Mn seasonal upwellings recorded in Lake Tanganyika mussels

International audienceBiogenic productivity of Lake Tanganyika is highly dependent on seasonal upwellings of anoxic deep waters. We investigated the shell of freshwater bivalve Pleiodon spekii as a geochemical archive of these periodic hydrological changes tuned by the monsoon regime. The results of a 2-years-long geochemical survey of the coastal waters performed on the dissolved and particulate fractions were put in perspective against laser ablation ICP-MS profiles of Mn in five aragonitic shells from the same lake location. Skeletal Mn profiles in 3 shells are very similar and dominated by episodic peaks that matched the Mn increase recorded in surface waters during the 2002 upwelling, while a shell collected during 2003 dry season detect both 2002 and 2003 upwelling events. Larger shells showing an extremely reduced growth display more than 8Mn peaks suggesting at least an 8 years record of seasonal changes in water composition

Manganese content records seasonal upwelling in Lake Tanganyika mussels

International audienceBiogenic productivity of Lake Tanganyika is highly dependent on seasonal upwellings of cold, oxygen-depleted, nutrient-rich deep waters. We investigated the shell of freshwater bivalve Pleiodon spekii as a geochemical archive of these periodic hydrological changes tuned by the monsoon regime. The results of a three-year-long limnological and geochemical survey of the coastal waters performed on the dissolved and particulate fractions were compared to LA-ICP-MS profiles of Mn in five aragonitic shells from the same lake location. Three shells present very similar Mn/Ca profiles dominated by a peak that matched the concomitant increase of Mn and chlorophyll a in surface waters during the 2002 upwelling, while a shell collected during 2003 dry season detect both 2002 and 2003 upwelling events. Larger shells showing an extremely reduced growth display more than 8 Mn/Ca peaks suggesting at least an 8-year-record of seasonal changes in water composition. We postulate that Mn/Ca in shells record the conjunction of an increase of biological activity with supplied of dissolved Mn and nutriments in coastal waters, resulting in an enhanced assimilation of biogenic Mn-rich particles. By combining the most recent generation of laser ablation system and the powerful High Resolution ICP-MS, the spatial resolution could be improved down to 5 to 10 µm crater size and end up in a better constrain of the relative variations of the annual Mn peaks. Such an approach on P. spekii from Lake Tanganyika has definitively a great potential to provide recent and past records on primary productivity associated with the monsoon climate system

Clues for a standardised thermal-optical protocol for the assessment of organic and elemental carbon within ambient air particulate matter

Along with some research networking programmes, the European Directive 2008/50/CE requires chemical speciation of fine aerosol (PM_2.5), including elemental (EC) and organic carbon (OC), at a few rural sites in European countries. Meanwhile, the thermal-optical technique is considered by the European and US networking agencies and normalisation bodies as a reference method to quantify EC–OC collected on filters. Although commonly used for many years, this technique still suffers from a lack of information on the comparability of the different analytical protocols (temperature protocols, type of optical correction) currently applied in the laboratories. To better evaluate the EC–OC data set quality and related uncertainties, the French National Reference Laboratory for Ambient Air Quality Monitoring (LCSQA) organised an EC–OC comparison exercise for French laboratories using different thermal-optical methods (five laboratories only). While there is good agreement on total carbon (TC) measurements among all participants, some differences can be observed on the EC / TC ratio, even among laboratories using the same thermal protocol. These results led to further tests on the influence of the optical correction: results obtained from different European laboratories confirmed that there were higher differences between OC_TOT and OC_TOR measured with NIOSH 5040 in comparison to EUSAAR-2. Also, striking differences between EC_TOT / EC_TOR ratios can be observed when comparing results obtained for rural and urban samples, with EC_TOT being 50% lower than EC_TOR at rural sites whereas it is only 20% lower at urban sites. The PM chemical composition could explain these differences but the way it influences the EC–OC measurement is not clear and needs further investigation. Meanwhile, some additional tests seem to indicate an influence of oven soiling on the EC–OC measurement data quality. This highlights the necessity to follow the laser signal decrease with time and its impact on measurements. Nevertheless, this should be confirmed by further experiments, involving more samples and various instruments, to enable statistical processing. All these results provide insights to determine the quality of EC–OC analytical methods and may contribute to the work toward establishing method standardisation

Behavior and Impact of Zirconium in the Soil–Plant System: Plant Uptake and Phytotoxicity

Because of the large number of sites they pollute, toxic metals that contaminate terrestrial ecosystems are increasingly of environmental and sanitary concern (Uzu et al. 2010, 2011; Shahid et al. 2011a, b, 2012a). Among such metals is zirconium (Zr), which has the atomic number 40 and is a transition metal that resembles titanium in physical and chemical properties (Zaccone et al. 2008). Zr is widely used in many chemical industry processes and in nuclear reactors (Sandoval et al. 2011; Kamal et al. 2011), owing to its useful properties like hardness, corrosion-resistance and permeable to neutrons (Mushtaq 2012). Hence, the recent increased use of Zr by industry, and the occurrence of the Chernobyl and Fukashima catastrophe have enhanced environmental levels in soil and waters (Yirchenko and Agapkina 1993; Mosulishvili et al. 1994 ; Kruglov et al. 1996)

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant

A Position Effect on the Heritability of Epigenetic Silencing

In animals and yeast, position effects have been well documented. In animals, the best example of this process is Position Effect Variegation (PEV) in Drosophila melanogaster. In PEV, when genes are moved into close proximity to constitutive heterochromatin, their expression can become unstable, resulting in variegated patches of gene expression. This process is regulated by a variety of proteins implicated in both chromatin remodeling and RNAi-based silencing. A similar phenomenon is observed when transgenes are inserted into heterochromatic regions in fission yeast. In contrast, there are few examples of position effects in plants, and there are no documented examples in either plants or animals for positions that are associated with the reversal of previously established silenced states. MuDR transposons in maize can be heritably silenced by a naturally occurring rearranged version of MuDR. This element, Muk, produces a long hairpin RNA molecule that can trigger DNA methylation and heritable silencing of one or many MuDR elements. In most cases, MuDR elements remain inactive even after Muk segregates away. Thus, Muk-induced silencing involves a directed and heritable change in gene activity in the absence of changes in DNA sequence. Using classical genetic analysis, we have identified an exceptional position at which MuDR element silencing is unstable. Muk effectively silences the MuDR element at this position. However, after Muk is segregated away, element activity is restored. This restoration is accompanied by a reversal of DNA methylation. To our knowledge, this is the first documented example of a position effect that is associated with the reversal of epigenetic silencing. This observation suggests that there are cis-acting sequences that alter the propensity of an epigenetically silenced gene to remain inactive. This raises the interesting possibility that an important feature of local chromatin environments may be the capacity to erase previously established epigenetic marks

Parental Genome Dosage Imbalance Deregulates Imprinting in Arabidopsis

In mammals and in plants, parental genome dosage imbalance deregulates embryo growth and might be involved in reproductive isolation between emerging new species. Increased dosage of maternal genomes represses growth while an increased dosage of paternal genomes has the opposite effect. These observations led to the discovery of imprinted genes, which are expressed by a single parental allele. It was further proposed in the frame of the parental conflict theory that parental genome imbalances are directly mirrored by antagonistic regulations of imprinted genes encoding maternal growth inhibitors and paternal growth enhancers. However these hypotheses were never tested directly. Here, we investigated the effect of parental genome imbalance on the expression of Arabidopsis imprinted genes FERTILIZATION INDEPENDENT SEED2 (FIS2) and FLOWERING WAGENINGEN (FWA) controlled by DNA methylation, and MEDEA (MEA) and PHERES1 (PHE1) controlled by histone methylation. Genome dosage imbalance deregulated the expression of FIS2 and PHE1 in an antagonistic manner. In addition increased dosage of inactive alleles caused a loss of imprinting of FIS2 and MEA. Although FIS2 controls histone methylation, which represses MEA and PHE1 expression, the changes of PHE1 and MEA expression could not be fully accounted for by the corresponding fluctuations of FIS2 expression. Our results show that parental genome dosage imbalance deregulates imprinting using mechanisms, which are independent from known regulators of imprinting. The complexity of the network of regulations between expressed and silenced alleles of imprinted genes activated in response to parental dosage imbalance does not support simple models derived from the parental conflict hypothesis

Evaluation of receptor and chemical transport models for PM10 source apportionment

In this study, the performance of two types of source apportionment models was evaluated by assessing the results provided by 40 different groups in the framework of an intercomparison organised by FAIRMODE WG3 (Forum for air quality modelling in Europe, Working Group 3). The evaluation was based on two performance indicators: z-scores and the root mean square error weighted by the reference uncertainty (RMSEu), with pre-established acceptability criteria. By involving models based on completely different and independent input data, such as receptor models (RMs) and chemical transport models (CTMs), the intercomparison provided a unique opportunity for their cross-validation. In addition, comparing the CTM chemical profiles with those measured directly at the source contributed to corroborate the consistency of the tested model results. The most commonly used RM was the US EPA- PMF version 5. RMs showed very good performance for the overall dataset (91% of z-scores accepted) while more difficulties were observed with the source contribution time series (72% of RMSEu accepted). Industrial activities proved to be the most difficult sources to be quantified by RMs, with high variability in the estimated contributions. In the CTMs, the sum of computed source contributions was lower than the measured gravimetric PM10 mass concentrations. The performance tests pointed out the differences between the two CTM approaches used for source apportionment in this study: brute force (or emission reduction impact) and tagged species methods. The sources meeting the z-score and RMSEu acceptability criteria tests were 50% and 86%, respectively. The CTM source contributions to PM10 were in the majority of cases lower than the RM averages for the corresponding source. The CTMs and RMs source contributions for the overall dataset were more comparable (83% of the z-scores accepted) than their time series (successful RMSEu in the range 25% - 34%). The comparability between CTMs and RMs varied depending on the source: traffic/exhaust and industry were the source categories with the best results in the RMSEu tests while the most critical ones were soil dust and road dust. The differences between RMs and CTMs source reconstructions confirmed the importance of cross validating the results of these two families of models