16 research outputs found
Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species
The mechanisms of stress tolerance in sessile animals, such as molluscs, can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges. One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genus Mytilus. We focus on the upstream region of Mytilus galloprovincialis Hsp90 genes and their structural and functional associations, using comparative genomics and network inference. Sequence comparison of this region provides novel evidence that the transcription of Hsp90 is regulated via a dense region of transcription factor binding sites, also containing a region with similarity to the Gamera family of LINE-like repetitive sequences and a genus-specific element of unknown function. Furthermore, we infer a set of gene networks from tissue-specific expression data, and specifically extract an Hsp class-associated network, with 174 genes and 2,226 associations, exhibiting a complex pattern of expression across multiple tissue types. Our results (i) suggest that the heat shock response in the genus Mytilus is regulated by an unexpectedly complex upstream region, and (ii) provide new directions for the use of the heat shock process as a biosensor system for environmental monitoring
Gene Expression Rhythms in the Mussel Mytilus galloprovincialis (Lam.) across an Annual Cycle
Seasonal environmental changes may affect the physiology of Mytilus
galloprovincialis (Lam.), an intertidal filter-feeder bivalve
occurring commonly in Mediterranean and Atlantic coastal areas. We investigated
seasonal variations in relative transcript abundance of the digestive gland and
the mantle (gonads) of males and females. To identify gene expression trends
– in terms of relative mRNA abundance- we used a medium-density cDNA
microarray (1.7 K probes) in dual-color competitive hybridization analyses.
Hierarchical clustering of digestive gland microarray data showed two main
branches, distinguishing profiles associated with the “hot” months
(May–August) from the other months. Genes involved in chitin metabolism,
associated with mussel nutrition and digestion showed higher mRNA levels during
summer. Moreover, we found different gene transcriptomic patterns in the
digestive glands of males when compared to females, during the four stages of
mussel gonadal development. Microarray data from gonadal transcripts also
displayed clear patterns during the different developmental phases respect to
the resting period (stage I) with peak relative mRNA abundance at the ripe phase
(stage III) for both sexes. These data showed a clear temporal pattern in
transcriptomic profiles of mussels sampled over an annual cycle. Physiological
response to thermal variation, food availability, and reproductive status across
months may contribute to variation in relative mRNA abundance
RNA preservation of Antarctic marine invertebrates
Fifteen species of marine invertebrate commonly
occurring in the near-shore environment of Rothera
base, Antarctica, were used to test tissue sample storage
protocols with regard to preservation of RNA integrity.
After animal collection, the tissues were either immediately
extracted for RNA or stored at -80C after having
been, either directly flash frozen in liquid nitrogen or
preserved in a commercial RNA storage solution, for
extraction in the UK. In four cases, direct flash freezing
produced enhanced RNA integrity compared with samples
in the commercial storage solution. A subset of samples
were further tested for the preferred temperature of storage
in the commercial reagent. RNA integrity was well preserved
at both ?4 and -20C over periods of 2 months,
but degradation was rapid in tissues stored at room temperature.
Eight out of the fifteen species only produced a
single ribosomal band on gel electrophoresis. This survey
provides a guide for tissue transport of Polar cold water
marine invertebrates.
Keywords Tissue preservation Tissue transport
28 s ribosomal RNA Echinoderms Molluscs
Introduction
RNA preservation is sometimes problematic in non-model
species but this is particularly the case when dealing with
environmental species. Logistical issues often surround the
ability to effectively preserve field-collected samples for
RNA analyses. Whilst rapid flash freezing in liquid nitrogen
generally solves this problem, it is not often available
because of the remote nature of the work. Even when such
a facility is available on site at a field station, it usually
cannot be transported to the actual, more remote specimen
collection site. Also, -80C storage may not be possible
during transportation from the field site to the main
research institute, often thousands of miles away. Antarctic
specimens have the additional issue of operating at temperatures that most species would consider cold and hence
cool stow is less effective at reducing tissue degradation
than with, for example, those taken from mammalian
species. Hence, we decided to carry out a study of effective
storage protocols for the most common invertebrates found
in the near-shore marine environment in Marguerite Bay
close to Rothera research station, Antarctica
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
EA Pôle EcolDurInternational audienceMicrobes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies