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Coastal mangroves, thriving at the interface between land and sea, provide robust flood risk reduction. Projected increases in the frequency and magnitude of climate impact drivers such as sea level rise and wind and wave climatology reinforce the need to optimize the design and functionality of coastal protection works to increase resilience. Doing so effectively requires a sound understanding of the local coastal system. However, data availability particularly at muddy coasts remains a pronounced problem. As such, this paper captures a unique dataset for the Guyana coastline and focuses on relations between vegetation (mangrove) density, wave attenuation rates and sediment characteristics. These processes were studied along a cross-shore transect with mangroves fringing the coastline of Guyana. The data are publicly available at the 4TU Centre for Research Data (4TU.ResearchData) via https://doi.org/10.4121/c.5715269 (Best et al., 2022) where the collection Advancing Resilience Measures for Vegetated Coastline (ARM4VEG), Guyana, comprises of six key datasets. Suspended sediment concentrations typically exceeded 1 g L−1 with a maximum of 60 g L−1, implying that we measured merely fluid-mud conditions across a 1 m depth. Time series of wind waves and fluid-mud density variations, recorded simultaneously with tide elevation and suspended sediment data, indicate that wave–fluid-mud interactions in the nearshore may be largely responsible for the accumulation of fine, muddy sediment along the coast. Sediment properties reveal a consolidated underlying bed layer. Vegetation coverage densities in the Avicennia-dominated forest were determined across the vertical with maximum values over the first 20 cm from the bed due to the roots and pneumatophores. Generalized total wave attenuation rates in the forest and along the mudflat were between 0.002–0.0032 m−1 and 0.0003–0.0004 m−1 respectively. Both the mangroves and the mudflats have a high wave-damping capacity. The wave attenuation in the mangroves is presumably dominated by energy losses due to vegetation drag, since wave attenuation due to bottom friction and viscous dissipation on the bare mudflats is significantly lower than wave dissipation inside the mangrove vegetation. Data collected corroborate the coastal defence function of mangroves by quantifying their contribution to wave attenuation and sediment trapping. The explicit linking of these properties to vegetation structure facilitates modelling studies investigating the mechanisms determining the coastal defence capacities of mangroves.

Building high dykes is a common measure of coping with floods and plays an important role in agricultural management in the Vietnamese Mekong Delta. However, the construction of high dykes causes considerable changes in hydrodynamics of the Mekong River. This paper aims to assess the impact of the high-dyke system on water level fluctuations and tidal propagation in the Mekong River branches. We developed a coupled 1-D to 2-D unstructured grid using Delft3D Flexible Mesh software. The model domain covered the Mekong Delta extending to the East (South China Sea) and West (Gulf of Thailand) seas, while the scenarios included the presence of high dykes in the Long Xuyen Quadrangle (LXQ), the Plain of Reeds (PoR) and the Trans-Bassac regions. The model was calibrated for the year 2000 high-flow season. Results show that the inclusion of high dykes changes the percentages of seaward outflow through the different Mekong branches and slightly redistributes flow over the low-flow and high-flow seasons. The LXQ and PoR high dykes result in an increase in the daily mean water levels and a decrease in the tidal amplitudes in their adjacent river branches. Moreover, the different high-dyke systems not only have an influence on the hydrodynamics in their own branch, but also influence other branches due to the Vam Nao connecting channel. These conclusions also hold for the extreme flood scenarios of 1981 and 1991 that had larger peak flows but smaller flood volumes. Peak flood water levels in the Mekong Delta in 1981 and 1991 are comparable to the 2000 flood as peak floods decrease and elongate due to upstream flooding in Cambodia. Future studies will focus on sediment pathways and distribution as well as climate change impact assessment.

Stable gonality is a multigraph parameter that measures the complexity of a graph. It is defined using maps to trees. Those maps, in some sense, divide the edges equally over the edges of the tree; stable gonality asks for the map with the minimum number of edges mapped to each edge of the tree. This parameter is related to treewidth, but unlike treewidth, it distinguishes multigraphs from their underlying simple graphs. Stable gonality is relevant for problems in number theory. In this paper, we show that deciding whether the stable gonality of a given graph is at most a given integer $k$ belongs to the class NP, and we give an algorithm that computes the stable gonality of a graph in $O((1.33n)^nm^m \text{poly}(n,m))$ time.

This article presents a novel approach to explore mangrove dynamics on a prograding delta by integrating unmanned aerial vehicle (UAV) and satellite imagery. The Porong Delta in Indonesia has a unique geographical setting with rapid delta development and expansion of the mangrove belt. This is due to an unprecedented mud load from the LUSI mud volcanic eruption. The mangrove dynamics analysis combines UAV-based Structure from Motion (SfM) photogrammetry and 11 years (2009–2019) satellite imagery cloud computing analysis by Google Earth Engine (GEE). Our analysis shows unique, high-spatiotemporal-resolution mangrove extent maps. The SfM photogrammetry analysis leads to a 3D representation of the mangrove canopy and an estimate of mangrove biophysical properties with accurate height and individual position of the mangroves stand. GEE derived vegetation indices resulted in high (three-monthly) resolution mangrove coverage dynamics over 11 years (2009–2019), yielding a value of more than 98% for the overall, producer and consumer accuracy. Combining the satellite-derived age maps and the UAV-derived spatial tree structure allowed us to monitor the mangrove dynamics on a rapidly prograding delta along with its structural attributes. This analysis is of essential value to ecologists, coastal managers, and policymakers.

In estuaries suspended sediment concentration (SSC) is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. Sediment dynamics differs depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. A robust sediment transport model is a first step in developing a chain of models enabling simulations of contaminants, phytoplankton and habitat conditions. This works aims to determine turbidity levels in the complex-geometry delta of the San Francisco estuary using a process-based approach (Delft3D Flexible Mesh software). Our approach includes a detailed calibration against measured SSC levels, a sensitivity analysis on model parameters and the determination of a yearly sediment budget as well as an assessment of model results in terms of turbidity levels for a single year, water year (WY) 2011. Model results show that our process-based approach is a valuable tool in assessing sediment dynamics and their related ecological parameters over a range of spatial and temporal scales. The model may act as the base model for a chain of ecological models assessing the impact of climate change and management scenarios. Here we present a modeling approach that, with limited data, produces reliable predictions and can be useful for estuaries without a large amount of processes data.

Previous work on morphodynamic evolution in the Yangtze Estuary (YE) is based on measured historical bathymetries. To evaluate the sensitivity of sand–mud interaction in the estuarine morpho-dynamics, a process-based morphodynamic model, Delft3D, is used to examine the morphodynamic behaviour from 1958 to 1997. Different scenarios concerning sand and mud and their combination are designed systematically. The scenarios considering multiple fractions, and especially with four fractions, improve the hindcasting evolution, suggesting the importance of including both sand and mud fractions and a sediment gradient setting of medium grain.

Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species.We linked a series of models to investigate responses of California's San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010-2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations.Most of these environmental indicators change substantially over the 21(st) century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

Background: Epithelial sodium channel (ENaC) hyperactivity has been implicated in the pathogenesis of cystic fibrosis (CF) by dysregulation of fluid and electrolytes in the airways. In the present study, we show proof-of-principle for ENaC inhibition by lentiviral-mediated RNA interference., Methods: Immortalized normal (H441) and CF mutant (CFBE) airway cells, and differentiated human bronchial epithelial cells in air liquid interface culture (HBEC-ALI) were transduced with a vesicular stomatitis virus G glycoprotein pseudotyped lentiviral (LV) vector expressing a short hairpin RNA (shRNA) targeting the α subunit of ENaC (ENaCα), and a marker gene. Efficacy of ENaCα down-regulation was assayed by the real-time polymerase chain reaction (PCR), membrane potential assay, western blotting, short-circuit currents and fluid absorption. Off-target effects were investigated by a lab-on-a-chip quantitative PCR array., Results: Transduction to near one hundred percentage efficiency of H441, CFBE and HBEC-ALI was achieved by the addition of the LV vector before differentiation and polarization. Transduction resulted in the inhibition of ENaCα mRNA and antigen expression, and a proportional decrease in ENaC-dependent short circuit current and fluid transport. No effect on transepithelial resistance or cAMP-induced secretion responses was observed in HBEC-ALI. The production of interferon α and pro-inflammatory cytokine mRNA, indicating Toll-like receptor 3 or RNA-induced silencing complex mediated off-target effects, was not observed in HBEC-ALI transduced with this vector., Conclusions: We have established a generic method for studying the effect of RNA interference in HBEC-ALI using standard lentiviral vectors. Down-regulation of ENaCα by lentiviral shRNA expression vectors as shown in the absence off-target effects has potential therapeutic value in the treatment of cystic fibrosis., (Copyright © 2012 John Wiley & Sons, Ltd.)

Isolated liver perfusion offers a unique prospect for safe, effective targeting of gene therapies that can be directed against allograft rejection or recurrent diseases such as reinfection by hepatitis C virus (HCV). We aimed to examine the effect of organ preservation solutions on vector-based gene therapy delivery under hypothermic conditions. University of Wisconsin (UW) solution, histidine tryptophan ketoglutarate (HTK), EloHaes, sodium-poly(ethylene glycol)-UW solution [Institut Georges Lopez 1 solution (IGL-1)], and Dulbecco's modified Eagle's medium (DMEM) culture medium (control) were tested at 2 degrees C or 37 degrees C for lentiviral vector transduction efficiencies to the hepatoma cell line Huh-7 and primary human or mouse hepatocytes. Lentiviral vectors expressing short hairpin RNA were used to target HCV replication. With a potent short hairpin RNA vector, transductions were directly correlated to the therapeutic effect, with low transduction yielding low knockdown and vice versa. Green fluorescent protein (GFP) reporter gene expression was observed with vector incubation times as short as 10 minutes. The highest transductions were seen, after 2-hour 37 degrees C incubation, in UW (62% +/- 6 SEM); they were significantly higher than those in HTK (21% +/- 7 SEM). Neither adenosine nor glutathione, present in UW, provided any increase in transduction when supplemented to HTK, although the addition of hydroxyethyl starch (HES) significantly improved transductions. To rule out size exclusion as a mechanism of HES, IGL-1 was tested but did not result in better transductions than HTK or DMEM. When supplemented to UW, anionic compounds reduced transduction, and this indicated a charge interaction mechanism of HES. In conclusion, this study demonstrates that effective vector delivery can be achieved under conditions of hypothermic liver perfusion. UW provides superior transduction to hepatocytes over nonstarch solutions.

Chronic hepatitis C virus (HCV) infection has a major medical impact and current treatments are often unsuccessful. RNA interference represents a promising new approach to tackling this problem. The current study details the design and testing of self-inactivating lentiviral vectors (LV) delivering RNA interference to prevent HCV replication and infection. Vectors were constructed with single, double, and triple cassettes expressing short hairpin RNAs (shRNAs) simultaneously targeting two regions of the HCV 1b genome and the host cell receptor, CD81. The shRNAs directed against HCV IRES or NS5b regions were shown to be effective in inhibiting HCV replication in vitro (82 and 98%, respectively). No evidence of shRNA-related interferon production was observed. Vectors containing CD81 shRNA reduced cell surface expression up to 83% and reduced cell binding of HCV surface protein E2 up to 82% while not affecting levels of unrelated surface protein (Ber-EP4) or HCV replication. Double or triple shRNA vectors were independently effective in simultaneously reducing HCV replication, CD81 expression, and E2 binding. This study demonstrates lentiviral delivery of multiple shRNA, inhibiting HCV in a specific, IFN-independent, manner. The targeting of multiple viral and host cell elements simultaneously by RNAi could increase the potency of antiviral gene therapies.

Treatment of congenital and acquired liver disease is one of the main issues in the field of gene therapy. Self-inactivating lentiviral vectors have several potential advantages over alternative systems. We have constructed a self-inactivating lentiviral vector (LV-ALBUGT) that expresses the human bilirubin UDP-glucuronosyltransferase (UGT1A1) from a liver-specific promoter. UGT1A1 is involved in the clearance of heme metabolites in the liver. This enzyme is deficient in Crigler-Najjar disease, a recessive inherited disorder in humans characterized by chronic severe jaundice, i.e., high plasma bilirubin levels. Gunn rats suffer from the same defect and are used as an animal model of this disease. We have treated juvenile Gunn rats by single intravenous injection with the LV-ALBUGT vector. Over 1 year after treatment with the highest dose (5 x 10(8) transducing units), we observed a stable reduction of bilirubin levels to near normal levels and normal secretion of bilirubin conjugates in the bile, in contrast to untreated animals. In situ hybridization showed expression of the therapeutic gene in more than 30% of liver parenchymal cells. Thus, we demonstrate stable and complete clinical remission of a congenital metabolic liver disease in an animal model, after systemic administration of a therapeutic lentiviral vector.