Digital Commons Network^™

Creation Of A Vector For Regulated Expression Of Antisense Rna In Escherichia Coli, Wen-Jun Wu

Masters Theses & Specialist Projects

A plasmid (pGEM-SD) was constructed in which the Shine-Dalgarno sequence had been deleted from pGEM-7zf(+) plasmid to generate a vector for regulated expression of antisense RNA. The binding of antisense RNA to mRNA provides a potent mechanism by which specific transcripts can be translationally inactivated. Although part of the lac operator sequence was deleted in pGEM-SD plasmid, it was proven that mRNA still can be induced under the control of lac promoter. Recombinant plasmids were generated by ligating bacterial genornic DNA into pGEM-SD plasmid, but the orientation of the inserted gene with respect to the lac promoter has not been …

Ua3/8/1 L.Y. Lancaster Professorship Report, Wku Ogden College Of Science & Technology

WKU Administration Documents

Report by Dr. Blaine Ferrell, L.Y. Lancaster Professor about activities for 1991-1992 funded by the Ogden Foundation.

A Brief Introduction To Aims And Methods For Image Processing Of Electron Micrographs Of Biological Specimens, Murray Stewart

Scanning Microscopy

A common problem with electron micrographs of biological objects is that fine details are usually faint and, moreover, tend to be obscured by background noise from stain and support film. Filtering is a useful way to improve the signal-to-noise ratio and is particularly important when trying to detect small changes (conformational or due to labelling) or when examining frozen hydrated objects, where the statistical definition of the image has been reduced because of the low-dose conditions needed to prevent radiation damage. Filtering can also be used to address the superposition effects that result from the large depth of focus of …

Three-Dimensional Crystallographic Reconstruction For Atomic Resolution, Kenneth H. Downing

Scanning Microscopy

Three-dimensional structures have recently been determined by electron crystallography at a resolution high enough to determine atomic arrangements in both protein and mineral specimens. The different nature of these two types of specimens produces some very significant differences in the way data is obtained and processed, although the principles are the same. The sensitivity of proteins to damage by the electron beam limits the signal-to-noise ratio in the image and the resolution to which data can be extracted from the image. A number of constraints, such as the amino acid sequence and the connectivity of atoms within amino acids, can …

Alignment, Classification, And Three-Dimensional Reconstruction Of Single Particles Embedded In Ice, Joachim Frank, Pawel Penczek, Weiping Liu

Scanning Microscopy

Cryo-electron microscopy of single biological particles poses new challenges to digital image processing due to the low signal-to-noise ratio of the data. New tools have been devised to deal with important aspects of 3-D reconstruction following the random-conical data collection scheme: (a) a new shift-invariant function has been derived, which promises to facilitate alignment and classification of single particle projections; (b) a new method of orientation search is proposed, which makes it possible to relate random-conical data sets to one another prior to reconstruction; and (c) the foundation is laid for a 3-D variance estimation which utilizes the oversampling of …

Confocal Microscopy And Three-Dimensional Reconstruction Of Thick, Transparent, Vital Tissue, Barry R. Masters

Scanning Microscopy

The three-dimensional visualization of the 400 micron thick, transparent, in situ cornea is described to demonstrate the use of confocal light microscopy for noninvasive imaging of living cells and thick tissues in their normal, vital conditions. Specimen preparation and physiological stability, as well as light attenuation corrections are critical to data acquisition. The technique to provide mechanical stability of the specimen during the duration of the image acquisition is explained. A laser scanning confocal light microscope (LSCM) was used to obtain optical serial sections from rabbit eyes that were freshly removed and placed in a physiological Ringer's solution. This study …

Structure Analysis Of Ice-Embedded Single Particles, M. Van Heel, H. Winkler, E. Orlova, M. Schatz

Scanning Microscopy

The conventional negative-stain preparation method for electron microscopy, in which biological macromolecules are contrasted using heavy metal salts (such as uranyl-acetate), is a simple and fast technique which has helped visualize hundreds of different molecular structures. Computer analysis of such negatively stained images of individual (i.e., non-crystalline) macromolecules using statistical pattern-recognition techniques has revealed considerable new structural information. Negative staining, however, has some disadvantages: the specimens are often severely flattened (as much as 25%-75%), they often exhibit strong preferential attachment of the molecules to the supporting carbon foil, and the molecular images may be difficult to interpret due to the …

Morphological Filtering And Granulometric Analysis On Scanning Electron Micrographs: Applications In Materials Science, Murielle Prod'homme, Michel Coster, Liliane Chermant, Jean-Louis Chermant

Scanning Microscopy

For many applications, scanning electron microscopy (SEM) images reflect the granular texture of analysed objects. So it is important to characterise the morphology of this texture and also to filter these images. Because the size of the texture is the main criterion to be studied, we have focused our paper on granulometric analysis.

