Carbon, nitrogen and Greenhouse gases budgets over a four years crop rotation in northern France

Croplands mainly act as net sources of the greenhouse gases carbon dioxide (CO₂) and nitrous oxide (N₂O), as well as nitrogen oxide (NO), a precursor of troposheric ozone. We determined the carbon (C) and nitrogen (N) balance of a four-year crop rotation, including maize, wheat, barley and mustard, to provide a base for exploring mitigation options of net emissions. The crop rotation had a positive net ecosystem production (NEP) of 4.4?±?0.7 Mg C ha^-1 y^-1 but represented a net source of carbon with a net biome production (NBP) of -1.3?±?1.1 Mg C?ha^-1 y^-1. The nitrogen balance of the rotation was correlated with the carbon balance and resulted in net loss (?24?±?28 kg N ha^-1 y^-1). The main nitrogen losses were nitrate leaching (?11.7?±1.0 kg N ha^-1 y^-1) and ammonia volatilization (?9 kg N ha^-1 y^-1). Dry and wet depositions were 6.7?±?3.0 and 5.9?±0.1 kg N ha^-1 y^-1, respectively. Fluxes of nitrous (N₂O) and nitric (NO) oxides did not contribute significantly to the N budget (N₂O: -1.8?±?0.04; NO: -0.7?±?0.04 kg N ha^-1 y^-1) but N₂O fluxes equaled 16% of the total greenhouse gas balance. The link between the carbon and nitrogen balances are discussed. Longer term experiments would be necessary to capture the trends in the carbon and nitrogen budgets within the variability of agricultural ecosystems.     

Identification of an interleukin-15alpha receptor-binding site on human interleukin-15

To identify the epitopes in human interleukin-15 (IL-15) that are responsible for binding to the interleukin-15 receptor alpha chain, antibody and receptor mapping by peptide scanning and site-directed mutagenesis was used. By using peptide scanning, we identified four regions in IL-15. The first region ((85)CKECEELEEKN(95)) is located in the C-D loop and is recognized by a set of non-inhibitory antibodies. The second region ((102)SFVHIVQMFIN(112)) is located in helix D and is recognized by two antibodies that are inhibitory of IL-15 bio-activity but not of IL-15 binding to IL-15Ralpha. The two remaining regions react with a recombinant soluble form of the IL-15Ralpha; the first ((44)LLELQVISL(52), peptide 1) corresponds to a sequence located in the B-helix and the second ((64)ENLII(68), peptide 2) to a sequence located in helix C. The latter is also contained in the epitope recognized by an antibody (monoclonal antibody B-E29) that prevents IL-15 binding to IL-15Ralpha. By site-directed mutagenesis, we confirmed that residues present in peptide 1 (Leu-45, Glu-46, Val-49, Ser-51, and Leu-52) and peptide 2 (Leu-66 and Ile-67) are involved in the binding of IL-15 to IL-15Ralpha. Furthermore, the results presented indicate that residues in the second peptide (Glu-64, Asn-65, and Ile-68) participate in IL-2Rbeta recruitment. This finding could have implications for the dynamics of receptor assembly. These results also indicate that the modes of interaction of IL-15 and IL-2 with their respective alpha chains are not completely analogous. Finally, some of the IL-15 mutants generated in this study displayed agonist or antagonist properties and may be useful as therapeutic agents.     

Protective effect of green tea polyphenols on the SH-SY5Y cells against 6-OHDA induced apoptosis through ROS-NO pathway

Green tea polyphenols (GTP) are thought to help prevent oxidative stress-related diseases, such as cancer, cardiovascular disease, neurodegenerative disease, and aging. We here investigate the protective mechanisms of GTP on SH-SY5Y cells against apoptosis induced by the pro-parkinsonian neurotoxin 6-hydroxydopamine (6-OHDA). GTP rescued the changes in condensed nuclear and apoptotic bodies, attenuated 6-OHDA-induced early apoptosis, prevented the decrease in mitochondrial membrane potential, and suppressed accumulation of reactive oxygen species (ROS) and of intracellular free Ca(2+). GTP also counteracted the 6-OHDA-induced nitric oxide increase and overexpression of nNOS and iNOS, and decreased the level of protein-bound 3-nitrotyrosine (3-NT). In addition, GTP inhibited the autooxidation of 6-OHDA and scavenged oxygen free radicals in a dose- and time-dependent manner. Our results show that the protective effects of GTP on SH-SY5Y cells are mediated, at least in part, by controlling the ROS-NO pathway.     

