•Urban grasslands are a big opportunity for biodiversity conservation in cities.•Reduction in mowing frequency dramatically increases plant diversity.•Management modification permit to switch from ...urban lawns to urban meadows.
In regions where intensive farming is the dominant land use, urban areas are an opportunity for biodiversity conservation. Thence there is an urgent need to promote more biodiversity-friendly cities. Lawns are widely distributed urban habitats which cover important surface in public and private places. However theses habitats are currently poor refuges for plant and animal communities due to their intensive management. This study assesses if a reduction in mowing frequency results in a more diverse plant community and changes functional ecological characteristics of urban lawns. We used a quasi-experimental situation resulting from 25 years differentiated management in public green spaces of Rennes (France) to evaluate the effect of reduced mowing frequency on plant taxonomic, functional and phylogenetic diversity. Our results clearly demonstrate that a reduction of mowing frequency induces a dramatic increase in the different components of plant community diversity that results in a switch from urban lawns to urban meadows.
1. Trait-based approaches applied to community ecology have led to a considerable advance in understanding the effect of environmental filters on species assembly. Although plant traits are known to ...vary both between and within species, little is known about the role of intraspecific trait variability in the non-random assembly mechanisms controlling the coexistence of species, including habitat filtering and niche differentiation. 2. We investigate the role of intraspecific variability in three key functional traits - specific leaf area (SLA), leaf dry matter content (LDMC) and height - in structuring grassland communities distributed along a flooding gradient. We quantified the contribution of intraspecific variability relative to interspecific differences in the trait-gradient relationship, and we used a null model approach to detect patterns of habitat filtering and niche differentiation, with and without intraspecific variability. 3. Community mean SLA and height varied significantly along the flooding gradient and intraspecific variability accounted for 44% and 32%, respectively, of these trait-gradient relationships. LDMC did not vary along the gradient, with and without accounting for intraspecific variability. Our null model approach revealed significant patterns of habitat filtering and niche differentiation for SLA and height, but not for LDMC. More strikingly, considering intraspecific trait variability greatly increased the detection of habitat filtering and was necessary to detect niche differentiation processes. 4. Synthesis. Our study provides evidence for a strong role of intraspecific trait variability in community assembly. Our findings suggest that intraspecific trait variability promotes species coexistence, by enabling species to pass through both abiotic and biotic filters. We argue that community ecology would benefit from more attention to intraspecific variability.
Despite being recognized as a promoter of diversity and a condition for local coexistence decades ago, the importance of intraspecific variance has been neglected over time in community ecology. ...Recently, there has been a new emphasis on intraspecific variability. Indeed, recent developments in trait-based community ecology have underlined the need to integrate variation at both the intraspecific as well as interspecific level. We introduce new T-statistics (‘T’ for trait), based on the comparison of intraspecific and interspecific variances of functional traits across organizational levels, to operationally incorporate intraspecific variability into community ecology theory. We show that a focus on the distribution of traits at local and regional scales combined with original analytical tools can provide unique insights into the primary forces structuring communities.
1. Climate change is expected to increase the magnitude and the frequency of extreme climatic events such as droughts. Better understanding how plant communities will respond to these droughts is a ...major challenge. We expect the response to be a shift in functional trait values resulting from both species turnover and intraspecific trait variability, but little research has addressed the relative contribution of both components. 2. We analysed the short-term functional response of subalpine grassland communities to a simulated drought by focusing on four leaf traits (LDMC: leaf dry matter content, SLA: specific leaf area, LNC: leaf nitrogen concentration and LCC: leaf carbon concentration). After evaluating species turnover and intraspecific variability separately, we determined their relative contribution in the community functional response to drought, reflected by changes in community-weighted mean traits. 3. We found significant species turnover and intraspecific variability, as well as significant changes in community-weighted mean for most of the traits. The relative contribution of intraspecific variability to the changes in community mean traits was more important (42–99%) than the relative contribution of species turnover (1–58%). Intraspecific variability either amplified (for LDMC, SLA and LCC) or dampened (for LNC) the community functional response mediated by species turnover. We demonstrated that the small contribution of species turnover to the changes in community mean LDMC and LCC was explained by a lack of covariation between species turnover and interspecific trait differences. 4. Synthesis. These results highlight the need for a better consideration of intraspecific variability to understand and predict the effect of climate change on plant communities. While both species turnover and intraspecific variability can be expected following an extreme drought, we report new evidence that intraspecific variability can be a more important driver of the short-term functional response of plant communities.
Cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) are pulmonary genetic disorders associated with inflammation and heterogeneous progression of the lung disease. We hypothesized that ...respiratory exosomes, nanovesicles circulating in the respiratory tract, may be involved in the progression of inflammation-related lung damage. We compared proteomic content of respiratory exosomes isolated from bronchoalveolar lavage fluid in CF and PCD to asthma (A), a condition also associated with inflammation but with less severe lung damage.
BALF were obtained from 3 CF, 3 PCD and 6 A patients. Exosomes were isolated from BALF by ultracentrifugations and characterized using immunoelectron microscopy and western-blot. Exosomal protein analysis was performed by high-resolution mass spectrometry using label-free quantification.
Exosome enrichment was validated by electron microscopy and immunodetection of CD9, CD63 and ALIX. Mass spectrometry analysis allowed the quantification of 665 proteins, of which 14 were statistically differential according to the disease. PCD and CF exosomes contained higher levels of antioxidant proteins (Superoxide-dismutase, Glutathione peroxidase-3, Peroxiredoxin-5) and proteins involved in leukocyte chemotaxis. All these proteins are known activators of the NF-KappaB pathway.
Our results suggest that respiratory exosomes are involved in the pro-inflammatory propagation during the extension of CF or PCD lung diseases.
The mechanism of local propagation of lung disease in cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) is not clearly understood. Differential Proteomic profiles of exosomes isolated from BAL from CF, PCD and asthmatic patients suggest that they carry pro-inflammatory proteins that may be involved in the progression of lung damage.
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•Exosomes were detected in BALF from CF, PCD and asthmatic patients•The exosomes from PCD and CF patients differed significantly from those isolated from asthmatic patients.•PCF and CF exosomes contained higher levels of antioxidant proteins
•A new index for the evaluation of vegetation conservation status (VCS).•Heathland habitats as a case study to test the performance of the VCS index.•The VCS index is consistent with expert ...assessments of conservation status.•The VCS index could potentially be applied to any habitat type.
Habitat degradation and fragmentation are recognized as major causes of biodiversity loss, and effective management to conserve habitats is highly dependent on our ability to assess their conservation status. In this study we introduce a new index (VCS, for vegetation conservation status) to assess the conservation status of plant communities, which reflect the identity of habitat types. The VCS index is based on the same probabilistic approach than the classical Simpson’s diversity index, but uses the concept of species pools to integrate the influence of ‘typical’ and ‘non-typical’ species on habitat conservation status. In addition to the effect of species identity, this index also allows the detection of change in conservation status because of variation in species-abundance distribution. As an example we applied the VCS index to two heathland habitats in French Brittany and we compared the values provided by the index to qualitative assessments by heathland experts. We also compared the performance of the VCS index against three other indices: species richness, species diversity and a more recent index of ‘favourable conservation status’. Among the four indices tested, the VCS index was the most effective in assessing the vegetation conservation status when compared against qualitative assessment by heathland experts. Moreover the VCS index, coupled with variance partitioning methods, allowed to quantify the contribution of expected causes of habitat degradation. This study demonstrates that the use of habitat-specific species pools to distinguish between typical and non-typical species, as well as the consideration of species abundances, are critical for an accurate assessment of the vegetation conservation status. The VCS index should therefore be a valuable tool for both managers and researchers involved in habitat conservation.
Methylmalonic acidemia (MMA) is a rare inborn error of metabolism caused by deficiency of the methylmalonyl-CoA mutase (MUT) enzyme. Downstream MUT deficiency, methylmalonic acid accumulates together ...with toxic metabolites from propionyl-CoA and other compounds upstream of the block in the enzyme pathway. The presentation is with life-threatening acidosis, respiratory distress, brain disturbance, hyperammonemia, and ketosis. Survivors develop poorly understood multi-organ damage, notably to the brain and kidneys. The HEK 293 cell line was engineered by CRISPR/Cas9 technology to knock out the
gene (MUT-KO). Shotgun label-free quantitative proteomics and bioinformatics analyses revealed potential damaging biological processes in MUT-deficient cells. MUT-KO induced alteration of cellular architecture and morphology, and ROS overproduction. We found the alteration of proteins involved in cytoskeleton and cell adhesion organization, cell trafficking, mitochondrial, and oxidative processes, as validated by the regulation of VIM, EXT2, SDC2, FN1, GLUL, and CHD1. Additionally, a cell model of MUT-rescuing was developed in order to control the specificity of MUT-KO effects. Globally, the proteomic landscape of MUT-KO suggests the cell model to have an increased susceptibility to propionate- and H
O
-induced stress through an impairment of the mitochondrial functionality and unbalances in the oxidation-reduction processes.
Protein Nα‐terminal acetylation represents one of the most abundant protein modifications of higher eukaryotes. In humans, six Nα‐acetyltransferases (Nats) are responsible for the acetylation of ...approximately 80% of the cytosolic proteins. N‐terminal protein acetylation has not been evidenced in organelles of metazoans, but in higher plants is a widespread modification not only in the cytosol but also in the chloroplast. In this study, we identify and characterize the first organellar‐localized Nat in eukaryotes. A primary sequence‐based search in Arabidopsis thaliana revealed seven putatively plastid‐localized Nats of which AT2G39000 (AtNAA70) showed the highest conservation of the acetyl‐CoA binding pocket. The chloroplastic localization of AtNAA70 was demonstrated by transient expression of AtNAA70:YFP in Arabidopsis mesophyll protoplasts. Homology modeling uncovered a significant conservation of tertiary structural elements between human HsNAA50 and AtNAA70. The in vivo acetylation activity of AtNAA70 was demonstrated on a number of distinct protein Nα‐termini with a newly established global acetylome profiling test after expression of AtNAA70 in E. coli. AtNAA70 predominately acetylated proteins starting with M, A, S and T, providing an explanation for most protein N‐termini acetylation events found in chloroplasts. Like HsNAA50, AtNAA70 displays Nε‐acetyltransferase activity on three internal lysine residues. All MS data have been deposited in the ProteomeXchange with identifier PXD001947 (http://proteomecentral.proteomexchange.org/dataset/PXD001947).
Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N‐α‐acetylation (NTA) and ε‐lysine acetylation (KA) are known to ...be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5‐related N‐acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid‐localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
Synopsis
A novel protein acetyltransferase family localized or associated to plant plastids is identified and characterised. These GCN5‐related N‐acetyltransferases (GNATs) have unique amino acid sequence characteristics and unambiguously possess dual N‐α‐ and ε‐lysine acetylation activities.
An in silico search for putative plastidial N‐terminal and lysine acetyltransferases reveals 10 putative GNAT candidates, showing unique features both at the level of the conserved motifs and key residues.
Localization to chloroplasts is confirmed for seven of them, while another one is either associated to chloroplasts or localized within the nucleus.
All plastid‐associated GNATs display distinct lysine acetyltransferase and relaxed N‐ terminal acetyltransferase substrate specificities.
Inactivation of GNAT2, the plastid GNAT involved in photosynthetic state transitions, results in NTA decreases confined to chloroplast proteins, next to the known decreases on photosynthetic KA target proteins.
A novel protein acetyltransferase family localized or associated to plant plastids is identified and characterised. These GCN5‐related N‐acetyltransferases (GNATs) have unique amino acid sequence characteristics and unambiguously possess dual N‐α‐ and ε‐lysine acetylation activities.
Focal and segmental glomerulosclerosis (FSGS) is a severe form of idiopathic nephrotic syndrome (INS), a glomerulopathy of presumably immune origin that is attributed to extrarenal pathogenic ...circulating factors. The recurrence of FSGS (rFSGS) after transplant occurs in 30% to 50% of cases. The direct analysis of patient plasma proteome has scarcely been addressed to date, mainly due to the methodological difficulties associated with plasma complexity and dynamic range. In this study, first, we compared different methods of plasma preparation, second, we compared the plasma proteomes of rFSGS and controls using two preparation methods, and third, we analyzed the early proximal signaling events in podocytes subjected to patient plasma, through a combination of phosphoproteomics and lipid-raft proteomics (raftomics). By combining immunodepletion and high pH fractionation, we performed a differential proteomic analysis of soluble plasma proteins and of extracellular vesicles (EV) obtained from healthy controls, non-INS patient controls, and rFSGS patients (n = 4). In both the soluble- and the EV-protein sets from the rFSGS patients, we found a statistically significant increase in a cluster of proteins involved in neutrophil degranulation. A group of lipid-binding proteins, generally associated with lipoproteins, was found to be decreased in the soluble set from the rFSGS patients. In addition, three amino acid transporters involved in mTORC1 activation were found to be significantly increased in the EV from the rFSGS. Next, we incubated human podocytes for 30 min with 10% plasma from both groups of patients. The phosphoproteomics and raftomics of the podocytes revealed profound differences in the proteins involved in the mTOR pathway, in autophagy, and in cytoskeleton organization. We analyzed the correlation between the abundance of plasma and plasma-regulated podocyte proteins. The observed changes highlight some of the mechanisms involved in FSGS recurrence and could be used as specific early markers of circulating-factor activity in podocytes.
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