Sequence assessment of comigrating AFLPTM bands in Echinacea — implications for comparative biological studies

Subbaiah M Mechanda; Bernard R Baum; Douglas A Johnson; John T Arnason

doi:10.1139/g03-094

Sequence assessment of comigrating AFLPTM bands in Echinacea — implications for comparative biological studies

Genome ◽

10.1139/g03-094 ◽

2004 ◽

Vol 47 (1) ◽

pp. 15-25 ◽

Cited By ~ 48

Author(s):

Subbaiah M Mechanda ◽

Bernard R Baum ◽

Douglas A Johnson ◽

John T Arnason

Keyword(s):

Comparative Studies ◽

Aflp Markers ◽

Size Group ◽

Polymorphic Band ◽

Sequence Identity ◽

Biological Studies ◽

Clone Sequence ◽

Monomorphic Band ◽

Different Populations

The extent of sequence identity among clones derived from monomorphic and polymorphic AFLPTM polymorphism bands was quantified. A total of 79 fragments from a monomorphic band of 273 bp and 48 fragments from a polymorphic band of 159 bp, isolated from individuals belonging to different populations, varieties, and species of Echinacea, were cloned and sequenced. The monomorphic fragments exhibited above 90% sequence identity among clones within samples. Sequence identity within variety ranged from 82.78% to 94.87% and within species from 75.82% to 98.9% and was 57.97% in the genus. The polymorphic fragments exhibited much less sequence identity. In some instances, even two clones from the same fragment were different in their size and sequence. Within sample, clone sequence identity ranged from 100% to 51.57%, within variety from 33.33% to 100% in one variety, and from 23.66% to 45% within species and was as low as 1.25% within the genus. In addition, sequences of the same size were aligned to verify the nature of their sequence dissimilarity/similarity. Within each size group, identical sequences were found across species and varieties. In general, comigrating bands cannot be considered homologous. Thus, the use of AFLPTM band data for comparative studies is appropriate only if the results emanating from such analyses are considered as approximations and are interpreted as phenotypic but not genotypic.Key words: AFLP markers, false homologies.

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Modification of the Electron Microscope for Investigation of Fully Hydrated Biological Specimens

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100064001 ◽

1969 ◽

Vol 27 ◽

pp. 418-419 ◽

Cited By ~ 2

Author(s):

R. C. Moretz ◽

D. F. Parsons

Keyword(s):

Electron Beam ◽

Electron Microscope ◽

Structural Damage ◽

Lower Percentage ◽

Vacuum Drying ◽

Total Removal ◽

Total Absence ◽

Biological Studies ◽

Electron Microscopes ◽

Beam Damage

Short lifetime or total absence of electron diffraction of ordered biological specimens is an indication that the specimen undergoes extensive molecular structural damage in the electron microscope. The specimen damage is due to the interaction of the electron beam (40-100 kV) with the specimen and the total removal of water from the structure by vacuum drying. The lower percentage of inelastic scattering at 1 MeV makes it possible to minimize the beam damage to the specimen. The elimination of vacuum drying by modification of the electron microscope is expected to allow more meaningful investigations of biological specimens at 100 kV until 1 MeV electron microscopes become more readily available. One modification, two-film microchambers, has been explored for both biological and non-biological studies.

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Design of Sensitive Photographic Materials for the High-Voltage Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100114402 ◽

1975 ◽

Vol 33 ◽

pp. 156-157

Author(s):

Murray Vernon King ◽

Donald F. Parsons

Keyword(s):

Electron Microscope ◽

Radiation Damage ◽

High Voltage ◽

Radiation Sensitivity ◽

Fast Electrons ◽

Voltage Electron ◽

High Voltage Electron Microscope ◽

High Voltage Electron ◽

Biological Studies ◽

Low Sensitivity

Effective application of the high-voltage electron microscope to a wide variety of biological studies has been restricted by the radiation sensitivity of biological systems. The problem of radiation damage has been recognized as a serious factor influencing the amount of information attainable from biological specimens in electron microscopy at conventional voltages around 100 kV. The problem proves to be even more severe at higher voltages around 1 MV. In this range, the problem is the relatively low sensitivity of the existing recording media, which entails inordinately long exposures that give rise to severe radiation damage. This low sensitivity arises from the small linear energy transfer for fast electrons. Few developable grains are created in the emulsion per electron, while most of the energy of the electrons is wasted in the film base.

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Application of stereological analysis of cell volume to isolated myocytes in culture with and without adrenergic innervation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010015962x ◽

1990 ◽

Vol 48 (3) ◽

pp. 416-417

Author(s):

Jane K. Rosenthal ◽

Dianne L. Atkins ◽

William J. Marvin ◽

Penny A. Krumm

Keyword(s):

Cardiac Myocytes ◽

Structural Changes ◽

Three Dimensional ◽

Adrenergic Innervation ◽

Culture Cell ◽

Serial Sections ◽

Newborn Rats ◽

Primary Culture Cell ◽

Biological Studies ◽

Cell Volumes

To comprehend structural changes in cardiac myocytes accompanying adrenergic innervation, it is essential that a three dimensional analysis be performed. To date, biological studies which utilize stereological methods have been limited to cells in tissue and in organs. Our laboratory has utilized current stereological techniques for measuring absolute volumes of individual myocytes in primary culture. Cell volumes are calculated for two distinct groups of cells at 96 hours in culture: isolated myocytes and myocytes innervated with adrenergic neurons (Figure 1).Cardiac myocytes are cultured from the ventricular apices of newborn rats. Cells are plated directly onto tissue culture dishes with or without preplated explants from the paravertebral thoracolumbar sympathetic chain. On day four cultures are photographed and marked for one-to-one cell location. Following conventional fixation and embeddment in eponate-12, the cells are relocated and mounted for microtomy. The cells are completely sectioned at 120nm in their parallel orientation to the surface of the dish (Figure 2). Serial sections are collected on formvar coated slotted grids and are recorded in sequence.

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