Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins

Addition of a 50 mM mixture of l-arginine and l-glutamic acid (RE) is extensively used to improve protein solubility and stability, although the origin of the effect is not well understood. We present Small Angle X-ray Scattering (SAXS) and Nuclear Magnetic Resonance (NMR) results showing that RE induces protein compaction by collapsing flexible loops on the protein core. This is suggested to be a general mechanism preventing aggregation and improving resistance to proteases and to originate from the polyelectrolyte nature of RE. Molecular polyelectrolyte mixtures are expected to display long range correlation effects according to dressed interaction site theory. We hypothesize that perturbation of the RE solution by dissolved proteins is proportional to the volume occupied by the protein. As a consequence, loop collapse, minimizing the effective protein volume, is favored in the presence of RE.

Colesteatoma: utilidade da sequência de difusão sem echo-planar

Colesteatomas são lesões císticas congênitas ou adquiridas que acometem as orelhas e que podem apresentar padrões típicos aos estudos de tomografia computadorizada, em função de suas características expansivas e tendência a promover erosão óssea. Entretanto, particularmente nos casos de resíduo ou recorrência pós-cirúrgica, a distinção entre colesteatoma e tecido inflamatório pode ser bastante difícil e, não raro, impossível com base somente nos achados tomográficos. A avaliação por ressonância magnética pode ser útil, particularmente neste contexto, uma vez que as sequências pós-contraste obtidas tardiamente e a difusão podem demonstrar padrões distintos nestas duas situações. Os artefatos condicionados pela interface ar/osso na região das mastoides podem limitar bastante a utilização da sequência de difusão echo-planar. A sequência de difusão sem echo-planar é uma alternativa na solução deste problema por estar menos sujeita a este tipo de artefato, fornecendo ainda imagens com maior resolução espacial e com espessuras de corte mais finas, as quais permitem a detecção de colesteatomas de pequenas dimensões.

Search and Discovery : OER's Open Loop

Open educational resources (OER) promise increased access, participation, quality, and relevance, in addition to cost reduction. These seemingly fantastic promises are based on the supposition that educators and learners will discover existing resources, improve them, and share the results, resulting in a virtuous cycle of improvement and re-use. By anecdotal metrics, existing web scale search is not working for OER. This situation impairs the cycle underlying the promise of OER, endangering long term growth and sustainability. While the scope of the problem is vast, targeted improvements in areas of curation, indexing, and data exchange can improve the situation, and create opportunities for further scale. I explore the way the system is currently inadequate, discuss areas for targeted improvement, and describe a prototype system built to test these ideas. I conclude with suggestions for further exploration and development.

Un análisis comparativo del papel del bucle fonológico versus la agenda visoespacial en el cálculo en niños de 7-8 años = A comparative analysis of the phonological loop versus the visuo-spatial sketchpad in mental arithmetic tasks in 7-8 y.o. children

En esta investigación se ha estudiado la relación entre dos subsistemas de la memoria de trabajo (buclefonológico y agenda viso-espacial) y el rendimiento en cálculo con una muestra de 94 niños españolesde 7-8 años. Hemos administrado dos pruebas de cálculo diseñadas para este estudio y seis medidassimples de memoria de trabajo (de contenido verbal, numérico y espacial) de la «Batería de Testsde Memoria de Treball» de Pickering, Baqués y Gathercole (1999), y dos pruebas visuales complementarias.Los resultados muestran una correlación importante entre las medidas de contenido verbaly numérico y el rendimiento en cálculo. En cambio, no hemos encontrado ninguna relación con las medidasespaciales. Se concluye, por lo tanto, que en escolares españoles existe una relación importanteentre el bucle fonológico y el rendimiento en tareas de cálculo. En cambio, el rol de la agenda viso-espaciales nulo

Conformações distorcida e planar do anel porfirínico em complexos e hemoproteínas: propriedades físico-químicas e implicações espectroscópicas

The different conformations of porphyrin rings are strongly related with the electronic configurations of the metallic center in the ferriheme coordination compounds and heme proteins. The usual electronic configuration, (d xy)²(d xz,d yz )³ presents a planar conformation of the porphyrin ring and the less common electronic configuration (d xz,d yz)4(d xy )¹ occurs in the case of a strongly ruffled ring. These states are responsible for distinct chemical and spectroscopic properties of the porphyrin systems. The importance of the ring conformations, their characteristics, implications and applications are discussed.

Determinação do íon ferro em preparações farmacêuticas através da cromatografia planar e espectrofotometria

Os autores estudaram o comportamento cromatográfico de preparações farmacêuticas comerciais contendo o íon Fe (II). Utilizando celulose microcristalina/Propanol: ácido clorídrico 4 N: ácido acético concentrado: ácido nítrico concentrado: clorofórmio (40: 5: 5: 10: 10), como sistema cromatográfico e alizarina como reagente de detecção, Fe (II), Mn (II), Mg (II), Cu (II), Zn (II) e Ca (II) foram separados e identificados pela Cromatografia Planar. O Fe (II) foi determinado pela reação com a ortofenantrolina, resultando em solução adequada para quantificação colorimétrica.

