Increases in intracellular calcium concentration ([Ca 2+ ] c ) mediate plant responses to stress by regulating the expression of genes encoding proteins that confer tolerance. Several plant stress genes have previously been shown to be calciumregulated, and in one case, a specific promoter motif Abscisic Acid Responsive-Element (ABRE) has been found to be regulated by calcium. A comprehensive survey of the Arabidopsis thaliana transcriptome for calcium-regulated promoter motifs was performed by measuring the expression of genes in Arabidopsis seedlings responding to three calcium elevations of different characteristics, using full genome microarray analysis. This work revealed a total of 269 genes upregulated by [Ca 2+ ] c in Arabidopsis. Bioinformatic analysis strongly indicated that at least four promoter motifs were [Ca 2+ ] c -regulated in planta. We confirmed this finding by expressing in plants chimeric gene constructs controlled exclusively by these cis-elements and by testing the necessity and sufficiency of calcium for their expression. Our data reveal that the C-Repeat/Drought-Responsive Element, Site II, and CAM box (along with the previously identified ABRE) promoter motifs are calcium-regulated. The identification of these promoter elements targeted by the second messenger intracellular calcium has implications for plant signaling in response to a variety of stimuli, including cold, drought, and biotic stress.

Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP−A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP−A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP−A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP−A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.

We investigated the gut microbiota of rabbit fish larvae at 3 locations in Vietnam (Thuan An: northern, Quang Nam: intermediate, Binh Dinh: southern sample site) over a three-year period. First, the Clostridiales order was the most predominant in the gut. Second, the location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1 and evenness. Last, the beta diversity 2 analysis indicated that the location had an effect on the microbiota. The year-by-year analysis showed that for 2014 the gut microbiota was different from the other years for Thuan An and Quang Nam. The location-by-location analysis indicated that in 2015, the gut microbiota was different for all locations and Quang Nam was different from Binh Dinh in 2014; Thuan An was different from the other locations in 2016. Thus, there seems to be a time-dependent trend in the North-South axis for the gut microbiota.Overall, this is the first study on the gut microbiota of migrating rabbit fish larvae. We found limited variation in the gut microbiota geographically and in time, and strong indications for a core microbiome.This suggest that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.

No abstract

Alkanes are saturated hydrocarbons that are ubiquitous in the environment. Microbial degradation pathways evolved to activate and catabolise these compounds in order to gain energy and building blocks for cell growth. These pathways involve a number of hydroxylases, which primarily differ according to the nature of the hydrocarbon itself (e.g. aromatic or aliphatic). Given the widespread distribution of alkanes in the environment, a number of variants of such enzymes are present among microbes. Hence, primers designed to detect such environmental variants would require a database with a sufficiently large number of sequences. In the present chapter, we selected the integral-membrane alkane hydroxylases (AlkB) and cytochrome P450 alkane hydroxylases (CYP153) superfamilies for sketching a general proposal of a design pipeline to target bacterial genes involved in aerobic alkane degradation. Further, we introduce HyDeg, a web-based tool that targets multiple subfamilies of enzymes involved in the microbial degradation of aromatic/aliphatic hydrocarbons. The website allows to retrieve amino acid and nucleotide sequences of the target family and proposes an evolutionary relationship for the selected enzyme.