Biological diversity and cultural heritage

In this paper some examples of the development of communities of microorganisms and plants on historic buildings and montiments are shown. When the building stones differ from the surrounding natural substrata, an increase in the biological diversity of the area is produced. In some cases, monuments can come to constitute a true refuge for a few species when the natural habitat is threatened. It is suggested that biological diversity, when it does not represent a threat for the cultural heritage, should be considered worthy of preservation.     

Biogeochemical mass-balances (C, N, P, Si) in three large reservoirs of the Seine Basin (France)

Three major reservoirs (Marne, Seine and Aube), situated in the upstream basin of the river Seine represent a storage capacity of 800 10⁶ m³. In order to quantify the possible role of these reservoirs as a sink or source of nutrients and organic matter for the river system, an input/output mass-balance of suspended matter, organic carbon, inorganic nitrogen forms, phosphorus and reactive silica was established, providing reliable estimates of their retention/elimination and export. The study was carried out over 3 years (1993, 1994 and 1995) in differing hydrological conditions. The retention times varied from 0.3 to 0.8 year, depending on the reservoir and the year, but was longer in 1993 that was a drier year than 1994 and 1995, hydrologically quite similar.Regarding retention (or elimination) and export, the behaviour of the three studied reservoirs was similar. A clear loss or retention of nitrogen, phosphorus and silica was observed in the reservoirs and represented about 40% of the incoming flux of nitrate, 50% of silica, and 60% of phosphate. The retention was lower for total phosphorus than for phosphate. The reservoirs are also sites of suspended matter deposition except during the decennial drawdown, when suspended matter is exported. For inorganic nitrogen, the average amount of nitrate retained in the Seine basin reservoirs upstream from Paris is 5000 tonnes y^–1 that is almost equal to the estimated retention by deposition or denitrification in river channel sediments for the whole drainage network. The retention in the reservoirs represents about 12% of the total flux of nitrate at the outlet of the basin upstream from Paris, and 5% at the mouth of the Seine River.We also calculated inlake C, N, P, Si budgets on the basis of direct process measurements. Measurements of planktonic primary and bacterial activity production led to annual net production of 4200 and 580 tonnes of carbon, respectively. A reasonable value (450 tonnes of carbon) of grazing was calculated. Corresponding N, P, Si fluxes were drawn from appropriate C:N:P:Si ratios. Benthic fluxes were measured with bell jars. The retention of P and Si represents a small fraction of important internal fluxes of phytoplanktonic uptake and recycling, while inorganic nitrogen retention depends mostly on benthic denitrification. The behaviour of P and Si differs in that P is mainly recycled in the water column, while Si dissolution occurs at the sediment interface. Nitrogen is recycled in both the planktonic and the benthic phase.     

Size‐based interactions and trophic transfer efficiency are modified by fish predation and cyanobacteria blooms in Lake Mývatn,Iceland

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Understanding the role of DNA methylation in successful biological invasions: a review

Biological invasions provide a unique opportunity to investigate rapid adaptation and evolution as the introduced taxa adapt to biogeographic contexts or habitats in which they have not evolved. The capacity of populations to evolve is generally thought to be constrained by their existing heritable genetic variation, which is usually associated with variation in genomic DNA nucleotide sequences. However, there is increasing acceptance that a range of mechanisms—collectively termed ‘epigenetics’ can alter gene function and affect ecologically important traits. Epigenetic processes may mediate adaptive phenotypic plasticity and provide heritable variation on a finer timescale than DNA sequence-based mutations. This review focuses on DNA methylation, a well-studied epigenetic mechanism known to be associated with biological adaptation to environmental stress. We explore the role of DNA methylation in characterising the adaptive potential of invasive species. We also provide an overview of studies focused on DNA methylation and invasive species to date, and identify knowledge gaps and potential ways to advance understanding of epigenetic-based adaptation. A summary of the literature suggests that DNA methylation could play a key role in the success of invasive species. Introduced populations with reduced genetic diversity often display increased DNA methylation variation in comparison with native populations, which could create phenotypic diversity when it is most required. Recent data show that DNA methylation could contribute to adaptation through both phenotypic plasticity and heritable variation, particularly through clonal reproduction. From a methodological perspective, recent advances in molecular techniques provide an exciting opportunity to explore the functional relevance of DNA methylation to successful biological invasions. Gaining a greater understanding of the adaptive and evolutionary processes that contribute to invasion success is critical for preventing and managing the future introduction, establishment and spread of invasive species.     

