Variation in fish community structure, richness, and diversity in 56 Danish lakes with contrasting depth, size, and trophic state: does the method matter?

Organisms inhabiting shallow near-shore waters are at risk of desiccation during water level fluctuations. Using laboratory experiments, we investigated the survival and behavioural defences of four freshwater amphipod species during substratum drying: three Ponto-Caspian invaders (Pontogammarus robustoides, Dikerogammarus haemobaphes and Dikerogammarus villosus) and the native Gammarus fossarum. We hypothesized that they would be able to survive air exposure events as well as to adjust their behaviour by following the decreasing water level and/or burying in the sediments. To test these hypotheses, we examined survival of each species on gradually drying sandy substratum as well as their horizontal and vertical migration behaviours. P. robustoides was most resistant to substratum drying and was the only species burying into the substratum. On the other hand, G. fossarum exhibited distinct horizontal migrations following the retreating waterline. These two species seem to be particularly well adapted to the drying environment. Defence mechanisms of D. haemobaphes and D. villosus were less efficient, though the former species also followed the retreating waterline to some extent. Our study demonstrates that exotic and native gammarids have several adaptations that enable them to invade and persist in habitats experiencing common water level fluctuations.     

Applying near-infrared spectroscopy in downstream processing: one calibration for multiple clarification processes of fermentation media

The use of near-infrared spectroscopy (NIRS) is demonstrated in the first downstream processing (DSP) steps of an active pharmaceutical ingredient (API) manufacturing process. The first method developed was designed to assess the API content in the filtrate stream (aqueous) of a rotary drum vacuum filter. The PLS method, built after spectral preprocessing and variable selection, had an accuracy of 0.01% (w/w) for an API operational range between 0.20 and 0.45% (w/w). The robustness and extrapolation ability of the calibration was proved when samples from ultrafiltration and nanofiltration processes, ranging from 0 to 2% (w/w), were linearly predicted (R2=0.99). The development of a robust calibration model is generally a very time-consuming task, and once established it is imperative that it can be useful for a long period of time. This work demonstrates that NIR procedures, when carefully developed, can be used in different process conditions and even in different process steps of similar unit operations.     

Numerical and structural chromosome variation in the swarm-founding wasp Metapolybia decorata Gribodo 1896 (Hymenoptera, Vespidae)

The Neotropical Polistinae wasps are diverse in taxonomy, social behavior, and nesting founding characteristics. Although some species in this group have been used as models for studies on wasp’s biology, they are poorly known in terms of cytogenetics. Here we reported an intraspecific numerical-structural chromosome variation in the swarm-founding wasp Metapolybia decorata from the Brazilian Atlantic Rainforest using conventional and molecular cytogenetic techniques. The observed structural chromosome change involved a telomeric fusion that resulted in a chromosome number range of 2n = 34–36. The origin and geographic distribution of the variant chromosome forms as well as their frequency and maintenance in the studied populations are discussed. In addition, we reported a novel and geographically restricted deletion in the fused chromosomes indicating that the species is undergoing a continued process of karyotype evolution leading to fused chromosome stabilization by elimination of inactive centromeric sequences. Evidence of differences in the telomeric sequences of this wasp was also found by in situ hybridization using the motif (T₂AG₂)₇ as probe.     

Density-dependent shift from facilitation to competition in a dwarf <Emphasis Type="Italic">Avicennia germinans</Emphasis> forest

The global effort to rehabilitate and restore destroyed mangrove forests is unable to keep up with the high mangrove deforestation rates, which exceed the average pace of global deforestation. Although facilitation theory presents new possibilities for the restoration of heavily degraded mangrove sites, knowledge of tree–tree interactions in stressed mangrove forest ecosystems is too limited to utilize facilitation appropriately. The aim was to determine the mode of local interaction among stressed mangrove trees by investigating the effect of clustering on tree size and crown morphology under contrasting stand densities. The study was conducted in a dwarf Avicennia germinans forest in Northern Brazil, in which tree growth is limited by infrequent inundation and high pore-water salinity. Autoregressive regression, Voronoi tessellation and spatial point pattern statistics were used to address the spatial processes underlying tree interaction. Under low stand density (1.2 trees m^?2) dwarf trees which grew in clustered cohorts of A. germinans had a less stunted crown morphology revealing the dominance of a positive neighborhood influence among plants. In contrast, dwarf trees in the denser forest stand (2.7 trees m^?2) were interacting competitively as indicated by the more negative effect of neighbors on crown morphology and size. The shift from facilitative to competitive interactions is an important feature of mangrove forest regeneration under harsh environmental conditions. If mangrove trees are unable to regenerate naturally on severely degraded sites, intraspecific facilitation could be used to assist regeneration by planting seedlings in clusters and not evenly spaced.     

