Novel microbicidal agents derived from Naja atra cardiotoxin 1 (CTX-1)

During my PhD course, I focused my research on antimicrobial peptides (AMPs), in particular on the aspects of their computational design and development. This work led to the development of a new family of AMPs that I designed, starting from the amino acid sequence of a snake venom toxin, the cardiotoxin 1 (CTX-1) of Naja atra. Naja atra atra cardiotoxin 1, produced by Chinese cobra snakes belonging to Elapidae family, is included in the three-finger toxin family and exerts high cytotoxicity and antimicrobial activity too. This toxin family is characterized by specific folding of three beta-sheet loops (“fingers”) extending from the central core and by four conserved disulfide bridges. Using as template the first loop of this toxin, different sequences of 20 amino acids linear cationic peptides have been designed in order to avoid toxic effects but to maintain and strengthen the antimicrobial activity. As a result, the sequence NCP-0 (Naja Cardiotoxin Peptide-0) was designed as ancestor and subsequently other 4 variant sequences of NCP0 were developed. These variant sequences have shown microbicidal activity towards a panel of reference strains of Gram-positive and Gram-negative bacteria, fungi and an enveloped virus. In particular, the sequence designed as NCP-3 (Naja Cardiotoxin Peptide-3) and its variants NCP-3a and NCP-3b have shown the best antimicrobial activity together with low cytotoxicity against eukaryotic cells and low hemolytic activity. Bactericidal activity has been demonstrated by minimum bactericidal concentration (MBC) assay at values below 10 μg/ml for Pseudomonas aeruginosa ATCC 27853, Acinetobacter baumannii ( clinical isolates), Moraxella catharralis ATCC 25238, MRSA ATCC 43400, while towards Staphylococcus aureus ATCC 25923, Enterococcus hirae ATCC 10541 and Streptococcus agalactiae ATCC 13813 the bactericidal activity was demonstrated even below 1.6 μg/ml concentration. This potent antimicrobial activity was confirmed even for unicellular fungi Candida albicans, Candida glabrata and Malassezia pachydermatis (MBC 32.26-6.4 μg/ml), and also against the fast-growing mycobacteria Mycobacterium smegmatis DSMZ 43756 and Mycobacterium fortuitum DSMZ 46621 (MBC 100 μg/ml). Moreover, NCP-3 has shown a virucidal activity on the enveloped virus Bovine Herpesvirus 1 (BoHV1) belonging to herpesviridae family. The bactericidal activity is maintained in a high salt concentration (125 and 250 mM NaCl) medium and PB +20% Mueller Hinton Medium for E. coli, MRSA and Pseudomonas aeruginosa reference strains. Considering these in vitro obtained data, we propose NCP-3 and its variants NCP-3a and NCP-3b as promising antimicrobial candidates. For this reason, the whole novel AMPs family has been protected by a national patent (n°102015000015951).

Emprego do ultra-som modo B e com efeito Doppler, termômetro infravermelho e medidas antropométricas na avaliação de uma formulação cosmética anticelulítica contendo extrato hidroglicólico de Trichilia catigua e Ptychopetalum olacoides Bentham

Hidrolipodistrofia ginóide (H.L.D.G.), a celulite, é comumente tratada com cosméticos contendo extratos vegetais. O estudo realizado foi: ultra-sonografia na avaliação da espessura da hipoderme e a microcirculação cutânea; uso de termômetro infravermelho na medida da temperatura e análise das medidas antropométricas da uma formulação cosmética anticelulítica contendo extrato hidroglicólico de Trichilia catigua e Ptychopetalum olacoides Bentham (catuaba e marapuama). Foram realizadas medidas iniciais e após aplicação da formulação. Os resultados apresentaram alterações estatisticamente significativas para a temperatura cutânea e medidas antropométricas. Não houve diferenças estatisticamente significativas nas medidas da hipoderme e microcirculação. Considerando os resultados, a formulação avaliada possui potencial ação coadjuvante na redução da hidrolipodistrofia ginóide. As técnicas podem ser associadas em conjunto com a avaliação sensorial e apreciabilidade cosmética. Os requisitos chaves para a reprodutibilidade das técnicas incluem ambiente controlado, monitoramento e climatização dos voluntários, procedimentos de medidas padronizados, protocolos de aplicação realístico e operadores qualificados.

