Modulation of cell-cycle dynamics is required to regulate the number of cerebellar GABAergic interneurons and their rhythm of maturation

The progenitors of cerebellar GABAergic interneurons proliferate up to postnatal development in the prospective white matter, where they give rise to different neuronal subtypes, in defined quantities and according to precise spatiotemporal sequences. To investigate the mechanisms that regulate the specification of distinct interneuron phenotypes, we examined mice lacking the G1 phase-active cyclin D2. It has been reported that these mice show severe reduction of stellate cells, the last generated interneuron subtype. We found that loss of cyclin D2 actually impairs the whole process of interneuron genesis. In the mutant cerebella, progenitors of the prospective white matter show reduced proliferation rates and enhanced tendency to leave the cycle, whereas young postmitotic interneurons undergo severe delay of their maturation and migration. As a consequence, the progenitor pool is precociously exhausted and the number of interneurons is significantly reduced, although molecular layer interneurons are more affected than those of granular layer or deep nuclei. The characteristic inside-out sequence of interneuron placement in the cortical layers is also reversed, so that later born cells occupy deeper positions than earlier generated ones. Transplantation experiments show that the abnormalities of cyclin D2(-/-) interneurons are largely caused by cell-autonomous mechanisms. Therefore, cyclin D2 is not required for the specification of particular interneuron subtypes. Loss of this protein, however, disrupts regulatory mechanisms of cell cycle dynamics that are required to determine the numbers of interneurons of different types and impairs their rhythm of maturation and integration in the cerebellar circuitry.     

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)

The global analysis of metabolism by liquid chromatography coupled to mass spectrometry is often hampered by a large amount of biological and technical variability. Here, we introduce an experimental and analytical strategy that can produce robust metabolome profiles in the face of this challenge. By applying a new computational approach based on concordance analysis to an extremely large number of analytical replicates, we are able to show that the overexpression of an antisense non-coding RNA targeting glutamine synthetase I results in a major reorganization of the metabolism of Streptomyces coelicolor, the model species of antibiotic-producing bacteria. We identified 97 metabolites with statistically significant reproducible dynamic behavior across the time series. The observed metabolic changes are very rapid, specific and widespread across metabolism, but focus on the nitrogen assimilation pathways. Our results demonstrate the power of highly replicated experimental designs for the robust characterization of metabolite dynamics. The identified global rearrangement of metabolism suggests the usefulness of RNA interference as an efficient strategy to manipulate the physiology of bacteria with wider biotechnological applicability in microorganisms.     

Peptides of type II collagen can induce the cleavage of type II collagen and aggrecan in articular cartilage.

The objective of this study was to determine whether a fragment(s) of type II collagen can induce cartilage degradation. Fragments generated by cyanogen bromide (CB) cleavage of purified bovine type II collagen were separated by HPLC. These fragments together with selected overlapping synthetic peptides were first analysed for their capacity to induce cleavage of type II collagen by collagenases in chondrocyte and explant cultures of healthy adult bovine articular cartilage. Collagen cleavage was measured by immunoassay and degradation of proteoglycan (mainly aggrecan) was determined by analysis of cleavage products of core protein by Western blotting. Gene expression of matrix metalloproteinases MMP-13 and MMP-1 was measured using Real-time PCR. Induction of denaturation of type II collagen in situ in cartilage matrix with exposure of the CB domain was identified with a polyclonal and monoclonal antibodies that only react with this domain in denatured but not native type II collagen. As well as the mixture of CB fragments and peptide CB12, a single synthetic peptide CB12-II (residues 195-218), but not synthetic peptide CB12-IV (residues 231-254), potently and consistently induced in explant cultures at 10 microM and 25 microM, in a time, cell and dose dependent manner, collagenase-induced cleavage of type II collagen accompanied by upregulation of MMP-13 expression but not MMP-1. In isolated chondrocyte cultures CB12-II induced very limited upregulation of MMP-13 as well as MMP-1 expression. Although this was accompanied by concomitant induction of cleavage of type II collagen by collagenases, this was not associated by aggrecan cleavage. Peptide CB12-IV, which had no effect on collagen cleavage, clearly induced aggrecanase specific cleavage of the core protein of this proteoglycan. Thus these events involving matrix molecule cleavage can importantly occur independently of each other, contrary to popular belief. Denaturation of type II collagen with exposure of the CB12-II domain was also shown to be much increased in osteoarthritic human cartilage compared to non-arthritic cartilage. These observations reveal that peptides of type II collagen, to which there is increased exposure in osteoarthritic cartilage, can when present in sufficient concentration induce cleavage of type II collagen (CB12-II) and aggrecan (CB12-IV) accompanied by increased expression of collagenases. Such increased concentrations of denatured collagen are present in adult and osteoarthritic cartilages and the exposure of chondrocytes to the sequences they encode, either in soluble or more likely insoluble form, may therefore play a role in the excessive resorption of matrix molecules that is seen in arthritis and development.     

