The limits of log-ratios

Background  

DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured expression levels for the two samples.     

Genetic regulation of endotoxin-induced airway disease

To identify novel genes regulating the biologic response to lipopolysaccharide (LPS), we used a combination of quantitative trait locus (QTL) analysis and microarray-based gene expression studies of C57BL/6J x DBA/2J(BXD) F2 and recombinant inbred (RI) mice. A QTL affecting pulmonary TNF-alpha production was identified on chromosome 2, and a region affecting both polymorphonuclear leukocyte recruitment and TNF-alpha levels was identified on chromosome 11. Microarray analyses of unchallenged and LPS-challenged BXD RI strains identified approximately 500 genes whose expression was significantly changed by inhalation of LPS. Of these genes, 28 reside within the chromosomal regions identified by the QTL analyses, implicating these genes as high priority candidates for functional studies. Additional high priority candidate genes were identified based on their differential expression in mice having high and low responses to LPS. Functional studies of these genes are expected to reveal important molecular mechanisms regulating the magnitude of biologic responses to LPS.     

Decline in Kelp in West Europe and Climate

Kelp ecosystems form widespread underwater forests playing a major role in structuring the biodiversity at a regional scale. Some seaweeds such as Laminaria digitata are also economically important, being exploited for their alginate and iodine content. Although some studies have shown that kelp ecosystems are regressing and that multiple causes are likely to be at the origin of the disappearance of certain populations, the extent to which global climate change may play a role remains speculative. Here we show that many populations of L. digitata along European coasts are on the verge of local extinction due to a climate-caused increase in sea temperature. By modeling the spatial distribution of the seaweed, we evaluate the possible implications of global climate change for the geographical patterns of the species using temperature data from the Coupled Model Intercomparison Project phase 5 (CMIP5). Projections of the future range of L. digitata throughout the 21st century show large shifts in the suitable habitat of the kelp and a northward retreat of the southern limit of its current geographic distribution from France to Danish coasts and the southern regions of the United Kingdom. However, these projections depend on the intensity of warming. A medium to high warming is expected to lead to the extirpation of the species as early as the first half of the 21st century and there is high confidence that regional extinction will spread northwards by the end of this century. These changes are likely to cause the decline of species whose life cycle is closely dependent upon L. digitata and lead to the establishment of new ecosystems with lower ecological and economic values.     

MFA for overdetermined systems reviewed and compared with rna expression data to elucidate the difference in shikimate yield between carbon- and phosphate-limited continuous cultures of E. coli W3110.shik1

The present contribution focuses on the mathematical techniques used to solve steady state metabolic models for the case of an overdetermined system. Even when parts of the system are underdetermined it is possible to solve the model partially and obtain statistically meaningful results. This is illustrated with data gathered from a set of E. coli W3110.shik1 phosphate- or carbon-limited continuous cultures. It is shown that the low yield in shikimate for C-limited cultures is not due to a lower flux going to the shikimate pathway but is caused by a high secretion of byproducts. Carbon-limited cultures could be better for shikimate production than carbon-abundant cultures provided the byproduct secretion is reduced. Finally, flux calculations are compared with RNA expression data.     

A first estimate of sea turtle bycatch in the industrial trawling fishery of Gabon

Gabon hosts nesting grounds for several sea turtle species, including the world’s largest rookery for the leatherback turtle (Dermochelys coriacea), Africa’s largest rookery for the olive ridley turtle (Lepidochelys olivacea) and smaller aggregations of the hawksbill turtle (Eretmochelys imbricata) and green turtle (Chelonia mydas). To assess the level of incidental captures of turtles by the Gabonese trawl fishery, an onboard observer program was conducted in the period 2012–2013. A total of 143 turtles were captured by 15 trawlers during 271 fishing days. The olive ridley turtle was the main species captured (80% of bycaught turtles), with mostly adult-sized individuals. The remaining 20% included green turtles, hawksbill turtles, leatherback turtles and undetermined species. Bycatch per unit of effort (BPUE) of olive ridley turtles varied greatly depending on the period of the year (range of means: 0.261–2.270). Dead and comatose turtles were 6.2 and 24.6% respectively (n = 65). By applying the available fishing effort to two BPUE scenarios (excluding or considering a seasonal peak), the total annual number of captures was estimated as ranging between 1026 (CI 95% 746–1343) and 2581 (CI 95% 1641–3788) olive ridley turtles, with a mortality ranging from 63 (CI 95% 13–135) to 794 (CI 95% 415–1282) turtles per year depending on the scenario and on the fate of comatose turtles. Such a potential mortality may be reason for concern for the local breeding population of olive ridley turtles and recommendations in terms of possible conservation measures and further research are given.     

Photosynthetic response to light and temperature in Laminaria digitata gametophytes from two French populations

Given the growing body of evidence on the general decline of kelp beds worldwide, it is crucial to understand the physiological responses of kelp gametophyte stages to environmental parameters. We investigated the physiological responses to light and temperature of gametophytes from two populations of Laminaria digitata in contrasting environments along the French coast of the English Channel. Gametophytes of both populations were highly tolerant of high light through an efficient down-regulation of photosynthesis triggered by the activation of the xanthophyll cycle. Temperature increases promoted photosynthesis and photosystem II showed high resistance to short-term exposure to high temperatures currently encountered in the field. Gametophytes from the two sites displayed some differences in their pigment content and photosynthetic characteristics, but low replication and difference in time of sampling precluded tests of potential local adaptation to the light conditions at each site, as observed in previously published results on adult sporophytes. Gametophytes of L. digitata appeared to be resistant to irradiation and temperature conditions currently experienced in the field, confirming their role in persistence of kelp species under stressful environmental conditions.     

Alpha fetoprotein in maternal blood during normal and pathological pregnancies]

AFP was assayed in serum of normal pregnant women and in patients with pathological pregnancy. Pathological levels of AFP, defined as increased or decreased concentrations compared with the normal distribution, was detected in 83.5 % of pregnant women who delivered a dysmature child and in 88 % of those whose placenta was macroscopically sclerous. A longitudinal determination of AFP appears to be useful in the follow-up of risk of abortion.