A Michaelis–Menten type equation for describing methylmercury dependence on inorganic mercury in aquatic sediments

Methylation of mercury (Hg) is the crucial process that controls Hg biomagnification along the aquatic food chains. Aquatic sediments are of particular interest because they constitute an essential reservoir where inorganic divalent Hg (Hg^II) is methylated. Methylmercury (MeHg) concentrations in sediments mainly result from the balance between methylation and demethylation reactions, two opposite natural processes primarily mediated by aquatic microorganisms. Thus, Hg availability and the activity of methylating microbial communities control the MeHg abundance in sediments. Consistently, some studies have reported a significant positive correlation between MeHg and Hg^II or total Hg (Hg_T), taken as a proxy for Hg^II, in aquatic sediments using enzyme-catalyzed methylation/demethylation mechanisms. By compiling 1,442 published and unpublished Hg_T–MeHg couples from lacustrine, riverine, estuarine and marine sediments covering various environmental conditions, from deep pristine abyssal to heavily contaminated riverine sediments, we show that a Michaelis–Menten type relationship is an appropriate model to relate the two parameters: MeHg = aHg_T/(K _m  + Hg_T), with a = 0.277 ± 0.011 and K _m  = 188 ± 15 (R ² = 0.70, p < 0.001). From K _m variations, which depend on the various encountered environmental conditions, it appears that MeHg formation and accumulation are favoured in marine sediments compared to freshwater ones, and under oxic/suboxic conditions compared to anoxic ones, with redox potential and organic matter lability being the governing factors.     

High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity,although bioinformatics pipelines do not perform equally

1. High‐throughput sequencing of amplicons (HTSA) has been proposed as an effective approach to evaluate taxonomic and genetic diversity at the same time. However, there are still uncertainties as to how the results produced by different bioinformatics treatments impact the conclusions drawn on biodiversity and population genetics indices.
2. We evaluated the ability of six bioinformatics pipelines to recover taxonomic and genetic diversity from HTSA data obtained from controlled assemblages. To that end, 20 assemblages were produced using 354 colonies of Botrylloides spp., sampled in the wild in ten marinas around Brittany (France). We used DNA extracted from preservative ethanol (ebDNA) after various time of storage (3, 6, and 12 months), and from a bulk of preserved specimens (bulkDNA). DNA was amplified with primers designed for targeting this ascidian genus. Results obtained from HTSA data were compared with Sanger sequencing on individual zooids (i.e., individual barcoding).
3. Species identification and relative abundance determined with HTSA data from either ebDNA or bulkDNA were similar to those obtained with traditional individual barcoding. However, after 12 months of storage, the correlation between HTSA and individual‐based data was lower than after shorter durations. The six bioinformatics pipelines were able to depict accurately the genetic diversity using standard population genetics indices (H_S and F_ST), despite producing false positives and missing rare haplotypes. However, they did not perform equally and dada2 was the only pipeline able to retrieve all expected haplotypes.
4. This study showed that ebDNA is a nondestructive alternative for both species identification and haplotype recovery, providing storage does not last more than 6 months before DNA extraction. Choosing the bioinformatics pipeline is a matter of compromise, aiming to retrieve all true haplotypes while avoiding false positives. We here recommend to process HTSA data using dada2, including a chimera‐removal step. Even if the possibility to use multiplexed primer sets deserves further investigation to expand the taxonomic coverage in future similar studies, we showed that primers targeting a particular genus allowed to reliably analyze this genus within a complex community.