Seed bank versus seed rain in the regeneration of a tropical pioneer tree

Summary We used the tropical pioneer tree, Cecropia obtusifolia to evaluate the relative importance of different sources of seeds in the regeneration of species that depend on ephemeral sites. We studied seed production in a population established in a 5 ha plot, and dispersal, dormancy and seed predation in two recent treefall gaps (<1 year-old), two building or successional forest patches (10–15 since disturbed), and two mature forest patches (>35 years since disturbed) for a one year period at Los Tuxtlas (Mexico). Flowers and fruits were counted at monthly intervals. Annual fecundity per tree ranged from 1.4×10⁴ to 1.4×10⁷ seeds. Seeds were continuously available on the trees and on the ground. Average annual seed rain per m² (as measured by 0.5×0.5 m seed traps) varied from 184 to 1925 among the six sites. Distance to nearest seed source and patch type explained more than 60% of the seed rain variation among sites. Soil seed density, estimated by counting seeds from ten samples (78.5 cm²×10 cm deep) collected from each site in October and January, ranged among the six sites from 269 to 4485 seeds per m² in January and from 204 to 5073 in October. Soil seed viabilities were much lower (17.1% in October and 5.1% in January) than those of rain seeds (48.26%). Annual survivorships of 2.2% were estimated for seeds artificially sown on the soil surface of a gap and a mature patch, and 3.75% in a building patch. In two other experiments seed removal rates ranged from 27% to 98% in 4 days. Removal rates were significantly higher in gap and mature patches than in building patches. Ants (Paratrechina vividula) and grasshopper nymphs (Hygronemobius. sp.) were the main predators. We draw three main conclusions from our data: (1) Pathogens and predators determine low survivorship of C. obtusifolia's seeds in the soil and a rapid turnover rate (1.07 to 1.02 years) of its seed bank; (2) a continuous and copious seed production and an abundant and extensive seed rain replenish the soil seed pool in patches with different disturbance ages at least up to 86 m from nearest source; (3) more than 90% of the seeds contributing to C. obtusifolia seedling recruitment in gaps are less than one year-old. We discuss our results in the context of previous similar studies for tropical forests.     

Influence of acclimation and determination temperature on the oxygen consumption of the brain in two species of anurans

1. 1. The effects of sudden changes by increasing or decreasing the measurement temperature on the oxygen consumption of the brains of Bufo arenarum and Leptodactylus ocellatus were determined.

2. 2. The experiments were carried at in vitro at temperatures which range from 4 to 37°C. The brain was oxygenated and stabilized for 20 min at each of the temperatures to which it was subjected before oxygen consumption measurements were made.

3. 3. A theoretical curve representing the variation of oxygen consumption with temperature was calculated according to the following exponential relationship; for Leptodactylus ocellatus y = 0.408 × 1.07^x and for Bufo arenarum y = 0.389 × 1.065^x.

4. 4. These results were compared with the brain oxygen consumption of animals acclimated to different temperatures, whose oxygen consumption was measured at a fixed temperature. Only Leptodactylus ocellatus had a significantly lower oxygen consumption in a high range of temperatures, indicating thermal compensation, probably to save metabolic reserves.

5. 5. No deterioration of the brain tissue was observed, as several passages from high to low temperatures in the range of 20°–30°C, showed a reversible oxygen consumption in acclimated and non-acclimated Bufo arenarum and Leptodactylus ocellatus.

The glucose‐deprivation network counteracts lapatinib‐induced toxicity in resistant ErbB2‐positive breast cancer cells

Dynamic interactions between intracellular networks regulate cellular homeostasis and responses to perturbations. Targeted therapy is aimed at perturbing oncogene addiction pathways in cancer, however, development of acquired resistance to these drugs is a significant clinical problem. A network‐based computational analysis of global gene expression data from matched sensitive and acquired drug‐resistant cells to lapatinib, an EGFR/ErbB2 inhibitor, revealed an increased expression of the glucose deprivation response network, including glucagon signaling, glucose uptake, gluconeogenesis and unfolded protein response in the resistant cells. Importantly, the glucose deprivation response markers correlated significantly with high clinical relapse rates in ErbB2‐positive breast cancer patients. Further, forcing drug‐sensitive cells into glucose deprivation rendered them more resistant to lapatinib. Using a chemical genomics bioinformatics mining of the CMAP database, we identified drugs that specifically target the glucose deprivation response networks to overcome the resistant phenotype and reduced survival of resistant cells. This study implicates the chronic activation of cellular compensatory networks in response to targeted therapy and suggests novel combinations targeting signaling and metabolic networks in tumors with acquired resistance.     

The gut microbiota in the metagenomics era: sometimes a friend, sometimes a foe

The normal intestinal microflora (microbiota) represents a complex, dynamic, and diverse collection of microorganisms, which usually inhabit the gastrointestinal tract. Normally, between this flora and the human host a mutually beneficial long-term symbiotic relationship is established, where the host contributes essential nutrients necessary for the survival of the microbiota and the latter fulfils multiple roles in host nutrition and development. Several achievements have recently converged to renew interest in studying the normal gut microbiota: the development of molecular methods of studying the microbial communities, the improved understanding of host-microbe interactions in health and disease, and the potential for therapeutic manipulation of the microbiota. We present recent data concerning the molecular technologies of studying the microbiota and new findings regarding the composition of the normal flora. We underline the beneficial activities of the gut flora on the human host. We emphasize the recent findings in the alterations of the microbiota in various medical conditions (celiac disease, irritable bowel syndrome, obesity, colorectal cancer, allergic disorders, and especially inflammatory bowel diseases). The results of these new studies suggest that changes of the microbiota could be linked to the etiopathogenesis of these diseases. These outstanding findings could be used for further diagnostic tools and/or therapy.