Gravel-bed river morphodynamics and large wood dynamics

International audienceThe gravel-bed rivers of the Gaspé Peninsula, Québec (Canada), a coastal drainage system of the St. Lawrence estuary, receive and transport vast quantities of large wood. The rapid rate of channel shifting caused by high-energy flows and noncohesive banks allows wood recruitment that in turn greatly influences the river morphodynamics. The delta of the Saint-Jean River has accumulated wood since 1960, leading to frequent avulsions over that time period. The wood raft in 2014 was more than 3-km long, which is unusual but natural. The jam configuration allows a unique opportunity to estimate a wood budget and to better understand the interactions between river morphodynamics and large wood flux at the basin scale. Airborne and ground photo/video images are used to evaluate channel changes, to determine the wood transport rates and the wood volume introduced by erosion and the wood deposited in the raft. Annual surveys were carried out from 2010 to 2013 to locate and describe more than 1000 jams and 2000 individual pieces of wood along the upstream 60 km long river section. Analysis of the morphodynamic trajectory of the river since 1960 (eroded floodplain, channel width, gravel-bar evolution, stream power…) combined with repeated field surveys allowed defining the morphological characteristics as well as the jam configuration that control wood mobility and deposit. The results indicate that the volumes of woods deposited along the 60 km section are 4 times higher in 2013 than in 2010. Increase in wood amount occurs mainly in upper alluvial sections whereas decrease is observed in the semi-alluvial sections. Wood transport rate and raft lengthening are only partly linked to peak flows so that some threshold conditions can control wood transfer within the basin. The four years analysis of the large woods dynamics in Saint-Jean river can assist river managers and develop management tools and strategies to deal with large wood in medium to large rivers and in rivers of cold areas

Response of Mediterranean Phytophagous Forest Insects to Climate Change (Abstract)

Mediterranean forest ecosystems have specific characteristics which, like other ecosystems, will very probably evolve during the 21st century under the influence of climate change. Variations in productivity, growth, phenology, fruit production and growing threats to survival of trees in connection with water stress and the risk of fire are already visible. The communities of phytophagous insects that inhabit Mediterranean forest ecosystems also show signs of being affected by climate change. These changes come about as a direct effect of climate on the demographics, phenology and geographic distribution of insects, and as an indirect effect of climate by modifying the quality, resistance and attraction of the trees they feed on. While some of the consequences of climate change on plant/insect interaction in these ecosystems appear to be predictable on the basis of these observations, much of these projections remain difficult to establish for two reasons: firstly, the impact of climate on insects is far less documented for Mediterranean areas than it is for temperate or boreal zones; secondly, the direct and indirect interactions of climate with both insects and trees increase the degree of complexity of long-term predictions for these sensitive ecosystems

Implementation and validation of large wood analysis for wood budgeting in a semi-alluvial river

International audienceThe semi-alluvial rivers of the Gaspé Peninsula, Québec (Canada), recruit and transport vast quantities of large wood. The rapid rate of channel shifting due to high-energy flows and non-cohesive banks allows the recruitment of large quantities of wood that in turn greatly influence river dynamics. The delta of the Saint-Jean River has accumulated a flux of wood since 1960, creating frequent avulsions, and now has a wood raft of more than 3 km in length. The Raft of the Saint-Jean River on the Gaspé Peninsula, Québec, Canada is an exceptional amount of wood that is unusual but natural. The river has complex large-wood dynamics that promote the formation of large wood jams in the river delta. The jam configuration allows a unique opportunity to apply a wood budget at the scale of a long river corridor and to better understand dynamics of large wood in river. A wood budget includes the evaluation of wood volumes (i) produced by bank erosion (input), (ii) still in transit in the river corridor (deposited on bars or channel edges), and (iii) accumulated in the delta (output). The budget is based on an analysis of aerial photos dating back to 1963 as well as surveys carried out between 2010 and 2014, all of which were used to locate and describe large wood accumulations along a 60 km river section. Understanding the interannual large wood dynamics in the Saint-Jean River can assist river managers determine sustainable solutions for the issue of wood rafts

Cross‐cultural assessment of HIV‐associated cognitive impairment using the Kaufman assessment battery for children: a systematic review

Introduction: Despite improved efficacy of, and access to, combination antiretroviral therapy (cART), HIV‐associated cognitive impairments remain prevalent in both children and adults. Neuropsychological tests that detect such impairment can help clinicians formulate effective treatment plans. The Kaufman Assessment Battery for Children (KABC), although developed and standardized in the United States, is used frequently in many different countries and cultural contexts to assess paediatric performance across various cognitive domains. This systematic review investigated the cross‐cultural utility of the original KABC, and its 2nd edition (KABC‐II), in detecting HIV‐associated cognitive impairment in children and adolescents.Methods: We entered relevant keywords and MeSH terms into the PubMed, PsycInfo, EBSCOHost, ProQuest, and Scopus databases, with search limits set from 1983–2017. Two independent reviewers evaluated the retrieved abstracts and manuscripts. Studies eligible for inclusion in the review were those that (a) used the KABC/KABC‐II to assess cognitive function in children/adolescents aged 2–18 years, (b) featured a definition of cognitive impairment (e.g. >2 SD below the mean) or compared the performance of HIV‐infected and uninfected control groups, and (c) used a sample excluded from population on which the instruments were normed.Results and discussion: We identified nine studies (eight conducted in African countries, and one in the United Kingdom) to comprise the review’s sample. All studies detected cognitive impairment in HIV‐infected children, including those who were cART‐naïve or who were cART treated and clinically stable. KABC/KABC‐II subtests assessing simultaneous processing appeared most sensitive. Evaluation of the methodological quality of the selected studies by two independent reviews suggested that shortcomings included reporting and selection biases.Conclusions: This systematic review provides evidence for the cross‐cultural utility of the KABC/KABC‐II, particularly the simultaneous processing subtests, in detecting cognitive impairment in HIV‐infected children (including those who are clinically stable). Although the current results suggest there is justification for using the KABC/KABC‐II primarily in East Africa, further investigation is required to explore the instrument’s utility in other HIV‐prevalent regions of the globe.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138351/1/jia21412.pd

Patterns and Factors of Soil Structure Recovery as Revealed From a Tillage and Cover-Crop Experiment in a Compacted Orchard

Degraded soil structure recovery is much less documented than structure degradation and in particular compaction. In this field experiment, the effects of rotary spade tillage followed by Sorghum cover crop (cover-crop treatment) on the degraded structure of the soil from an orchard were evaluated on undisturbed soil samples collected at 5–10 cm and 20–25 cm depth, respectively, using CoreVESS visual scoring of structure quality and shrinkage analysis. The cover-crop treatment took place from April to September and despite a particularly dry climate, the development of Sorghum was good. A large and significant improvement of the structure quality scores were obtained at both depths. Similar recovery trends in the physical properties were observed at the two depths, however the changes were significant at 5–10 cm depth only and were associated with a small increase of soil organic carbon (SOC) content. Analysis of covariance revealed a significant impact of the tillage and root development on the structure recovery, larger than the effect of SOC content. The structure recovery showed an increase of the positive role of SOC content on the physical properties. This structural change pattern was similar to those reported from other structure degradation or compaction studies. The slopes of the relationship between physical properties and SOC is an indicator of structure quality in general. Though the observed final structure quality of the top layer was good, we assume that its vulnerability remains large due to its small SOC to clay ratio. Our results are in close agreement with previous studies highlighting the relationships between SOC to clay ratio and structure quality

Endocortical bone loss in osteoporosis: The role of bone surface availability

Age-related bone loss and postmenopausal osteoporosis are disorders of bone remodelling, in which less bone is reformed than resorbed. Yet, this dysregulation of bone remodelling does not occur equally in all bone regions. Loss of bone is more pronounced near and at the endocortex, leading to cortical wall thinning and medullary cavity expansion, a process sometimes referred to as "trabecularisation" or "cancellisation". Cortical wall thinning is of primary concern in osteoporosis due to the strong deterioration of bone mechanical properties that it is associated with. In this paper, we examine the possibility that the non-uniformity of microscopic bone surface availability could explain the non-uniformity of bone loss in osteoporosis. We use a computational model of bone remodelling in which microscopic bone surface availability influences bone turnover rate and simulate the evolution of the bone volume fraction profile across the midshaft of a long bone. We find that bone loss is accelerated near the endocortical wall where the specific surface is highest. Over time, this leads to a substantial reduction of cortical wall thickness from the endosteum. The associated expansion of the medullary cavity can be made to match experimentally observed cross-sectional data from the Melbourne Femur Collection. Finally, we calculate the redistribution of the mechanical stresses in this evolving bone structure and show that mechanical load becomes critically transferred to the periosteal cortical bone.Comment: 13 pages, 3 figures. V2: minor stylistic improvements in text/figures; more accurately referenced subsection "Internal mechanical stress distribution"; some improved remarks in the Discussion sectio

The nonstructural NS1 protein of influenza viruses modulates TP53 splicing through host factor CPSF4

International audienceInfluenza A viruses (IAV) are known to modulate and "hijack" several cellular host mechanisms, including gene splicing and RNA maturation machineries. These modulations alter host cellular responses and enable an optimal expression of viral products throughout infection. The interplay between the host protein p53 and IAV, in particular through the viral nonstructural protein NS1, has been shown to be supportive for IAV replication. However, it remains unknown whether alternatively spliced isoforms of p53, known to modulate p53 transcriptional activity, are affected by IAV infection and contribute to IAV replication. Using a TP53 minigene, which mimics intron 9 alternative splicing, we have shown here that the NS1 protein of IAV changes the expression pattern of p53 isoforms. Our results demonstrate that CPSF4 (cellular protein cleavage and polyadenylation specificity factor 4) independently and the interaction between NS1 and CPSF4 modulate the alternative splicing of TP53 transcripts, which may result in the differential activation of p53-responsive genes. Finally, we report that CPSF4 and most likely beta and gamma spliced p53 isoforms affect both viral replication and IAV-associated type I interferon secretion. All together, our data show that cellular p53 and CPSF4 factors, both interacting with viral NS1, have a crucial role during IAV replication that allows IAV to interact with and alter the expression of alternatively spliced p53 isoforms in order to regulate the cellular innate response, especially via type I interferon secretion, and perform efficient viral replication

Developmental origins for kidney disease due to Shroom3 deficiency

CKD is a significant health concern with an underlying genetic component. Multiple genome-wide association studies (GWASs) strongly associated CKD with the shroomfamilymember 3 (SHROOM3) gene, which encodes an actin-associated protein important in epithelial morphogenesis. However, the role of SHROOM3 in kidney development and function is virtually unknown. Studies in zebrafish and rat showed that alterations in Shroom3 can result in glomerular dysfunction. Furthermore, human SHROOM3 variants can induce impaired kidney function in animal models. Here, we examined the temporal and spatial expression of Shroom3 in the mammalian kidney. We detected Shroom3 expression in the condensing mesenchyme, Bowman\u27s capsule, and developing and mature podocytes in mice. Shroom3 null (Shroom3Gt/Gt) mice showed marked glomerular abnormalities, including cystic and collapsing/degenerating glomeruli, and marked disruptions in podocyte arrangement and morphology. These podocyte-specific abnormalities are associated with altered Rho-kinase/myosin II signaling and loss of apically distributed actin. Additionally, Shroom3 heterozygous (Shroom3Gt/+) mice showed developmental irregularities that manifested as adult-onset glomerulosclerosis and proteinuria. Taken together, our results establish the significance of Shroom3 in mammalian kidney development and progression of kidney disease. Specifically, Shroom3 maintains normal podocyte architecture in mice via modulation of the actomyosin network, which is essential for podocyte function. Furthermore, our findings strongly support the GWASs that suggest a role for SHROOM3 in human kidney disease

E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient

Background. An influenza A(H1N1)pdm09 infection was diagnosed in a hematopoietic stem cell transplant recipient during conditioning regimen. He was treated with oral oseltamivir, later combined with intravenous zanamivir. The H275Y neuraminidase (NA) mutation was first detected, and an E119D NA mutation was identified during zanamivir therapy. Methods. Recombinant wild-type (WT) E119D and E119D/H275Y A(H1N1)pdm09 NA variants were generated by reverse genetics. Susceptibility to NA inhibitors (NAIs) was evaluated with a fluorometric assay using the 2′-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid (MUNANA) substrate. Susceptibility to favipiravir (T-705) was assessed using plaque reduction assays. The NA affinity and velocity values were determined with NA enzymatic studies. Results. We identified an influenza A(H1N1)pdm09 E119D mutant that exhibited a marked increase in the 50% inhibitory concentrations against all tested NAIs (827-, 25-, 286-, and 702-fold for zanamivir, oseltamivir, peramivir, and laninamivir, respectively). The double E119D/H275Y mutation further increased oseltamivir and peramivir 50% inhibitory concentrations by 790- and >5000-fold, respectively, compared with the WT. The mutant viruses remained susceptible to favipiravir. The NA affinity and velocity values of the E119D variant decreased by 8.1-fold and 4.5-fold, respectively, compared with the WT. Conclusions. The actual emergence of a single NA mutation conferring pan-NAI resistance in the clinical setting reinforces the pressing need to develop new anti-influenza strategie