Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

<p>Abstract</p> <p>Background</p> <p>Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.</p> <p>Methods</p> <p>We generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.</p> <p>Results and conclusion</p> <p>We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as <it>fpair </it>and propose to use it for evaluation of the accuracy of multiple protein docking.</p

Novel Strategies for Upstream and Downstream Processing of Tannin Acyl Hydrolase

Tannin acyl hydrolase also referred as tannase is an enzyme with important applications in several science and technology fields. Due to its hydrolytic and synthetic properties, tannase could be used to reduce the negative effects of tannins in beverages, food, feed, and tannery effluents, for the production of gallic acid from tannin-rich materials, the elucidation of tannin structure, and the synthesis of gallic acid esters in nonaqueous media. However, industrial applications of tannase are still very limited due to its high production cost. Thus, there is a growing interest in the production, recovery, and purification of this enzyme. Recently, there have been published a number of papers on the improvement of upstream and downstream processing of the enzyme. These papers dealt with the search for new tannase producing microorganisms, the application of novel fermentation systems, optimization of culture conditions, the production of the enzyme by recombinant microorganism, and the design of efficient protocols for tannase recovery and purification. The present work reviews the state of the art of basic and biotechnological aspects of tannin acyl hydrolase, focusing on the recent advances in the upstream and downstream processing of the enzyme

La internacionalización de los bancos domésticos y el canal del crédito de la política monetaria

¿Cómo afecta la expansión de los bancos domésticos en los mercados internacionales el canal del crédito bancario de la política monetaria? Usando datos a nivel de banco-firma-préstamo, este estudio encuentra que el crecimiento del crédito y las tasas de interés de los créditos otorgados por los bancos internacionales (i.e., bancos domésticos que se expandieron en los mercados internacionales) responden menos a cambios en la política monetaria y que la internacionalización mitiga parcialmente el canal de la toma de riesgos de la política monetaria. Encontramos también que los bancos con una mayor presencia internacional tienden a tolerar mejor su exposición al riesgo de crédito frente a los bancos domésticos. Además, identificamos que los bancos internacionales tienden a usar más el fondeo externo cuando cambian las tasas de política, lo que les permite aislar en mayor medida su oferta de crédito de los cambios de la política monetaria en comparación con los bancos domésticos. Este resultado es consistente con las predicciones de la hipótesis de los mercados de capital internos. Se muestra que la regulación cambiaria macroprudencial reduce el acceso al fondeo externo por parte de los bancos con alta exposición cambiaria, lo que contribuye a la transmisión de la política monetaria. En general, los resultados sugieren que la internacionalización de los bancos disminuye la potencia del canal del crédito bancario y reduce el canal de la toma de riesgos de la política monetaria dentro del límite establecido por la regulación cambiaria macroprudencial.How does the expansion of domestic banks in international markets affect the bank lending channel of monetary policy? Using bank-firm loan-level data, we find that loan growth and loan rates from international banks respond less to monetary policy changes than domestic banks and that internationalization partially mitigates the risk-taking channel of monetary policy. Banks with a large international presence tend to tolerate more their credit risk exposition relative to domestic banks. Moreover, international banks tend to rely more on foreign funding when policy rates change, allowing them to insulate better the monetary policy changes from their credit supply than domestic banks. This result is consistent with the predictions of the internal