Does contamination buildup limit throughput for automated cryoEM?

The development of automated systems for data acquisition in cryo electron microscopy has enabled the possibility of acquiring very large number of images from a single specimen grid. We have demonstrated that over images of 250,000 single particles can be acquired in a 24 h period. This has raised questions as to whether contamination buildup on the specimen limits the quality of the data that can be acquired during these long duration experiments and also whether the data acquisition session could be extended to allow acquisition of more than 1,000,000 particles. We report here a systematic characterization of contamination of specimens maintained for long periods of time at liquid nitrogen temperatures using standard side entry cryo stages. As part of this characterization we developed a more reliable method for accurately estimating specimen ice thickness. Using the method, we were able to calibrate image contrast against ice thickness under a variety of magnifications, objective aperture positions, and defoci, and demonstrated the strong dependence of the calibration curve on these parameters. The results show the anti-contamination aperture is, as expected, critical to the prevention of contamination and that loading film into the microscope dramatically increases the contamination rate, particularly in the first 3 h after the insertion of the film box. In the absence of film, we were able to reproducibly demonstrate that the contamination rate can be limited to a rate of approximately 1 angstrom/h providing reassurance that contamination will not be a major limiting factor for long term cryoEM experiments if a CCD camera is used for the imaging.     

Microbial control of black cutworm (Lepidoptera: Noctuidae) in turfgrass using Agrotis ipsilon multiple nucleopolyhedrovirus

Agrotis ipsilon multiple nucleopolyhedrovirus (family Baculoviridae, genus Nucleopolyhedrovirus, AgipMNPV), a naturally occurring baculovirus, was found infecting black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae), on central Kentucky golf courses. Laboratory, greenhouse, and field studies investigated the potential of AgipMNPV for managing black cutworms in turfgrass. The virus was highly active against first instars (LC50 = 73 occlusion bodies [OBs] per microl with 2-microl dose; 95% confidence intervals, 55-98). First instars that ingested a high lethal dose stopped feeding and died in 3-6 d as early second instars, whereas lethally infected fourth instars continued to feed and grow for 4-9 d until death. Sublethal doses consumed by third or fifth instars had little or no effect on subsequent developmental rate or pupal weight. Horizontal transmission of AgipMNPV in turfgrass plots was shown. Sprayed suspensions of AgipMNPV (5 x 10(8) - 6 x 10(9) OBs/m2) resulted in 75 to > 93% lethal infection of third or fourth instars in field plots of fairway-height creeping bentgrass, Agrostis stolonifera (Huds.), and on a golf course putting green collar. Virus spray residues (7 x 10(9) OBs/m2) allowed to weather on mowed and irrigated creeping bentgrass field plots significantly increased lethal infection of implanted larvae for at least 4 wk. This study, the first to evaluate a virus against a pest in turfgrass, suggests that AgipMNPV has potential as a preventive bioinsecticide targeting early instar black cutworms. Establishing a virus reservoir in the thatch and soil could suppress successive generations of that key pest on golf courses and sport fields.     

Do holly leaf spines really deter herbivory?

Summary Although spinose teeth of holly leaves have been widely cited as an example of a physical defense against herbivores, this assumption is based largely on circumstantial evidence and on general misinterpretation of a single, earlier experiment. We studied the response of third and fifth instar larvae of the fall webworm, Hyphantria cunea Drury, a generalist, edge-feeding caterpillar, to intact American holly leaves and to leaves that had been modified by blunting the spines, by removing sections of leaf margin between the spines, or by removing the entire leaf margin. The results suggest that the thick glabrous cuticle and tough leaf margin of Ilex opaca are more important than the spinose teeth in deterring edge-feeding caterpillars. Microscopic examination of mature leaves revealed that the epidermis is thickened at the leaf margin, and that the leaf is cirucumscribed by a pair of fibrous veins. In simple choice tests neither domesticated rabbits nor captive whitetailed deer discriminated between spinescent holly foliage and foliage from which spines were removed. Nevertheless, we found little evidence of herbivory by mammals in the field, either on small experimental trees or in the forest understory. While it is possible that spinose teeth contribute to defense by reducing acceptibility of holly relative to other palatable plant species, we suggest that the high concentrations of saponins and poor nutritional quality of holly foliage may be more important than spines in deterring vertebrate herbivores. The degree of leaf spinescence and herbivory was compared at different heights with the tree canopy to test the prediction that lower leaves should be more spinescent as a deterrent to browsers. Leaves on lower branches of mature forest trees were slightly more spinescent than were upper leaves, and juvenile trees were slightly more spinescent than were mature trees. However, there was no relationship between degree of spinescence and feeding damage. The greater spinescence of holly leaves low in the canopy is probably an ontogenetic phenomenon rather than a facultative defense against browsers.The investigation reported in this paper (No. 87-7-8-77) is in connection with a project of the Kentucky Agricultural Experiment Station and is published with the approval of the Dirctor     

Acetylcholine and Choline in Neuronal Tissue Measured by HPLC with Electrochemical Detection

Abstract: A simple, rapid method is presented for the determination of acetylcholine (ACh) and choline (Ch) in neuronal tissue using HPLC with electrochemical detection. The method is based on the separation of ACh and Ch by reverse-phase HPLC and mixing the effluent as it emerges from the column with acetylcholinesterase and Ch oxidase, which converts endogenous Ch and Ch produced by the hydrolysis of ACh to betaine and hydrogen peroxide. Production of hydrogen peroxide is continuously monitored electrochemically. The sensitivity of the procedure is 1 pmol for Ch and 2 pmol for ACh. Specificity of the method is based on HPLC, two specific enzymatic reactions, and the detection of hydrogen peroxide.     

Immunochemical identification of the serine protease inhibitor alpha 1-antichymotrypsin in the brain amyloid deposits of Alzheimer's disease

Two approaches--molecular cloning and immunochemical analysis--have identified one of the components of Alzheimer's disease amyloid deposits as the serine protease inhibitor alpha 1-antichymotrypsin. An antiserum against isolated Alzheimer amyloid deposits detected immunoreactivity in normal liver. The antiserum was then used to screen a liver cDNA expression library, yielding three related clones. DNA sequence analysis showed that these clones code for alpha 1-antichymotrypsin. Antisera against purified alpha 1-antichymotrypsin stained Alzheimer amyloid deposits, both in situ and after detergent extraction from brain. The anti-amyloid antiserum recognizes at least two distinct epitopes in alpha 1-antichymotrypsin, further supporting the presence of this protein in Alzheimer amyloid deposits. In addition to being produced in the liver and released into the serum, alpha 1-antichymotrypsin is expressed in Alzheimer brain, particularly in areas that develop amyloid lesions. Models by which alpha 1-antichymotrypsin could contribute to the development of Alzheimer amyloid deposits are discussed.     

Development of the alt Mutant of Pisum sativum L

The alt (albina-terminalis) mutant of Pisum sativum L. germinates normally, produces several nodes, and then above a sharp transition produces 2 to 3 bleached nodes, ceases growth, and eventually dies. Green nodes have normal chlorophyll content, absorption spectra, photosynthetic rates, and ultrastructure. In bleaching tissues, the chloroplasts degenerate rapidly, followed by extensive disruption and loss of the remaining cytoplasm and organelles. Application of tissue extracts of normal genotypes of pea, corn, and bean stimulates apical development of alt. The resulting tissues have essentially normal structure and function. Application of thiamine, thiamine monophosphate, and thiamine pyrophosphate also stimulate normal apical development at concentrations of 1 micromolar and above. Partial characterization of the stimulus from pea seed extracts is consistent with thiamine as the active factor.     

Factors influencing the characteristics of fish assemblages in a large subtropical marine embayment

Mean number of species and density of fishes in nearshore shallow waters of Shark Bay, a large subtropical embayment, were c . seven and 19.5 times greater in seagrass than over bare sand, where protection from predators and the abundance of potential invertebrate prey were less. The number of fish species and density of fishes over bare sand were lower in nearshore than offshore waters, where there was a greater amount of organic material and thus presumably a greater density of benthic macroinvertebrate prey. Species composition in vegetated and unvegetated habitats differed markedly, with species such as Monacanthus chinensis, Apogon rueppellii and Pelates quadrilineatus being largely confined to seagrass, whereas others such as Pseudorhombus jenynsii, Torquigener whitleyi and Engyprosopon grandisquama were found predominantly or exclusively over bare sand. The ichthyofauna in beds of Posidonia australis , in which the canopy is uniformly dense, differed in composition and comprised a greater number of species and density of fishes than that in Amphibolis antarctica , in which an open space is present beneath the terminal clusters of relatively short leaves. Species composition in the beds of both of these seagrass species underwent well defined cyclical changes, caused by out-of-phase sequential changes in the densities of certain species. Such changes were less common over bare sand, where the ichthyofaunal composition was more variable. The number of species and density of fishes over bare sand were greater at night than during the day, reflecting, in part, a tendency for species such as A. rueppellii to move into unvegetated areas to feed at night, when the likelihood of predation by visual predators would be reduced. Within Shark Bay, ichthyofaunal composition is influenced most by habitat type (vegetated v . unvegetated), followed in general by water depth and then region in the bay and time of year.     

Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides

Thermotoga neapolitana (Tne) DNA polymerase belongs to the DNA polymerase I (Pol I) family. The O-helix region of these polymerases is involved in dNTP binding and also plays a role in binding primer–template during DNA synthesis. Here we report that mutations in the O-helix region of Tne DNA polymerase (Arg722 to His, Tyr or Lys) almost completely abolished the enzyme’s ability to catalyze the template-independent addition of a single base at the 3′-end of newly synthesized DNA in vitro. The mutations did not significantly affect the DNA polymerase catalytic activity and reduced base misinsertions 5- to 50-fold. The same Arg722 mutations dramatically increased the ability of the enzyme’s 3′→5′ exonuclease to remove mispaired 3′ bases in a primer extension assay. These mutant DNA polymerases can be used to accurately amplify target DNA in vitro for gene cloning and genotyping analysis.