The ‘shifting baseline’ phenomenon: a global perspective

In this paper we demonstrate that low level ‘artisanal’ fishing can dramatically affect populations of slow-growing, late-maturing animals and that even on remote oceanic islands, stocks have been depleted and ecosystems degraded for millennia. Industrialised fisheries have developed during different decades in different regions of the world, and this has almost always been followed by a period of massive stock decline. However, ecosystems were not pristine before the onset of industrial fishing and it is difficult to assess the ‘virgin’ state of a population given that it may have been subject to moderate or even high levels of fishing mortality for many centuries. A wide range of information is available to help define or deduce historic marine population status. These include ‘traditional’ written sources but also less conventional sources such as archaeological remains, genetic analyses or simple anecdotal evidence. Detailed information, collected specifically for the purpose of determining fish stock biomass tends to exist only for recent decades, and most fishery assessments around the world (and thus time-series of biomass estimates), are less than 30 years long. Here we advocate using a wider range of multidisciplinary data sources, although we also recognise that it can be difficult to separate natural variability associated with changing climatic conditions from human-induced changes through fishing. We consider whether or not recovery of degraded ecosystems is ever possible and discuss a series of one-way ratchet like processes that can make it extremely difficult to return to a former ecosystem state.     

The Impact of Message Mutation on the Fitness of a Genetic Code

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness ``load' that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code. Received: 4 April 2001 / Accepted: 22 October 2001     

Dynamics of Aboveground and Soil Carbon and Nitrogen Stocks and Cycling of Available Nitrogen along a Land-use Gradient in Rondônia,Brazil

High rates of deforestation in the Brazilian Amazon have the potential to alter the storage and cycling of carbon (C) and nitrogen (N) across this region. To investigate the impacts of deforestation, we quantified total aboveground biomass (TAGB), aboveground and soil pools of C and N, and soil N availability along a land-use gradient in Rondônia, Brazil, that included standing primary forest, slashed primary and secondary forest, shifting cultivation, and pasture sites. TAGB decreased substantially with increasing land use, ranging from 311 and 399 Mg ha^–1 (primary forests) to 63 Mg ha^–1 (pasture). Aboveground C and N pools declined in patterns and magnitudes similar to those of TAGB. Unlike aboveground pools, soil C and N concentrations and pools did not show consistent declines in response to land use. Instead, C and N concentrations were strongly related to percent clay content of soils. Concentrations of NO₃-N and NH₄-N generally increased in soils following slash-and-burn events along the land-use gradient and decreased with increasing land use. Increasing land use resulted in marked declines in NO₃-N pools relative to NH₄-N pools. Rates of net nitrification and N-mineralization were also generally higher in postfire treatments relative to prefire treatments along the land-use gradient and declined with increasing land use. Results demonstrate the linked responses of aboveground C and N pools and soil N availability to land use in the Brazilian Amazon; steady reductions in aboveground pools along the land-use gradient were accompanied by declines in inorganic soil N pools and transformation rates.     

Modeling Neisseria meningitidis B metabolism at different specific growth rates

Neisseria meningitidis is a human pathogen that can infect diverse sites within the human host. The major diseases caused by N. meningitidis are responsible for death and disability, especially in young infants. At the Netherlands Vaccine Institute (NVI) a vaccine against serogroup B organisms is currently being developed. This study describes the influence of the growth rate of N. meningitidis on its macro-molecular composition and its metabolic activity and was determined in chemostat cultures. In the applied range of growth rates, no significant changes in RNA content and protein content with growth rate were observed in N. meningitidis. The DNA content in N. meningitidis was somewhat higher at the highest applied growth rate. The phospholipid and lipopolysaccharide content in N. meningitidis changed with growth rate but no specific trends were observed. The cellular fatty acid composition and the amino acid composition did not change significantly with growth rate. Additionally, it was found that the PorA content in outer membrane vesicles was significantly lower at the highest growth rate. The metabolic fluxes at various growth rates were calculated using flux balance analysis. Errors in fluxes were calculated using Monte Carlo Simulation and the reliability of the calculated flux distribution could be indicated, which has not been reported for this type of analysis. The yield of biomass on substrate (Y(x/s)) and the maintenance coefficient (m(s)) were determined as 0.44 (+/-0.04) g g(-1) and 0.04 (+/-0.02) g g(-1) h(-1), respectively. The growth associated energy requirement (Y(x/ATP)) and the non-growth associated ATP requirement for maintenance (m(ATP)) were estimated as 0.13 (+/-0.04) mol mol(-1) and 0.43 (+/-0.14) mol mol(-1) h(-1), respectively. It was found that the split ratio between the Entner-Doudoroff and the pentose phosphate pathway, the sole glucose utilizing pathways in N. meningitidis, had a minor effect on ATP formation rate but a major effect on the fluxes going through for instance the citric-acid cycle. For this reason, we presented flux ranges for underdetermined parts of metabolic network rather than presenting single flux values, which is more commonly done in literature.     

