Architecture of an Antagonistic Tree/Fungus Network: The Asymmetric Influence of Past Evolutionary History

Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions.Based on a long-term (1972-2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns.Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependent on recent ecological processes

The conserved coiled-coil protein CCCP1 and the endosomal complex EARP regulate dense-core vesicle cargo sorting

Thesis (Ph.D.)--University of Washington, 2018The regulated release of peptide hormones (e.g. insulin), neuropeptides, and monoamines depends on their being packaged into dense-core vesicles (DCVs). How these vesicles are made and how their cargo is properly selected is not well understood, especially at the molecular level. DCVs are generated at the trans-Golgi network (TGN) and go through maturation steps including peptide processing and removal of improperly loaded cargo. Screens in C. elegans have identified several conserved molecules that are important for DCV function. These include the small G protein RAB2, its effector the conserved coiled-coil protein 1 (CCCP1), the endosome-associated recycling complex (EARP), and the EARP interacting protein 1 (EIPR1). All these proteins function in C. elegans neurons in the same genetic pathway. In mutants of these proteins, DCVs are generated normally but they contain reduced levels of cargo suggesting a role in cargo sorting. To determine whether CCCP1 and EIPR1 are important for the formation of DCVs in mammalian endocrine cells, we generated Cccp1KO and Eipr1KO insulin-secreting pancreatic beta 832/13 cells. We have observed that the KO cells have reduced insulin secretion and that insulin is retained near or at the TGN suggesting that both proteins are required for sorting insulin into DCVs. In a proximity labelling BioID screen, I found that CCCP1 is in close proximity to the transmembrane protein carboxypeptidase D (CPD). CPD localizes to the TGN and to immature DCVs (iDCVs), but gets removed from iDCVs during maturation. Interestingly, I have shown that in Cccp1KO and in Eipr1KO cells, CPD is missorted and remains in mature DCVs. In subcellular localization studies, I found that both CCCP1 and EIPR1/EARP partially colocalize with TGN and iDCV markers, while a second pool of EARP localizes to recycling endosomes. By super-resolution microscopy, I observed that CCCP1 forms circles (~200 nm diameter) that surround proinsulin; suggesting that CCCP1 localizes around immature DCV membranes, around proinsulin positive TGN subdomains, or to both. Together, these localization and functional studies suggest that CCCP1 and EIPR1 are novel regulators of DCV cargo sorting in neurons and endocrine cells. The data is consistent with a model in which CCCP1 and EIPR1 control insulin sorting into DCVs at the TGN and remove cargo not destined to the regulated secretory pathway in a post-Golgi step. To gain insights into the function of CCCP1, I have performed a detailed structure-function study of CCCP1. I have shown that its C-terminal coiled-coil CC3 domain is necessary and sufficient for its localization in vivo, while its middle coiled-coil domain CC2 is required for recruiting EARP complex (likely EARP positive membrane compartment). Finally, in biophysical studies of CCCP1, I have found that the protein has features reminiscent of golgins, a family of membrane tethers. Together, my findings are consistent with a speculative model in which a membrane tethering step between TGN/iDCVs membranes and EARP positive membranes might be required for cargo sorting to DCVs

Surface Lagrangian Remeshing: A new tool for studying long term evolution of continental lithosphere from 2D numerical modelling

International audienceIn this paper we present a new local remeshing algorithm that is dedicated to the problem of erosion in finite element models whose grid follows the movement of the free surface. The method, which we name Surface Lagrangian Remeshing (SLR), is adapted to 2D Lagrangian models which couple surface erosion with deformation of Earth materials. The remeshing procedure preserves nodes defining the surface submitted to erosion and removes nodes belonging to surface elements whose internal angles or area is critically low. This algorithm is ideally suited to track long term surface evolution. To validate the method we perform a set of numerical tests, using triangular finite elements, which compare the results obtained with the SLR algorithm with global remeshing and with analytical results. The results show good agreements with analytical solutions. Interpolation errors associated with remeshing are generated locally and numerical diffusion is restricted to the remeshed domain itself. In addition this method is computationally costless compared to classical global remeshing algorithm. We propose to couple the SLR method with the Dynamical Lagrangian Remeshing (DLR) algorithm to enable local remeshing only of Lagrangian models coupling large deformation of Earth materials with large erosion

Towards the hydrologic and bed load monitoring from high-frequency seismic noise in a braided river: The "torrent de St Pierre", French Alps

International audienceWe explore the use of seismic noise produced by rivers to monitor the bed load transport in the case of a low-discharge braided river in the French Alps: the "torrent de St Pierre". For this purpose, we deployed two dedicated seismic networks during summers 2007 and 2008, for which the characteristics of the recorded continuous signal are similar despite changes in the sensor locations. For dry weather conditions, only melting of nearby glaciers controls the supply of water to the stream. In these conditions, the river hydrology and the seismic energy in the 2-80 Hz frequency band both follow a diurnal fluctuation similar to the thermal amplitude. In contrast during rainfall episodes, the temperature variation fails to explain the hydrodynamic changes. Dense cloud covers reduce glacier melting and the recorded seismic energy denotes bursts of high-frequency seismic noise well correlated with water level data. Comparisons between the recorded seismic signals and the collected hydrological and sediment load data indicate that a frequency band of 3-9 Hz best explains the water level changes and thus the seismic waves coming from the flow turbulence. These analyses also reveal the presence of a seismic noise threshold that might be linked to the water shear stress exerted by the flowing water. Using the seismic energy in this frequency band as a proxy of the fluvial shear stress, the seismic-hydrologic relationship may be sensitive to variations in bed load transport. The spectral content of the seismic energy shows patterns consistent with the mobilization of sediment particles. From the interpretations of the seismic wave attenuation of river sources, we finally propose that stations at a distance from the stream less than 50 m are able to record most sediment particles. Farther stations are still useful during extreme events when largest grain sizes are mobilized. More generally this study demonstrates the feasibility of using the river seismic signal to survey bed load transport in various river types from small braided mountain rivers like the "torrent de St Pierre" to the large entrenched Himalayan rivers

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Turnover rates of hepatic collagen and circulating collagen-associated proteins in humans with chronic liver disease.

Accumulation and degradation of scar tissue in fibrotic liver disease occur slowly, typically over many years. Direct measurement of fibrogenesis, the rate of scar tissue deposition, may provide valuable therapeutic and prognostic information. We describe here results from a pilot study utilizing in vivo metabolic labeling to measure the turnover rate of hepatic collagen and collagen-associated proteins in plasma for the first time in human subjects. Eight subjects with chronic liver disease were labeled with daily oral doses of 2H2O for up to 8 weeks prior to diagnostic liver biopsy and plasma collection. Tandem mass spectrometry was used to measure the abundance and fractional synthesis rate (FSR) of proteins in liver and blood. Relative protein abundance and FSR data in liver revealed marked differences among subjects. FSRs of hepatic type I and III collagen ranged from 0.2-0.6% per day (half-lives of 4 months to a year) and correlated significantly with worsening histologic fibrosis. Analysis of plasma protein turnover revealed two collagen-associated proteins, lumican and transforming growth factor beta-induced-protein (TGFBI), exhibiting FSRs that correlated significantly with FSRs of hepatic collagen. In summary, this is the first direct measurement of liver collagen turnover in vivo in humans and suggests a high rate of collagen remodeling in advanced fibrosis. In addition, the FSRs of collagen-associated proteins in plasma are measurable and may provide a novel strategy for monitoring hepatic fibrogenesis rates

Genome wide association and gene validation studies for early root vigor to improve direct seeding of rice

Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigor traits in breeding programs. In a genome wide association study using an indica‐predominantdiversity panel we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS‐11, explained was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds and a predicted glycosyl hydrolase, TIPS‐11‐9, was identified as the causal gene for observed phenotypic differences. TIPS‐11‐9 was differentially expressed in emerging lateral roots of contrasting qTIPS‐11 haplotypes, which was likely due to differences in cis‐regulatory elements and auxin‐responsiveness. Abolishment of Tips‐11‐9 function through T‐DNA insertion in a qTIPS‐11‐positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous‐limiting conditions. Marker‐assisted introgression of qTIPS‐11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia

Subject Demographics.

<p>*both scores 0 to 4 (Batts Ludwig, 1995)</p><p>Details regarding diagnosis, heavy water labeling duration, pathology scoring and tissue samples analyzed from each clinical subject. Abbreviations: autoimmune hepatitis (AIH); hepatitis C virus (HCV); human immunodeficiency virus (HIV); orthotopic liver transplantation (OLT).</p><p>Subject Demographics.</p

List of 20 hepatic proteins with relative abundances observed to most significantly positively correlate with histological fibrosis score.

<p>List of 20 hepatic proteins with relative abundances observed to most significantly positively correlate with histological fibrosis score.</p

Comparison of Hepatic Collagen Kinetics and Histologic Fibrosis Score.

<p>(A) Linear regression of hepatic type I collagen FSR (% new per day) and histopathologic fibrosis score in human subjects with chonic liver disease. (B,C) Bar graphs depicting the relative abundance of unlabeled (old) and labeled (new) hepatic type I collagen (B) and type III collagen (C) per unit mass of liver protein, normalized to 30 days of labeling <i>in vivo</i>. Collagen FSR values (% new per 30 days) are displayed above each bar. Values shown represent the subject or the mean of subjects with each histopathology score. Abbreviation: fractional synthesis rate (FSR).</p