Showing papers by "Stockholm University published in 2000"
TL;DR: A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
4,268 citations
TL;DR: If the growing aquaculture industry is to sustain its contribution to world fish supplies, it must reduce wild fish inputs in feed and adopt more ecologically sound management practices.
Abstract: Global production of farmed fish and shellfish has more than doubled in the past 15 years. Many people believe that such growth relieves pressure on ocean fisheries, but the opposite is true for some types of aquaculture. Farming carnivorous species requires large inputs of wild fish for feed. Some aquaculture systems also reduce wild fish supplies through habitat modification, wild seedstock collection and other ecological impacts. On balance, global aquaculture production still adds to world fish supplies; however, if the growing aquaculture industry is to sustain its contribution to world fish supplies, it must reduce wild fish inputs in feed and adopt more ecologically sound management practices.
2,931 citations
TL;DR: The authors examined inflation targeting in a small open economy with forward-looking aggregate supply and demand with microfoundations, and with stylized realistic lags in the different monetary-policy transmission channels.
1,108 citations
TL;DR: There is growing interest in the possibility that genetic compatibility may drive mate choice, including gamete choice, particularly from the perspective of understanding why females frequently mate with more than one male, and whether there is any evidence for mate choice driven by these factors.
Abstract: There is growing interest in the possibility that genetic compatibility may drive mate choice, including gamete choice, particularly from the perspective of understanding why females frequently mate with more than one male. Mate choice for compatibility differs from other forms of choice for genetic benefits (such as ‘good genes’) because individuals are expected to differ in their mate preferences, changing the evolutionary dynamics of sexual selection. Recent experiments designed to investigate genetic benefits of polyandry suggest that mate choice on the basis of genetic compatibility may be widespread. However, in most systems the mechanisms responsible for variation in compatibility are unknown. We review potential sources of variation in genetic compatibility and whether there is any evidence for mate choice driven by these factors. Selfish genetic elements appear to have the potential to drive mate compatibility mate choice, though as yet there is only one convincing example. There is abundant evidence for assortative mating between populations in hybrid zones, but very few examples where this is clearly a result of selection against mating with genetically less compatible individuals. There are also numerous cases of inbreeding avoidance, but little evidence that mate choice or differential fertilization success driven by genetic compatibility occurs between unrelated individuals. The exceptions to this are a handful of situations where both the alleles causing incompatibility and the alleles involved in mate choice are located in a chromosome region where recombination is suppressed. As yet there are only a few potential sources of genetic compatibility which have clearly been shown to drive mate choice. This may reflect limitations in the potential for the evolution of mate choice for genetic compatibility within populations, although the most promising sources of such incompatibilities have received relatively little research.
902 citations
TL;DR: In this paper, the generalized Schur form is used to solve a system of linear expectational difference equations (a multivariate linear rational expectations model) and the method is simple to understand and to use, and is applicable to a large class of rational expectations models.
888 citations
TL;DR: The evidence for the existence of dark matter in the universe is reviewed in this paper, where a general picture emerges, where both baryonic and non-baryonic dark matter is needed to explain current observations.
Abstract: The evidence for the existence of dark matter in the universe is reviewed. A general picture emerges, where both baryonic and non-baryonic dark matter is needed to explain current observations. In particular, a wealth of observational information points to the existence of a non-baryonic component, contributing between around 20 and 40% of the critical mass density needed to make the universe geometrically flat on large scales. In addition, an even larger contribution from vacuum energy (or cosmological constant) is indicated by recent observations. To the theoretically favoured particle candidates for non-baryonic dark matter belong axions, supersymmetric particles, and of less importance, massive neutrinos. The theoretical foundation and experimental situation for each of these is reviewed. Direct and indirect methods for detection of supersymmetric dark matter are described in some detail. Present experiments are just reaching the required sensitivity to discover or rule out some of these candidates, and major improvements are planned over the coming years.
837 citations
TL;DR: In this paper, the role of disturbance for coral reef ecosystem dynamics has been examined and the implications of these changes for reef-associated human activities, such as fishing and tourism, can be substantial.
