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Bioinspired peptides are considered as the most promising alternative for drug design nowadays, acting as anticancer, antiinflammatory, antimicrobial, and delivery agents, as well as inhibitors of amyloidogenesis. However, it is essential to search for efficient and precise strategies to deliver these bioactive molecules into the host system and also to maintain their bioavailability. In this scenario, the design of diastereomeric and all- d -peptides has been applied to increase bioactive peptides’ resistance to endogenous enzymes, as well as their bioavailability. In addition, studies have also proposed the design of d -AMPs organized in the reverse sequence of their parent l -AMPs, known as retro-inverso AMPs, which present high topochemical similarities with their precursors, suggesting equivalent bioactivities. In this context, this chapter will report new advances and obstacles in the engineering of diastereomeric, all- d -enantiomeric and retro-inverso bioactive peptides, with a focus on antimicrobial peptides, mainly highlighting their therapeutic potential.

Data regarding the epidemiology and diagnosis of invasive aspergillosis in the critically ill population are limited, with data regarding elderly patients (=75 years old) even scarcer. We aimed to further compare the epidemiology, characteristics and outcome of elderly versus nonelderly critically ill patients with invasive aspergillosis (IA) Prospective, international, multicenter observational study (AspICU) including adult intensive care unit (ICU) patients, with a culture and/or direct examination and/or histopathological sample positive for Aspergillus spp. at any site.We compared clinical characteristics and outcome of IA in ICU patients using two different diagnostic algorithms. Elderly and nonelderly ICU patients with IA differed in a number of characteristics, including comorbidities, clinical features of the disease, mycology testing, and radiological findings. No difference regarding mortality was found. According to the clinical algorithm, elderly patients were more likely to be diagnosed with putative IA. Elderly patients had less diagnostic radiological findings and when these findings were present they were detected late in the disease course. The comparison between elderly survivors and nonsurvivors demonstrated differences in clinical characteristics of the disease, affected sites and supportive therapy needed. All patients who were diagnosed with proven IA died. Increased vigilance combined with active search for mycological laboratory evidence and radiological confirmation are necessary for the timely diagnosis of IA in the elderly patient subset. Although elderly state per se is not a particular risk factor formortality, a high SOFA score and the decision not to administer antifungal therapy may have an impact on survival of elderly patients. © The Author(s) 2017.

The biological activities and the structural arrangement of adevonin, a novel antimicrobial peptide, were investigated. The trypsin inhibitor ApTI, isolated from Adenanthera pavonina seeds, was used as a template for screening 18-amino acid peptides with predicted antimicrobial activity. Adevonin presented antimicrobial activity and minimum inhibitory concentrations (MIC) ranging from 1.86 to 7.35 µM against both Gram-positive and – negative bacterial strains. Moreover, adevonin exerted time-kill effects within 10 min and both susceptible and drug-resistant bacterial strains were affected by the peptide. In vitro and in vivo assays showed that, at MIC concentration, adevonin did not affect human fibroblasts (MRC-5) viability or Galleria mellonella survival, respectively. Hemolytic activity was observed only at high peptide concentrations. Additionally, nucleic acid efflux assays, gentian violet uptake and time-kill kinetics indicate that the antimicrobial activity of adevonin may be mediated by bacterial membrane damage. Furthermore, molecular dynamic simulation in the presence of SDS micelles and anionic membrane bilayers showed that adevonin acquired a stable α-helix secondary structure. Further studies are encouraged to better understand the mechanism of action of adevonin, as well as to investigate the anti-infective activity of this peptide.

Antimicrobial peptides (AMPs) have been widely isolated from most organisms in nature. This class of antimicrobials may undergo changes in their sequence for improved physicochemical properties, including charge, hydrophobicity, and hydrophobic moment. It is known that such properties may be directly associated with AMPs' structural arrangements and, consequently, could interfere in their modes of action against microorganisms. In this scenario, biophysical methodologies, such as nuclear magnetic resonance spectroscopy, X-ray crystallography, and cryo-electron microscopy, allied to in silico approaches, including molecular modeling, docking, and dynamics nowadays represent an enormous first step for the structural elucidation of AMPs, leading to further structure-function annotation. In this context, this chapter will focus on the main atomic-level experimental and computational tools used for the structural elucidation of AMPs that have assisted in the investigation of their functions.

Confluences with low discharge and momentum ratios, where narrow steep tributaries with high sediment load join a wide low-gradient main channel that provides the main discharge, are often observed in high mountain regions such as in the upper- Rhone river catchment in Switzerland. Few existing studies have examined the hydro-morphodynamics of this type of river confluence while considering sediment discharge in both confluent channels. This paper presents the evolution of the bed morphology and hydrodynamics as observed in an experimental facility with a movable bed. For that purpose, one experiment was carried out in a laboratory confluence with low discharge and momentum ratios, where constant sediment rates were supplied to both flumes. During the experiment, bed topography and water surface elevations were systematically recorded. When the bed topography reached a steady state (so-called equilibrium) and the outgoing sediment rate approximated the incoming rate, flow velocity was measured at 12 different points distributed throughout the confluence, and the grain size distribution of the bed surface was analyzed. Typical morphodynamic features of discordant confluences such as a bank-attached bar and a flow deflection zone are identified in this study. Nevertheless, the presence of a marked scour hole in the discordant confluence and distinct flow regimes for the tributary and main channel, differ from results obtained in previous studies. Strong acceleration of the flow along the outer bank of the main channel is responsible for the scour hole. This erosion is facilitated by the sediment discharge into the confluence from the main channel which inhibits bed armoring in this region. The supercritical flow regime observed in the tributary is the hydrodynamic response to the imposed sediment rate in the tributary. Copyright © 2015 John Wiley & Sons, Ltd.

Currently, one of the major global public health concerns is related to the transmission of dengue/yellow fever virus by the vector Aedes aegypti. The most abundant digestive enzymes in Ae. aegypti midgut larvae are trypsin and chymotrypsin. Since protease inhibitors have the capacity to bind to and inhibit the action of insect digestive proteinases, we investigated the short- and long-term effects of Adenanthera pavonina seed proteinase inhibitor (ApTI) on Ae. aegypti larvae, as well as a possible mechanism of adaptation. ApTI had a significant effect on Ae. aegypti larvae exposed to a non-lethal concentration of ApTI during short- and long-duration assays, decreasing survival, weight and proteinase activities of midgut extracts of larvae. The zymographic profile of ApTI demonstrated seven bands; three bands apparently have trypsin-like activity. Moreover, the peritrophic membrane was not disrupted. The enzymes of ApTI-fed larvae were found to be sensitive to ApTI and to have a normal feedback mechanism; also, the larval digestive enzymes were not able to degrade the inhibitor. In addition, ApTI delayed larval development time. Histological studies demonstrated a degeneration of the microvilli of the posterior midgut region epithelium cells, hypertrophy of the gastric caeca cells and an augmented ectoperitrophic space in larvae. Moreover, Ae. aegypti larvae were incapable of overcoming the negative effects of ApTI, indicating that this inhibitor might be used as a promising agent against Ae. aegypti. In addition, molecular modeling and molecular docking studies were also performed in order to construct three-dimensional theoretical models for ApTI, trypsin and chymotrypsin from Ae. aegypti, as well as to predict the possible interactions and affinity values for the complexes ApTI/trypsin and ApTI/chymotrypsin. In this context, this study broadens the base of our understanding about the modes of action of proteinase inhibitors in insects, as well as the way insects adapt to them.

Crop protection is the basis of plant production and food security. Additionally, there are many efforts focused on increasing defensive mechanisms in order to avoid the damaging effects of insects, which still represent significant losses worldwide. Plants have naturally evolved different mechanisms to discourage herbivory, including chemical barriers such as the induction of defensive proteins and secondary metabolites, some of which have a historical link with bio-farming practices and others that are yet to be used. In the context of global concern regarding health and environmental impacts, which has been translated into political action and restrictions on the use of synthetic pesticides, this review deals with a description of some historical commercial phytochemicals and promising proteinaceous compounds that plants may modulate to defeat insect attacks. We present a broader outlook on molecular structure and mechanisms of action while we discuss possible tools to achieve effective methods for the biological control of pests, either by the formulation of products or by the development of new plant varieties with enhanced chemical defenses.

In the present study, a new physically sound approach to experimentally obtain the contribution of each complex pier component to the ensemble scour depth is presented and illustrated. The ...

The accurate prediction of depth-averaged streamwise velocity, boundary shear stress and lateral shear stress are important requisites for the estimation of the flow depth associated with flood events in compound river channels composed of main channel and floodplain. This engineering problem may be tackled through the analytical solution of the depth-averaged momentum equation. Under uniform flow, this solution relies on the calibration of three descriptors of the bottom friction, secondary currents and lateral shear stress. In this paper, the analytical solution materialized in the Lateral Distribution Method is revisited through the consideration of a new panel division. Accurate measurements of streamwise and spanwise velocities as well as of boundary shear stress are used to obtain new predictors of the coefficients describing the effects of bottom friction, secondary currents and lateral shear. The new lateral division of the compound channel into four panels is physically based on the mixing layer width, which is computed by an iterative procedure easily implemented in practical applications.

The aim of the study was to analyze a series of Brazilian patients with Niemann-Pick disease type C (NP-C). Method Correlations between clinical findings, laboratory data, molecular findings and treatment response are presented. Result The sample consisted of 5 patients aged 8 to 26 years. Vertical supranuclear gaze palsy, cerebellar ataxia, dementia, dystonia and dysarthria were present in all cases. Filipin staining showed the “classical” pattern in two patients and a “variant” pattern in three patients. Molecular analysis found mutations in the NPC1 gene in all alleles. Miglustat treatment was administered to 4 patients. Conclusion Although filipin staining should be used to confirm the diagnosis, bone marrow sea-blue histiocytes often help to diagnosis of NP-C. The p.P1007A mutation seems to be correlated with the “variant” pattern in filipin staining. Miglustat treatment response seems to be correlated with the age at disease onset and disability scale score at diagnosis. O objetivo desse estudo foi analisar uma série de casos de pacientes brasileiros com doença de Niemann-Pick tipo C (NP-C). Método Correlação entre manifestações clínicas, alterações laboratoriais, estudo molecular e resposta ao tratamento foram realizadas. Resultado A amostra consiste de 5 pacientes com idade entre 8 e 26 anos. Paralisia do olhar vertical supranuclear, ataxia cerebelar, demência, distonia e disartria estavam presentes em todos os casos. Coloração de filipina na cultura de fibroblastos mostrou padrão “clássico” em dois pacientes e padrão “variante” em três casos. O estudo molecular encontrou mutações no gene NPC1 em todos os alelos. O tratamento com miglustate foi realizado em 4 pacientes. Conclusão Embora coloração de filipina seja utilizada para confirmar o diagnóstico, o histiócito azul-marinho no aspirado de medula óssea frequentemente auxilia a confirmar o diagnóstico de NP-C. A mutação p.P1007A está correlacionada com o padrão “ variante” na coloração de filipina. A resposta ao tratamento com miglustate parece estar correlacionada com a idade e escore de desabilidade no momento do diagnóstico.

The Indianmeal moth, Plodia interpunctella, is one of the most damaging pests of stored products. We investigated the insecticidal properties of ApKTI, a Kunitz trypsin inhibitor from Adenanthera pavonina seeds, against P. interpunctella larvae through bioassays with artificial diet. ApKTI-fed larvae showed reduction of up to 88% on larval weight and 75% in survival. Trypsin enzymes extracted from P. interpunctella larvae were inhibited by ApKTI, which also demonstrated capacity to bind to chitin. Kinetic studies revealed a non-competitive inhibition mechanism of ApKTI for trypsin, which were further corroborated by molecular docking studies. Furthermore, we have demonstrated that ApKTI exhibits a hydrophobic pocket near the reactive site loop probably involved in chitin interactions. Taken together, these data suggested that the insecticidal activity of ApKTI for P. interpunctella larvae involves a dual and promiscuous mechanisms biding to two completely different targets. Both processes might impair the P. interpunctella larval digestive process, leading to larvae death before reaching the pupal stage. Further studies are encouraged using ApKTI as a biotechnological tool to control insect pests in field conditions.

Biofilm-related infections represent an enormous clinical challenge nowadays. In this context, diverse studies are underway to develop effective antimicrobial agents targeting bacterial biofilms. Here, we describe the antibacterial and anti-biofilm activities of a short, cationic peptide named R5F5, obtained from sliding-window analysis based on a peptide (PcDBS1R5) derived from Plasmodium chabaudi. Ten fragments were generated (R5F1 to F10) and submitted to initial antibacterial assays against Pseudomonas aeruginosa. As a result, R5F5 showed the highest antimicrobial activity. We therefore carried out further antibacterial and anti-biofilm assays against P. aeruginosa and Klebsiella pneumoniae carbapenemase-producing bacterial strains. R5F5 revealed selective anti-biofilm activity, as the peptide inhibited >60% biofilm formation in all cases from 8 to 64 μg·mL−1. Moreover, R5F5 was not hemolytic against mice erythrocytes at 640 μg mL−1. Cytotoxic effects on human lung fibroblast cells were not detected at 160 μg·mL−1. Structural studies revealed that R5F5 presents random coil conformations in water and 50% 2,2,2-trifluoroethanol (TFE)/water (v/v), whereas amphipathic, extended conformations were observed in contact with sodium dodecyl sulfate (SDS) micelles. Thus, here we report a novel peptide with selective anti-biofilm activity against susceptible and resistant bacterial strains, with no toxicity toward mammalian cells and that adopts a stable structure in anionic environment.

The reported experimental study assesses the effects of flow non-uniformity on the momentum flux in straight compound channels. Two flumes were used, featuring vertical and sloping banks. Starting with uniform flow condition, various imbalances in the upstream discharge distribution were introduced. This resulted in a time-averaged lateral flow and advective transport of momentum, which interacted with the shear-layer turbulence generated by the compound geometry. To investigate this interaction, the three contributions to transverse momentum flux (depth-averaged flow, shear-layer turbulence and dispersive term of spanwise velocity) are assessed. The first two contributions were strengthened by the sloping banks, while the third becomes important for the case of the vertical bank. With a lateral flow towards the main channel, the first contribution rises at the expense of the second. With a lateral flow towards the floodplain, the first two contributions have the same order of magnitude, and the Boussines...

Gram-positive and -negative bacteria are dangerous pathogens that may cause human infection diseases, especially due to the increasingly high prevalence of antibiotic resistance, which is becoming one of the most alarming clinical problems. In the search for novel antimicrobial compounds, snake venoms represent a rich source for such compounds, which are produced by specialized glands in the snake's jawbone. Several venom compounds have been used for antimicrobial effects. Among them are phospholipases A2, which hydrolyze phospholipids and could act on bacterial cell surfaces. Moreover, metalloproteinases and L-amino acid oxidases, which represent important enzyme classes with antimicrobial properties, are investigated in this study. Finally, antimicrobial peptides from multiple classes are also found in snake venoms and will be mentioned. All these molecules have demonstrated an interesting alternative for controlling microorganisms that are resistant to conventional antibiotics, contributing in medicine due to their differential mechanisms of action and versatility. In this review, snake venom antimicrobial compounds will be focused on, including their enormous biotechnological applications for drug development.

An experimental campaign of 21 long-duration tests on scouring at complex piers of different configurations was performed to investigate the effect of pile cap thickness on the temporal evolution of the maximum scour depth and the development of equilibrium conditions. Two test series were performed with two significantly different pile cap thicknesses over a wide range of pile cap elevations with respect to the expected scour hole and the approach flow depth. In addition, the accuracy of existing methods to calculate the maximum scour depth was evaluated and discussed. The results show that, in general, the thicker the pile cap, the deeper the corresponding scour hole. The increase in scour depth that is attributable to the pile cap thickness depends on the distance between the pile cap and the original bed level. The observed maximum scour depth was greater with the thicker pile cap (with respect to the thinner pile cap) when it was entirely immerged into the flow, partially buried, or totally buried at a small depth from the initial bed level. Depending on the distance between the pile cap and initial bed level, the pile cap thickness may also influence the temporal evolution of the maximum scour depth by increasing or reducing the scouring rate. DOI: 10.1061/(ASCE)HY.1943-7900.0000704. © 2013 American Society of Civil Engineers.

Scientific Reports 6: Article number: 2138510.1038/srep21385; published online: February 26 2016; updated: July 20 2016 In this Article, there is a typographical error in the Results section. “Pa-MAP 1.9 (NH2-LAAKLTKAATKLTAALTKLAAALT-COOH) was designed …” should read: “Pa-MAP 1.9 (NH2-LAAKLTKAATKLTAALTKLAAALTAAAT-COOH) was designed …”

Made available in DSpace on 2018-12-11T17:01:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-02-26 Stingrays commonly cause human envenoming related accidents in populations of the sea, near rivers and lakes. Transcriptomic profiles have been used to elucidate components of animal venom, since they are capable of providing molecular information on the biology of the animal and could have biomedical applications. In this study, we elucidated the transcriptomic profile of the venom glands from two different freshwater stingray species that are endemic to the Paraná-Paraguay basin in Brazil, Potamotrygon amandae and Potamotrygon falkneri. Using RNA-Seq, we identified species-specific transcripts and overlapping proteins in the venom gland of both species. Among the transcripts related with envenoming, high abundance of hyaluronidases was observed in both species. In addition, we built three-dimensional homology models based on several venom transcripts identified. Our study represents a significant improvement in the information about the venoms employed by these two species and their molecular characteristics. Moreover, the information generated by our group helps in a better understanding of the biology of freshwater cartilaginous fishes and offers clues for the development of clinical treatments for stingray envenoming in Brazil and around the world. Finally, our results might have biomedical implications in developing treatments for complex diseases. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília Centro de Análises Proteômicas e Bioquímicas Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília Departamento de Ciências Fisiológicas Programa de Pós-Graduação em Biologia Animal Universidade de Brasília Programa de Pós-Graduação em Patologia Molecular Universidade de Brasília S-Inova Biotech Pós-graduação em Biotecnologia Universidade Católica Dom Bosco UNESP - Universidade Estadual Paulista Júlio de Mesquita Filho Campus Experimental de Registro UNESP - Universidade Estadual Paulista Júlio de Mesquita Filho Campus Experimental de Registro

Most studies on scouring seem to have overlooked the effect of viscosity, the assumption being that the flow is free of viscous effects inside the scour hole because of the presence of highly turbulent flow structures such as down-flow, horseshoe vortex, and wake vortices irrespective of the approach flow regime. The present work reports the results of experiments conceived to revisit the effect of viscosity on scouring. The experiments were performed by changing the Reynolds-like numbers for two flow shallowness values and keeping constant the remaining dimensionless parameters that control the scour process. The values of the Reynolds number corresponded to transitional approach flows. The experimental results indicate that scouring does depend on viscosity in usual laboratory conditions, the viscous effect leading to scour depths in the safety side

A Background Oriented Schlieren (BOS) experiment was designed to measure density gradients in a transparent medium. The BOS technique presented here consists on a comparison between a reference image of a dot matrix and another image of the same matrix behind the flow of a transparent gas. The presence of the flow induces changes in the refractive index, so the dots in the matrix appear displaced in the second image. The displacement of each dot is determined through a cross-correlation algorithm between both images. From the displacement, the changes in the refractive index can be determined, which in turn are related to the density by the Gladstone-Dale equation. In the experiment described in this paper, two different gases with known properties were used for the calibration.

© 2016 Published by Elsevier B.V., Recently, several peptides have been studied regarding the defence process against pathogenic microorganisms, which are able to act against different targets, with the purpose of developing novel bioactive compounds. The present work focuses on the structural and functional evaluation of the palindromic antimicrobial peptide Pa-MAP2, designed based on the peptide Pa-MAP from Pleuronectes americanus. For a better structural understanding, molecular modelling analyses were carried out, together with molecular dynamics and circular dichroism, in different media. Antibacterial activity against Gram-negative and positive bacteria was evaluated, as well as cytotoxicity against human erythrocytes, RAW 264.7, Vero and L6 cells. In silico docking experiments, lipid vesicle studies, and atomic force microscopy (AFM) imaging were carried out to explore the activity of the peptide. In vivo studies on infected mice were also done. The palindromic primary sequence favoured an α-helix structure that was pH dependent, only present on alkaline environment, with dynamic N- and C-terminals that are stabilized in anionic media. Pa-MAP2 only showed activity against Gram-negative bacteria, with a MIC of 3.2 μM, and without any cytotoxic effect. In silico, lipid vesicles and AFM studies confirm the preference for anionic lipids (POPG, POPS, DPPE, DPPG and LPS), with the positively charged lysine residues being essential for the initial electrostatic interaction. In vivo studies showed that Pa-MAP2 increases to 100% the survival rate of mice infected with Escherichia coli. Data here reported indicated that palindromic Pa-MAP2 could be an alternative candidate for use in therapeutics against Gram-negative bacterial infections., This work was supported by the Brazilian funding agencies CNPq, CAPES, FADPDF, FINEP and FUNDECT, by Fundação para a Ciência e a Tecnologia — Ministério da Ciência, Tecnologia e Ensino Superior (FCT-MCTES, Portugal), and by Marie Skłodowska-Curie Research and Innovation Staff Exchange (MSCA-RISE, European Union) project INPACT (call H2020-MSCA-RISE-2014, grant agreement 644167). MRF also acknowledges FCT-MCTES fellowship SPRH/BD/100517/2014.

5 pages, 3 figures, 1 table, This technical note focuses on the plan geometry of riprap mattresses to protect spill-through abutments against local scour through edge failure. Two non-standard riprap apron geometries are experimentally studied. The performance of the new geometries is evaluated by comparing it with that of the standard design in terms of apron width and total riprap volume needed to guarantee stability. For comparatively short abutments, it is demonstrated that one of the new proposed geometries allows reductions between 15% and 25% in the total riprap volume without any increase in both design complexity and building difficulty, G. Simarro was supported by the Spanish Government through the Ramón y Cajal program. The authors thank Eduardo Diaz for his help in preparing the experiments

An experimental investigation of riprap stability at spill-through abutments has been carried out in two similar horizontal-bed flumes, avoiding riprap failure modes other than shear failure and erosion failure. Tests were conducted for two common abutment side slopes, sub-critical flow regime, short to intermediate abutment lengths and high bed roughness. The aim of the experiments was to determine the size of stone riprap necessary to resist (a) shear failure in aprons placed at the base of spill-through abutments, and (b) erosion failure over their side slopes. Results are compared with predictions of stone riprap size given by expressions found in the literature. The predictor of Pagán–Ortiz is confirmed as being appropriate for shear failure at abutment aprons and can be adapted to account for erosion failure over abutment side slopes. Alternatively, two new expressions, written in terms of the (critical) approach flow intensity required to make the riprap stones move, are suggested.

The main objective of this study was the definition of a predictor of time to equilibrium on the basis of experimental evidence. The study used the results of an important number of long-lasting experiments, run under clear-water flow conditions for large abutment lengths. These experiments have already been reported by the present authors in recently published papers. It is concluded that time to equilibrium scour at thin vertical-wall abutments, protruding at right angles from the side wall of fully developed, uniform flows in wide rectangular channels on flat bed of uniform non-ripple forming sand depends mostly on the relative abutment length. It can also be concluded that time to equilibrium may be rather large in the field.

This paper presents the comparison between numerical results obtained with a conceptual model proposed in a companion paper and experimental results collected from previous studies. The numerical model is based on a finite difference approximation using the MacCormack scheme with a total variation diminishing high-resolution correction term for the mixture mass and momentum conservation equations and an artificial viscosity term for the sediment mass conservation equation. From the comparison between numerical and experimental results, it can be verified that the model generally gives results in good agreement with the experimental data and the wave structure is in accordance with what has been reported in previous studies. The estimation of model parameters based on existing sheet-flow data seems a promising way of developing models without arbitrary choice of values for tuning parameters. Some limitations can be identified, namely the equilibrium sediment transport approach implies that the model cannot simulate the hydraulic jump formed in the higher mobility bed for dry bed conditions. The use of a constant friction factor does not allow simulating the exact wave-front location for all instants in time.

The present study aims at understanding the changes in the channel conveyance and in the turbulent flow structure due to the presence of both submerged vegetation in the floodplains and riparian vegetation. An experimental campaign was carried out comprising uniform compound channels flows (i) without any kind of vegetation, (ii) with synthetic grass in the floodplains, (iii) with synthetic grass in the floodplains and rods in the interface between main channel and the floodplain and (iv) with synthetic grass in the floodplains and artificial shrubs in the interface between main channel and the floodplain. For comparison, the water depth in all flow cases was kept constant. Accurate acoustic Doppler velocimetry was used to evaluate the 3d velocity field and the turbulence structures characteristics.

This experimental study focuses the influence of bed material mobility and initial downstream water level on maximum water level and time to peak of dam-break waves. It covers horizontal bed conditions on fixed bed, sand bed, and pumice bed. Results include water surface level time evolution, maxima wave levels and time to peak. The influence of bed material mobility and downstream water level was identified and characterized, stressing the importance of using mathematical models with appropriate sediment transport formulations instead of purely hydrodynamic models to simulate dam-break waves on mobile bed channels.

Mathematical modelling of river processes is, nowadays, a key element in river engineering and planning. River modelling tools should rest on conceptual models drawn from mechanics of sediment transport, river mechanics, and river hydrodynamics. The objectives of the present work are (i) to describe conceptual models of sediment transport, deduced from grain-scale mechanics of sediment transport and turbulent flow hydrodynamics, and (ii) to present solutions to specific river morphology problems. The conceptual models described are applicable to the morphologic evolution of rivers subjected to the transport of poorly sorted sediment mixtures at low shear stresses and to geomorphic flows featuring intense sediment transport at high shear stresses. In common, these applications share the fact that sediment transport and flow resistance depend, essentially, on grain-scale phenomena. The idealized flow structures are presented and discussed. Numerical solutions for equilibrium and nonequilibrium sediment transport are presented and compared with laboratory and field data.

This study addresses the design of riprap mattresses as a scour countermeasure near vertical-wall bridge abutments under clear water flow conditions. It specifically deals with the diameter of riprap, Dr50, the lateral extent of mattresses, w, and their thickness, t. Experiments were performed in a rectangular, sand-bed open channel using different abutment lengths, three riprap stone sizes, and two different sands. The minimum size of stable stones as well as the mattress dimensions depend on the ratio between the abutment length and the flow depth. New equations for the evaluation of Dr50 and w are suggested. The geometric properties of the scour holes which develop at the edge of riprap mattresses are similar to those reported in the literature for spill-through abutments. Although it is not possible to fully arrest scour by winnowing, the corresponding scour depth is negligible when the mattress layer thickness is at least 6Dr50.

Results are presented and discussed from two laboratory experimental campaigns specifically designed to investigate the behavior of a slot as countermeasure against local scouring at a smooth circular bridge pier, close to threshold flow conditions of initiation of uniform sediment motion. The investigation was aimed at evaluating the effectiveness of the slot by changing its sinking depth into a sand bed, and assessing the dependence of the scour depth on different dimensionless groups. The results showed that the slot reduces the local scour at pier. The maximum reduction of the scour depth was about 30% (about 70% for both scour area and volume) in the best configurations. A combined countermeasure is also proposed and tested, consisting of a slot and a bed sill placed downstream of the pier and adjacent to it: in the best configuration, the scour reduction in front of the pier reached about 45% on average (with about 80 and 90% for scour area and volume, respectively). This last result shows that a combination of slot and bed sill may be a very effective countermeasure against local scouring at bridge piers.

Results are presented from laboratory experiments to investigate the effectiveness of bed sills as countermeasures against local scouring at a smooth circular bridge pier, for flow conditions near the threshold of uniform sediment motion. The bed sill was located downstream of the pier, and its effectiveness with the distance between pier and sill was evaluated. The dependence of the scour depth on different dimensionless groups was defined. The results showed that a bed sill placed at a short distance downstream of the pier reduces the scour depth, area, and volume. In particular, the smaller the distance between the two structures, the larger the effectiveness of the countermeasure. The bed sill seems to take effect some time after the beginning of the test, as the scour hole downstream of the bridge pier develops sufficiently and interacts with the countermeasure.

Technical note discusses a detailed approach to dimensional analysis for the bridge pier scour phenomenon and the introduction of flow intensity. It demonstrates the dependence of critical upstream velocity on the rest of the parameters describing the process and its implications on dimensional analysis. Assuming that the viscous effects are negligible in the local scour phenomenon, it is concluded that the flow intensity of the approaching undisturbed flow is not an adequate parameter to describe the process in usual laboratory conditions. A new proposal is established.

Bacteria predominantly exist as multicellular aggregates known as biofilms that are associated with at least two thirds of all infections and exhibit increased adaptive resistance to conventional antibiotic therapies. Therefore, biofilms are major contributors to the global health problem of antibiotic resistance, and novel approaches to counter them are urgently needed. Small molecules of the innate immune system called host defense peptides (HDPs) have emerged as promising templates for the design of potent, broad-spectrum antibiofilm agents. Here, we review recent developments in the new field of synthetic antibiofilm peptides, including mechanistic insights, synergistic interactions with available antibiotics, and their potential as novel antimicrobials against persistent infections caused by biofilms. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.

The accurate prediction of flood levels and velocities is a prerequisite to any appropriate management of river valleys, where the mitigation of environmental, economic or human losses caused by flood events is of paramount importance. During these events, rivers frequently acquire a compound channel configuration. Due to the 3D nature of compound channel flows, the stage–discharge curves are not as easily predicted as in single channels. Despite the availability of 2D and 3D flow models that may solve this question, 1D methods are often preferred due to the reduced data required and to the much shorter processing time. In the last five decades, important research efforts have been devoted to the improvement of 1D predictors of stage–discharge curves in compound channels. In this study, the accuracy of seven of those methods is assessed by comparing their predictions with a large experimental dataset, comprising symmetrical and asymmetrical compound channels with vertical and inclined main channel sidewalls, and smooth and rough floodplains. To the authors’ best knowledge, this is the most comprehensive assessment of stage–discharge predictors for straight compound channels since it involves the highest number of predictors applied to the widest data set. It was concluded that the methods that account for the momentum transfer between the main channel and the floodplains display considerably better results than the traditional methods. For relative depth (ratio between floodplain and main channel flow depths) higher than 0.25, predicted discharges for the methods that account for the turbulent momentum exchange are within 5% of observed values. Depending on whether the flow depth or the flow discharge is the pertinent variable, two different methods seem to be the most appropriate to produce precise and safe predictions. 62-67pp Volume 45 DHA/NRE Flow Measurement and Instrumentation

