Infrastructure for the life sciences: design and implementation of the UniProt website

Background  

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the domain was switched to the newly developed site described in this paper in July 2008.     

Allelopathy of Aquatic Autotrophs

Allelopathy in aquatic environments may provide a competitive advantage to angiosperms, algae, or cyanobacteria in their interaction with other primary producers. Allelopathy can influence the competition between different photoautotrophs for resources and change the succession of species, for example, in phytoplankton communities. Field evidence and laboratory studies indicate that allelopathy occurs in all aquatic habitats (marine and freshwater), and that all primary producing organisms (cyanobacteria, micro- and macroalgae as well as angiosperms) are capable of producing and releasing allelopathically active compounds. Although allelopathy also includes positive (stimulating) interactions, the majority of studies describe the inhibitory activity of allelopathically active compounds. Different mechanisms operate depending on whether allelopathy takes place in the open water (pelagic zone) or is substrate associated (benthic habitats). Allelopathical interactions are especially common in fully aquatic species, such as submersed macrophytes or benthic algae and cyanobacteria. The prevention of shading by epiphytic and planktonic primary producers and the competition for space may be the ultimate cause for allelopathical interactions. Aquatic allelochemicals often target multiple physiological processes. The inhibition of photosynthesis of competing primary producers seems to be a frequent mode of action. Multiple biotic and abiotic factors determine the strength of allelopathic interactions. Bacteria associated with the donor or target organism can metabolize excreted allelochemicals. Frequently, the impact of surplus or limiting nutrients has been shown to affect the overall production of allelochemicals and their effect on target species. Similarities and differences of allelopathic interactions in marine and freshwater habitats as well as between the different types of producing organisms are discussed. Referee: Dr. Friedrich Jüttner, Universität Zürich-Limnologische Station, Institut für Pflanzen biologie, Universität Zürich, Seestrasse 187, Ch-8802 Klichberg ZH, Switzerland     

Disproportionately elevated fasting proinsulin levels in normoglycemic patients with thalassemia major are correlated to the degree of iron overload

OBJECTIVE: To analyze the secretion of the insulin precursor proinsulin in patients with beta-thalassemia and its possible relation to iron overload. METHODS: We assessed fasting proinsulin, insulin, C-peptide and glucose levels from 34 patients with beta-thalassemia and 33 healthy controls. The correlation to age, body mass index, hepatic iron concentration, serum ferritin and serum AST was analyzed. RESULTS: Fasting proinsulin (p < 0.002) and proinsulin-to-insulin ratio (p < 0.02) were significantly increased in patients with thalassemia irrespective of the degree of glucose tolerance. They correlated positively to serum ferritin, liver iron, patient age and serum AST (all p < 0.05). CONCLUSIONS: Disproportionately elevated proinsulin levels in thalassemic patients indicate early beta-cell dysfunction due to siderosis. An additional biological significance of hyperproinsulinemia and its possible ability to predict long-term iron toxicity in these patients remain to be clarified.     

Validation of a method for quantification of ketobemidone in human plasma with liquid chromatography-tandem mass spectrometry

A liquid chromatography tandem mass spectrometry (LC-MS-MS) method for determination of the analgesic aminophenol ketobemidone in human plasma is presented. Two preparation methods for plasma samples containing ketobemidone were compared, liquid-liquid extraction (LLE) and solid-phase extraction (SPE). Both methods showed good precision (n=10), 1.7% and 2.9%, respectively (0.04 micro M) and 1.1% and 2.5%, respectively (0.14 micro M). The accuracy was 98% and 103%, respectively (0.04 micro M) and 105% and 99%, respectively (0.14 micro M). Ketobemidone could be quantified at 0.43 nM, with a relative standard deviation of 17.5% (n=19) using LLE and 18.6% (n=10) using SPE. This level was an order of magnitude lower than earlier reported quantification limits. Quantitative data from plasma samples analyzed with LC-MS-MS were in good agreement with those obtained by gas chromatography with chemical ionization mass spectrometry (GC-CI/MS). This indicates that LC-MS-MS is a good alternative method to GC-MS as it is more sensitive and time-consuming derivatization can be avoided.     

Conjugative plasmid transfer in gram-positive bacteria.

Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer.     