O elemento finito T6-3i na análise de placas e dinâmica de cascas.

O método dos elementos finitos é o método numérico mais difundido na análise de estruturas. Ao longo das últimas décadas foram formulados inúmeros elementos finitos para análise de cascas e placas. As formulações de elementos finitos lidam bem com o campo de deslocamentos, mas geralmente faltam testes que possam validar os resultados obtidos para o campo das tensões. Este trabalho analisa o elemento finito T6-3i, um elemento finito triangular de seis nós proposto dentro de uma formulação geometricamente exata, em relação aos seus resultados de tensões, comparando-os com as teorias analíticas de placas, resultados de tabelas para o cálculo de momentos em placas retangulares e do ANSYSr, um software comercial para análise estrutural, mostrando que o T6-3i pode apresentar resultados insatisfatórios. Na segunda parte deste trabalho, as potencialidades do T6-3i são expandidas, sendo proposta uma formulação dinâmica para análise não linear de cascas. Utiliza-se um modelo Lagrangiano atualizado e a forma fraca é obtida do Teorema dos Trabalhos Virtuais. São feitas simulações numéricas da deformação de domos finos que apresentam vários snap-throughs e snap-backs, incluindo domos com vincos curvos, mostrando a robustez, simplicidade e versatilidade do elemento na sua formulação e na geração das malhas não estruturadas necessárias para as simulações.

Strength of the Iberian intraplate lithosphere: Cenozoic deformations and seismicity

Previous studies about the strength of the lithosphere in the center of Iberia fail to resolve the depth of earthquakes because of the rheological uncertainties. Therefore, new contributions are considered (the crustal structure from a density model) and several parameters (tectonic regime, mantle rheology, strain rate) are checked in this paper to properly examine the role of lithospheric strength in the intraplate seismicity and the Cenozoic evolution. The strength distribution with depth, the integrated strength, the effective elastic thickness and the seismogenic thickness have been calculated by a finite element modelling of the lithosphere across the Central System mountain range and the bordering Duero and Madrid sedimentary basins. Only a dry mantle under strike-slip/extension and a strain rate of 10-15 s-1, or under extension and 10-16 s-1, causes a strong lithosphere. The integrated strength and the elastic thickness are lower in the mountain chain than in the basins. This heterogeneity has been maintained since the Cenozoic and determine the mountain uplift and the biharmonic folding of the Iberian lithosphere during the Alpine deformations. The seismogenic thickness bounds the seismic activity in the upper–middle crust, and the decreasing crustal strength from the Duero Basin towards the Madrid Basin is related to a parallel increase in Plio–Quaternary deformations and seismicity. However, elasto–plastic modelling shows that current African–Eurasian convergence is resolved elastically or ductilely, which accounts for the low seismicity recorded in this region.

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics

Background: Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results: Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions: Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.

Paleogene-Aquitanian Tectonic Breakup in the Eastern External Betic Zone (Alicante, SE Spain)

Six Paleogene-Aquitanian successions have been reconstructed in the Alicante area (eastern External Betic Zone). The lithofacies association evidences “catastrophic” syn-sedimentary tectonic processes consisting of slumps, mega-olisthostromes, “pillow-beds” and turbiditic deposits. This kind of sedimentation is related to unconformity surfaces delimiting sequence and para-sequence cycles in the stratigraphic record. The data compiled have enabled the reconstruction of the Paleogene-Aquitanian paleogeographic and geodynamic evolution of this sector of the External Betics. During the Eocene the sedimentary basin is interpreted as a narrow trough affected by (growth) folding related to blind thrust faulting with a source area from the north-western margin, while the southeastern margin remained inactive. During the Oligocene-Aquitanian, the sourcing margin becames the southeastern margin of the basin affected by a catastrophic tectonic. The activity of the margins is identified from specific sediment source areas for the platform-slope-trough system and from tectofacies analysis. The southeastern South Iberian Margin is thought to be closer to the Internal Betic Zone, which was tectonically pushing towards the South Iberian Margin. This pushing could generate a lateral progressive elimination of subbetic paleogeographic domains in the eastern Betics. This geodynamic frame could explain the development of such “catastrophic” tectono-sedimentary processes during the Late Oligocene-Early Miocene.