We present basic parameters, morphological filtering and granulometry for Rⁿ•R functions and their properties with local knowledge and anamorphosis.

Some applications in the domain of materials science illustrate these methods and present their suitable possibilities.

Application Of The Wavelet Transform To The Digital Image Processing Of Electron Micrographs And Of Backreflection Electron Diffraction Patterns, A. Gómez, L. Beltrán Del Río, D. Romeu, M. Jose Yacamán

Scanning Microscopy

In this work we explore the use of the so-called wavelet transform in the digital image processing of micrographs. The wavelet transform of an image f(x,y) is defined as:

Wf(s,u,v)

= f(x,y) s Ψ(s(x-u),s(y-v)) dxdy

where Ψ is an analyzing function called "wavelet" and which is in our examples always taken to be the "Mexican hat" given by

Ψ(x)=(2-(x²+y²))exp(-(x²+y²)/2)

Some synthetic images are shown in which it can be clearly seen how the wavelet transform can be useful to reveal edges and to emphasize the boundaries of the clusters.

The technique is …

Image Algebra And Restoration, P. W. Hawkes

Scanning Microscopy

The arrival of image algebras has made it possible to express a vast amount of the heterogeneous material in the image processing literature in a convenient and consistent manner. Furthermore, this type of formulation has proved very fertile and many new ideas have emerged. Image restoration has, however, been studied very much less than enhancement and analysis. We explain briefly the use of one such algebra in this field and show that such tasks as reconstruction from focal series and three-dimensional reconstruction can easily be incorporated.

A Robust Solution To The Super-Resolution Phase Problem In Scanning Transmission Electron Microscopy, J. M. Rodenburg, B. C. Mccallum

Scanning Microscopy

From a set of images, each of poor resolution, recorded in a transmission microscope under many different incident angles of coherent illumination, it is possible to obtain wavelength-limited resolution even if there is a narrow aperture lying in the back-focal plane of the imaging lens. This is achieved by a deconvolution algorithm which retrieves the phase of the Fourier transform of the specimen. The method accounts for complex components in the transfer function of the lens, is not very sensitive to defocus and is remarkably resilient to noise. It may have important applications in overcoming the resolution limit in the …

The Detection And Quantification Of Straight-Lined Irregularities On Surfaces, J. Alan Swift

Scanning Microscopy

Under the microscope, scratches or abrasions on hard otherwise flat surfaces are usually revealed as straight-lined irregularities. At a more macroscopic level creases in thin sheets such as of paper and textile fabrics are also observed to be straight-lined. A computer-aided image analytical method is described here not only for identifying such features but also for counting them, measuring their lengths and evaluating their contrast. Further measures are derived that are in accord with the qualitative visual impact of each line within the milleau of lines in the original image. The method makes use of a parametric transformation from two …

Multi-Dimensional Data Analysis And Processing In Electron-Induced Microanalysis, N. Bonnet, P. Trebbia

Scanning Microscopy

The new facilities offered by computer controlled data capturing devices allow one to open the field of data acquisition from one or two-dimensional spaces to multi-dimensional ones. The methods used for analysing and processing such data sets have to move in parallel towards multi-dimensionality. Multivariate Statistical Analysis is one of the tools which appear to be promising in : data analysis, data reduction, data processing (multivariate noise filtering), data interpolation and extrapolation. Illustrations of these different possibilities are given in the fields of spatially resolved spectroscopy, time-dependent spectroscopy and elemental mapping from Electron Energy Loss Spectroscopy.

