Multi Station Calibration of 3D Flexible Mesh Model: A Case Study of the Columbia Estuary

A model calibration based on the distributed multi stations approach is necessary towards model implementation in the operational phase. In this study, a tree dimensional (3D) hydrodynamic and salinity dynamic model of an estuary was simulated using DFlow Flexible Mesh program, which is developed by Deltares. Specifically, this research was focused on the Columbia Estuary case study, which is situated in Oregon, United States. The preconfigured model was calibrated based on 15 measurement stations that are spread along the estuary. Furthermore, a detail portion data with an average interval of 1 minute were used during the calibration process. The model performances were improved by considering the data denial concept. The data denial concept was introduced by neglecting inconsistence data across its temporal and spatial variability. In this particular case, it was revealed that the downstream data, which have high salinity value, tends to produce high contribution to the root mean square error of the model result. In conclusion, the upstream data have immense variable fluctuation rate and therefore it is more sensitive to give lower coefficient of determination. Therefore, there must be a trade of between good estuary model performance and upstream station data reliability

Decadal-timescale estuarine geomorphic change under future scenarios of climate and sediment supply

© The Authors, 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Estuaries and Coasts 33 (2010): 15-29, doi:10.1007/s12237-009-9244-y.Future estuarine geomorphic change, in response to climate change, sea-level rise, and watershed sediment supply, may govern ecological function, navigation, and water quality. We estimated geomorphic changes in Suisun Bay, CA, under four scenarios using a tidal-timescale hydrodynamic/sediment transport model. Computational expense and data needs were reduced using the morphological hydrograph concept and the morphological acceleration factor. The four scenarios included (1) present-day conditions; (2) sea-level rise and freshwater flow changes of 2030; (3) sea-level rise and decreased watershed sediment supply of 2030; and (4) sea-level rise, freshwater flow changes, and decreased watershed sediment supply of 2030. Sea-level rise increased water levels thereby reducing wave-induced bottom shear stress and sediment redistribution during the wind-wave season. Decreased watershed sediment supply reduced net deposition within the estuary, while minor changes in freshwater flow timing and magnitude induced the smallest overall effect. In all future scenarios, net deposition in the entire estuary and in the shallowest areas did not keep pace with sea-level rise, suggesting that intertidal and wetland areas may struggle to maintain elevation. Tidal-timescale simulations using future conditions were also used to infer changes in optical depth: though sea-level rise acts to decrease mean light irradiance, decreased suspended-sediment concentrations increase irradiance, yielding small changes in optical depth. The modeling results also assisted with the development of a dimensionless estuarine geomorphic number representing the ratio of potential sediment import forces to sediment export forces; we found the number to be linearly related to relative geomorphic change in Suisun Bay. The methods implemented here are widely applicable to evaluating future scenarios of estuarine change over decadal timescales.This study was supported by the US Geological Survey’s Priority Ecosystems Science program, CALFED Bay/ Delta Program, and the University of California Center for Water Resources

Genomic Sequence Analysis of Granulovirus Isolated from the Tobacco Cutworm, Spodoptera litura

Background: Spodoptera litura is a noctuid moth that is considered an agricultural pest. The larvae feed on a wide range of plants and have been recorded on plants from 40 plant families (mostly dicotyledons). It is a major pest of many crops. To better understand Spodoptera litura granulovirus (SpliGV), the nucleotide sequence of the SpliGV DNA genome was determined and analyzed. Methodology/Principal Findings: The genome of the SpliGV was completely sequenced. The nucleotide sequence of the SpliGV genome was 124,121 bp long with 61.2 % A+T content and contained 133 putative open reading frames (ORFs) of 150 or more nucleotides. The 133 putative ORFs covered 86.3 % of the genome. Among these, 31 ORFs were conserved in most completely sequenced baculovirus genomes, 38 were granulovirus (GV)-specific, and 64 were present in some nucleopolyhedroviruses (NPVs) and/or GVs. We proved that 9 of the ORFs were SpliGV specific. Conclusions/Significance: The genome of SpliGV is 124,121 bp in size. One hundred thirty-three ORFs that putatively encode proteins of 50 or more amino acid residues with minimal overlap were determined. No chitinase or cathepsin genes, which are involved in the liquefaction of the infected host, were found in the SpliGV genome, explaining why SpliGVinfected insects do not degrade in a typical manner. The DNA photolyase gene was first found in the genus Granulovirus. When phylogenic relationships were analyzed, the SpliGV was most closely related to Trichoplusia ni granulovirus (TnGV

Pre-Clinical Evaluation of a Replication-Competent Recombinant Adenovirus Serotype 4 Vaccine Expressing Influenza H5 Hemagglutinin

Influenza virus remains a significant health and social concern in part because of newly emerging strains, such as avian H5N1 virus. We have developed a prototype H5N1 vaccine using a recombinant, replication-competent Adenovirus serotype 4 (Ad4) vector, derived from the U.S. military Ad4 vaccine strain, to express the hemagglutinin (HA) gene from A/Vietnam/1194/2004 influenza virus (Ad4-H5-Vtn). Our hypothesis is that a mucosally-delivered replicating Ad4-H5-Vtn recombinant vector will be safe and induce protective immunity against H5N1 influenza virus infection and disease pathogenesis.The Ad4-H5-Vtn vaccine was designed with a partial deletion of the E3 region of Ad4 to accommodate the influenza HA gene. Replication and growth kinetics of the vaccine virus in multiple human cell lines indicated that the vaccine virus is attenuated relative to the wild type virus. Expression of the HA transgene in infected cells was documented by flow cytometry, western blot analysis and induction of HA-specific antibody and cellular immune responses in mice. Of particular note, mice immunized intranasally with the Ad4-H5-Vtn vaccine were protected against lethal H5N1 reassortant viral challenge even in the presence of pre-existing immunity to the Ad4 wild type virus.Several non-clinical attributes of this vaccine including safety, induction of HA-specific humoral and cellular immunity, and efficacy were demonstrated using an animal model to support Phase 1 clinical trial evaluation of this new vaccine

Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor

<div><p>Macrophages are a diverse group of phagocytic cells acting in host protection against stress, injury, and pathogens. Here, we show that the scavenger receptor SR-A6 is an entry receptor for human adenoviruses in murine alveolar macrophage-like MPI cells, and important for production of type I interferon. Scavenger receptors contribute to the clearance of endogenous proteins, lipoproteins and pathogens. Knockout of SR-A6 in MPI cells, anti-SR-A6 antibody or the soluble extracellular SR-A6 domain reduced adenovirus type-C5 (HAdV-C5) binding and transduction. Expression of murine SR-A6, and to a lower extent human SR-A6 boosted virion binding to human cells and transduction. Virion clustering by soluble SR-A6 and proximity localization with SR-A6 on MPI cells suggested direct adenovirus interaction with SR-A6. Deletion of the negatively charged hypervariable region 1 (HVR1) of hexon reduced HAdV-C5 binding and transduction, implying that the viral ligand for SR-A6 is hexon. SR-A6 facilitated macrophage entry of HAdV-B35 and HAdV-D26, two important vectors for transduction of hematopoietic cells and human vaccination. The study highlights the importance of scavenger receptors in innate immunity against human viruses.</p></div

Using viral vectors as gene transfer tools (Cell Biology and Toxicology Special Issue: ETCS-UK 1 day meeting on genetic manipulation of cells)

In recent years, the development of powerful viral gene transfer techniques has greatly facilitated the study of gene function. This review summarises some of the viral delivery systems routinely used to mediate gene transfer into cell lines, primary cell cultures and in whole animal models. The systems described were originally discussed at a 1-day European Tissue Culture Society (ETCS-UK) workshop that was held at University College London on 1st April 2009. Recombinant-deficient viral vectors (viruses that are no longer able to replicate) are used to transduce dividing and post-mitotic cells, and they have been optimised to mediate regulatable, powerful, long-term and cell-specific expression. Hence, viral systems have become very widely used, especially in the field of neurobiology. This review introduces the main categories of viral vectors, focusing on their initial development and highlighting modifications and improvements made since their introduction. In particular, the use of specific promoters to restrict expression, translational enhancers and regulatory elements to boost expression from a single virion and the development of regulatable systems is described

Uniendo ingeniería y ecología: la protección costera basada en ecosistemas

En un contexto de crecientes impactos y riesgos socio-económicos en las costas del planeta, la protección costera basada en ecosistemas surge como un nuevo paradigma que une los principios de protección, sostenibilidad y resiliencia, a la vez que proporciona múltiples beneficios. Este artículo ofrece una perspectiva sobre qué son y cómo se pueden utilizar las defensas naturales en el diseño, planificación y gestión de costas. La política pública muestra un creciente interés por su implementación general y el cuerpo de conocimiento y experiencia alrededor de la también denominada infraestructura ?verde? es creciente, pero aún existen importantes barreras que salvar. Una de ellas es estandarizar su diseño en términos ingenieriles, así como reconocer los aspectos que los diferencian respecto a enfoques tradicionales. La adaptación climática y la reducción de riesgos son áreas en las que su utilización puede ser más significativa, debido a la variedad de servicios que ofrecen. Tanto desde el punto de vista técnico como económico, existen argumentos sólidos para evitar la degradación de los ecosistemas, avanzando su restauración y conservación, como también desde la perspectiva de la defensa de las costas.In a context of increasing socio-economic impacts and risks in the coastal areas of the planet, coastal protection based on ecosystem features becomes a new paradigm that combines the principles of conservation, sustainability and resilience, while providing multiple benefits. This paper provides a perspective on what these are and how they can be used in the design, planning and management of the coastal zones. Policy-makers are calling for further uptake and implementation across the board and the body of knowledge and experience around the socalled ?green? infrastructure is growing, but there are still major barriers for a widespread uptake. One of them is to standardize designs in engineering terms, recognizing the different characteristics compared to traditional engineering solutions. Climate adaptation and risk reduction are areas where its use may be more significant, for the variety of services they offer. Both technically and economically, there are strong arguments to prevent degradation of ecosystems and to advance in their restoration and conservation, as well as from a coastal defense perspective

Water resource assessment along the Blue Nile River, north Africa with a one-dimensional model

The water resource of the Blue Nile River in north Africa is under increasing pressure due to rapid population growth and economic development. The situation is aggravated by a lack of coordinated management and governance, partly caused by incomplete knowledge of the water supplies, uses and needs. Proper water management is particularly important now, considering the recently completed and planned mega dams on the Blue Nile River network. This paper reports on the construction of a one-dimensional hydrodynamic model covering the entire Blue Nile River system, from Lake Tana to the confluence with the White Nile, with the aim of quantifying water availability throughout the year, for different conditions. The work included an extensive field measurement campaign along the Blue River and its tributaries, both in Ethiopia and Sudan. Calibrated and validated with independent datasets, the model was used to quantify water uses in the period 2008–2010, which were then compared with the official figures. The results show that the dry season is characterised by extra water losses that should be taken into account when quantifying water needs, especially during the filling up phase of new reservoirs