Habitat specific growth rates and condition indices for the sympatric soles Solea solea (Linnaeus, 1758) and Solea senegalensis Kaup 1858, in the Tagus estuary, Portugal, based on otolith daily increments and RNA-DNA ratio

Habitat specific growth rates and condition indices were estimated for Solea solea and Solea senegalensis, in two nursery areas within the Tagus estuary, at the end of the estuarine colonization process, in 2005. While in the uppermost nursery area the two species of sole live in sympatry, in the lower nursery only S. senegalensis is present. Daily increments of left lapillar otoliths were used to estimate age (in days) and determine growth rates (mm per day). Condition indices were assessed through RNA‐DNA ratio in muscle samples. Growth rates were higher for S. senegalensis (0.970and 1.180 mm per day in nursery A and B, respectively) than for S. solea (0.767 mm per day in nursery A). Growth rates of S. senegalensis from the uppermost nursery area were lower when compared to those obtained for the other nursery. The RNA/DNA condition index followed the general trend given by the growth rate estimates, i.e. values were higher for S. senegalensis than for S. solea. However, no significant differences were detected in S. senegalensis from the two nurseries. Larger variations in salinity (10‰ amplitude in the uppermost nursery vs 0.2‰ in the lower nursery) and highest pollution loads may be important factors lowering the habitat quality of the uppermost nursery in comparison to the lower nursery. The use of growth rate estimates based on otolith readings and the RNA/DNA index as tools for habitat quality assessment was discussed.     

Estuarine colonization, population structure and nursery functioning for 0-group sea bass (Dicentrarchus labrax), flounder (Platichthys flesus) and sole (Solea solea) in a mesotidal temperate estuary

The function of the Mondego estuary as a fish nursery habitat was investigated from June 2003 to June 2004 by comparing the timing of estuarine colonization with juveniles of sea bass Dicentrarchus labrax, flounder Platichthys flesus, and sole Solea solea, while also analysing their population structure, growth and diet composition. Differences in the onset of estuarine colonization were observed, since sole juveniles were the first to enter the estuary (in January), followed by flounder in April and sea bass in June. The estuarine population of these species consisted of several age‐groups, although the majority of individuals belonged to age‐groups 0 and 1. The growth rates determined for 0‐group fish were within the range of those reported for other European estuarine systems. Some differences were also recognized regarding the timing of estuarine colonization and the length of the growing season. Diet of 0‐group sea bass consisted mainly of Crustacea, Polychaeta and Mollusca. Flounder juveniles fed chiefly on Amphipoda (especially Corophium spp.), with Polychaeta, Isopoda and Decapoda also being common prey. The diet of 0‐group sole was dominated by Polychaeta, with Amphipoda, Mollusca and Decapoda ranking highest, with other important benthic organisms also being present. Dietary overlap among these species was relatively low.     

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution

Background and Aims

Species'' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species'' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species'' identification.

Methods

Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.

Key Results

Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species'' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.

Conclusions

The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.Key words: Chromosome number, Christensonella, Cymbidieae, cytotaxonomy, fluorochrome staining, Maxillaria, Maxillariinae, molecular phylogenetics, species delimitation     

Simple and easy method for the determination of fungal growth and decolourative capacity in solid media

A technique was developed for studying the biodegradative ability of white rot fungi in different solid media. This technique enables the gravimetric determination of fungal growth (increase of biomass) and the spectrometric measurement of fungal decolourization ability (both by the determination of the production of the extracellular enzyme manganese-dependent peroxidase (MnP) and by the rate of decolourization of dyes). Bjerkandera sp., strain BOS55, was grown in different solid media. Its growth rate, decolourization of solophenil blue 2BL (azoic dye), neutral red (eurhodin dye), methyl green and crystal violet (triphenylmethane dyes) and the production of MnP were determined. Application of this technique enabled a spectrometric quantification of enzymatic activity. Assays indicate that greater amounts of MnP were present in agar plate cultures of Bjerkandera sp. than in liquid cultures.     

Importance of discards of a beam trawl fishery as input of organic matter into nursery areas within the Tagus estuary

The brown-shrimp beam trawl fishery carried out within the Tagus estuary produces discards due to the little commercial interest of most of the species caught. Between 1994 and 1996, monthly samples were collected in the two major fishing areas within the Tagus estuary, using a beam trawl, in order to estimate the amount of fish and crustaceans caught per unit of effort. The fishing effort of the commercial fleet was determined based on surveys of professional fishermen. Mortality estimates of discards were also evaluated experimentally. The main fish and crustacean species discarded after capture were Crangon crangon (Linnaeus, 1758), Liza ramada (Risso, 1826), Carcinus maenas (Linnaues, 1758) and Pomatoschistus minutus (Pallas, 1770). The estimated total amount of fishery discards in the upper part of the Tagus estuary is approximately 1500 tonnes per year, which represents ca. 90% of the captures. The mortality rate of the fishes and crustaceans discarded varied according to species and season, with the highest rates during Summer months. Considering nitrogen and carbon content of the main discarded species, an input of particulate organic matter of more than 140 tonnes of carbon and 35 tonnes of nitrogen per year were estimated for these estuarine areas.     

