High-altitude stream faunas in the Mt Pelion East-Mt Doris area of Tasmania

A survey was carried out of the aquatic fauna of the headwaters of two high-altitude 0170-1355 m) streams draining Mt Doris and two streams draining Mt Pelion East in Tasmania. Although the fauna above the treeline appeared to be characterised primarily by the loss of downstream fauna, three Trichoptera (Notoperata maculata, an unidentified genus from the Kokiriidae, and Plectrotarsus sp.) and one crustacean (Neoniphargus sp.) may form part of a specialised high-altitude fauna. The amphipod Neoniphargus sp. was collected from above the treeline only, whereas the other amphipod recorded, Antipodeus sp., was found at or below the treeline only. Cluster analyses enabled five habitat and three species groupings to be recognised. Since the habitat groupings were generally well defined by their physico-chemical characteristics as well as by the faunal groups, it is concluded that they reflect a genuine series of identifiable high-altitude stream habitats

The role of input noise in transcriptional regulation

Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise associated with the inputs to transcriptional regulation, the random arrival and binding of transcription factors to their target sites along the genome. This noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, global models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.Comment: 11 pages, 5 figures minor correction

Trade-Offs and Constraints in Allosteric Sensing

Sensing extracellular changes initiates signal transduction and is the first stage of cellular decision-making. Yet relatively little is known about why one form of sensing biochemistry has been selected over another. To gain insight into this question, we studied the sensing characteristics of one of the biochemically simplest of sensors: the allosteric transcription factor. Such proteins, common in microbes, directly transduce the detection of a sensed molecule to changes in gene regulation. Using the Monod-Wyman-Changeux model, we determined six sensing characteristics – the dynamic range, the Hill number, the intrinsic noise, the information transfer capacity, the static gain, and the mean response time – as a function of the biochemical parameters of individual sensors and of the number of sensors. We found that specifying one characteristic strongly constrains others. For example, a high dynamic range implies a high Hill number and a high capacity, and vice versa. Perhaps surprisingly, these constraints are so strong that most of the space of characteristics is inaccessible given biophysically plausible ranges of parameter values. Within our approximations, we can calculate the probability distribution of the numbers of input molecules that maximizes information transfer and show that a population of one hundred allosteric transcription factors can in principle distinguish between more than four bands of input concentrations. Our results imply that allosteric sensors are unlikely to have been selected for high performance in one sensing characteristic but for a compromise in the performance of many

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

A multivariate morphometric investigation to delineate stock structure of gangetic whiting, Sillaginopsis panijus (Teleostei: Sillaginidae)

This study was conducted to delineate the stock structure of Sillaginopsis paniijus based on morphometric characters of the species. A total of 194 specimens were collected from the Meghna, Tentulia and Baleswar rivers located in the southern coastal zone of Bangladesh. Data were subjected to univariate ANOVA, multivariate ANOVA, discriminate function analysis (DFA), and principal component analysis. Mean variations of ten morphometric characters; HD, HBD, LBD, PsOL, ED, SnL, SPrDL, HAF, LSDB and LPB showed significant differences (p < 0.05) among 27 morphometric traits that were selected for the study. In DFA, the overall assignments of individuals into their correctly classified original groups were 71.1 and 70.6 % for male and female, respectively. A scatter plot of the first two discriminant functions was used to visually depict the discrimination among the populations. The results showed different stocks of S. panijus in the rivers of Baleswar, Tentulia and Meghna in southwest coast of Bangladesh

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Parental transfer of the antimicrobial protein LBP/BPI protects Biomphalaria glabrata eggs against oomycete infections

Copyright: © 2013 Baron et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by ANR (ANR-07-BLAN-0214 and ANR-12-EMMA-00O7-01), CNRS and INRA. PvW was financially supported by the BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Gastrointestinal stromal tumour and hypoglycemia in a Fjord pony: Case report

<p>Abstract</p> <p>Background</p> <p>Neoplasia may cause hypoglycemia in different species including the horse, but hypoglycemia has not previously been reported in the horse associated with gastrointestinal stromal tumours.</p> <p>Case presentation</p> <p>A case of a gastrointestinal stromal tumour in a Fjord pony with severe recurrent hypoglycemia is presented. The mechanism causing the hypoglycemia was not established.</p> <p>Conclusion</p> <p>This case indicates that a gastrointestinal stromal tumour may cause hypoglycemia also in the horse.</p