Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

Effects Of Aromatic-Hydrocarbons On The Metabolism Of The Digestive Gland Of The Mussel Mytilus-Edulis-L

1. The results presented in this paper show that the exposure of mussels to a sublethal concentration of oil-derived aromatic hydrocarbons (30 μg 1−1) for a period of 4 months significantly decreases the protein level in the digestive gland of the animals (−17%). 2. The activity of the nuclear RNA polymerase I and II is also significantly decreased in the digestive gland of hydrocarbon-exposed mussels (−64% and −18%, respectively). 3. The RNAase(s) activity present in the nuclei from the digestive gland cells increases following the exposure of the mussels to aromatic hydrocarbons. This effect is particularly evident at high ionic strength [200 mM (NH4)2SO4]. 4. The analysis of some characteristics of the nuclear RNAase(s) (most of which is soluble and shows a maximum of activity at pH 4−5) could indicate that part of this hydrolytic enzyme may have a lysosomal origin. 5. This fact appears to be in agreement with the finding that in the mussels exposed for 4 months to aromatic hydrocarbons the lysosomal stability decreases drastically and the total content of lysosomal enzymes is significantly increased (+42.4%).

Hormesis - The Stimulation Of Growth By Low-Levels Of Inhibitors

Hormesis is the name given to the stimulatory effects caused by low levels of potentially toxic agents. When this phenomenon was first identified it was called the Arndt-Schulz Law or Hueppe's Rule, because it was thought to occur generally. Although this generalisation is not accepted today, there has never been more evidence in its support, justifying a re-examination of the phenomenon. Evidence from the literature shows that not only has growth hormesis been observed in a range of taxa after exposure to a variety of agents, but also that the dose-response data have a consistent form. While there are a number of separate hypotheses to explain specific instances of hormesis, the evidence presented here suggests that different examples might have a common explanation, and the possibility of a general theory is considered.