiation (340–400 nm) induced both an immediate (<4 h) and a delayed (>20 h) apoptotic mechanism, while UVB or UVC radiation induced only the delayed mechanism. The role of membrane damage was examined using a lipophilic free-radical scavenger, vitamin E. Immediate apoptosis and membrane permeability increased in a UVA1 dose-dependent manner, both of which were reduced by vitamin E. However, vitamin E had little effect on UVR-induced delayed apoptosis. In contrast, the DNA damaging agents 2,4- and 2,6-diaminotoluene exclusively induced delayed apoptosis. Thus, immediate apoptosis can be initiated by UVA 1-induced membrane damage, while delayed apoptosis can be initiated by DNA damage. Moreover, the results suggest that immediate and delayed apoptosis are two independent mechanisms that exist beyond the realm of photobiology.     

UV doses worldwide

UV radiation affects human health. Human exposure to UV radiation causes a few beneficial health effects like vitamin D3 formation but it causes many detrimental health effects: sunburn, ocular damage, photoaging, immune suppression, DNA damage and skin cancer. In countries with fair-skinned populations, skin cancer is the most diagnosed of all cancers. In the United States in 2002, there were over one million new skin cancer cases. That means one out of every 285 people got skin cancer. Skin cancer of fair-skinned individuals is increasing at an alarming rate (4-6% per year) around the world and has now reached so-called "pandemic" proportions. Thus, it is important to know what UV doses people around the world get throughout their lives. This review covers how the outdoor UV doses are weighted for different biological effects, the most commonly used measuring devices for terrestrial and personal UV doses, the natural and other effects on terrestrial and personal UV doses, the time people spend outside, their ambient exposures and the terrestrial and personal UV doses of adult outdoor and indoor workers as well as children and adolescents around the world. Overall, outdoor-working adults get about 10%, while indoor-working adults and children get about 3% (2-4%) of the total available annual UV (on a horizontal plane). People's UV doses increase with increasing altitude and decreasing latitude; most indoor-working adult Europeans get 10,000-20,000 J/m2 per year, Americans get 20,000-30,000 J/m2 per year and Australians are estimated to get 20,000-50,000 J/m2 per year (excluding vacation, which can increase the dose by 30% or more).     

Three new mussel tissue standard reference materials (SRMs) for the determination of organic contaminants

Three new mussel tissue standard reference materials (SRMs) have been developed by the National Institute of Standards and Technology (NIST) for the determination of the concentrations of organic contaminants. The most recently prepared material, SRM 1974b, is a fresh frozen tissue homogenate prepared from mussels (Mytilus edulis) collected in Boston Harbor, Massachusetts. The other two materials, SRMs 2977 and 2978, are freeze-dried tissue homogenates prepared from mussels collected in Guanabara Bay, Brazil and Raritan Bay, New Jersey, respectively. All three new mussel tissue SRMs complement the current suite of marine natural-matrix SRMs available from NIST that are characterized for a wide range of contaminants (organic and inorganic). SRM 1974b has been developed to replace its predecessor SRM 1974a, Organics in Mussel Tissue, for which the supply is depleted. Similarly, SRMs 2977 and 2978 were developed to replace a previously available (supply depleted) freeze-dried version of SRM 1974a, SRM 2974, Organics in Freeze-Dried Mussel Tissue. SRM 1974b is the third in a series of fresh frozen mussel tissue homogenate SRMs prepared from mussels collected in Boston Harbor starting in 1988. SRM 1974b has certified concentration values for 22 polycyclic aromatic hydrocarbons (PAHs), 31 polychlorinated biphenyl congeners (PCBs), and 7 chlorinated pesticides. Reference values are provided for additional constituents: 16 PAHs, 8 PCBs plus total PCBs, 6 pesticides, total extractable organics, methylmercury, and 11 trace elements. PAH concentrations range from about 2 ng g^–1 dry mass (cyclopenta[cd]pyrene) to 180 ng g^–1 dry mass (pyrene). PCB concentrations range from about 2 ng g^–1 dry mass (PCB 157) to 120 ng g^–1 dry mass (PCB 153). The reference value for total PCBs in SRM 1974b is (2020 ± 420) ng g^–1 dry mass. Pesticide concentrations range from about 4 ng g^–1 dry mass (4,4-DDT) to 40 ng g^–1 dry mass (4,4-DDE). SRM 2977 has certified values for 14 PAHs, 25 PCB congeners, 7 pesticides, 6 trace elements, and methylmercury. Reference values for 16 additional PAHs and 9 inorganic constituents are provided, and information values are given for 23 additional trace elements. SRM 2978 has certified and reference concentrations for 41 and 22 organic compounds, respectively, and contains contaminant levels similar to those of SRM 1974b. Organic contaminant levels in SRM 2977 (mussels from Guanabara Bay, Brazil) are typically a factor of 2 to 4 lower than those in SRM 1974b and SRM 2978. The organic contaminant concentrations in each new mussel tissue SRM are presented and compared in this paper. In addition, a chronological review of contaminant concentrations associated with mussels collected in Boston Harbor is discussed as well as a stability assessment of SRM 1974a.Electronic Supplementary Material Supplementary material is available in the online version of this article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Molecular dynamics simulations of pregelification mixtures for the production of imprinted xerogels

A series of molecular dynamics (MD) simulations of different pregelification mixtures representing intermediate stages of the sol-gel process were set up to gain insight into the molecular imprinting process in xerogels, namely, to assess the template-gel affinity and template self-aggregation. The physical plausibility of the parametrization was checked, confirming the reliability of the simulations. The simulated mixtures differed in the water/methanol ratio (1:3, 5:3, and 5:1) and in the absence/presence of an organic functional group (phenylaminopropyl-) in the silicate species. The simulation results, expressed mainly by the radial distribution functions and respective coordination numbers, showed that the affinity of the template molecule, damascenone (a hydrophobic species), for the gel backbone would not be attained without the tested functional group, phenylaminopropyl-. The affinity, related to the capability to trap the template within the gel network, was derived mostly from the hydrophobic interaction. It was also inferred from MD simulations that lower water contents (methanol-richer mixtures) would facilitate a better dispersion of both the functional group and the template within the final gel, therefore favoring the imprinting process. From the experimental counterparts of the simulated mixtures, a series of imprinted and nonimprinted xerogels were obtained. There was only one xerogel exhibiting the imprinting effect, namely, the one containing the organic group obtained at the lower water/methanol ratio (1:3), in agreement with predictions from the MD simulations. Such congruence demonstrates the ability of MD simulations to provide information regarding the fine aspects of molecular interactions in pregelification mixtures for imprinting.     

A Novel Synthesis of 3-Amido-5-phenyl-benzazepin-2-one via an Intramolecular Amidoalkylation

A synthesis of N-(8-Methyl-2-oxo-5-phenyl-2,3-dihydro-1H-benz[b]azepin-3-yl)-benzamide 2 via an intramolecular amidoalkylation is described.     

Commercialization of biomass ethanol technology

Applied Biochemistry and Biotechnology - With the recent commissioning of the National Renewable Energy Laboratory’s (NREL) process development unit, through the support of the US Department...