Fluvial geomorphic elements in modern sedimentary basins and their potential preservation in the rock record : A review

We appreciate very helpful reviews by Dr. Martin Stokes and three anonymous reviewers and editor Dr. Richard Marston. We also appreciate the encouragement for writing this paper from Dr. Timothy Horscroft. We acknowledge support of the sponsors of the Fluvial Systems Research Group consortium, BP, BG, Chevron, ConocoPhillips and Total.Peer reviewedPostprin

Lagging Response of Belowground Functional Traits to Environmental Cues in a Mature Amazonian Tropical Rainforest

Context/Purpose: The stress-dominance hypothesis (SDH) is a model of community assembly predicting that the relative importance of environmental filtering increases and competition decreases along a gradient of increasing environmental stress. Therefore, trait variation at the community level should increase as resources are more available. Although the SDH was designed to explain spatial changes in plant communities based on aboveground traits, it is possible that root communities show similar switches in strategies at temporal scales in response to pulses in resource availability. Methods: To test this hypothesis we sampled for two years the morphological changes in root systems in a mature tropical forest in Central Amazon. Thirty-six samples along a 500 m transect were taken each three months from February 2016 to February 2018, separating the uppermost organic layer (0-5 cm) from the mineral soil (5-15 cm). Besides root biomass, we scanned approximately 20% of the total root systems to calculate specific root length (SRL), average diameter (D), root tissue density (RTD), and branching index (BI). Spatially, we expected shifts from acquisitive to conservative syndromes as roots penetrate in the mineral soil. Temporarily, we hypothesized that traits associated with resource acquisition (SRL, SRTA, BI) will increase with soil moisture. Moreover, we expected that trait range will increase as resources become more available. Results: We found significant differences in biomass and morphological traits between the organic and mineral soils. We found no patterns between biomass increases in seasonality, but mean community traits change significantly with seasonal rain patterns. More interestingly, changes in mean and range values were more strongly associated with rain events three months before the collecting date, suggesting a lagging between rain events and belowground community responses. Conclusions: Belowground dynamics are structured spatially and temporarily in tropical forests, in synchrony with the availability of resources, as predicted by the SHD. Our results suggest that species tend to show similar traits during stressful times but diverge during acquisition periods. The results suggest a belowground dimension to niche segregation little explored in tropical biomes to date

Fine roots stimulate nutrient release during early stages of leaf litter decomposition in a Central Amazon rainforest

Purpose Large parts of the Amazon rainforest grow on weathered soils depleted in phosphorus and rock-derived cations. We tested the hypothesis that in this ecosystem, fine roots stimulate decomposition and nutrient release from leaf litter biochemically by releasing enzymes, and by exuding labile carbon stimulating microbial decomposers. Methods We monitored leaf litter decomposition in a Central Amazon tropical rainforest, where fine roots were either present or excluded, over 188 days and added labile carbon substrates (glucose and citric acid) in a fully factorial design. We tracked litter mass loss, remaining carbon, nitrogen, phosphorus and cation concentrations, extracellular enzyme activity and microbial carbon and nutrient concentrations. Results Fine root presence did not affect litter mass loss but significantly increased the loss of phosphorus and cations from leaf litter. In the presence of fine roots, acid phosphatase activity was 43.2% higher, while neither microbial stoichiometry, nor extracellular enzyme activities targeting carbon- and nitrogen-containing compounds changed. Glucose additions increased phosphorus loss from litter when fine roots were present, and enhanced phosphatase activity in root exclusions. Citric acid additions reduced litter mass loss, microbial biomass nitrogen and phosphorus, regardless of fine root presence or exclusion. Conclusions We conclude that plant roots release significant amounts of acid phosphatases into the litter layer and mobilize phosphorus without affecting litter mass loss. Our results further indicate that added labile carbon inputs (i.e. glucose) can stimulate acid phosphatase production by microbial decomposers, highlighting the potential importance of plant-microbial feedbacks in tropical forest ecosystems

Perspectives in visual imaging for marine biology and ecology: from acquisition to understanding

Durden J, Schoening T, Althaus F, et al. Perspectives in Visual Imaging for Marine Biology and Ecology: From Acquisition to Understanding. In: Hughes RN, Hughes DJ, Smith IP, Dale AC, eds. Oceanography and Marine Biology: An Annual Review. 54. Boca Raton: CRC Press; 2016: 1-72

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript