A quantitative ultrastructural study of Chromatium minus in the bacterial layer of Lake Cisó (Spain)

A quantitative ultrastructural study was performed with samples taken throughout a layer of the purple sulfur bacterium Chromatium minus in Lake Cisó (Spain). Ultrathin sections of cells were analyzed by transmission electron microscopy, in order to study the size, number and volume of intracytoplasmic membranes (ICM), sulfur globules and poly--hydroxybutyrate (PHB) granules per unit volume of cell. Important differences were seen between cells from the top (receiving 60 E · m^–2 · s^–1 at noon) on the one hand, and cells from the peak and bottom parts of the bacterial layer (receiving less than 1 E · m^–2 · s^–1) on the other hand. The amount of ICM per cell increased as a function of depth being about three times higher in bottom cells than in top cells. Neither statistically significant differences in cell size, nor in numbers of sulfur globules were found, but the ultrastructure changed with depth. Finally, the most important changes throughout depth were detected in PHB granules. Top cells had 0.5% of their volume occupied by PHB granules, whereas in the bottom cells the corresponding value was 12.2%. These changes were due to the number of PHB granules per unit volume of cell since globule size was constant.Non-common abbreviations ECM intracytoplasmic membrane systems - PHB poly--hydroxybutyrate - Bchl bacteriochlorophyll - SED sphere equivalent diameter     

The aquarium trade as a potential source of fish introductions in southwestern Europe

The aquarium trade has been identified as an important vector of aquatic invasive species but this question has mostly been investigated in North America. We investigated the variation in diversity and species composition in different trade types in southwestern Europe (three major international wholesalers, different retail store types, and local internet forums), mostly in Spain and Portugal. As in previous studies, the diversity of fishes in the aquarium trade was vast, with a total of 20 orders, 79 families, and 1,133 fish species detected in the trade types analyzed. 248 species were observed in a single metropolitan area (Barcelona), with estimates of about 294 species being present. International wholesalers had higher species richness and evenness, with a single one having over 700 species. General pet stores had much lower evenness but due to high turnover had a total richness of over 200 species. Internet forums had the lowest evenness but similar richness. The different commerce types varied significantly in relative species abundance with about a dozen of popular fish species (e.g., goldfish, Siamese fighting fish, common carp, guppy, swordtails) dominating the retail stores, particularly the general pet stores. Our results imply that frequency in the trade varies strongly among species and commerce types and although general pet stores have usually low diversity, this is compensated with a higher species turnover. Many of the most popular species are well known invasive species and some of the species available are temperate species that might establish in Europe, reinforcing the need for more careful implementation of education programs, regulation and monitoring of trade, and internalization of environmental costs by the industry.     

Rudd (Scardinius erythrophthalmus) introduced to the Iberian peninsula: feeding ecology in Lake Banyoles

The first data on the ecology of rudd (Scardinius erythrophthalmus) introduced to the Iberian peninsula are presented. The habitat and diet variation of rudd were studied in Lake Banyoles (Spain), an oligotrophic karstic lake dominated by exotic fish species. Rudd were strictly littoral and the diet was based on detritus and plant material. The most important animal prey were the cladocerans Daphnia longispinaand Scapholeberis rammneri, amphipods and several late stages of nematoceran dipterans. Rudd were more zooplanktivorous in spring and autumn and less in summer. There was also a size-dependent diet shift, from microcrustaceans to macroinvertebrates. The diet of rudd was also distinguished by the importance of plant material and various small neustonic invertebrates, particularly S. rammneriand late stages of nematocerans, showing a strong resource partitioning with other fish species. The degree of herbivory in Lake Banyoles was lower than usual.     

JNK Controls the Onset of Mitosis in Planarian Stem Cells and Triggers Apoptotic Cell Death Required for Regeneration and Remodeling