Abstract: Facing a human-dominated world, ecologists are now reconsidering the role of disturbance for coral reef ecosystem dynamics. Human activities alter the natural disturbance regimes of coral reefs by transforming pulse events into persistent disturbance or even chronic stress, by introducing new disturbance, or by suppressing or removing disturbance. Adding these alterations to natural disturbance regimes will probably result in unknown synergistic effects. Simultaneously, humans are altering the capacity of reefs to cope with disturbance (e.g. by habitat fragmentation and reduction of functional diversity), which further exacerbates the effects of altered disturbance regimes. A disturbance that previously triggered the renewal and development of reefs might, under such circumstances, become an obstacle to development. The implications of these changes for reef-associated human activities, such as fishing and tourism, can be substantial.
781 citations
TL;DR: It is suggested that individuals who exercised at least two to three times a week experienced significantly less depression, anger, cynical distrust, and stress than those exercising less frequently or not at all.
691 citations
TL;DR: It now appears clear that the polar-aromatic residues Trp and Tyr have a specific affinity for a region near the lipid carbonyls, whereas positively charged residues extend into the lipid phosphate region.
665 citations
TL;DR: An extensive literature survey on knowledge management explores knowledge management with respect to its content, its definition and domain in theory and practice, its use and implications, and to point out some problems inherent in the concept.
Abstract: Over the past several years there have been intensive discussions about the importance of knowledge management within our society. The management of knowledge is promoted as an important and necessary factor for organisational survival and maintenance of competitive strength. To remain at the forefront organisations need a good capacity to retain, develop, organise, and utilise their employees’ capabilities. Knowledge and the management of knowledge appear to be regarded as increasingly important features for organisational survival. Explores knowledge management with respect to its content, its definition and domain in theory and practice, its use and implications, and to point out some problems inherent in the concept. The main contribution of this paper is an extensive literature survey on knowledge management.
593 citations
TL;DR: Phylogenetic analysis places the two Neanderthals from the Caucasus and western Germany together in a clade that is distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool.
Abstract: The expansion of premodern humans into western and eastern Europe ∼40,000 years before the present led to the eventual replacement of the Neanderthals by modern humans ∼28,000 years ago1. Here we report the second mitochondrial DNA (mtDNA) analysis of a Neanderthal, and the first such analysis on clearly dated Neanderthal remains. The specimen is from one of the eastern-most Neanderthal populations, recovered from Mezmaiskaya Cave in the northern Caucasus2. Radiocarbon dating estimated the specimen to be ∼29,000 years old and therefore from one of the latest living Neanderthals3. The sequence shows 3.48% divergence from the Feldhofer Neanderthal4. Phylogenetic analysis places the two Neanderthals from the Caucasus and western Germany together in a clade that is distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool. Comparison with modern populations provides no evidence for the multiregional hypothesis of modern human evolution.
TL;DR: Support of the chemical structure was obtained through the demonstration that AA is formed in the heating of the feed and that the level of AA in the fried feed is compatible with the measured levels of the CEV adduct.
Abstract: Exposure to acrylamide (AA) has been monitored by mass spectrometric detection of the adduct, N-(2-carbamoylethyl)valine (CEV), to the N-termini of hemoglobin (Hb), according to the N-alkyl Edman method In these studies, a conspicuous background level, about 40 pmol/g of globin, of apparently the same adduct was regularly observed in Hb from persons without known exposure to AA For testing of the hypothesis that this adduct originates from AA formed in cooking, rats were fed fried animal standard diet for 1 or 2 months These animals exhibited a strong increase of the level of the studied Hb adduct, compared to control rats fed unfried diet By gas chromatography/tandem mass spectrometry, the identity with CEV was confirmed by the concordance of the product ion spectrum of the studied adduct with that of a verified standard and by interpretation of the fragment ions Further support of the chemical structure, at the same time pinpointing AA as the causative reactive factor, was obtained through the demo
TL;DR: There is negative correlation between x and the amount y that 2 allocates to 1, however, there is positive correlation between y and 2's expectation of 1's expectations of y.