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4, Due to the growing concern about antibiotic-resistant microbial infections, increasing support has been given to new drug discovery programs. A promising alternative to counter bacterial infections includes the antimicrobial peptides (AMPs), which have emerged as model molecules for rational design strategies. Here we focused on the study of Pa-MAP 1.9, a rationally designed AMP derived from the polar fish Pleuronectes americanus. Pa-MAP 1.9 was active against Gram-negative planktonic bacteria and biofilms, without being cytotoxic to mammalian cells. By using AFM, leakage assays, CD spectroscopy and in silico tools, we found that Pa-MAP 1.9 may be acting both on intracellular targets and on the bacterial surface, also being more efficient at interacting with anionic LUVs mimicking Gram-negative bacterial surface, where this peptide adopts α-helical conformations, than cholesterolenriched LUVs mimicking mammalian cells. Thus, as bacteria present varied physiological features that favor antibiotic-resistance, Pa-MAP 1.9 could be a promising candidate in the development of tools against infections caused by pathogenic bacteria., Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number R21AI098701, and by a grant from the Canadian Institutes. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. R.E.W.H. holds a Canada Research Chair in Health and Genomics. C.D.L.F.-N. received a scholarship from the Fundación “la Caixa” and Fundación Canadá (Spain), and currently holds a postdoctoral scholarship from Fundación Ramón Areces (Spain). This work was also supported by Fundaçao para a Ciencia e a Tecnologia–Ministério da Educaçao e Ciencia (FCT-MEC, Portugal), including the fellowship SPRH/BD/100517/2014 to M.R.F., and by Marie Skłodowska-Curie Research and Innovation Staff Exchange (MSCA-RISE, European Union) project INPACT (call H2020-MSCA-RISE-2014, grant agreement 644167). M.H.C., L.M. and O.L.F. acknowledge funding from CNPq, CAPES, FUNDECT and FAPDF.

There has been an increasing acknowledgement of debris flows as one of the most relevant geomorphic modifiers of many steepland valleys and fans. Despite it being a well-known phenomenon, debris flows are somehow unpredictable and complex to simulate. Due to several past harmful debris flows worldwide, there are already a significant number of mitigation structures with water and sediment control functions, which are essential features of short-term countermeasures against debris flows. This paper is based on laboratory experiments carried out to test slit dams (open-type retention dams), usually used as a structural countermeasure to mitigate debris flows in steep torrential channels. Flume tests were conducted using a straight channel to assess the influence of different slit-dam solution types on the sediment retention efficiency against stony-type debris flows. Inspired by common slit dam solutions, two different piers layouts in plan view were tested. The experiments were performed with two different discharges and two different slopes. Experimental results about the sediment control efficiency are presented for the different tested solutions.

This work is concerned with the role that friction and inertia effects can play on the magnitude of dam-break wave-front celerity. Classic analytical solutions are presented. A large collection of experimental data is used, covering a wide range of different initial conditions: fixed bed or mobile bed (five types of bed material), dry or wet bed downstream, and with or without bed step. To overcome the limitations of analytical solutions, a numerical model is used. The model is based on the shallow-water approach with contact-load dominated sediment transport, and it makes use of developments recently made in the study of sheet flows. The analytical and numerical results are compared with experimental data. It was found that the celerity is mainly dictated by the friction coefficient, by the sediment inertia, by the initial downstream water depth, and by the initial bed step height. For good data fitting, the friction coefficient must be influenced by the type of bed, fixed or mobile. In the latter, the coefficient must vary with the bed material characteristics. The dissimilarities between the experimental, analytical, and numerical results are interpreted.