Consistent probabilistic outputs for protein function prediction

In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one another; for example, the predictor may assign a specific GO term to a given protein ('purine nucleotide binding') but not assign the parent term ('nucleotide binding'). Such predictions are difficult to interpret. In this work, we focus on methods for calibrating and combining independent predictions to obtain a set of probabilistic predictions that are consistent with the topology of the ontology. We call this procedure 'reconciliation'. We begin with a baseline method for predicting GO terms from a collection of data types using an ensemble of discriminative classifiers. We apply the method to a previously described benchmark data set, and we demonstrate that the resulting predictions are frequently inconsistent with the topology of the GO. We then consider 11 distinct reconciliation methods: three heuristic methods; four variants of a Bayesian network; an extension of logistic regression to the structured case; and three novel projection methods - isotonic regression and two variants of a Kullback-Leibler projection method. We evaluate each method in three different modes - per term, per protein and joint - corresponding to three types of prediction tasks. Although the principal goal of reconciliation is interpretability, it is important to assess whether interpretability comes at a cost in terms of precision and recall. Indeed, we find that many apparently reasonable reconciliation methods yield reconciled probabilities with significantly lower precision than the original, unreconciled estimates. On the other hand, we find that isotonic regression usually performs better than the underlying, unreconciled method, and almost never performs worse; isotonic regression appears to be able to use the constraints from the GO network to its advantage. An exception to this rule is the high precision regime for joint evaluation, where Kullback-Leibler projection yields the best performance.     

Age-based demography and reproductive biology of three <Emphasis Type="Italic">Epinephelus</Emphasis> groupers, <Emphasis Type="Italic">E. polyphekadion,E. tauvina,</Emphasis> and <Emphasis Type="Italic">E. howlandi</Emphasis> (Serranidae), inhabiting coral reefs in Okinawa

The demography and reproductive biology of three Epinephelus groupers (Serranidae), namely E. polyphekadion, E. tauvina, and E. howlandi in the Yaeyama Islands, Okinawa, were examined based on age assessment using otoliths and gonadal histology. The maximum ages for these three species were 26 year, 23 year, and 17 year. The von Bertalanffy growth functions were also determined for each species. The size and age at 50% female maturity were estimated to be 358 mm in total length (TL) and 6.0 year for E. polyphekadion, 371 mm TL and 6.7 year for E. tauvina, and 327 mm TL and 4.1 year for E. howlandi, respectively. Significant differences between the sexes in size and age frequencies were found in all three species, with males being larger and older than females, or transitional individuals. These results strongly indicated that the population of these three grouper species showed monandric protogynous hermaphroditism. The sex ratios of E. polyphekadion and E. tauvina were biased in favor of females, but that of E. howlandi was equivalent between sexes. The relative sizes of ripe testes indicated that the intensity of sperm competition varied among species suggesting different mating system of each species. Reproductive seasonality was similar among species, with active vitellogenesis coinciding with the annual rise in water temperature. The active spawning period was determined to be between April and May for E polyphekadion, in May for E. howlandi, and from March to June for E. tauvina.     

Evaluating the effect of silver nanoparticles on testes of adult albino rats (histological,immunohistochemical and biochemical study)

Silver nanoparticles (AgNPs) are widely used in medicine, however, they have toxic impacts on different organs. AgNPs distribution to the testes was reported, so, we aimed to study the effect of intraperitoneal injection of AgNPs, at different concentrations and different time durations, on adult rat testes. Sixty healthy adult male Wistar albino rats were divided into three groups; control group (Group I) and two experimental groups (Groups II & III), each of which were subdivided into two subgroups. Rats in group II were exposed for 7 days to low and high doses of AgNPs, respectively. Rats in group III were exposed for 28 days to low and high doses of AgNPs, respectively. Testicular sections were stained with H&E, Toluidine blue, Immunohistochemical staining for Ki-67 and CD68 and Electron microscope examination were performed. Serum testosterone level and Quantitative Real-Time PCR for spermatogenesis genes were measured. Group IIa & IIb showed thickened capsule studded with nanoparticles, congested blood vessels, disorganized seminiferous tubules (Sts) and detached germinal epithelium. Group IIIa & IIIb showed marked reduction in the germinal epithelium, and shrunken Sts with the absence of sperms in most of them, which was more evident with higher doses of AgNPs. Significant decrease in cell proliferation and increase in interstitial tissue macrophages were more detected in groups II & III than in the control group. Decreased serum testosterone and decreased expression levels of spermatogenesis genes in groups IIa, IIb & IIIa, IIIb than in the control group were observed. In conclusion: intraperitoneal injection of AgNPs adversely affected the structure of adult rat testes. The tissue damage was more manifested with increased dose and duration of exposure.     

Impacts of enhanced UVB radiation on photosynthetic characteristics of the marine diatom <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis> (Bacillariophyceae,Heterokontophyta)

Solar ultraviolet B (UVB) irradiance at the Earth’s surface is increasing due to anthropogenic influences. To evaluate the effects of enhanced UVB radiation on photosynthetic characteristics of the marine diatom Phaeodactylum tricornutum, the species was exposed to four levels of UVB radiation, 0, 0.25, 0.75, and 1.50 KJ m^?2 day^?1 for 7 days. Effects of UVB stress on net photosynthetic rate, net respiration rate, variable chlorophyll (Chl) fluorescence parameters, Chl a and carotenoid contents, and UV-absorbing compounds (UVACs) were investigated. Results showed that there were no significant differences in terms of net respiration rate or maximal photochemical efficiency of photosystem II (F_v/F_m) between the treatments in the short or long term. However, enhanced UVB radiation at an intensity of 0.16 W m^?2 had a negative effect on the net photosynthetic rate, electron transport rate, and on the pathway of excess energy dissipation over the short term (1 to 5 days). Carotenoid and UVACs content increased under UVB radiation. Photosynthetic parameters were unaffected by UVB radiation on the seventh day indicating that P. tricornutum can adapt to UVB radiation in the long term. Results of the present study indicate that there is a dynamic balance between damage and adaptation in microalgae that enables them to adapt to UVB-induced photosystem alterations during both short-term and long-term exposure.