TL;DR: In this paper, the authors show that the results developed in N. Singh and X. Vives (1984, Rand J. Econ.15, 546-554) are sensitive to the duopoly assumption and that prices may be higher under price competition than under quantity competition.
TL;DR: In this article, a model of ocean and sediment geochemistry is used to evaluate the current proposals for explaining the glacial/interglacial pCO2 cycles within the context of the ocean carbon cycle.
Abstract: Fifteen years after the discovery of major glacial/interglacial cycles in the CO2 concentration of the atmosphere, it seems that all of the simple mechanisms for lowering pCO2 have been eliminated. We use a model of ocean and sediment geochemistry, which in- cludes new developments of iron limitation of biological production at the sea surface and anoxic diagenesis and its effect on CaCO3 preservation in the sediments, to evaluate the current proposals for explaining the glacial/ interglacial pCO2 cycles within the context of the ocean carbon cycle. After equilibration with CaCO3 the model is unable to generate glacial pCO2 by increasing ocean NO3 but predicts that a doubling of ocean H4SiO4 might suffice. However, the model is unable to generate a doubling of ocean H4SiO4 by any reasonable changes in SiO2 weathering or production. Our conclusions force us to challenge one or more of the assumptions at the foundations of chemical oceanography. We can abandon the stability of the "Redfield ratio" of nitrogen to phos- phorus in living marine phytoplankton and the ultimate limitation of marine photosynthesis by phosphorus. We can challenge the idea that the pH of the deep ocean is held relatively invariant by equilibrium with CaCO3 .A third possibility, which challenges physical oceanogra- phers, is that diapycnal mixing in ocean circulation mod- els exceeds the rate of mixing in the real ocean, dimin- ishing the model pCO2 sensitivity to biological carbon uptake.
TL;DR: This paper showed that recombinant recombinant IL-1Ra or its selective endogenous overexpression in astrocytes under the control of glial acidic fibrillary protein promoter potently inhibits motor and electroencephalographic seizures induced by bicuculline methiodide in mice.
Abstract: IL-1beta and its endogenous receptor antagonist (IL-1Ra) are rapidly induced by seizures in the rodent hippocampus. Exogenously applied IL-1beta prolongs seizures in an IL-1R type I-mediated manner. This effect depends on N-methyl-d-aspartate receptor activation. We report here that intrahippocampal application of recombinant IL-1Ra or its selective endogenous overexpression in astrocytes under the control of glial acidic fibrillary protein promoter potently inhibits motor and electroencephalographic seizures induced by bicuculline methiodide in mice. Accordingly, transgenic mice show a reduced seizure-related c-fos mRNA expression in various forebrain areas compared with their wild-type littermates. Recombinant IL-1Ra was ineffective in mice deficient in IL-1R type I, having per se a delayed onset to generalized convulsions. These results demonstrate that IL-1Ra mediates potent anticonvulsant effects acting on IL-1R type I and suggest that the balance between brain IL-1beta and IL-1Ra represents a crucial mechanism to control seizure generalization.
TL;DR: It is proposed that YidC, homologous to Saccharomyces cerevisiae Oxa1p, is involved in the insertion of hydrophobic sequences into the lipid bilayer after initial recognition by the SecAYEG translocase.
Abstract: In Escherichia coli, both secretory and inner membrane proteins initially are targeted to the core SecYEG inner membrane translocase. Previous work has also identified the peripherally associated SecA protein as well as the SecD, SecF and YajC inner membrane proteins as components of the translocase. Here, we use a cross-linking approach to show that hydrophilic portions of a co-translationally targeted inner membrane protein (FtsQ) are close to SecA and SecY, suggesting that insertion takes place at the SecA/Y interface. The hydrophobic FtsQ signal anchor sequence contacts both lipids and a novel 60 kDa translocase-associated component that we identify as YidC. YidC is homologous to Saccharomyces cerevisiae Oxa1p, which has been shown to function in a novel export pathway at the mitochondrial inner membrane. We propose that YidC is involved in the insertion of hydrophobic sequences into the lipid bilayer after initial recognition by the SecAYEG translocase.