capital markets hypothesis. We also show that macroprudential FX regulation reduces banks with high FX exposition access to foreign funding, ultimately contributing to monetary policy transmission. Overall, our results suggest that the internationalization of banks lowers the potency of the bank lending channel. Furthermore, it diminishes the risk-taking channel of monetary policy within the limit established by macroprudential FX regulations.Enfoque La internacionalización de la banca puede traer beneficios en términos de la diversificación de riesgos y menores costos de fondeo; pero a su vez, puede aumentar la exposición de los bancos a choques externos y debilitar la transmisión de la política monetaria. En Colombia, los principales bancos domésticos realizaron una expansión internacional sin precedentes que cambió la estructura del sistema financiero. Entre 2006 y 2017 los activos de los bancos colombianos en Centroamérica crecieron 7,5 veces, al pasar de USD 10 billones a 85 USD billones; mientras que el número de subsidiarias y oficinas en esa región pasó de 17 a 234. La internacionalización de la banca colombiana ha traído consigo importantes cambios en la supervisión y regulación bancaria, dados los potenciales riesgos que pueden enfrentar los bancos locales al operar en economías con una regulación bancaria más laxa y mayores vulnerabilidades. Asimismo, la regulación macroprudencial del Banco de la República se ha venido adaptando para reducir la exposición cambiaria de los bancos y mitigar, por esa vía, su impacto sobre la estabilidad financiera. En la medida que los bancos cumplan con la regulación bancaria y macroprudencial se asume que dichos riesgos están siendo controlados. Sin embargo, los efectos de la internacionalización de la banca sobre la transmisión de la política monetaria son más complejos evaluar. Contribución En este trabajo estudiamos los efectos de la internacionalización de la banca en Colombia sobre la transmisión de la política monetaria bajo el enfoque del canal del crédito de la política monetaria. El trabajo extiende la evidencia sobre la transmisión de la política monetaria al evaluar los efectos de la internacionalización de los bancos, la toma de riesgos de la política monetaria y el papel de las medidas cambiarias macroprudenciales. En la identificación usamos micro-datos del universo de préstamos entre bancos y firmas de la Superintendencia Financiera de Colombia (SFC) para el periodo 2006-2017 y modelos de datos panel con efectos fijos que controlan por la demanda de crédito, entre otros aspectos (Khwaja and Mian, 2008). Resultados Los resultados indican que el crecimiento del crédito y la variación en las tasas de interés de los préstamos otorgados por los bancos internacionales (i.e., bancos domésticos que se expandieron en los mercados internacionales) responden menos a cambios en la política monetaria en comparación con los bancos domésticos (i.e., bancos sin subsidiarias en el exterior). Encontramos además que los bancos con una mayor presencia internacional tienden a tolerar mejor su exposición al riesgo de crédito frente a los bancos domésticos y en efecto, ante reducciones de la tasa de política, su oferta de crédito hacia las firmas riesgosas crece en menor magnitud que la observada por parte de los bancos domésticos. Al analizar la estructura de fondeo de los bancos encontramos que los bancos internacionales tienden a usar más el fondeo externo cuando cambian las tasas de política, lo que les permite aislar en mayor medida su oferta de crédito de los cambios de la política monetaria. Este resultado es consistente con las predicciones de la hipótesis de los mercados de capital internos. Por último, se muestra que la regulación cambiaria macroprudencial es efectiva en reducir el acceso al fondeo externo de los bancos con alta exposición cambiaria, lo que contribuye a incrementar la tracción de la política monetaria. En general, los resultados sugieren que la internacionalización de los bancos disminuye la potencia del canal del crédito bancario y reduce el canal de la toma de riesgos de la política monetaria, dentro del límite establecido por la regulación cambiaria macroprudencial

Typical Mexican agroindustrial residues as supports for solid-state fermentation

Biological wastes contain several reusable substances of high value such as soluble sugars and fiber. Direct disposal of such wastes to soil or landfill causes serious environmental problems. Thus, the development of potential value-added processes for these wastes is highly attractive. These biological wastes can be used as support-substrates in Solid-State Fermentation (SSF) to produce industrially relevant metabolites with great economical advantage. In addition, it is an environment friendly method of waste management. In this study were analyzed six different Mexican agro industrial residues to evaluate their suitability as support-substrate in SSF, between physicochemical properties that have included Water Absorption Index (WAI), Critical Moisture Point (CHP) and Packing Density (PD). The selection of an appropriate solid substrate plays an important role in the development of an efficient SSF process. The results provided important knowledge about the characteristics of these materials revealing their potential for use in fermentation processes.(undefined

Desinformação em contextos de polarização social: a greve nacional na Colômbia do dia 21N

Disinformation emerges as a worldwide phenomenon that affects public opinion. The article’s purpose is to analyze the contents evaluated as disinformation by three fact-checking media during Colombia’s national strike (November 21st, 2019). Specifically, the objective is to understand how disinformation negatively affects the intangible assets (legitimacy, reputation, and trust) of social &amp; political actors, and institutions. Methodologically, we carried out both quantitative and ethnographic content analysis to analyze data and, identify the prominent arguments and relationships. Through this, we linked the disinformation and the costs of the intangible assets associated with these actors and institutions. The results highlight that the disinformation contents’ key drivers were the violence and punishable acts that affected both social actors and the Public Force, particularly the Esmad and the police. These contents delegitimized and discredited both the reasons for the protest and the function of guaranteeing public order and security. Regarding the disinformation linked to political actors, the leader of the left-side was the most affected due to inaccurate content that polarized and proclaimed extreme positions close to subversion. Finally, we discuss the implications of disinformation and how it affects legitimacy, reputation, and trust. Moreover, disinformation imitates media outlet aesthetics as a necessity of a kind of legitimacy and credibility set of news practice in the eye of the beholder.&nbsp;La desinformación se ha convertido en un fenómeno mundial que incide en la opinión pública. El objetivo de este artículo es analizar los contenidos evaluados como desinformación por tres medios de verificación durante el paro nacional del 21 de noviembre del 2019. Específicamente, se pretende conocer cómo la desinformación afecta negativamente los bienes intangibles (legitimidad, reputación y confianza) de actores sociales, políticos e instituciones. Metodológicamente, se realizó un análisis de contenido cuantitativo y etnográfico para analizar los datos e identificar argumentos y patrones de relación de la desinformación con su afectación en la intangibilidad de estos clústeres de actores. Los resultados obtenidos destacan que la desinformación propagada vinculó la violencia y los actos punibles tanto a los actores sociales como a la fuerza pública, especialmente al Esmad y a la policía, con el fin de deslegitimar y desacreditar las razones de la protesta o bien su labor de garantizar el orden público y la seguridad. Respecto a la desinformación vinculada con los actores políticos se observa que el líder de la izquierda fue el más afectado por contenidos que polarizaban y proclamaban posiciones extremas cercanas a la subversión. Por último, se discuten las implicaciones de la desinformación en la ciudadanía y cómo incide sobre la legitimidad, reputación y confianza. Además, se evidencia que la desinformación imita la estética de medios de comunicación para dotarse de una falsa legitimidad y credibilidad ante los ojos de la audiencia.A desinformação se há convertido em um fenômeno mundial que infringe na opinião pública.O objetivo desse artigo é analisar os conteúdos vistos como desinformação por ter meios deverificação durante a greve nacional do dia 21 de novembro de 2019. Especificamente, busca-seconhecer como a desinformação afeta negativamente os bens intangíveis (legitimidade, reputaçãoe confiança) de atores sociais, políticos e instituições. Metodologicamente, realizou-se umaanálises do conteúdo quantitativo e etnográfico para analisar os dados e identificar argumentose padrões de relação da desinformação com sua afetação na intangibilidade propagada vinculoua violência e os atos puníveis tanto aos atores sociais como a força pública, especialmente oEsmad e a polícia, com o fim de deslegitimar e desacreditar as razões da paralisação ou bemseu trabalho de garantir a ordem pública e a segurança. Respeito a desinformação atreladacom os atores políticos observa-se que o líder da esquerda foi o mais afetado pelos conteúdosde polarizaram e proclamavam posições extremas. Por último, discutem-se as implicações dadesinformação na cidadania e como incide sobre a legitimidade, reputação e confiança. Oque mais se percebe é que a desinformação imita a estética dos meios de comunicação paraequipar-se de uma falsa legitimidade e credibilidade ante os olhos da audiência

CÁLCULO DE LA RIGIDEZ DE UN ROBOT INDUSTRIAL DE SEIS GRADOS DE LIBERTAD

ResumenComo parte de una investigación para producir un sistema de compensación on-line para el proceso de Roll Hemming, proponemos un método para calcular la matriz de rigidez de las juntas de un robot industrial de seis grados de libertad. Este análisis fue hecho aplicando solo una fuerza sobre la el punto central de la herramienta, esta fuerza solo actuaba en la dirección Z del marco de referencia. El experimento puede ser mejorado sin embargo los resultados pueden ser utilizados como referencia para experimentos relacionados con robots industriales.Palabra(s) Clave: Rigidez, Robot Industrial, Roll Hemming. CALCULATION OF THE RIGIDITY OF AN INDUSTRIAL ROBOT OF SIX DEGREES OF FREEDOM AbstractAs part of a research to produce an on-line compensation system for Roll Hemming process, we propose a method to calculate the joint stiffness matrix of an industrial robot of six degrees of freedom. This analysis was done applying only one force over the tool center point, this force only acted in the Z world frame reference direction. The experiment can be improved nevertheless the values can be used as reference for experiments related with industrial robots.Keywords: Industrial robot, Roll Hemming, Stiffness

Fructo-oligosaccharides (FOS) production by fungal submerged culture using aguamiel as a low-cost by-product

Supplementary data to this article can be found online at https:// doi.org/10.1016/j.lwt.2018.12.020.Fructooligosaccharides (FOS) are important ingredients in the functional food industry because they have different biological properties such as decrease level of triglycerides, cholesterol and phospholipids and stimulate growth of probiotics for enhancement of microflora in large intestine. However, current strategies for the FOS production through simple and economical bioprocess has been necessary. The aim of this work was evaluated the capacity of three fungal strains (Aspergillus niger GH1, Aspergillus niger PSH and Aspergillus oryzae DIA-MF) to produce fructooligosaccharides (FOS) using aguamiel from Agave salmiana as an economical substrate. In addition, Czapek Dox medium supplemented with sucrose as carbon source was used as a control medium for the FOS production. A. oryzae DIA-MF was a fungi producer of FOS using aguamiel or Czapek Dox medium as substrate at 24?h of fermentation. However, the yield of FOS was increased two folds (20.30?g/L), with a productivity of 0.84?g FOS/l.h when aguamiel was used as substrate. On the other hand, A. niger GH1 and A. niger PSH showing only hydrolytic activity on sucrose under the studied conditions. In conclusion, this study shown excellent compatibility of A. oryzae DIA-MF using aguamiel as an economical substrate for the FOS production under a simple bioprocess.Authors thank all technical support and comments made by Dra. Adriana C. Flores-Gallegos and Dra. Abril Flores-Maltos. Authors thank National Council for Science and Technology (CONACYT) of Mexico by the financial support through the project No. CB-2011-C01-167764. Author D. B. Muñiz-Márquez also thank CONACYT for the financial support during her postgraduate program (Doctorate) in Food Science and Technology offered by the University Autonomous of Coahuila, Mexico.info:eu-repo/semantics/publishedVersio

Evaluation of Culture Conditions for Tannase Production by Aspergillus niger GH1

Ispitana je ekstracelularna i intracelularna proizvodnja tanaze submerznim uzgojem plijesni Aspergillus niger GH1 u tekućoj te površinskim uzgojem na čvrstoj podlozi pri različitim temperaturama (30, 40 i 50 °C). Istražen je utjecaj koncentracije početnog supstrata (taninske kiseline), vremena inkubacije i temperature na proizvodnju tanaze pri uzgoju na čvrstoj podlozi. Soj A. niger GH1 proizveo je najviše tanaze (2291 U/L) tijekom prvih 20 sati uzgoja pri koncentraciji taninske kiseline od 50 g/L. U tim uvjetima proizvodnje enzim je u potpunosti bio ekstracelularan. Opadanje aktivnosti tanaze nakon 20 sati ugoja povezano je s pratećim porastom aktivnosti proteaze.Extra- and intracellular tannase production by Aspergillus niger GH1 has been evaluated using submerged (SmF) and solid-state fermentation (SSF) at different temperatures (30, 40 and 50 °C). Effects of initial substrate (tannic acid) concentration, incubation time and temperature on tannase production in SSF have been studied. A. niger GH1 produced the highest tannase level (2291 U/L) in SSF at 30 °C during the first 20 h of culture at tannic acid concentration of 50 g/L, and under these conditions enzyme production was entirely extracellular. The decline in tannase activity after 20 h of incubation was associated with a concomitant increase in protease activity

Fungal Invertase Expression in Solid-State Fermentation

U ovom je istraživanju ocijenjena ekspresija aktivnosti invertaze u soju plijesni Aspergillus niger Aa-20 pri različitim koncentracijama dvaju supstrata tijekom rasta na čvrstoj podlozi od poliuretanske pjene. Kao represor upotrijebljena je glukoza, a kao induktor saharoza. Proizvodnja invertaze povećala se dodatkom do 100 g glukoze na litru podloge, a pri većim koncentracijama se smanjila. Omjer indukcije i represije pri svim koncentracijama glukoze bio je 2,5 puta veci od onog pri osnovnim uvjetima (bez induktora).In this study invertase activity expression in Aspergillus niger Aa-20 was evaluated under different concentrations of two substrates using solid-state fermentation (SSF) on polyurethane foam. Glucose was used as repressor and sucrose was the inducer. Invertase production increased when glucose was present in the medium (up to 100 g/L); however, higher concentration than this reduced the enzyme production. Induction-repression ratio obtained using any glucose concentration was at least 2.5 times higher than that under basal conditions (without inducer)

Isolation and Evaluation of Tannin-degrading Fungal Strains from the Mexican Desert

Eleven fungal strains (4 Penicillium commune, 2 Aspergillus niger, 2 Aspergillus rugulosa, Aspergillus terricola, Aspergillus ornatus and Aspergillus fumigatus) were isolated, characterized morphologically and by their capacity to degrade tannins. Aspergillus niger Aa-20 was used as control strain. Several concentrations of hydrolysable tannin (tannic acid) were used as sole carbon source. All strains were able to degrade hydrolysable tannins. Aspergillus niger GH1 and PSH showed the highest tannin-degrading capacity (67 and 70%, respectively). Also, the fungal capacity to degrade condensed tannin (catechin) was tested. Aspergillus niger PSH and Penicillium commune EH2 degraded 79.33% and 76.35% of catechin. The results demonstrated the capacity of fungi to use hydrolysable and condensed tannins as carbon source