A Unique Prestressed Concrete Pedestrian Bridge in Spain

This paper describes the so-called Kiss Bridge. This structure resembles a kiss, a subtle touch of structures. The beams have been structurally designed to adapt the Japanese art of paper folding called "origami." The material used for constructing the floating beams is white reinforced concrete in the form of folded shells. The two geometrically different parts have distinct structural behaviors. The length of the main pathway of both structures is over 60 m. The pedestrian bridge crosses an artificial rainwater channel with a skew of 45° with respect to the referred channel. The joint between the cantilever structure and the Y-shaped one is located over the middle of the channel. Each stretch has different transversal sections. The pedestrian bridge is made with prestressed self-compacting reinforced concrete of 60 MPa. The foundation is shallow, comprising footings and footing beams made of 25 MPa conventional concrete. The cantilever structure with its foundations is designed as a semi-integral bridge whereas the Y-shaped one is an integral structure. The dynamic behavior of the structure was carefully studied to ensure that the dynamic loads generated by pedestrians do not cause excessive vibrations, especially to the cantilever structure, which could present dynamic interactions with the pedestrians walking. The bridge was recognized, in the 2014 edition of the fib Awards for Outstanding Concrete Structures, for having made a valuable contribution to the image and promotion of concrete structures.

Convergence analysis and validation of low cost distance metrics for computational cost reduction of the Iterative Closest Point algorithm

The Iterative Closest Point algorithm (ICP) is commonly used in engineering applications to solve the rigid registration problem of partially overlapped point sets which are pre-aligned with a coarse estimate of their relative positions. This iterative algorithm is applied in many areas such as the medicine for volumetric reconstruction of tomography data, in robotics to reconstruct surfaces or scenes using range sensor information, in industrial systems for quality control of manufactured objects or even in biology to study the structure and folding of proteins. One of the algorithm’s main problems is its high computational complexity (quadratic in the number of points with the non-optimized original variant) in a context where high density point sets, acquired by high resolution scanners, are processed. Many variants have been proposed in the literature whose goal is the performance improvement either by reducing the number of points or the required iterations or even enhancing the complexity of the most expensive phase: the closest neighbor search. In spite of decreasing its complexity, some of the variants tend to have a negative impact on the final registration precision or the convergence domain thus limiting the possible application scenarios. The goal of this work is the improvement of the algorithm’s computational cost so that a wider range of computationally demanding problems from among the ones described before can be addressed. For that purpose, an experimental and mathematical convergence analysis and validation of point-to-point distance metrics has been performed taking into account those distances with lower computational cost than the Euclidean one, which is used as the de facto standard for the algorithm’s implementations in the literature. In that analysis, the functioning of the algorithm in diverse topological spaces, characterized by different metrics, has been studied to check the convergence, efficacy and cost of the method in order to determine the one which offers the best results. Given that the distance calculation represents a significant part of the whole set of computations performed by the algorithm, it is expected that any reduction of that operation affects significantly and positively the overall performance of the method. As a result, a performance improvement has been achieved by the application of those reduced cost metrics whose quality in terms of convergence and error has been analyzed and validated experimentally as comparable with respect to the Euclidean distance using a heterogeneous set of objects, scenarios and initial situations.

El sueño de un barrio y la problemática del ensanche: la obra inconclusa de Benalúa de Alicante (1883-1896)

El presente artículo describe la construcción de Benalúa, según proyecto del arquitecto José Guardiola Picó (1883), una de las áreas más singulares de la ciudad de Alicante -España-. Se realiza una exposición cronológica desde su concepción, documentando las tramitaciones legales que conllevaron su aprobación, hasta el cese en sus funciones de la Sociedad Anónima Los Diez Amigos, promotora y constructora del barrio (1896), sin finalizar con éxito el proyecto emprendido. Del estudio se concluyen tanto los aspectos más relevantes que caracterizaron el desarrollo de las obras del barrio como las causas que propiciaron el abandono de la Sociedad, siendo éstas exclusivamente económicas, con especial interés en la problemática que llegó a generar el proyecto y ejecución del Ensanche de Alicante.

Memorandum of contract with carpenters, Moore, and others, [ca. 1814]

Estimate for $5942.68 for the completion of the interior fixtures of University Hall including folding doors, pew arrangement in the chapel, and architraves to doors, windows, and fireplaces.

Structural evolution of the Lesser Himalayan fold-thrust belt of west central Nepal

The Lesser Himalayan fold-thrust belt on the south flank of the Jajarkot klippe in west central Nepal was mapped in detail between the Main Central thrust in the north and the Main Boundary thrust in the south. South of the Jajarkot klippe, the fold-thrust belt involves sandstone, shale and carbonate rocks that are unmetamorphosed in the foreland and increase in metamorphic grade with higher structural position to sub-greenschist facies towards the hinterland. The exposed stratigraphy is correlative with the Proterozoic Ranimata, Sangram, Galyang, Syangia Formations and Lakharpata Group of Western Nepal and overlain by the Paleozoic Tansen and Kali Gandaki Groups. Based on field mapping and cross-section construction, three distinct thrust sheets were identified separated by top-to-the-south thrust faults. From the foreland (south) to the hinterland (north), the first thrust sheet in the immediate hanging wall of the Main Boundary thrust defines an open syncline. The second thrust sheet contains a very broad synformal duplex, which is structurally stacked against the third thrust sheet containing a homoclinal panel of the oldest exposed Proterozoic stratigraphy. Outcrop scale folds throughout the study area are predominantly south vergent, open, and asymmetric reflecting the larger regional scale folding style, which corroborate the top-to-the-south deformation style seen in the faults of the region. Field techniques were complemented with microstructural and quartz crystallographic c-axis preferred orientation analyses using a petrographic microscope and a fabric analyzer, respectively. Microstructural analysis identified abundant strain-induced recrystallization textures and occasional occurrences of top-to-the-south shear-sense indicators primarily in the hinterland rocks in the immediate footwall of the Main Central Thrust. Top-to-the-south shearing is also supported by quartz crystallographic c-axis preferred orientations. Quartz recrystallization textures indicate an increase in deformation temperature towards the Main Central thrust. A line balance estimate indicates that approximately 15 km of crustal shortening was accommodated by folding and faulting in the fold-thrust belt south of the Jajarkot klippe. Additionally, estimations of shortening velocity suggest that the shortening velocity operating in this section of the fold-thrust belt between 23 to 14 Ma was slower than what is currently observed as a result of the ongoing deformation of the Sub-Himalayan fold-thrust belt.

Calcium carbonate, total and organic carbon and accumulation rate characteristics at DSDP Leg 78A Holes

Bulk sediment accumulation rates and carbonate and carbonate-free accumulation rates corrected for tectonic tilting have been calculated for Leg 78A sediments. These rates are uniformly low, ranging from 0.1 to 6.8 g/(cm**2 x 10**3 yr.), reflecting the pelagic-hemipelagic nature of all the sediments drilled in the northern Lesser Antilles forearc. Rates calculated for Sites 541 and 542 [0.6-6.8 g/(cm**2 x 10**3 yr.)], located on the lower slope of the accretionary prism, are significantly greater than the Neogene rates calculated for oceanic reference Site 543 [0.1-2.4 g/(cm**2 x 10**3)]. This difference could be the result of (1) tectonic thickening of accretionary prism sediments due to folding, small-scale faulting, and layer-parallel shortening; (2) deposition in shallower water farther above the CCD (carbonate compensation depth) resulting in preservation of a greater percentage of calcareous microfossils; or (3) a greater percentage of foraminiferal sediment gravity flows. Terrigenous turbidites are not documented in the Leg 78A area because of (1) great distance from South American sources; (2) damming effects of east-west trending tectonic elements; and (3) location on the Tiburon Rise (Site 543). This lack of terrigenous material, characteristic of intraoceanic convergent margins, suggests that published sedimentation models for active continental convergent margins with abundant terrigenous influxes are not applicable to intraoceanic convergent margin settings.