CFD Simulation of Two-phase and Three-phase Flows in Internal-loop Airlift

Airlift reactors are pneumatically agitated reactors that have been widely used in chemical, petrochemical, and bioprocess industries, such as fermentation and wastewater treatment. Computational Fluid Dynamics (CFD) has become more popular approach for design, scale-up and performance evaluation of such reactors. In the present work numerical simulations for internal-loop airlift reactors were performed using the transient Eulerian model with CFD package, ANSYS Fluent 12.1. The turbulence in the liquid phase is described using κ- ε the model. Global hydrodynamic parameters like gas holdup, gas velocity and liquid velocity have been investigated for a range of superficial gas velocities, both with 2D and 3D simulations. Moreover, the study of geometry and scale influence on the reactor have been considered. The results suggest that both, geometry and scale have significant effects on the hydrodynamic parameters, which may have substantial effects on the reactor performance. Grid refinement and time-step size effect have been discussed. Numerical calculations with gas-liquid-solid three-phase flow system have been carried out to investigate the effect of solid loading, solid particle size and solid density on the hydrodynamic characteristics of internal loop airlift reactor with different superficial gas velocities. It was observed that averaged gas holdup is significantly decreased with increasing slurry concentration. Simulations show that the riser gas holdup decreases with increase in solid particle diameter. In addition, it was found that the averaged solid holdup increases in the riser section with the increase of solid density. These produced results reveal that CFD have excellent potential to simulate two-phase and three-phase flow system.

Kaivoslastauskoneen hybridisointianalyysi virtuaali- ja in-loop -simuloinnin avulla

Työssä tutkitaan raskaiden työkoneiden hybridisointimitoitusta simuloimalla. Työssä esitetään simulation-in-the-loop-simulointiin perustuva järjestelmä, jolla esimerkkitapauksena oleva kaivoslastauskone työympäristöineen voidaan mallintaa mekaaniselta osaltaan monikappaledynamiikkaan perustuvalla ohjelmistolla ja hybridijärjestelmän osalta Simulinkissa. Yhdistetty simulointi mahdollistaa hybridityökoneen virtuaalimallin ohjaamisen käyttäjän toimesta reaaliajassa. Simuloinnista saadaan tuloksena mm. työsykli, jota voidaan käyttää hybridisointimitoitukseen. Hybridisointi toteutetaan kahdella erilaisella kokoonpanolla, joista analysoidaan suorituskykyä sekä polttoaineen kulutusta. Tuloksia verrataan pelkästään dieselmoottoria voimanlähteenä käyttävään lastauskoneeseen. Työssä tehty tutkimus osoittaa, että (sarja-) hybridisoinnilla voidaan saavuttaa merkittäviä etuja raskaiden työkoneiden polttoainetehokkuudessa. Dieselmoottoria voidaan ajaa sellaisessa staattisessa toimintapisteessä, jonka hyötysuhde on korkea riippumatta työkoneen kuormituksesta. Saavutettu hyöty on toteutetussa tutkimuksessa parhaimmillaan jopa 56 % vähennys polttoaineenkulutuksessa. Lisäksi tarvittava dieselin nimellisteho pienenee huomattavasti. Tutkimuksen osana esitellään myös Hardware-in-the-Loop -laitteisto, jonka avulla voidaan liittää oikea sähkömoottori ja taajuudenmuuttaja osaksi virtuaalisesti simuloitua työkonetta.

Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for rapid detection of Actinobacillus pleuropneumoniae based the dsbE-like gene

This paper reports on the development and validation of a loop-mediated isothermal amplification assay (LAMP) for the rapid and specific detection of Actinobacillus pleuropneumoniae (A. pleuropneumoniae). A set of six primers were designed derived from the dsbE-like gene of A.pleuropneumoniae and validate the assay using 9 A. pleuropneumoniae reference/field strains, 132 clinical isolates and 9 other pathogens. The results indicated that positive reactions were confirmed for all A. pleuropneumoniae strains and specimens by LAMP at 63ºC for 60 min and no cross-reactivity were observed from other non-A.pleuropneumoniae including Haemophilus parasuis, Escherichia coli, Pasteurella multocida, Bordetella bronchiseptica, Streptococcus suis, Salmonella enterica, Staphylococcus, porcine reproductive and respiratory syndrome virus (PRRSV), and Pseudorabies virus. The detection limit of the conventional PCR was 10² CFU per PCR test tube, while that of the LAMP was 5 copies per tube. Therefore, the sensitivity of LAMP was higher than that of PCR. Moreover, the LAMP assay provided a rapid yet simple test of A. pleuropneumoniae suitable for laboratory diagnosis and pen-side detection due to ease of operation and the requirement of only a regular water bath or heat block for the reaction.

Rapid and sensitive detection of Bordetella bronchiseptica by loop-mediated isothermal amplification (LAMP)

Bordetella bronchiseptica causes acute and chronic respiratory infections in diverse animal species and occasionally in humans. In this study, we described the establishment of a simple, sensitive and cost-efficient loop-mediated isothermal amplification (LAMP) assay for the detection of B. bronchiseptica. A set of primers towards a 235 bp region within the flagellum gene of B. bronchiseptica was designed with online software.. The specificity of the LAMP assay was examined by using 6 porcine pathogens and 100 nasal swabs collected from healthy pigs and suspect infected pigs. The results indicated that positive reactions were confirmed for all B. bronchiseptica and no cross-reactivity was observed from other non-B. bronchiseptica. In sensitivity evaluations, the technique successfully detected a serial dilutions of extracted B. bronchiseptica DNA with a detection limit of 9 copies, which was 10 times more sensitive than that of PCR. Compared with conventional PCR, the higher sensitivity of LAMP method and no need for the complex instrumentation make this LAMP assay a promising alternative for the diagnosis of B. bronchiseptica in rural areas and developing countries where there lacks of complex laboratory services.

Cyanobacterial occurrence and detection of microcystin by planar chromatography in surface water of Billings and Guarapiranga Reservoirs, SP, Brazil

Billings and Guarapiranga Reservoirs were deeply affected by environmental disturbances, which more evident consequence are the cyanobacterial blooms. Microcystins are the most common cyanotoxin in freshwaters and more than 70 types are known. Different methods for microcystins analysis in water can be used, among which ELISA and HPLC are the most frequently employed. However, less sophisticated and more economic methods can also be used. This is the case of planar chromatography (thin-layer chromatography) method previously used in cyanotoxins purification but gradually replaced by others. Posterior optimization of the microcystin chromatography conditions and because of its simplicity, rapidity, efficiency and low cost, this method is again considered an option for the analysis of microcystins and nodularins. Considering the importance of Billings and Guarapiranga Reservoirs for drinking water supplies and the few scientific data about cyanobacteria and cyanotoxins in these water bodies, the aims of this work are to analyze the biodiversity of cyanobacteria in the Billings and Guarapiranga Reservoirs and the detection of dissolved microcystins in the water. It was possible to identify 17 species of cyanobacteria, 9 of them being potentially toxic. In Billings Reservoir Microcystis aeruginosa (Kützing) Kützing and Cylindrospermopsis raciborskii (Woloszynska) Seenayya & Subba Raju are the most common species, while in Guarapiranga Reservoir only M. aeruginosa was considered as a common species. Microcystins were detected in all Billings Reservoir samples and in only one sample from Guarapiranga Reservoir.

Hygro-elasto-plastic behavior of planar orthotropic material

The mechanical and hygroscopic properties of paper and board are factors affecting the whole lifecycle of a product, including paper/board quality, production, converting, and material and energy savings. The progress of shrinkage profiles, loose edges of web, baggy web causing wrinkling and misregistration in printing are examples of factors affecting runnability and end product quality in the drying section and converting processes, where paper or board is treated as a moving web. The structural properties and internal stresses or plastic strain differences built up during production also cause the end-product defects related to distortion of the shape of the product such as sheet or box. The objective of this work was to construct a model capable of capturing the characteristic behavior of hygroscopic orthotropic material under moisture change, during different external in-plane stretch or stress conditions. Two independent experimental models were constructed: the elasto-plastic material model and the hygroexpansivity-shrinkage model. Both describe the structural properties of the sheet with a fiber orientation probability distribution, and both are functions of the dry solids content and fiber orientation anisotropy index. The anisotropy index, introduced in this work, simplifies the procedure of determining the constitutive parameters of the material model and the hygroexpansion coefficients in different in-plane directions of the orthotropic sheet. The mathematically consistent elasto-plastic material model and the dry solids content dependent hygroexpansivity have been constructed over the entire range from wet to dry. The presented elastoplastic and hygroexpansivity-shrinkage models can be used in an analytical approach to estimate the plastic strain and shrinkage in simple one-dimensional cases. For studies of the combined and more complicated effects of hygro-elasto-plastic behavior, both models were implemented in a finite element program for a numerical solution. The finite element approach also offered possibilities for studying different structural variations of orthotropic planar material, as well as local buckling behavior and internal stress situations of the sheet or web generated by local strain differences. A comparison of the simulation examples presented in this work to results published earlier confirms that the hygro-elasto-plastic model provides at least qualitatively reasonable estimates. The application potential of the hygro-elasto-plastic model is versatile, including several phenomena and defects appearing in the drying, converting and end-use conditions of the paper or board webs and products, or in other corresponding complex planar materials.

The role of autolysis loop in determining the specificity of coagulation proteases

We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system) of activated protein C (APC) with the corresponding loop of factor Xa (fXa) renders the APC mutant (APC/fX143-154) susceptible to inhibition by antithrombin (AT) in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154). Unlike an ~500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved ~10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.