Creatine supplementation attenuates corticosteroid-induced muscle wasting and impairment of exercise performance in rats.

The objective of the present study was to investigate whether creatine (Cr) could attenuate the deleterious effects of high doses of dexamethasone (Dexa) on body mass, exercise performance, and respiratory variables of rodents. Forty-four Wistar rats performed incremental maximal exercise tests. They were then assigned to four groups: G1: subcutaneous (s.c.) and intraperitoneal (i.p.) saline; G2: s.c. saline and i.p. Cr (250 mg x kg(-1) x day(-1)); G3: s.c. Dexa (7.5 mg x kg(-1) x day(-1)) and i.p. saline; G4: s.c. Dexa and i.p. Cr. New exercise tests and analysis of the respiratory pattern under resting conditions and after stimulation with doxapram (2 mg/kg i.p.) were performed after 18 days. Post- minus pretreatment differences were compared between groups. G3 and G4 showed a significant impairment in body mass gain compared with G1 and G2 (P < 0.05) (G1: 65.3 +/- 26.1, G2: 93.1 +/- 27.4, G3: -18.4 +/- 20.1, G4: 9.8 +/- 23.1 kg x 10(-3)). Similar results were observed for maximal oxygen consumption (G1: 9.5 +/- 8.5, G2: 25.8 +/- 14.5, G3: -25.5 +/- 6.0, G4: -4.8 +/- 9.5 ml x kg(-1) x min(-1)) and test duration (G1: 43.0 +/- 45.0, G2: 72.0 +/- 59.5, G3: -165.0 +/- 60.6, G4: -48.0 +/- 48.5 s). Simultaneous use of Cr significantly attenuated the Dexa-induced impairment of the last two variables. Cr attenuated Dexa-induced gastrocnemius and diaphragm muscle weight losses and the atrophy of gastrocnemius type IIb fibers. Cr supplementation had only small effects on Dexa-induced respiratory changes. These results suggest that Cr may play a role in the prophylaxis or treatment of steroid-induced myopathy.     

Molecular Phylogeny and Historical Biogeography of the Neotropical Swarm-Founding Social Wasp Genus Synoeca (Hymenoptera: Vespidae)

The Neotropical Region harbors high biodiversity and many studies on mammals, reptiles, amphibians and avifauna have investigated the causes for this pattern. However, there is a paucity of such studies that focus on Neotropical insect groups. Synoeca de Saussure, 1852 is a Neotropical swarm-founding social wasp genus with five described species that is broadly and conspicuously distributed throughout the Neotropics. Here, we infer the phylogenetic relationships, diversification times, and historical biogeography of Synoeca species. We also investigate samples of the disjoint populations of S. septentrionalis that occur in both northwestern parts of South America through Central American and the Brazilian Atlantic rainforests. Our results showed that the interspecific relationships for Synoeca could be described as follows: (S. chalibea + S. virginea) + (S. cyanea + (S. septentrionalis/S. surinama)). Notably, samples of S. septentrionalis and S. surinama collected in the Atlantic Forest were interrelated and may be the result of incomplete lineage sorting and/or mitochondrial introgression among them. Our Bayesian divergence dating analysis revealed recent Plio-Pleistocene diversification in Synoeca. Moreover, our biogeographical analysis suggested an Amazonian origin of Synoeca, with three main dispersal events subsequently occurring during the Plio-Pleistocene.     

Epipona media cooper (Hymenoptera: Vespidae), a social wasp new to the Brazilian Atlantic Forest

An occupied nest of Epipona media Cooper was discovered and collected in a cabruca (cocoa plantation with native tree cover). This is the first record of E. media from Bahia State. We described the nest structure and compared the adults with the closely related species Epipona tatua Cuvier.     