The inositol phosphatase SHIP-1 inhibits NOD2-induced NF-κB activation by disturbing the interaction of XIAP with RIP2

SHIP-1 is an inositol phosphatase predominantly expressed in hematopoietic cells. Over the ten past years, SHIP-1 has been described as an important regulator of immune functions. Here, we characterize a new inhibitory function for SHIP-1 in NOD2 signaling. NOD2 is a crucial cytoplasmic bacterial sensor that activates proinflammatory and antimicrobial responses upon bacterial invasion. We observed that SHIP-1 decreases NOD2-induced NF-κB activation in macrophages. This negative regulation relies on its interaction with XIAP. Indeed, we observed that XIAP is an essential mediator of the NOD2 signaling pathway that enables proper NF-κB activation in macrophages. Upon NOD2 activation, SHIP-1 C-terminal proline rich domain (PRD) interacts with XIAP, thereby disturbing the interaction between XIAP and RIP2 in order to decrease NF-κB signaling.     

Serine/threonine protein phosphatases PP1 and PP2A are key players in apoptosis

The reversible phosphorylation of proteins controlled by protein kinases and protein phosphatases is a major mechanism that regulates a wide variety of cellular processes. In contrast to C. elegans, recent studies in mammalian cells have highlighted a major role of serine/threonine protein phosphorylation in apoptosis. To illustrate the importance of dephosphorylation processes in apoptosis, this review will focus on recent studies suggesting that the interaction of the serine/threonine protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) with certain regulators of the Bcl-2 family is critically involved in the control of apoptosis.     

Localization of NADPH-protochlorophyllide reductase in plastids of barley at different greening stages

The localization of protochorophyllide (Pchlide) and of NADPH-protochlorophyllide oxidoreductase (POR, EC 1.6.99.1) within (etio)chloroplasts has been investigated at selected stages of greening of barley seedlings. Pchlide pigment and POR protein contents were evaluated in different plastid membrane fractions by fluorescence spectroscopy and immunoblot analysis using a monospecific polyclonal antibody raised against the purified enzyme. Fluorescence analysis showed the presence of Pchlide in both the envelope and thylakoid membranes. During greening, the Pchlide content, expressed on a total protein basis, decreased in thylakoid membranes, whereas it increased in the envelope membranes. POR proteins were detected mainly in thylakoid membranes at early greening stages. In contrast, the weak amount of POR proteins was associated more specifically with envelope membranes of mature chloroplasts. Whatever the greening stage, thylakoid-bound Pchlide and POR proteins were more abundant in the thylakoid regions which remained unsolubilized after mild Triton treatment used as standard procedure to prepare PS II particles. This suggests the preferential association of Pchlide and POR to the appressed regions of thylakoids. This revised version was published online in June 2006 with corrections to the Cover Date.     

The influence of anionic lipids on SHIP2 phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase activity

The SH2 domain containing inositol 5-phosphatase 2 (SHIP2) catalyzes the dephosphorylation of phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P₃) to phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P₂) and participates in the insulin signalling pathway in vivo. In a comparative study of SHIP2 and the phosphatase and tensin homologue deleted on chromosome 10 (PTEN), we found that their lipid phosphatase activity was influenced by the presence of vesicles of phosphatidylserine (PtdSer). SHIP2 PtdIns(3,4,5)P₃ 5-phosphatase activity was greatly stimulated in the presence of vesicles of PtdSer. This effect appears to be specific for di-C8 and di-C16 fatty acids of PtdIns(3,4,5)P₃ as substrate. It was not observed with inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P₄) another in vitro substrate of SHIP2, nor with Type I Ins(1,4,5)P₃/Ins(1,3,4,5)P₄ 5-phosphatase activity, an enzyme which acts on soluble inositol phosphates. Vesicles of phosphatidylcholine (PtdCho) stimulated only twofold PtdIns(3,4,5)P₃ 5-phosphatase activity of SHIP2. Both a minimal catalytic construct and the full length SHIP2 were sensitive to the stimulation by PtdSer. In contrast, PtdIns(3,4,5)P₃ 5-phosphatase activity of the Skeletal muscle and Kidney enriched Inositol Phosphatase (SKIP), another member of the mammaliam Type II phosphoinositide 5-phosphatases, was not sensitive to PtdSer. Our enzymatic data establish a specificity in the control of SHIP2 lipid phosphatase activity with PtdIns(3,4,5)P₃ as substrate which is depending on the fatty acid composition of the substrate.     

Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria

The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems.