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Manning's roughness coefficient is one of the input parameters in many surface irrigation simulation models. It affects the velocity of flow and thereby its variation with time and distance along the field length influence water application. In this study, variation of Manning's roughness coefficient was studied for a furrow plot consisting of three 40 m long free drained furrows of parabolic shape and having a top width of 0.30 m, a depth of 0.15 m and a slope of 0.5%. The irrigation experiments were carried out with the inflow rates of 0.2, 0.3, 0.4, and 0.5 L [s.sup.1]; and 0.3, 0.4, 0.5, 0.6, and 0.7 L [s.sup.-1] under bare; and cropped field conditions, respectively. Furrow cross-section data were collected before each irrigation event at 0.5, 13, 26 and 39.5 m from the head end along the center furrow using a profilometer. During the irrigation event, water depth and velocity of flow were measured at these locations at an interval of 15 min using point gauge and color dye, respectively. The furrow cross-section data were fitted into a second-degree polynomial equation to determine the furrow shape parameters that were used along with the flow depth data for determining the wetted area and wetted perimeter. The wetted area, wetted perimeter, and the velocity data were used to estimate Manning's roughness coefficient spatially and temporally. It is found that for both bare and cropped field conditions, Manning's roughness coefficient was more at second and last quarter of the furrow due to soil erosion at these locations. Manning's roughness coefficient at these locations varied from 0.019 to 0.022 and 0.015 to 0.018 for bare field whereas from 0.02 to 0.024, and 0.019 to 0.022 for cropped field, respectively. The temporal variation of Manning's roughness coefficient for both bare and cropped furrow conditions decreased with the elapsed time. However, these decreasing trends were observed more for lower inflow rates. Further, the average Manning's roughness coefficient for the subsequent irrigations was varied from 0.018 to 0.02 and from 0.019 to 0.0245 for bare and cropped conditions, respectively. Thus, the values of Manning's roughness coefficients were more for cropped furrow conditions than for bare furrow. DOI: 10.1061/(ASCE)0733-9437(2008)134:2(185) CE Database subject headings: Furrow irrigation; Hydraulic roughness; Coefficient; Velocity; Simulation models; Parameters.

TDR was used to estimate furrow infiltration, which is a key component in furrow irrigation system design and management. Furrow irrigation experiments were conducted on bare and cropped fields consisting of three 40 m long parabolic shaped furrows spaced at 0.8 m on a slope of 0.5%. The centre furrow was taken as the study furrow and the other two provided a buffer to the centre furrow. Altogether, 22 irrigations were conducted during 2004 and 2005 with inflow rates ranging from 0.1 to 0.7 l s−1. TDR probes were installed vertically around the centre furrow at four locations 0.5 (S1), 13 (S2), 26 (S3) and 39.5 m (S4) from the inlet end. The S1 and S3 locations had four TDR probes installed at 0.15, 0.30, 0.45 and 0.60 m depths whereas the S2 and S4 locations had two probes each at 0.15 and 0.30 m depths. Soil moisture data collected at 5-min intervals were used to determine the average soil moisture content of the field. The change in moisture content was used to estimate the furrow infiltration which was compared with that measured using an inflow–outflow (IO) method. The performance of the TDR method was studied by calculating the absolute prediction error (APE), root mean square error (RMSE) and index of agreement ( I a). It was found that the TDR-method estimated furrow infiltration well for higher inflow rates and during the initial stages of irrigation. APE decreased and I a increased with increase in flow rate for both bare and cropped conditions. The APE and RMSE were found to be larger for a cropped field than the bare field when irrigated at the same inflow rate. The accuracy of the TDR-method for estimating total infiltration was improved by using the average field moisture content of 30 or 45 min after the recession phase ceased. These results indicate that TDR can be used to estimate in situ infiltration under furrow irrigation. [ABSTRACT FROM AUTHOR]

Flood forecasting is of increasing importance as it comes to an increasing variability in global and local climates. But rainfall-runoff models are far from being perfect. In order to achieve a better prediction for emerging flood events, the model outputs have to be continuously updated. This contribution introduces a rather simple, yet effective updating procedure for the conceptual semi-distributed rainfall-runoff model PREVAH, whose runoff generation module relies on similar algorithms as the HBV-Model. The current conditions of the system, i.e. the contents of the upper soil reservoirs, are updated by the proposed method. The testing of the updating procedure on data from two mountainous catchments in Switzerland reveals a significant increase in prediction accuracy with regards to peak flow. [ABSTRACT FROM AUTHOR]

Flood forecasting is of increasing importance as it comes to an increasing variability in global and local climates. But rainfall-runoff models are far from being perfect. In order to achieve a better prediction for emerging flood events, the model outputs have to be continuously updated. This contribution introduces a rather simple, yet effective updating procedure for the conceptual distributed rainfall-runoff model PREVAH, whose runoff generation module relies on similar algorithms as the HBV-Model. The current conditions of the system, i.e. the contents of the upper soil reservoirs, are updated by the proposed method. The testing of the updating procedure on data from two mountainous catchments in Switzerland reveals a significant increase in prediction accuracy with regards to peak flow. [ABSTRACT FROM AUTHOR]

Inverse methods are often used for estimating soil hydraulic parameters from experiments on flow of water through soil. We propose here an alternative method using neural networks. We teach a problem-adapted network of radial basis functions(RBF) the relationship between soil parameters and transient flow patterns using a numerical flow model. The trained RBF network accurately identifies soil parameters from flow patterns not contained in the training scenarios. A comparison with the inverse method(Annealing-Simplex) reveals a similarly good prediction by both approaches for randomly perturbed data and data from the real world. Nonetheless, the inverse method showed dependency on initial parameter estimates not required by the RBF network. Training demands moderately more computation and manpower than the inverse technique, but the absolutely stable and simple network application requires negligible resources. Thus, for individual applications, the network approach is slightly surpassed by the Annealing-Simplex method. However, the RBF network has to be trained only once and, subsequently, it can be applied easily and without effort upon any number of laboratory experiments with standardized experimental setups. [ABSTRACT FROM AUTHOR]

The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO 2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover., (© 2024 The Author(s). Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

The ephrin type-A receptor 2 (EPHA2) kinase belongs to the largest family of receptor tyrosine kinases. There are several indications of an involvement of EPHA2 in the development of infectious diseases and cancer. Despite pharmacological potential, EPHA2 is an under-examined target protein. In this study, we synthesized a series of derivatives of the inhibitor NVP-BHG712 and triazine-based compounds. These compounds were evaluated to determine their potential as kinase inhibitors of EPHA2, including elucidation of their binding mode (X-ray crystallography), affinity (microscale thermophoresis), and selectivity (Kinobeads assay). Eight inhibitors showed affinities in the low-nanomolar regime (K D <10 nM). Testing in up to seven colon cancer cell lines that express EPHA2 reveals that several derivatives feature promising effects for the control of human colon carcinoma. Thus, we have developed a set of powerful tool compounds for fundamental new research on the interplay of EPH receptors in a cellular context., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

An effective malaria vaccine remains a global health priority and vaccine immunogens which prevent transmission of the parasite will have important roles in multi-component vaccines. One of the most promising candidates for inclusion in a transmission-blocking malaria vaccine is the gamete surface protein Pfs48/45, which is essential for development of the parasite in the mosquito midgut. Indeed, antibodies which bind Pfs48/45 can prevent transmission if ingested with the parasite as part of the mosquito bloodmeal. Here we present the structure of full-length Pfs48/45, showing its three domains to form a dynamic, planar, triangular arrangement. We reveal where transmission-blocking and non-blocking antibodies bind on Pfs48/45. Finally, we demonstrate that antibodies which bind across this molecule can be transmission-blocking. These studies will guide the development of future Pfs48/45-based vaccine immunogens., (© 2022. The Author(s).)

Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron-sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron-sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H 2 O 2 . Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis., (open access.)

A detailed understanding of the interaction between the highly variant Plasmodium falciparum erythrocyte membrane proteins 1 (PfEMP1) and their human binding partners is essential to explain their roles in disease development in malaria, as well as to understand how antibodies can inhibit these interactions and how the parasite manages to evade such an immune response. This chapter focuses on using surface plasmon resonance (SPR) as a reproducible, high-throughput method to quantitatively characterize these interactions. We describe how to utilize protein A or A/G and streptavidin for protein immobilization on SPR sensor chips and provide instructions on how to biotinylate proteins for this purpose and how to use SPR for binding competition assays. Since these experiments rely on recombinant proteins, we also present a method to verify their structural integrity using circular dichroism spectroscopy., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The overexpression of (basic)helix-loop-helix ((b)HLH) transcription factors (TFs) is frequent in malignant glioma. We investigated molecular effects upon disruption of the (b)HLH network by a dominant-negative variant of the E47 protein (dnE47). Our goal was to identify novel molecular subgroup-specific therapeutic strategies., Methods: Glioma cell lines LN229, LNZ308, and GS-2/GS-9 were lentivirally transduced. Functional characterization included immunocytochemistry, immunoblots, cytotoxic, and clonogenic survival assays in vitro, and latency until neurological symptoms in vivo. Results of cap analysis gene expression and RNA-sequencing were further validated by immunoblot, flow cytometry, and functional assays in vitro., Results: The induction of dnE47-RFP led to cytoplasmic sequestration of (b)HLH TFs and antiglioma activity in vitro and in vivo. Downstream molecular events, ie, alterations in transcription start site usage and in the transcriptome revealed enrichment of cancer-relevant pathways, particularly of the DNA damage response (DDR) pathway. Pharmacologic validation of this result using ataxia telangiectasia and Rad3 related (ATR) inhibition led to a significantly enhanced early and late apoptotic effect compared with temozolomide alone., Conclusions: Gliomas overexpressing (b)HLH TFs are sensitive toward inhibition of the ATR kinase. The combination of ATR inhibition plus temozolomide or radiation therapy in this molecular subgroup are warranted., (© The Author(s) 2020. Published by Oxford University Press, the Society for Neuro-Oncology and the European Association of Neuro-Oncology.)

A major determinant of pathogenicity in malaria caused by Plasmodium falciparum is the adhesion of parasite-infected erythrocytes to the vasculature or tissues of infected individuals. This occludes blood flow, leads to inflammation, and increases parasitemia by reducing spleen-mediated clearance of the parasite. This adhesion is mediated by PfEMP1, a multivariant family of around 60 proteins per parasite genome which interact with specific host receptors. One of the most common of these receptors is intracellular adhesion molecule-1 (ICAM-1), which is bound by 2 distinct groups of PfEMP1, A-type and B or C (BC)-type. Here, we present the structure of a domain from a B-type PfEMP1 bound to ICAM-1, revealing a complex binding site. Comparison with the existing structure of an A-type PfEMP1 bound to ICAM-1 shows that the 2 complexes share a globally similar architecture. However, while the A-type PfEMP1 bind ICAM-1 through a highly conserved binding surface, the BC-type PfEMP1 use a binding site that is more diverse in sequence, similar to how PfEMP1 interact with other human receptors. We also show that A- and BC-type PfEMP1 present ICAM-1 at different angles, perhaps influencing the ability of neighboring PfEMP1 domains to bind additional receptors. This illustrates the deep diversity of the PfEMP1 and demonstrates how variations in a single domain architecture can modulate binding to a specific ligand to control function and facilitate immune evasion., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

The Plasmodium falciparum variant surface antigen PfEMP1 expressed on the surface of infected erythrocytes is thought to play a major role in the pathology of severe malaria. As the sequence pool of the var genes encoding PfEMP1 expands there are opportunities, despite the high degree of sequence diversity demonstrated by this gene family, to reconstruct full-length var genes from small sequence tags generated from patient isolates. To test whether this is possible we have used a set of recently laboratory adapted ICAM-1-binding parasite isolates to generate sequence tags and, from these, to identify the full-length PfEMP1 being expressed by them. In a subset of the strains available we were able to produce validated, full-length var gene sequences and use these to conduct biophysical analyses of the ICAM-1 binding regions.

Human infective parasites, such as those that cause malaria, are highly adapted to evade clearance by the immune system. In situations where they must maintain prolonged interactions with molecules of their host, they often use parasite surface protein families. These families are highly diverse to prevent immune recognition, and yet, to promote parasite survival, their members must retain the ability to interact with specific human receptors. One of the best understood of the parasite surface protein families is the PfEMP1 proteins of Plasmodium falciparum. These molecules cause infected erythrocytes to adhere to human receptors found on blood vessel and tissue surfaces. This protects the parasite within from clearance by the spleen and also causes symptoms of severe malaria. The PfEMP1 are exposed to the immune system during infection and are therefore excellent vaccine candidates for use in an approach to prevent severe disease. A key question, however, is whether their extensive diversity precludes them from forming components of the malaria vaccines of the future?, (© 2017 The Author(s).)

Borna disease virus (BDV) is a non-segmented negative-stranded RNA virus that maintains a strictly neurotropic and persistent infection in affected end hosts. The primary target cells for BDV infection are brain cells, e.g. neurons and astrocytes. The exact mechanism of how infection is propagated between these cells and especially the role of the viral glycoprotein (GP) for cell-cell transmission, however, are still incompletely understood. Here, we use different cell culture systems, including rat primary astrocytes and mixed cultures of rat brain cells, to show that BDV primarily spreads through cell-cell contacts. We employ a highly stable and efficient peptidomimetic inhibitor to inhibit the furin-mediated processing of GP and demonstrate that cleaved and fusion-active GP is strictly necessary for the cell-to-cell spread of BDV. Together, our quantitative observations clarify the role of Borna disease virus-glycoprotein for viral dissemination and highlight the regulation of GP expression as a potential mechanism to limit viral spread and maintain persistence. These findings furthermore indicate that targeting host cell proteases might be a promising approach to inhibit viral GP activation and spread of infection., (© 2015 John Wiley & Sons Ltd.)

The virulence of Plasmodium falciparum is linked to the ability of infected erythrocytes (IE) to adhere to the vascular endothelium, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). In this article, we report the functional characterization of an mAb that recognizes a panel of PfEMP1s and inhibits ICAM-1 binding. The 24E9 mouse mAb was raised against PFD1235w DBLβ3&#95;D4, a domain from the group A PfEMP1s associated with severe malaria. 24E9 recognizes native PfEMP1 expressed on the IE surface and shows cross-reactivity with and cross-inhibition of the ICAM-1 binding capacity of domain cassette 4 PfEMP1s. 24E9 Fab fragments bind DBLβ3&#95;D4 with nanomolar affinity and inhibit ICAM-1 binding of domain cassette 4-expressing IE. The antigenic regions targeted by 24E9 Fab were identified by hydrogen/deuterium exchange mass spectrometry and revealed three discrete peptides that are solvent protected in the complex. When mapped onto a homology model of DBLβ3&#95;D4, these cluster to a defined, surface-exposed region on the convex surface of DBLβ3&#95;D4. Mutagenesis confirmed that the site most strongly protected is necessary for 24E9 binding, which is consistent with a low-resolution structure of the DBLβ3&#95;D4::24E9 Fab complex derived from small-angle x-ray scattering. The convex surface of DBLβ3&#95;D4 has previously been shown to contain the ICAM-1 binding site of DBLβ domains, suggesting that the mAb acts by occluding the ICAM-1 binding surface. Conserved epitopes, such as those targeted by 24E9, are promising candidates for the inclusion in a vaccine interfering with ICAM-1-specific adhesion of group A PfEMP1 expressed by P. falciparum IE during severe malaria., (Copyright © 2015 The Authors.)

The Lassa virus nucleoprotein (NP) is a multifunctional protein that plays an essential role in many aspects of the viral life cycle, including RNA encapsidation, viral transcription and replication, recruitment of ribonucleoprotein complexes to viral budding sites, and inhibition of the host cell interferon response. While it is known that NP is capable of forming oligomers, both the oligomeric state of NP in mammalian cells and the significance of NP oligomerization for its various functions remain unclear. Here, we demonstrate that Lassa virus NP solely forms trimers upon expression in mammalian cells. Using a minigenome assay we show that mutants that are not able to form stable trimers are no longer functional during transcription and/or replication of the minigenome, indicating that NP trimerization is essential for transcription and/or replication of the viral genome. However, mutations leading to destabilization of the NP trimer did not impact the incorporation of NP into virus-like particles or its ability to suppress interferon-induced gene expression, two important functions of arenavirus NP.

In this paper we present a new simulation-based integrated water management tool for sustainable water resources management in arid coastal environments. This tool delivers optimised groundwater withdrawal scenarios considering saltwater intrusion as a result of agricultural and municipal water abstraction. It also yields a substantially improved water use efficiency of irrigated agriculture. To allow for a robust and fast operation we unified process modelling with artificial intelligence tools and evolutionary optimisation techniques. The aquifer behaviour is represented using an artificial neural network (ANN) which emulates a numerical density-dependent groundwater flow model. The impact of agriculture is represented by stochastic crop water production functions (SCWPF). Simulation-based optimisation techniques together with the SCWPF and ANN deliver optimal groundwater abstraction and cropping patterns. To address contradicting objectives, e.g. profit-oriented agriculture vs. sustainable abstraction scenarios, we performed multi-objective optimisations using a multi-criteria optimisation algorithm.

Arenaviruses are a family of enveloped negative-stranded RNA viruses that can cause severe human disease ranging from encephalitis symptoms to fulminant hemorrhagic fever. The bi‑segmented RNA genome encodes four polypeptides: the nucleoprotein NP, the surface glycoprotein GP, the polymerase L, and the RING finger protein Z. Although it is the smallest arenavirus protein with a length of 90 to 99 amino acids and a molecular weight of approx. 11 kDa, the Z protein has multiple functions in the viral life cycle including (i) regulation of viral RNA synthesis, (ii) orchestration of viral assembly and budding, (iii) interaction with host cell proteins, and (iv) interferon antagonism. In this review, we summarize our current understanding of the structural and functional role of the Z protein in the arenavirus replication cycle.

Mature glycoprotein spikes are inserted in the Lassa virus envelope and consist of the distal subunit GP-1, the transmembrane-spanning subunit GP-2, and the signal peptide, which originate from the precursor glycoprotein pre-GP-C by proteolytic processing. In this study, we analyzed the oligomeric structure of the viral surface glycoprotein. Chemical cross-linking studies of mature glycoprotein spikes from purified virus revealed the formation of trimers. Interestingly, sucrose density gradient analysis of cellularly expressed glycoprotein showed that in contrast to trimeric mature glycoprotein complexes, the noncleaved glycoprotein forms monomers and oligomers spanning a wide size range, indicating that maturation cleavage of GP by the cellular subtilase SKI-1/S1P is critical for formation of the correct oligomeric state. To shed light on a potential relation between cholesterol and GP trimer stability, we performed cholesterol depletion experiments. Although depletion of cholesterol had no effect on trimerization of the glycoprotein spike complex, our studies revealed that the cholesterol content of the viral envelope is important for the infectivity of Lassa virus. Analyses of the distribution of viral proteins in cholesterol-rich detergent-resistant membrane areas showed that Lassa virus buds from membrane areas other than those responsible for impaired infectivity due to cholesterol depletion of lipid rafts. Thus, derivation of the viral envelope from cholesterol-rich membrane areas is not a prerequisite for the impact of cholesterol on virus infectivity.