Effect of visible light on superoxide dismutase (SOD) activity in the red alga Gracilariopsis tenuifrons (Gracilariales, Rhodophyta)

Superoxide dismutase (SOD) was studied in the agarophyte Gracilariopsis tenuifrons. Similar SOD activity (130 ± 9U mg^-1) was observed in material from different regions of SouthAmerica, from different phases of the life cycle (gametophytes andtetrasporophytes), and from apical and basal sections of the thallus.In alga grown under a light-dark cycle, SOD activity in samples takenat different times exhibited a diurnal rhythm. The activity measured duringthe day phase was twice as much as during the night phase. This rhythm didnot persist under constant light, indicating light regulation of SOD activity.SOD activity was tested in algae submitted to different light intensities anddifferent wavelengths. It increased with the light intensity. The blue lightwavelength exerted a greater induction of SOD activity than other specificwavelengths.     

Yeast genes YOL002C and SUL1 are involved in neomycin resistance

In previous studies we suggested the importance of the control of plasma membrane H⁺-ATPase by a phosphatidylinositol-like pathway for cellular proton extrusion in Saccharomyces cerevisiae (Brandão et al. 1994; Coccetti et al. 1998). The observations that provided the model above include the inhibition of the glucose-induced activation of the plasma membrane H⁺-ATPase as well as the inhibition of the glucose-induced external acidification by neomycin, a known inhibitor of the phosphatidylinositol turnover in eukaryotic cells. In this work, using two libraries, we isolated two yeast clones that were able to prevent the inhibition of glucose-induced activation of the H⁺-ATPase by neomycin. We show that the YOL002C gene, which encodes a protein of unknown function, and the SUL1 gene, which is a sulphate transporter belonging to the major facilitator superfamily, suppress growth inhibition by neomycin. However, they are not required for glucose-induced activation of the plasma membrane H⁺-ATPase. The resistance of the clones to neomycin is probably related to the level and/or activity of proteins functioning as drug extrusion pumps.     

Differentiation of Human Umbilical Cord Matrix Mesenchymal Stem Cells into Neural-Like Progenitor Cells and Maturation into an Oligodendroglial-Like Lineage

Mesenchymal stem cells (MSCs) are viewed as safe, readily available and promising adult stem cells, which are currently used in several clinical trials. Additionally, their soluble-factor secretion and multi-lineage differentiation capacities place MSCs in the forefront of stem cell types with expected near-future clinical applications. In the present work MSCs were isolated from the umbilical cord matrix (Wharton''s jelly) of human umbilical cord samples. The cells were thoroughly characterized and confirmed as bona-fide MSCs, presenting in vitro low generation time, high proliferative and colony-forming unit-fibroblast (CFU-F) capacity, typical MSC immunophenotype and osteogenic, chondrogenic and adipogenic differentiation capacity. The cells were additionally subjected to an oligodendroglial-oriented step-wise differentiation protocol in order to test their neural- and oligodendroglial-like differentiation capacity. The results confirmed the neural-like plasticity of MSCs, and suggested that the cells presented an oligodendroglial-like phenotype throughout the differentiation protocol, in several aspects sharing characteristics common to those of bona-fide oligodendrocyte precursor cells and differentiated oligodendrocytes.     

Macroecology in the age of Big Data – Where to go from here?

Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space- and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data-driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.     

Development of process flow sheets for the purification of supercoiled plasmids for gene therapy applications.

Human clinical trial of gene therapy with nonviral vectors demands large amounts of pharmaceutical-grade plasmid DNA. Since standard molecular biology methods cannot be used for this purpose, there is a need for the development of processing methodologies for the large-scale production and purification of plasmids. This work describes several studies that were undertaken during the development of process flow-sheets for the downstream processing of supercoiled plasmids. Anion-exchange HPLC was used as a routine technique for monitoring plasmid purity in process streams. The use of RNase or high temperatures during alkaline lysis was proved unnecessary. Instead, RNA could be completely removed by performing sequentially clarification with a chaotropic salt, concentration with PEG, and ion-exchange and size-exclusion chromatography. Also, clarification of streams by precipitation was independent of the chaotropic salt used. Furthermore, by proceeding directly from cell lysis to chromatography it was possible to obtain plasmid with purity/quality identical to that of the one obtained when clarification and concentration were included in the process. This strategy has the advantage of increasing the overall process yield to 38%. The plasmid thus purified was depleted of RNA, chromosomal DNA, and proteins. Additionally, no animal-derived enzymes, alcohols, or toxic solvents were used, rendering validation potentially easier. The results described in this report also indicate that downstream processing times and costs can be considerably reduced without affecting plasmid purity.