Plankton distribution across a slope current-induced front in the southern Bay of Biscay

Relatively warm (12.50–12.75°C) and high-salinity[<35.640 practical salinity units (PSU)] water flowing eastwardwas detected at the shelf-break during a cruise carried Outin the southern Bay of Biscay in Spring 1987. The slope currentinduced the formation of a convergent front separating well-mixedoceanic waters from haline-stratified coastal waters. Very highconcentrations of dissolved oxygen (295 µmol kg^–1)and chlorophyll a(>4.5 mg m^–3) were found at the outeredge of the frontal boundary. Small autotrophic flagellatesdominated the phytoplankton community. Primary production peakedat the boundary region. Estimated phytoplankton growth ratesindicated that active growth was taking place, with lower turnovertimes integrated over the water column at the frontal station(2.5–5 days) than at coastal (1.5–2.8 days) or oceanic(1.5–3.5 days) stations. The lowest doubling times (1–2days) were calculated for surface frontal populations. Accumulationof zooplankton was also observed associated with the convergentphysical structure, although this relationship was less markedthan for phytoplankton. Copepods, mainly Paracalanus parvus,Acartia clausi and Oithona helgolandica, formed the bulk ofthe mesozooplankton biomass. Compatibility between the sizeof phytoplankton cells and copepod size spectra indicate highfood availability for these animals, particularly in the vicinityof the front. The distribution of fish eggs and fish larvaewas also coupled with the slope current-induced front. Sardinelarvae were more abundant at the coastal side of the front,whereas larval stages of blue whiting reached the highest densitiesat off-shelf stations. Larvae of lamellibranch molluscs andbryozoa were restricted to nearshore waters, as the frontalboundary prevented larval dispersion to the open ocean. Theresults presented in this paper suggest that the Iberian slopecurrent and its associated shelf-break frontal structure werecrucial in controlling phytoplankton primary production, activityof grazers, distribution of larvae of fishes and benthic invertebrates,and ultimately in determining the structure of the pelagic foodweb in the southern Bay of Biscay during the seasonal periodof vertical mixing.     

Ethanol-hypersensitive and ethanol-dependent cdc − mutants in Schizosaccharomyces pombe

Ethanol-hypersensitive strains (ets mutants), unable to grow on media containing 6% ethanol, were isolated from a sample of mutagenized Schizosaccharomyces pombe wild-type cells. Genetic analysis of these ets strains demonstrated that the ets phenotype is associated with mutations in a large set of genes, including cell division cycle (cdc) genes, largely non-overlapping with the set represented by the temperature conditional method; accordingly, we isolated some ets non-ts cdc ^? mutants, which may identify novel essential genes required for regulation of the S. pombe cell cycle. Conversely, seven well characterized ts cdc ^? mutants were tested for their ethanol sensitivity; among them, cdc1–7 and cdc13–117 exhibited a tight ets phenotype. Ethanol sensitivity was also tested in strains bearing different alleles of the cdc2 gene, and we found that some of them were ets, but others were non-ets; thus, ethanol hypersensitivity is an allele-specific phenotype. Based on the single base changes found in each particular allele of the cdc2 gene, it is shown that a single amino acid substitution in the p34^cdc2 gene product can produce this ets phenotype, and that ethanol hypersensitivity is probably due to the influence of this alcohol on the secondary and/or tertiary structure of the target protein. Ethanol-dependent (etd) mutants were also identified as mutants that can only be propagated on ethanol-containing media. This novel type of conditional phenotype also covers many unrelated genes. One of these etd mutants, etd1-1, was further characterized because of the lethal cdc ^? phenotype of the mutant cells under restrictive conditions (absence of ethanol). The isolation of extragenic suppressors of etd1-1, and the complementation cloning of a DNA fragment encompassing the etd1 ⁺ wild-type gene (or an extragenic multicopy suppressor) demonstrate that current genetic techniques may be applied to mutants isolated by using ethanol as a selective agent.     

Identification of the gene encoding an N-acetylpuromycin N-acetylhydrolase in the puromycin biosynthetic gene cluster from Streptomyces alboniger.

The biologically inactive compound N-acetylpuromycin is the last intermediate of the puromycin antibiotic biosynthetic pathway in Streptomyces alboniger. Culture filtrates from either this organism or Streptomyces lividans transformants harboring the puromycin biosynthetic gene cluster cloned in low-copy-number cosmids contained an enzymic activity which hydrolyzes N-acetylpuromycin to produce the active antibiotic. A gene encoding the deacetylase enzyme was located at one end of this cluster, subcloned in a 2.5-kb DNA fragment, and expressed from a high-copy-number plasmid in S. lividans.     

Enumeration of Obesumbacterium proteus in brewery yeasts and characterization of isolated strains using Biolog GN microplates and protein fingerprinting

Of a range of media tested for enumeration of Obesumbacterium proteus in brewers' yeast, Universal Beer agar and Wallerstein Laboratories Differential medium were most effective. MacConkey agar (several types) and Membrane Lauryl Sulphate agar were least effective. Other media (Wort agar, YM agar) were of intermediate efficacy. Nine O. proteus strains from commercial yeast samples were characterized using the API 20E test kit, the Biolog GN microplate (BGNM) and by SDS-PAGE of their total soluble proteins. Both the BGNM and SDS-PAGE techniques allowed the strains to be differentiated from one another: the API 20E kit did not. All strains isolated from UK breweries belonged to O. proteus biogroup II. Four of these strains displayed a branching cell morphology not hitherto described in any member of the Enterobacteriaceae.     

Use of Synthetic Peptides to Study the Function of GTPases Regulating Vesicular Traffic

We describe the application of synthetic peptides to explore the function of GTPases regulating vesicular traffic through the constitutive and regulated exocytic pathways. The utility of the approach is discussed in the context of the parameters that limit or enhance the effectiveness of these reagents in eliciting a biologically relevant response.     

Combined effect of ambient temperature and solar radiation on maned sloths' behaviour and detectability

Changes in ambient temperature and solar radiation may affect sloths' metabolic rate and body temperature, with consequent changes in activities, postures and microhabitat selection. Although the separate effect of temperature and solar radiation on sloth's behaviour have been previously studied, the combined effect of these climatic factors on behavioural aspects of sloths has never been systematically evaluated in field conditions. Here we evaluated the influence of hourly ambient temperature variation on maned sloth (Bradypus torquatus) activities, postures and tree crown positions, under sunny and cloudy conditions; and tested if any of the animal posture and position increase their exposure to human detection. We performed 350 h of visual observation on eight maned sloths, equipped with radio-backpacks, in northern Bahia, Brazil, recording their activities, and their resting postures and positions on tree crowns. We also recorded the time taken to visualize the sloths on 58 days to analyse if sloths' detection is affected by posture and position. Higher ambient temperature, within a range of 21–33°C, increased the sloths' activity levels in cloudy conditions but reduced their activity in sunny conditions. Increasing ambient temperature also reduced the frequency of huddled posture and increased the frequency of extended posture and permanence in the inner tree crown. Lastly, the postures and positions did not influence sloths' detectability. Thus, the direction of the temperature–activity relationship depends on climatic conditions (sunny/cloudy), and individuals rely on resting postures and positions to thermoregulate. The warmer and drier future climate, expected to occur in the northern Atlantic Forest, may impose change in the diurnal activity levels and postural pattern for this threatened species, leading maned sloths to reduce its activity on sunny and warmer days and adopting an extended posture.     

Hepatic changes during a carrageenan induced granuloma in rats

Hepatic changes during inflammation were studied in rats bearing a carrageenan induced granuloma. In spite of a decrease in the metabolic capacity of microsomes to induce lipid peroxidation during inflammation, the endogenous lipid peroxidation remained unchanged and unrelated with the hepatic activities measured. The continuous increase in hepatic cAMP observed during acute and chronic phases could be related to adenylate cyclase stimulation by mediators, and could be an initial step in the hepatocyte adaptation leading to the increased level of hepatic caeruloplasmin, to the reduction of cytochrome P-450 level and to the modifications of Ca(2+) sequestration by microsomes.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.