Na12Ge17 is prepared from the elements at 1025 K in sealed niobium ampoules. The crystal structure reinvestigation reveals a doubling of the unit cell (space group:P21/c; a = 22.117(3)A, b = 12.803(3)A, c = 41.557(6)A, β = 91.31(2)°, Z = 16; Pearson code: mP464), furthermore, weak superstructure reflections indicate an even larger C-centred monoclinic cell. The characteristic structural units are the isolated cluster anions [Ge9]4— and [Ge4]4— in ratio 1:2, respectively. The crystal structure represents a hierarchical cluster replacement structure of the hexagonal Laves phase MgZn2 in which the Mg and Zn atoms are replaced by the Ge9 and Ge4 units, respectively. The Raman spectrum of Na12Ge17 exhibits the characteristic breathing modes of the constituent cluster anions at ν = 274 cm—1 ([Ge9]4—) and ν = 222 cm—1 ([Ge4]4—) which may be used for identification of these clusters in solid phases and in solutions. Raman spectra further prove that Na12Ge17 is partial soluble both in ethylenediamine and liquid ammonia. The solution and the solid extract contain solely [Ge9]4—. The remaining insoluble residue is Na4Ge4. By heating the solvate Na4Ge9(NH3)n releases NH3 and decomposes irreversibly at 742 K, yielding Na12Ge17 and Ge. Na12Ge17: Eine Verbindung mit den Zintl-Anionen [Ge4]4— und [Ge9]4—: Darstellung, Kristallstruktur und Ramanspektrum Na12Ge17 wurde durch direkte Umsetzung der Elemente in verschweisten Nb-Ampullen bei 1025 K synthetisiert. Die erneute Bestimmung der Kristallstruktur ergab eine Verdopplung der Elementarzelle (Raumgruppe P21/c, a = 22.117(3)A, b = 12.803(3)A, c = 41.557(6)A, β = 91.31(2)°, Z = 16; Pearsonsymbol: mP464), jedoch zeigen schwache Uberstrukturreflexe eine noch grosere C-zentrierte monokline Elementarzelle an. Die charakteristischen Strukturelemente sind isolierte Clusteranionen [Ge9]4— und [Ge4]4— im Molverhaltnis 1:2. Die Kristallstruktur ist eine hierarchische Cluster-Ersetzungs-Struktur der hexagonalen Laves-Phase MgZn2, in welcher die Mg- bzw. Zn-Atome durch die Cluster [Ge9]4— bzw. [Ge4]4— ersetzt sind. Das Ramanspektrum von Na12Ge17 zeigt die charakteristischen Pulsationsfrequenzen der Clusteranionen bei ν = 274 cm—1 ([Ge9]4—) und ν = 222 cm—1 ([Ge4]4—), die also zur Identifizierung dieser Einheiten in fester Phasen und Losungen verwendet werden konnen. Ferner beweisen die Ramanspektren, dass Na12Ge17 sowohl in Ethylendiamin als auch in flussigem Ammoniak partiell loslich ist. Die Losung und das Feststoffextrakt enthalten ausschlieslich [Ge9]4—, wahrend der unlosliche Ruckstand nur aus Na4Ge4 besteht. Bei Erhitzen von Na4Ge9(NH3)n wird NH3 abgespalten und die Verbindung zersetzt sich bei 742 K zu Na12Ge17 und Ge.

BY PEDRO J.M. MORETA and JUAN PEDRO MARTIN-VIDE, Journal of Hydraulic Research Vol. 48, No. 2 (2010), pp. 169–177 The discussers congratulate the authors for their valuable study of the apparent sh...

River widening is commonly used as a solution for the rehabilitation of rivers with the main purposes of allowing the river to adjust to its natural dynamics and to improve riparian and instream habitat for flora and fauna, by increasing the heterogeneity in substrate, flow and morphology. Local widening may also be used for confluences rehabilitation as, for many of them, the heterogeneity and fragmentation of the river system were severely affected by previous human interventions. Local tributary widening amplifies the morphodynamic processes, enhancing the diversity in sediment substrate, flow velocities and flow depths. In addition, widening should neither affect aspects such as water level in the tributary nor in the main channel, which is an important consideration for flood safety. The aim of this paper is to analyze the differences in terms of bed morphology and flow dynamics induced by different confluence angles in widen channel confluences.

A previsão rigorosa da profundidade de cavidades de erosão associadas a pilares complexos, utilizados como apoio de tabuleiros de pontes, pode não ser garantida pela utilização dos métodos actualmente existentes. De entre esses métodos, destacam-se os de Auckland, o HEC-18 e o do FDOT. Neste artigo, analisa-se o respetivo desempenho comparando as previsões que fornecem com conjuntos de dados obtidos em laboratório para seis modelos de pilares, cinco dos quais publicados em literatura da especialidade. A esses dados, adicionaram-se os de ensaios conduzidos no LNEC para um modelo de pilar de dimensões mais próximas de dimensões reais do que as dos outros pilares estudados. Os três modelos de cálculo apresentam desvios de previsão em relação às medições que dependem da posição do maciço de encabeçamento relativamente ao nível inicial do leito; em geral, os maiores desvios ocorrem quando o maciço se encontra parcialmente enterrado. Em face dos resultados da análise dos desvios, conclui-se que o modelo FDOT é aquele a que está associada uma menor probabilidade de previsões por defeito, ou seja, aquele que produz previsões seguras para uma maior percentagem de situações que podem ocorrer na prática da engenharia. 5-22 DOI:10.5894/rh35n1-1 Volume 35, Nº 1 DHA/NRE Revista Recursos Hídricos

Plant immune responses involve a wide diversity of physiological reactions that are induced by the recognition of pathogens, such as hypersensitive responses, cell wall modifications, and the synthesis of antimicrobial molecules including antimicrobial peptides (AMPs). These proteinaceous molecules have been widely studied, presenting peculiar characteristics such as conserved domains and a conserved disulfide bond pattern. Currently, many AMP classes with diverse modes of action are known, having been isolated from a large number of organisms. Plant AMPs comprise an interesting source of studies nowadays, and among these there are reports of different classes, including defensins, albumins, cyclotides, snakins and several others. These peptides have been widely used in works that pursue human disease control, including nosocomial infections, as well as for agricultural purposes. In this context, this review will focus on the relevance of the structural-function relations of AMPs derived from plants and their proper use in applications for human health and agribusiness.