     

Targeted-antibacterial-plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity

The global emergence of drug-resistant bacteria leads to the loss of efficacy of our antibiotics arsenal and severely limits the success of currently available treatments. Here, we developed an innovative strategy based on targeted-antibacterial-plasmids (TAPs) that use bacterial conjugation to deliver CRISPR/Cas systems exerting a strain-specific antibacterial activity. TAPs are highly versatile as they can be directed against any specific genomic or plasmid DNA using the custom algorithm (CSTB) that identifies appropriate targeting spacer sequences. We demonstrate the ability of TAPs to induce strain-selective killing by introducing lethal double strand breaks (DSBs) into the targeted genomes. TAPs directed against a plasmid-born carbapenem resistance gene efficiently resensitise the strain to the drug. This work represents an essential step toward the development of an alternative to antibiotic treatments, which could be used for in situ microbiota modification to eradicate targeted resistant and/or pathogenic bacteria without affecting other non-targeted bacterial species.     

LOCALISATION MITOCHONDRIALE D'ENZYMES LIEES AU METABOLISME DU GLYCOGENE DANS LE SPERMATOZOIDE DE L'ESCARGOT

The mitochondrial derivative of the sperm cell of the Gastropod Helix is endowed with a compartment loaded with glycogen (Personne et André, 1964). The aim of this work is to establish whether this mitochondrial glycogen is synthesized in the mitochondrial derivative itself or elsewhere in the cell. For this purpose, living sperm were first incubated in a medium containing glucose 1-phosphate, then fixed, sectioned, and stained specifically for polysaccharides by the phosphotungstic acid technique or the periodic acid-thiosemicarbazide-silver proteinate technique. Comparison with controls shows that a synthesis of glycogen occurred during the time of incubation. It can be inferred from this result that an amylophosphorylase system controlling the metabolism of polysaccharides is present in the mitochondrial derivative itself. Results obtained with the iodine technique indicate that the original glycogen molecules are elongated during the experiment. It seems probable that the amylophosphorylase system demonstrated here accounts for at least a part of the proteinaceous coat morphologically detectable around each individual glycogen particle.     

Tobacco pollen tubes as cellular models for ion dynamics: improved spatial and temporal resolution of extracellular flux and free cytosolic concentration of calcium and protons using pHluorin and YC3.1 CaMeleon

The presence of both calcium (Ca²⁺) and proton (H⁺) apical gradients is necessary for polarized cell elongation to occur in pollen tubes. So far, most of these studies have been carried out in lily pollen tubes, using chemical probes. Yet, lily is a refractory model for molecular genetics, with no easy protocol available for the construction of stable transgenic lines. Tobacco, however, is well suited for both transformation and cell biology, with sexual organs that are accessible, easy to handle and visualize. Pollen tubes are in an ideal size range for sub-cellular imaging analyses using modern microscopy techniques. Ion homeostasis in tobacco pollen tubes has not been precisely characterized so far. Here, we characterize the H⁺ and Ca²⁺ spatial and temporal patterns in tobacco pollen tubes by the use of two fluorescent genetic probes, pHluorin and the YC3.1 yellow CaMeleon, and direct measurement of extracellular flux by ion-sensitive vibrating probes. A distinct 0.4 pH unit acidic gradient was found to stretch from the tip up to 40 μm into the tube shank. This gradient intensity displayed 1–4 min period oscillations and is reduced in the non-growing phase of an oscillatory cycle. Furthermore, sub-membrane and sub-apical alkaline domains were detected. Extracellular H⁺ fluxes oscillated between 10 and 40 pmol cm⁻² s⁻¹. Fourier and continuous wavelet analyses showed tubes with one or two major oscillatory components in both extra and intracellular H⁺ oscillations. Cytosolic Ca²⁺ was imaged by confocal microscopy, showing a V-shaped 40 μm gradient extending from the tip, from 0.2 to 1.0 μM, which oscillates with a 1–4 min period, but with only one major oscillatory component. Extracellular Ca²⁺ fluxes oscillate in most pollen tubes, between 2 and 50 pmol cm⁻² min⁻¹ and, like in H⁺, with one or two major oscillatory peaks. A combination of confocal and widefield microscopy showed that H⁺ and Ca²⁺ displayed different patterns and shapes inside the cell, sometimes suggesting a structurally complementary role for these 2 second messengers in the growth process. These data suggest that fluxes at the apex of the pollen tube are directly responsible for establishment and maintenance of the gradient. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.