Improving cluster-based missing value estimation of DNA microarray data

We present a modification of the weighted K-nearest neighbours imputation method (KNNimpute) for missing values (MVs) estimation in microarray data based on the reuse of estimated data. The method was called iterative KNN imputation (IKNNimpute) as the estimation is performed iteratively using the recently estimated values. The estimation efficiency of IKNNimpute was assessed under different conditions (data type, fraction and structure of missing data) by the normalized root mean squared error (NRMSE) and the correlation coefficients between estimated and true values, and compared with that of other cluster-based estimation methods (KNNimpute and sequential KNN). We further investigated the influence of imputation on the detection of differentially expressed genes using SAM by examining the differentially expressed genes that are lost after MV estimation. The performance measures give consistent results, indicating that the iterative procedure of IKNNimpute can enhance the prediction ability of cluster-based methods in the presence of high missing rates, in non-time series experiments and in data sets comprising both time series and non-time series data, because the information of the genes having MVs is used more efficiently and the iterative procedure allows refining the MV estimates. More importantly, IKNN has a smaller detrimental effect on the detection of differentially expressed genes.     

Safety and whole-body antioxidant potential of a novel anthocyanin-rich formulation of edible berries

Edible berry extracts rich in anthocyanins possess a broad spectrum of therapeutic, pharmacologic and anti-carcinogenic properties. Six berry extracts (wild blueberry, bilberry, cranberry, elderberry, raspberry seeds and strawberry), singly and in combination, were studied in our laboratories for antioxidant efficacy, cytotoxic potential, cellular uptake and anti-angiogenic properties. Combinations of edible berry extracts were evaluated to develop a synergistic formula, OptiBerry, which exhibited high oxygen radical absorbance capacity (ORAC) value, low cytotoxicity and superior anti-angiogenic properties compared to the other combinations tested. The current study sought to determine the broad spectrum safety and antioxidant potential of OptiBerry in vivo. Acute oral LD₅₀ of OptiBerry was greater than 5 g/kg in rats. Acute dermal LD₅₀ of OptiBerry was greater than 2 g/kg. No changes in the body weight or adverse effects were observed following necropsy. Primary skin and eye irritation studies were conducted in New Zealand albino rabbits. OptiBerry was classified as slightly irritating to the skin (primary skin irritation index 0.3) and minimally irritating to the eye (maximum mean total score 6.0). The antioxidant potential of OptiBerry was investigated in rats and mice by assessing GSH redox status in tissues as well as by a unique state-of-the-art electron paramagnetic resonance (EPR) imaging of whole-body redox status. A clinically relevant hyperbaric oxygen (HBO) exposure system (2 atm, 2 h) was employed to study the antioxidant properties of OptiBerry. OptiBerry feeding (8 weeks) significantly prevented HBO-induced GSH oxidation in the lung and liver of vitamin E-deficient Sprague Dawley rats. Furthermore, OptiBerry-fed mice, when exposed to HBO, demonstrated significant protection in whole-body HBO-induced oxidation compared to the unfed controls by EPR imaging. Taken together, these results indicate that OptiBerry is reasonably safe and possess antioxidant properties.     

Absence of Classical Heat Shock Response in the Citrus Pathogen <Emphasis Type="Italic">Xylella fastidiosa</Emphasis>

The fastidious bacterium Xylella fastidiosa is associated with important crop diseases worldwide. We have recently shown that X. fastidiosa is a peculiar organism having unusually low values of gene codon bias throughout its genome and, unexpectedly, in the group of the most abundant proteins. Here, we hypothesized that the lack of codon usage optimization in X. fastidiosa would incapacitate this organism to undergo quick and massive changes in protein expression as occurs in a classical stress response. Proteomic analysis of the response to heat stress in X. fastidiosa revealed that no changes in protein expression can be detected. Moreover, stress-inducible proteins identified in the closely related citrus pathogen Xanthomonas axonopodis pv citri were found to be constitutively expressed in X. fastidiosa. These proteins have extremely high codon bias values in the X. citri and other well-studied organisms, but low values in X. fastidiosa. Because biased codon usage is well known to correlate to the rate of protein synthesis, we speculate that the peculiar codon bias distribution in X. fastidiosa is related to the absence of a classical stress response, and, probably, alternative strategies for survival of X. fastidiosa under stressfull conditions.