TL;DR: Seed size was positively correlated with the probability of successful establishment of seeds and negatively correlated with patch occupancy, suggesting that dispersal limitation is an important structuring factor in temperate-forest herb communities.
Abstract: The distribution of species depends on the availability of suitable habitats, the capacity to disperse to these habitats, and the capacity of populations to persist after establishment. Dispersal limitation implies that not all suitable habitat patches will be occupied by a species. However, the extent to which dispersal limits local distribution is poorly known. In this study, we transplanted seeds, bulbils, and juvenile plants to examine patterns of dispersal limitation and patch occupancy in seven temperate-forest herbs. Recruitment was recorded during four years in 48 patches. The investigated species varied considerably in their natural abundance in the patches. Patterns of seedling emergence and establishment among patches were not related to any of nine investigated abiotic factors. In contrast, the availability of seeds or bulbils was found to limit recruitment in six of the investigated species. Establishment was also successful in many patches where the species did not occur naturally. Estimated patch occupancy in the investigated species ranged from 17.2% to 94.6%. Seed size was positively correlated with the probability of successful establishment of seeds and negatively correlated with patch occupancy. The results suggest that dispersal limitation is an important structuring factor in temperate-forest herb communities. The distribution of species can be perceived as the result of processes operating both among and within patches. Seed size is a key trait in these processes.
TL;DR: In this article, massive summer blooms of nitrogenfixing cyanobacteria have been documented in the Baltic Sea since the 19th century, but are reported to have increased in frequency, biomass, and duration in recen
Abstract: Massive summer blooms of nitrogen-fixing cyanobacteria have been documented in the Baltic Sea since the 19th century, but are reported to have increased in frequency, biomass, and duration in recen
TL;DR: This work proposes a model based on multiplicative frailties with a multivariate log-normal joint distribution with a generalization of the one presented by McGilchrist (1993, Biometrics 49, 221-225) based on Laplace approximation of the likelihood function.
Abstract: Summary. There exists a growing literature on the estimation of gamma distributed multiplicative shared frailty models. There is, however, often a need to model more complicated frailty structures, but attempts to extend gamma frailties run into complications. Motivated by hip replacement data with a more complicated dependence structure, we propose a model based on multiplicative frailties with a multivariate log-normal joint distribution. We give a justification and an estimation procedure for this generally structured frailty model, which is a generalization of the one presented by McGilchrist (1993, Biometrics49, 221-225). The estimation is based on Laplace approximation of the likelihood function. This leads to estimating equations based on a penalized fixed effects partial likelihood, where the marginal distribution of the frailty terms determines the penalty term. The tuning parameters of the penalty function, i.e., the frailty variances, are estimated by maximizing an approximate profile likelihood. The performance of the approximation is evaluated by simulation, and the frailty model is fitted to the hip replacement data.
TL;DR: A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures of flexible or rigid molecules is presented, which allows use of most types of conventional molecular-mechanical force fields and contains a variety of auxiliary terms for inter- and intramolecular interactions, including an harmonic bond-stretchings.
TL;DR: This study definitively identifies the chloroplast protease acting on the D1 protein during its light-induced turnover, and represents a novel class of FtsH substrate— functionally assembled proteins that have undergone irreversible photooxidative damage and cleavage.
Abstract: The photosystem II reaction center D1 protein is known to turn over frequently. This protein is prone to irreversible damage caused by reactive oxygen species that are formed in the light; the damaged, nonfunctional D1 protein is degraded and replaced by a new copy. However, the proteases responsible for D1 protein degradation remain unknown. In this study, we investigate the possible role of the FtsH protease, an ATP-dependent zinc metalloprotease, during this process. The primary light-induced cleavage product of the D1 protein, a 23-kD fragment, was found to be degraded in isolated thylakoids in the dark during a process dependent on ATP hydrolysis and divalent metal ions, suggesting the involvement of FtsH. Purified FtsH degraded the 23-kD D1 fragment present in isolated photosystem II core complexes, as well as that in thylakoid membranes depleted of endogenous FtsH. In this study, we definitively identify the chloroplast protease acting on the D1 protein during its light-induced turnover. Unlike previously identified membrane-bound substrates for FtsH in bacteria and mitochondria, the 23-kD D1 fragment represents a novel class of FtsH substrate— functionally assembled proteins that have undergone irreversible photooxidative damage and cleavage.
