Aging of Xenopus tropicalis Eggs Leads to Deadenylation of a Specific Set of Maternal mRNAs and Loss of Developmental Potential

As first shown more than 100 years ago, fertilization of an aged (overripe) egg increases the rate of malformations and embryonic loss in several vertebrates, including possibly humans as well. Since the molecular events in aging eggs may be similar in these species, we established in the frog Xenopus tropicalis a defined protocol for delayed fertilization of eggs. A three-hour delayed fertilization led to a dramatic increase in malformation and mortality. Gene expression profiling revealed that 14% of the polyadenylated maternal transcripts were downregulated upon aging. These transcripts were not degraded, but rather deadenylated as shown for specific maternal mRNAs. The affected transcripts are characterized by a relatively short 3′UTR and a paucity of cytoplasmic polyadenylation elements (CPE) and polyadenylation signals (PAS). Furthermore, maternal mRNAs known to be deadenylated during egg maturation as well as after fertilization were preferentially deadenylated in aged eggs. Taken together our analysis of aging eggs reveals that unfertilized eggs are in a dynamic state that was previously not realized. On the one hand deadenylation of transcripts that are typically deadenylated during egg maturation continues and this implies overripeness of the aged egg in the truest sense of the word. On the other hand transcripts that normally are deadenylated after fertilization loose their poly(A) in the aged egg and this implies that the egg awaiting fertilization starts processes that are normally only observed after fertilization. Based on our novel finding we postulate that the imbalance of the polyadenylated maternal transcripts upon egg aging contributes to the loss of developmental potential. Based on this hypothesis the developmental consequences of downregulation of specific transcripts can be analyzed in future

From genome to toxicity: a combinatory approach highlights the complexity of enterotoxin production in Bacillus cereus

In recent years Bacillus cereus has gained increasing importance as a food poisoning pathogen. It is the eponymous member of the Bacillus cereus sensu lato group that consists of eight closely related species showing impressive diversity of their pathogenicity. The high variability of cytotoxicity and the complex regulatory network of enterotoxin expression have complicated efforts to predict the toxic potential of new Bacillus cereus isolates. In this study, comprehensive analyses of enterotoxin gene sequences, transcription, toxin secretion and cytotoxicity were performed. For the first time, these parameters were compared in a whole set of Bacillus cereus strains representing isolates of different origin (food or food poisoning outbreaks) and of different toxic potential (enteropathogenic and apathogenic) to elucidate potential starting points of strain-specific differential toxicity. While toxin gene sequences were highly conserved and did not allow for differentiation between high and low toxicity strains, comparison of nheB and hblD enterotoxin gene transcription and Nhe and Hbl protein titers revealed not only strain-specific differences but also incongruence between toxin gene transcripts and toxin protein levels. With one exception all strains showed comparable capability of protein secretion and so far, no secretion patterns specific for high and low toxicity strains were identified. These results indicate that enterotoxin expression is more complex than expected, possibly involving the orchestrated interplay of different transcriptional regulator proteins, as well as posttranscriptional and posttranslational regulatory mechanisms plus additional influences of environmental conditions

CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli

Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. In: Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. Vol 129. ELSEVIER SCIENCE BV; 2007: 279-289

Resonant photoacoustic CO2 spectroscopy with LED light source

We have applied resonant photoacoustic sensing for carbon dioxide (CO2) detection using a mid-infrared LED light source at 4.3μm. The pressure signals are detected using a MEMS microphone. A simple cell design has been adapted to achieve an optimal enhancement of the acoustic signal. The cell can be operated both in closed and open configuration, allowing a permanent gas flow. With the components we used a compact and low-cost CO2 sensor can be realized. We present first results of our photoacoustic sensor using the binary gas mixture CO2 / nitrogen. The signals were evaluated measuring the shift in the resonance frequency of the system. The sensor shows sensitivities down to a few percent CO2. Ideas to further enhance the sensitivity of the sensor are discussed

N6-Adenosine Methylation in MiRNAs

<div><p>Methylation of N6-adenosine (m6A) has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs) has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression.</p></div