A comparison of the nitrogen metabolic networks of Kluyveromyces marxianus and Saccharomyces cerevisiae

In grape must, nitrogen is available as a complex mixture of various compounds (ammonium and amino acids). Wine yeasts assimilate these multiple sources in order to suitably fulfil their anabolic requirements during alcoholic fermentation. Nevertheless, the order of uptake and the intracellular fate of these sources are likely to differ between strains and species. Using a two-pronged strategy of isotopic filiation and RNA sequencing, the metabolic network of nitrogen utilization and its regulation in Kluyveromyces marxianus were described, in comparison with those of Saccharomyces cerevisiae. The data highlighted differences in the assimilation of ammonium and arginine between the two species. The data also revealed that the metabolic fate of certain nitrogen sources differed, thereby resulting in the production of various amounts of key wine aroma compounds. These observations were corroborated by the gene expression analysis.     

Neuronal Shot Noise and Brownian 1/f2 Behavior in the Local Field Potential

We demonstrate that human electrophysiological recordings of the local field potential (LFP) from intracranial electrodes, acquired from a variety of cerebral regions, show a ubiquitous 1/f² scaling within the power spectrum. We develop a quantitative model that treats the generation of these fields in an analogous way to that of electronic shot noise, and use this model to specifically address the cause of this 1/f² Brownian noise. The model gives way to two analytically tractable solutions, both displaying Brownian noise: 1) uncorrelated cells that display sharp initial activity, whose extracellular fields slowly decay in time and 2) rapidly firing, temporally correlated cells that generate UP-DOWN states.     

Mayday - integrative analytics for expression data

Background  

DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.     

Potentiation by naltrexone of d-amphetamine-induced behavioral suppression and its reversal by clonidine

Rats were trained to perform a fixed ratio-15 operant for food reinforcement during a 30 minute daily session. Naltrexone, in doses up to 45 mg/kg administered 15 min before the behavioral session, failed to disrupt responding. However, 0.3 and 1.0 mg naltrexone/kg produced a dose related potentiation of the operant behavioral suppression induced by 1.0 mg d-amphetamine/kg injected immediately before the session. The naltrexone/d-amphetamine combination also produced excessive salivation and postural abnormalities not seen when either drug was administered alone. [A subsequent study indicated that the salivation induced by naltrexone in combination with d-amphetamine may require previous exposure to naltrexone and/or d-amphetamine.] Blockade of dopamine receptors with pimozide did not modify the interaction. Functional noradrenergic blockade with a low dose of clonidine significantly reversed the potentiated suppression, of operant behavior, as well as the excessive salivation and abnormal posture. These data suggest that there is an important noradrenergic component to the interaction of naltrexone with d-amphetamine. The impressive interaction of behaviorally inactive doses of naltrexone with a moderate dose of d-amphetamine reported here for rats may have clinical implications for detoxified opiate addicts maintained on naltrexone in antagonist therapy programs.     

Climate‐driven rampant speciation of the Cape flora

Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine‐driven climate change. Location Middle to Late Miocene in the south‐east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south‐east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south‐western African coast are the disappearance of Podocarpus‐dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi‐arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre‐date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine‐driven climate change in south‐western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae.     

Seasonality in the altitude–diversity pattern of Alpine moths

Altitudinal gradients are frequently used to study environmental effects on species diversity. Recent quantitative studies on Lepidoptera focussed on tropical mountain systems and often reported unimodal diversity peaks at “mid-elevations”;, a pattern also often found in other taxa. Here we used methodologically comparable, nocturnal Macrolepidoptera samples from the Swiss Alps to analyze environmental correlates of diversity. Using seasonal data (monthly samples from April to November at altitudes between 600 and 2400 m a.s.l.) allowed to decouple altitude and some climate variables for analyses. We found that the altitude–diversity pattern changes with season. In spring and autumn, diversity decreased with increasing altitude, while we found a unimodal peak of diversity at mid-elevations during summer. This excluded all hypothetical causes of diversity variation that do not allow for seasonality. Temperature was an important correlate of diversity, whereas precipitation was not. These results were separately corroborated for the two most common families (Noctuidae and Geometridae). However, diversity patterns of the two families were not particularly close, and unexplained variance of climatic explanations was substantial in all cases. The patterns of faunal overlap did not explain the unimodal diversity pattern, and we claim that we lack a generally valid explanation for this common phenomenon.     

OLIGOAGARS ELICIT A PHYSIOLOGICAL RESPONSE IN GRACILARIA CONFERTA (RHODOPHYTA)

Gracilaria conferta (Schousboe ex Montagne) J. et G. Feldmann responded with an oxidative burst and rapid increases in respiration and halogenating activity when agar, agarose, or the agarose degradation products neoagarotetraose and neoagarohexaose were added to the growth medium. In contrast, carrageenan, oligocarrageenans, neoagarobiose, l-galactose, d-galactose, and several other mono- and oligosaccharides did not have any effect. Sixfold increases in respiration were observed 3 min after addition of neoagarohexaose. The response could only be induced in species of the genera Gracilaria and Gracilariopsis. Neoagarohexaose also elicited a release of hydrogen peroxide in less than 15 min, resulting in an immediate increase in algal brominating activity. Bleached thallus tips appeared a few hours after the addition of neoagarohexaose. This effect was dependent on the release of hydrogen peroxide and exposure to light. Exposure to light and oligosaccharide elicitors increased the production of reactive oxygen species, which reached destructive concentrations when both mechanisms were simultaneously active. Concentrations of 0.1 to 3.3 μM agarose or agars were sufficient to trigger an increase in respiration, an oxidative burst response, and tip bleaching. However, higher concentrations of neoagarohexaose and neoagarotetraose were necessary to elicit the responses, indicating that the alga is more sensitive to oligoagars with degrees of biose-polymerization > 3. The extremely short reaction time and high specificity indicate that intermediates of agar degradation are recognized by Gracilaria as messengers when microbial degradation of its cell wall occurs. The physiological responses may represent the early stages of algal defense mechanisms involved in repression of pathogen ingress.