Processing Multi-Spectral Scanning Electron Microscopy Images For Quantitative Microfabric Analysis, N. K. Tovey, D. L. Dent, W. M. Corbett, D. H. Krinsley

Scanning Microscopy

Multi-spectral image analysis is a powerful method to characterise quantitatively the mineralogy and microfabric of soils, sediments, and other particulate materials. Backscattered scanning electron microscope (SEM) images of polished, resin-impregnated samples are grouped with the corresponding X-ray elemental maps using classification methods commonly used in remote sensing. However, the resulting mineral-segmented images require processing to render them suitable for quantification. In the past, this has been done subjectively and interactively, but the new objective methods described in this paper largely eliminate this subjectivity. An intensity gradient magnitude image of the original backscattered electron image is used as the basis of …

Image Segmentation Applied To Scanning Electron Microscopy Multi-Images Of Weathered Stones Of Monuments, M. Rautureau, R. Harba, G. Jacquet

Scanning Microscopy

This paper describes a three complementary images processing method. The three images are coming from a scanning electron microscope (SEM) during the analysis of a particular stone: the Tuffeau used in most monuments of the Loire valley (France). The goal is to separate two classes of particles (calcareous and siliceous) from the porosity to give more information to experts who evaluate the damage of weathering on monuments. A specific process is developed: a first threshold on the good quality image allows separation of particles from porosity. Then, the complementarity of the three images gives the two other thresholds. Granulometry, percentages …

Random Access Direct Parallel Detection Of Electron Energy Loss Spectra With A New Photodiode Array, Stephan La Barré, Eckhard Quandt, Heinz Niedrig

Scanning Microscopy

A new type of photodiode array (PDA) which allows the individual access of single diodes is used to record energy loss electrons directly without electron photon conversion.

The detector is part of an electron energy loss parallel detection system which consists of a sector field spectrometer and a quadrupole lens system to magnify the spectra electron-optically.

The parallel detector is a new random access PDA (RAPDA) which allows the individual access of single diodes. Therefore, different parts of the spectrum with dramatically different electron rates (zero loss peak, plasmon loss, ionization edges) can be recorded, each with optimum acquisition time …

On-Line Processing And Computer Control In High Resolution Transmission Electron Microscopy, F. A. Ponce, H. Hikashi

Scanning Microscopy

Recent advances in hardware and software make it possible to perform real-time image processing, and to do simultaneous analysis of the image characteristics in the transmission electron microscope (TEM). We have used a commercially available image processor and a suitable computer/TEM interface to build a automated computer-control system for a JEOL 4000EX TEM. We report here the characteristics of the system, which has direct access to all electronic controls of a JEOL 4000EX. The various microscope parameters are set by changing one parameter at a time while the image processor measures a specific image variable such as the variance. From …

Quantification Of High-Resolution Lattice Images And Electron Holograms, W. J. De Ruijter, M. Gajdardziska-Josifovska, M. R. Mccartney, R. Sharma, David J. Smith, J. K. Weiss

Scanning Microscopy

Progress towards the quantification of high-resolution electron microscopy and electron holograms has been achieved using digital acquisition with a slow-scan charge-coupled device (CCD) camera. Two applications are described: the precise measurement of lattice-fringe spacings and the determination of the mean inner potential. Lattice images can be characterized by a finite sum of two-dimensional sinusoids. A new method for measurement of the frequency, amplitude and phase of each sinusoid, based on an interpolation technique in reciprocal space, is presented. The method offers considerably higher precision for measurement of lattice fringes than the optical bench and is applicable to images recorded with …

Digital Image Processing Of Electron Micrographs: The Pic System Ii, Benes L. Trus, Michael Unser, Thierry Pun, Alasdair C. Steven

Scanning Microscopy

The PIC system, an integrated package of Fortran programs and subroutines designed to run on the Digital Equipment Corporation VAX family of computers, has been developed for analysis of electron micrographs with emphasis on the particular requirements for structural analysis of biological macromolecules. The substantially improved VAX version of PIC reported here has been developed from an earlier PDP-11 version which was, in turn, developed from a set of IBM 370 programs called MDPP. PIC now encompasses over 150 commands or processing operations that afford a comprehensive range of image processing operations including image restoration, enhancement, Fourier analysis, correlation averaging, …

Specimen Catalog, Tom A. Collins

Division of Mammals - Field Notes and Catalogs

No abstract provided.

Specimen Catalog, Sandra L. Brantley

Division of Mammals - Field Notes and Catalogs

No abstract provided.

Patterns Of Survival, Growth, And Maturation In Snakes And Lizards, Richard Shine, Eric Charnov

Biology Faculty & Staff Publications

Dimensionless invariants for reptile life-histories are discussed

A Comparative Study Of The Oxygen Dissociation Curves Of Deer Mouse (Peromyscus Leucopus) And Meadow Vole (Microtus Pennsylvanicus) Hemoglobin, James Loeffelholz

Honors Theses, 1963-2015

Oxygen equilibrium curves of dilute hemoglobin solutions from deer mice (Peromyscus leucopus) and meadow voles (Microtus pennsylvanicus) were determined by optical tonometry at pH 6.8 and pH 7.4. For deer mouse hemoglobin, P50 6.8 = 4.54 KPa, n7.4 (cooperativity index at pH 7.4) = 1.13, n6.8 = 1.60 and Bohr shift = 1.91. For meadow vole hemoglobin P50 7.4 = 2.74 KPa, P50 6.8 = 6.16 KPa, n7.4 = 1.11, n6.8 = 1.63, and Bohr shift = 2.35. The method was evaluated for use in the undergraduate laboratory.

Revival Of Metabolism In Rehydrated Marasmius Oreades, Lorie J. Warren

Honors Theses, 1963-2015

Mushrooms from the genus Marasmius have the ability to revive -- viz., dried specimens regain their original shape when moistened. The purpose of this study was to determine if the basidiocarps are metabolically active upon revival or whether they simply absorb moisture like a sponge. The reduction of tetrazolium chloride to a red, water-insoluble formazan pigment was used as a measure of respiratory activity. Basidiocarp samples were incubated in a phosphate buffer containing 1% tetrasolium chloride. After a suitable period, the samples were extracted with MeOH to remove any formazan pigment and the absorbance measured at 530 nm. Fresh M. …

Fluorescence Quenching In The Varied Photosynthetic Modes Of Portulacaria Afra (L.) Jacq, Lonnie J. Guralnick, Guillermo Goldstein, Robert L. Heath, Irwin P. Ting

Arts & Sciences Faculty Publications

No abstract provided.

Aspects Of Air Pollution, And Its Effect On The Respiratory System, Jennifer Randall

Presidential Scholars Theses (1990 – 2006)

This report centers around one of today's most prominent environmental issues-- air pollution. First, the major pollutants are defined and explained. Chloroflourocarbons, ozone, carbon monoxide, carbon dioxide, methane, sulfur dioxide, nitrogen oxides, and suspended particulate matter all receive attention.

Next, air pollution's effect on the Earth is explained. The "greenhouse effect", global warming, acid rain, and ozone depletion all have an enormous impact on Earth's climate and atmosphere.

The report proceeds on to discuss options for controlling and so lving the air pollution problem. Se+ective catalytic reduction, noncatalytic reduction, tradeable permits-- these three processes are examples of large scale attempts …

Effects Of Forest Fragmentation On Neotropical Migrant Landbirds In East-Central Illinois, Eric Thomas Linder

Masters Theses

No abstract provided.

Localization Of A Collagenous Protein In The Organic Matrix Of Spicules From The Octocoral Leptogorgia Virgulata (Cnidaria: Gorgonacea), Jeffrey L. Dupree

Master's Theses

Calcareous body inclusions are commonly found throughout the invertebrate taxa. Elaborately structured calcium carbonate spicules are the major mineralized body inclusions of the gorgonian, Leptogorgia virgulata. Spicule formation in this octocoral, as well as other calcium carbonate invertebrate structures, is apparently regulated by the intra-spicule organic matrix. Recent findings show that the insoluble fraction of the spicule organic matrix is collagenous. Collagen, although integral to calcium phosphate structures found in vertebrates is not usually associated with the formation of invertebrate calcium carbonate structures. Interestingly, collagen is present in the organic matrix during the summer but absent in winter. This suggests …

Experimental Manipulations Of The Organic Chemistry Of Seawater: Implications For Studies Of Energy Budgets In Marine Invertebrate Larvae, William Jaeckle

Scholarship

Correct measurement of changes in biomass and metabolic rates over time are two essential elements for the accurate construction of energy budgets for invertebrate larvae. Both components of larval energetics are altered by changes in the organic chemistry of the seawater. Axenic (bacteria-free) veliger larvae (88 µm shell length) of the bivalve Crassostrea gigas (Thunberg, 1795) had a 53% enhancement of their metabolic rate relative to control values (5.8 ± 0.6 pmol larva -1 h -1 , x¯ ± 1 SE) when exposed to seawater to which 1 µM glucose had been added. Gastrulae increased their rate of respiration by …

"A New Genus And Species Of Fresh-Water Crab From Cameroon, West Africa" , Neil Cumberlidge, Paul F. Clark

Journal Articles

No abstract provided.