Tab. 1: Rates of advance of the frontal push-moraines of 19 lobes in front of an approx. 4.5 km long margin of the Kötlujökull

In the last years masses of ice, about 5 km long, have been protruding from the lowest part of an advancing glacier margin of the Kötlujökull in Southern Iceland. In the summer of 1983, they appeared as sediment-covered lobes, 10-60 m long, bordering the glacier rnargin like agarland. 1 to 3 push-rnoraines without ice core, rnostly sickle-shaped, occured first in the frontal parts of the lobes: behind thern came several ice-cored moraines with heights of up to several metres. The active ice in front of the precipice of the glacier is called the "glacier-foot" in this paper. The digging out of 9 lobes and the measuring of the advance of 19 lobes showed that in most cases this glacierfoot had split up at its distal end into several plate- or stem-shaped pieces of ice which were situated one upon the other, separated by moraine deposits and proceeding irregularly into the foreland at the rate of several mm/h, The sometimes different rate of advance in the same lobe and different rates of advanee in adjoining lobes (some being entirely inactive) point to a type of rnovement which is independent of the general advance of the glacier. Research in the winter of 1983/84 showed less activity in 3 examined lobes, but the activity had not ceased. The advancement of the lower parts of the glacier-foot into and across the sands of the foreland implies the following genesis of pushmoraines: Shoving off a plate of sand, folding it and pushing it over the foreland at average rates of up to 7,2 mm/h, according to the investigations in thc summer of 1983. At a certain stage of the folding process, new folds begin to develop in front of the old, and the old folds are shifted onto the backslope of thc folds in front of them until they are completely unired. In this way, "püe-moraines" arise, which become higher and higher. They include two or more folds declining towards the glacier. Systems of small moraines presumably of the same genesis occur on old moraine areas in front of the Kötlujökull. The possible cause of formation of a glacier-foot is discussed, and the moraines of the Kötlujökull are compared with certain pleistocene push-moraines.

Description of recent sediments of Nile Delta, Red Sea and Gulf of Aden (Table 1-3)

The study of textural, structural, chemical, and physical properties of fine-grained recent marine sediments leads to the conclusion that only a few compositional factors are responsible for significant changes in mass physical characteristics in the upper meters below sea bottom. Fossil-induced porosity increases water content and liquid limit. It also seems to have partially influenced the plastic limit and plasticity index of calcareous sandy silts from the Red Sea and the western Gulf of Aden so that they become similar to the montmorillonite rich prodelta clays from the Nile Delta. Diagrams based on liquid limit and plasticity loose their original meaning in these cases. Activity of sediments rich in microorganisms can be higher than that of montmorillonitic clay. The shear strength-depth relationship of normally consolidated sediments is surprisingly little influenced by changes in sand or clay content and clay mineralogy. Only high lime content, submarine erosion and beginning cementation increase the strength considerably. Erosional disconformities near the present surface can be deduced from the strength-depth curve when as little as 1 or 2 m sediment have been removed. Flat or irregular strength-depth curves indicate beginning cementation and probably discontinuous sedimentation, provided the composition of the material remains in some degree constant. In our samples diagenetic pyrite, but no recristallisation of carbonates could be detected under the microscope. Underconsolidation and excess pore-water pressure, factors which tend to foster submarine slides, mud lumps, and diapiric folding, seem to be restricted Varito areas with mainly rapidly deposited, homogeneous or layered sediments. But where an abundance of burrowing organisms increases the vertical permeability of the sediment, normal consolidation and stable deposits are to be expected, at least in the upper meters below the present surface. According to 14C-determinations on calcareous microorganisms the rate of deposition of the investigated sediments seems to range from 26 to 167 cm per 1000 years.

50 year means of oxygen isotope data from ice core NGRIP

Two deep ice cores from central Greenland, drilled in the 1990s, have played a key role in climate reconstructions of the Northern Hemisphere, but the oldest sections of the cores were disturbed in chronology owing to ice folding near the bedrock. Here we present an undisturbed climate record from a North Greenland ice core, which extends back to 123,000 years before the present, within the last interglacial period. The oxygen isotopes in the ice imply that climate was stable during the last interglacial period, with temperatures 5 °C warmer than today. We find unexpectedly large temperature differences between our new record from northern Greenland and the undisturbed sections of the cores from central Greenland, suggesting that the extent of ice in the Northern Hemisphere modulated the latitudinal temperature gradients in Greenland. This record shows a slow decline in temperatures that marked the initiation of the last glacial period. Our record reveals a hitherto unrecognized warm period initiated by an abrupt climate warming about 115,000 years ago, before glacial conditions were fully developed. This event does not appear to have an immediate Antarctic counterpart, suggesting that the climate see-saw between the hemispheres (which dominated the last glacial period) was not operating at this time.