TL;DR: Atlantic cod chronically exposed to mechanically dispersed crude oil showed increased levels of PAH metabolites in bile and a slight induction of CYP1A, as well as formation of DNA adducts when compared with control fish, a novel finding.
TL;DR: There is an increasing recognition of the necessity to consider the heterogeneity of geosorbents, and in particular the condensed carbon facies fraction, to improve prediction of hydrophobic pollut....
Abstract: There is an increasing recognition of the necessity to consider the heterogeneity of geosorbents, and in particular the condensed carbon facies fraction, to improve prediction of hydrophobic pollut...
TL;DR: It is demonstrated that various environmentally relevant PCB-OHs are extremely potent inhibitors of human estrogen sulfotransferase, strongly suggesting that they indirectly induce estrogenic activity by increasing estradiol bioavailability in target tissues.
Abstract: Polychlorinated biphenyls (PCBs) are persistent environmental pollutants which exert a variety of toxic effects in animals, including disturbances of sexual development and reproductive function. The estrogenic effects of PCBs may be mediated in part by hydroxylated PCB metabolites (PCB-OHs), but the mechanisms by which they are brought about are not understood. PCBs as well as PCB-Hs show low affinities for both alpha and beta estrogen receptor isoforms. In the present study we demonstrate that various environmentally relevant PCB-OHs are extremely potent inhibitors of human estrogen sulfotransferase, strongly suggesting that they indirectly induce estrogenic activity by increasing estradiol bioavailability in target tissues.
TL;DR: The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching to identify proteins that possess the twin arginine motif that is characteristic for substrates of the TAT pathway.
Abstract: The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching. After correcting to eliminate possible isoforms and post-translational modifications, we estimated that there are at least 200 to 230 different lumenal and peripheral proteins. Sixty-one proteins were identified; for 33 of these proteins, a clear function or functional domain could be identified, whereas for 10 proteins, no function could be assigned. For 18 proteins, no expressed sequence tag or full-length gene could be identified in the databases, despite experimental determination of a significant amount of amino acid sequence. Nine previously unidentified proteins with lumenal transit peptides are presented along with their full-length genes; seven of these proteins possess the twin arginine motif that is characteristic for substrates of the TAT pathway. Logoplots were used to provide a detailed analysis of the lumenal targeting signals, and all nuclear-encoded proteins identified on the two-dimensional gels were used to test predictions for chloroplast localization and transit peptides made by the software programs ChloroP, PSORT, and SignalP. A combination of these three programs was found to provide a useful tool for evaluating chloroplast localization and transit peptides and also could reveal possible alternative processing sites and dual targeting. The potential of proteomics for plant biology and homology-based searching with mass spectrometry data is discussed.
TL;DR: This paper reviews and discusses, from an ecological perspective, the causes behind the development and spreading of pathogens in shrimp aquaculture.
TL;DR: Undetectable coenzyme Q10 and results of radiolabelling experiments in cultured fibroblasts supported the diagnosis of widespread coen enzyme Q10 deficiency, and particular attention should be paid to multiple quinone-responsive respiratory-chain enzyme deficiency, which can be successfully treated by oral ubidecarenone.
TL;DR: This work finds that activation of this innate immune response in Drosophila is preceded by rapid proteolytic cleavage of Relish into two parts, different from previously described mechanisms for Rel factor activation.
Abstract: The Rel/NF-κB transcription factor Relish plays a key role in the humoral immune response in Drosophila. We now find that activation of this innate immune response is preceded by rapid proteolytic cleavage of Relish into two parts. An N-terminal fragment, containing the DNA-binding Rel homology domain, translocates to the nucleus where it binds to the promoter of the Cecropin A1 gene and probably to the promoters of other antimicrobial peptide genes. The C-terminal IκB-like fragment remains in the cytoplasm. This endoproteolytic cleavage does not involve the proteasome, requires the DREDD caspase, and is different from previously described mechanisms for Rel factor activation.