The Influence of water salinity on the free amino acid concentration in muscle and hepatopancreas of adult shrimps, Penaeus japonicus

Variations of the total free amino acid (FAA) pool and the content of specific amino acids have been measured in the muscle and hepatopancreas of adult shrimps, Penaeus japonicus, acclimatized at five water salinities: 38, 32, 26, 20 and 14%‰ The FAA content is always higher in muscle than in hepatopancreas at all tested salinites. On the other hand, the hepatopancreas exhibits the highest concentrations of essential amino acids. Two steps in the evolution of FAA content can be observed, the first one regarding decrease in salinity from 38 to 20%‰ and the second one, when salinity goes below 20%_°. The first step can be characterized by a 16% decrease of total FAA content in the muscle and a 36% increase in the hepatopancreas. In muscle, the variations are mainly due to changes in non-essential FAA content, whereas in the hepatopancreas, they are linked to variations in essential FAA content. The other step is characterized by a drastic increase in moisture and decrease in FAA content in both studied organs when water salinity is 14%‰ The total FAA content is about 40% lower in shrimps at 14%_° compared to 38%‰ seawater salinity. During adaptation, the FAA pool (mainly NEFAAs) of muscle seems to be directly related to osmoregulation, whereas in the hepatopancreas, its evolution seems to be linked with energy expenditure and protein synthesis. The results are evaluated in order to elucidate the role of FAA in intracellular osmoregulation and in relation to animal ecology.     

Primary astroglial cultures

Conclusion Primary cultures from neonatal rat brain consist mainly of astroglial cells, immunohistochemically identified by GFAp and S-100. As other cells than astrocytes may survice in the culture, specific markers for the expected cells were used. Cells with phagocytic properties, endothelial-like cells, oligoblasts, ependymal cells and mesenchymal cells were identified. No neurons have so far been detected.The astroglial cells have a high-affinity uptake for glutamate, aspartate GABA, taurine and hypotaurine, while there is probably a non-saturable uptake of norepinephrine, dopamine and 5-HT. The enzymes MAO, COMT, GABA-T and GS have been demonstrated. It thus seems that astrocytes take part in the inactivation of neurotransmitters, although amino acids and monoamines are taken up with different mechanisms.The presence of receptors for different neurotransmitters and neuromodulators has been demonstrated on astrocytes.Astroglial-enriched cultures from various brain regions have shown that the cells express specialized functional properties concerning neurotransmitter uptake, metabolizing enzymes and receptor density.Astroglial cell differentiation in culture is shortly reviewed and one possibility to affect this maturation by co-cultivation with neuronal containing cultures is point out.     

Complete elimination of hostplant quinolizidine alkaloids by larvae of a polyphagous lycaenid butterfly,Callophrys rubi

Caterpillars of the lycaenid butterfly Callophrys rubi accept a variety of hostplants. When fed inflorescences or leaves of Genista tinctoria (a natural hostplant) or Lupinus polyphyllus (a non-host), the larvae completely eliminate quinolizidine alkaloids ingested from their food in their frass. No alkaloids are stored. Infestation by the parasitoid wasp Distatrix sancus (Braconidae) did not affect alkaloid elimination. The presence of an effective anti-toxin system is discussed with reference to the evolution of hostplant relationships in the genus Callophrys. There is no evidence that in the secondarily myrmecoxenous larvae of C. rubi hostplantderived chemical defense takes the place of former myrmecophily.     

Hunting and consumption of rodents by children in the Lassa fever endemic area of Faranah,Guinea

As a consequence of the Ebola outbreak, human–animal contact has gained importance for zoonotic transmission surveillance. In Faranah (Upper Guinea), daily life is intertwined with rodents, such as the Natal multimammate mouse, Mastomys natalensis; a reservoir for Lassa virus (LASV). However, this contact is rarely perceived as a health risk by residents, although Lassa fever (LF) is known to be endemic to this region. Conversely, these observations remain a great concern for global health agendas. Drawing on ethnographic research involving interviews, focus group discussions, participant observations, and informal discussions over four months, we first identified factors that motivated children to hunt and consume rodents in Faranah villages, and thereafter, explored the knowledge of LF infection in children and their parents. Furthermore, we studied two dimensions of human-rodent encounters: 1) space-time of interaction and 2) factors that allowed the interaction to occur and their materiality. This approach allowed us to contextualize child-rodent contacts beyond domestic limits in the fallow fields, swamps, and at other times for this practice. A close look at these encounters provided information on rodent trapping, killing, and manipulation of cooking techniques and the risk these activities posed for the primary transmission of LASV. This research facilitated the understanding of children’s exposure to M. natalensis during hunting sessions and the importance of rodent hunting, which is a part of their boyish identity in rural areas. Determination of when, where, why, and how children, rodents, and environments interacted allowed us to understand the exposures and risks important for human and animal surveillance programs in the Lassa-endemic region.