Regeneration of lost tissues depends on the precise interpretation of molecular signals that control and coordinate the onset of proliferation, cellular differentiation and cell death. However, the nature of those molecular signals and the mechanisms that integrate the cellular responses remain largely unknown. The planarian flatworm is a unique model in which regeneration and tissue renewal can be comprehensively studied in vivo. The presence of a population of adult pluripotent stem cells combined with the ability to decode signaling after wounding enable planarians to regenerate a complete, correctly proportioned animal within a few days after any kind of amputation, and to adapt their size to nutritional changes without compromising functionality. Here, we demonstrate that the stress-activated c-jun–NH₂–kinase (JNK) links wound-induced apoptosis to the stem cell response during planarian regeneration. We show that JNK modulates the expression of wound-related genes, triggers apoptosis and attenuates the onset of mitosis in stem cells specifically after tissue loss. Furthermore, in pre-existing body regions, JNK activity is required to establish a positive balance between cell death and stem cell proliferation to enable tissue renewal, remodeling and the maintenance of proportionality. During homeostatic degrowth, JNK RNAi blocks apoptosis, resulting in impaired organ remodeling and rescaling. Our findings indicate that JNK-dependent apoptotic cell death is crucial to coordinate tissue renewal and remodeling required to regenerate and to maintain a correctly proportioned animal. Hence, JNK might act as a hub, translating wound signals into apoptotic cell death, controlled stem cell proliferation and differentiation, all of which are required to coordinate regeneration and tissue renewal.     

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry

We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies, simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.     

Life history and parasites of the invasive mosquitofish (Gambusia holbrooki) along a latitudinal gradient

The eastern mosquitofish (Gambusia holbrooki) is among the most invasive fish worldwide and yet, while very abundant in most Mediterranean countries, it is unable to tolerate the colder winters of northern and central Europe. Understanding the effects of latitude on its life-history traits is essential to predict the potential for its invasion of central Europe in current scenarios of climate change. We studied the variation of life-history traits and parasite load in the eastern mosquitofish along a latitudinal gradient from southern France to southern Spain, sampling mosquitofish populations in eight Mediterranean river mouths ranging 5° in latitude. Southern mosquitofish populations displayed higher catch rates, allocated more energy to reproduction (gonadosomatic index and gonadal weight after accounting for fish size) and had a lower condition (total weight and eviscerated weight after accounting for fish size) than in northern populations. Despite variability among populations, size-at-maturity (L₅₀) significantly varied with latitude and northern individuals matured at smaller size (lower L₅₀). Parasite prevalence ranged from 0.0 to 26.7% but parasite richness was very low; all the parasites identified were larvae of pleurocercoid cestodes belonging to the order Pseudophyllidea. The abundance of mosquitofish parasites decreased with latitude and the presence and number of parasites infecting the mosquitofish had a significant negative effect on fish condition. The significant effects of latitude on the catch rates, life history and parasites of mosquitofish highlight the importance of latitudinal studies of invasive species to understand the interactive mechanisms of climate change and biological invasions.     

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

Background

Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of gene-sets used by many current enrichment analysis software works against this ideal.

Principal Findings

To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed “Enrichment Map”, a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges represent gene overlap between sets. Automated network layout groups related gene-sets into network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret the enrichment results.

Conclusions

Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).     

Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation

Assembly of the active site of the [NiFe]-hydrogenase enzymes involves a multi-step pathway and the coordinated activity of many accessory proteins. To analyze complex formation between these factors in Escherichia coli, they were genomically tagged and native multi-protein complexes were isolated. This method validated multiple interactions reported in separate studies from several organisms and defined a new complex containing the putative chaperone HybG and the large subunit of hydrogenase 1 or 2. The complex also includes HypE and HypD, which interact with each other before joining the larger complex.     

Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4

RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal-domain protein that is important for recovery from DNA damage during S phase. Rtt107 is a substrate of the checkpoint protein kinase Mec1, although the mechanism by which Rtt107 is targeted by Mec1 after checkpoint activation is currently unclear. Slx4, a component of the Slx1-Slx4 structure-specific nuclease, formed a complex with Rtt107. Deletion of SLX4 conferred many of the same DNA-repair defects observed in rtt107delta, including DNA damage sensitivity, prolonged DNA damage checkpoint activation, and increased spontaneous DNA damage. These phenotypes were not shared by the Slx4 binding partner Slx1, suggesting that the functions of the Slx4 and Slx1 proteins in the DNA damage response were not identical. Of particular interest, Slx4, but not Slx1, was required for phosphorylation of Rtt107 by Mec1 in vivo, indicating that Slx4 was a mediator of DNA damage-dependent phosphorylation of the checkpoint effector Rtt107. We propose that Slx4 has roles in the DNA damage response that are distinct from the function of Slx1-Slx4 in maintaining rDNA structure and that Slx4-dependent phosphorylation of Rtt107 by Mec1 is critical for replication restart after alkylation damage.