Sistemas Computacionais para Auxílio na Cicatrização de Feridas: Revisão de Escopo / Computer Systems to Aid in Wound Healing: Scope Review / Sistemas Informáticos para Ayudar en la Cicatrización de Heridas: Revisión del Alcance

Objetivo:Investigar estudos que apresentem sistemas computacionais de auxílio à cicatrização de feridas e quais sistemas se referem ao uso de laser de baixa intensidade. Método: Revisão de escopo que visou responder à questão de pesquisa: Quais sistemas computacionais auxiliam na cicatrização de feridas? Uma subquestão foi: quais sistemas computacionais se referem ao uso do laser de baixa intensidade? Resultados: A partir da busca, aplicando os critérios de elegibilidade, 49 artigos compuseram a amostra final. Os sistemas apresentaram várias finalidades de apoio à cicatrização de feridas, em que a maioria apresentou como usuário do sistema o profissional de saúde, sendo a medicina a área profissional mais mencionada, embora a enfermagem esteja envolvida com o manejo do cuidado às pessoas com feridas. Foi relatada com frequência a inovação na assistência a partir do uso do sistema computacional, o que demonstra a importância desse tipo de ferramenta para a prática clínica. Verificou-se com frequência o uso de plataforma mobile, como tendência da atualidade. Conclusão: Os sistemas computacionais têm sido utilizados como ferramentas para apoiar pacientes e principalmente profissionais na cicatrização de feridas. Quanto ao laser de baixa intensidade, houve escassez de sistemas computacionais com essa finalidade, com apenas um estudo.

Objective:To investigate studies that present computational systems to aid healing and systems which refer to the use of low-level laser. Method: Scope review that aimed to answer the question: Which computer systems help in wound healing? A subquestion was: Which of the computer systems refer to the use of low-level laser? Results: From the search, applying the eligibility criteria, 49 articles made up the final sample. The systems served multiple purposes in support of wound healing; the majority presented the health professional as a user of the system; medicine was the most mentioned professional area despite nursing being involved in the management of care for people with wounds. Innovation in care using the computer system was frequently reported, demonstrating the importance of this type of tool for clinical practice. There was a high frequency of the mobile platform, showing that this is a current trend. Conclusion: Computer systems have been used as tools to support patients and especially professionals in wound healing. Regarding the systems aimed at the low intensity laser, there was a shortage of computer systems for this purpose, with a study.

Objetivo:Investigar estudios que presenten sistemas computacionales de ayuda a la cicatrización y sistemas que se refieran al uso de láser de bajo nivel. Método: Revisión de alcance que tuvo como objetivo responder a la pregunta: ¿Qué sistemas informáticos ayudan en la cicatrización de heridas? Una subpregunta fue: ¿Cuál de los sistemas informáticos se refieren al uso de láser de bajo nivel? Resultados: A partir de la búsqueda, aplicando los criterios de elegibilidad, 49 artículos conformaron la muestra final. Los sistemas sirvieron para múltiples propósitos en apoyo de la cicatrización de heridas; la mayoría presentó al profesional de la salud como usuario del sistema; la medicina fue el área profesional más mencionadas, a pesar de que la enfermería está involucrada en la gestión del cuidado de las personas con heridas. La innovación en la atención basada en el uso del sistema informático fue relatada con frecuencia, demostrando la importancia de este tipo de herramienta para la práctica clínica. Hubo una alta frecuencia de la plataforma móvil, lo que demuestra que esta es una tendencia actual. Conclusión: Los sistemas informáticos se han utilizado como herramientas de apoyo a los pacientes y especialmente a los profesionales en la cicatrización de heridas. En cuanto a los sistemas dirigidos al láser de baja intensidad, hubo escasez de sistemas informáticos para este fin, con un estudio.

Application and development of systems biology in computer-aided drug design / 中国中药杂志

With the advances in medicine, people have deeply understood the complex pathogenesis of diseases. Revealing the mechanism of action and therapeutic effect of drugs from an overall perspective has become the top priority of drug design. However, the traditional drug design methods cannot meet the current needs. In recent years, with the rapid development of systems biology, a variety of new technologies including metabolomics, genomics, and proteomics have been used in drug research and development. As a bridge between traditional pharmaceutical theory and modern science, computer-aided drug design(CADD) can shorten the drug development cycle and improve the success rate of drug design. The application of systems biology and CADD provides a methodological basis and direction for revealing the mechanism and action of drugs from an overall perspective. This paper introduces the research and application of systems biology in CADD from different perspectives and proposes the development direction, providing reference for promoting the application.

Systems biology applied to the study of papaya fruit ripening: the influence of ethylene / Biologia de sistemas aplicada ao estudo do amadurecimento de mamões: a influência do etileno

Fruit ripening is a biochemical process that results in flavor, odor, texture, and color suitable for human consumption, in addition to providing access to important nutrients. Although ripening promotes sensory and nutritional increases in fruits, there is also an increased susceptibility to physical damage, as is the case with papaya. These transformations occur due to changes in gene expression patterns at different stages of maturity, whose control and coordination result from the combined action of plant hormones, especially ethylene. As the action of this hormone in the regulation of gene expression is still elusive, this dissertation sought to address the global analysis of the transcriptome in an overview study of molecular processes involved in the ripening of ethylene-treated and non-treated papaya. Transcription factors related to ethylene synthesis and signaling had increased activity towards exogenous-ethylene treatment. Consequently, ethylene-induced enzymes had their coding genes differentially expressed, like genes related to the synthesis of carotenoids, linalool, and vitamins, which increase color, aroma, and antioxidant activity, respectively. Metabolic pathways related to the synthesis of sugars were suppressed while genes encoding the enzyme responsible for sucrose synthesis maintained a basal expression, showing that the accumulation of sugars occurs before the ripening process. The firmness of the peel and pulp of the fruits were strongly influenced by the treatment with ethylene and by the time of the experiment, suffering the action of numerous enzymes related to the degradation of the cell wall. The main enzyme responsible for softening the pulp was polygalacturonase, together with the activity of other pectinases and cellulases. In contrast to the need for the pre-climacteric action of pectate lyase and pectinesterase reported in other fleshy fruits, such as tomatoes and strawberries, papaya did not show a significant difference in their expression. The meta-analysis of several papaya ripening transcriptomes confirmed the expression profile observed in the previous RNA-seq, besides providing statistical enrichment to the biological narratives. Finally, the present study gathered a range of robust information on the gene regulation of the papaya ripening process, which opens possibilities for future approaches to transcriptomic analysis and validates the use of papaya as a model for such studies

O amadurecimento de frutos é um processo bioquímico que resulta em sabor, odor, textura e cor adequados para o consumo humano, além de propiciar o acesso a nutrientes importantes. Apesar do amadurecimento promover incrementos sensoriais e nutricionais nos frutos, ocorre também um aumento da suscetibilidade a danos físicos, como é o caso do mamão. Essas transformações ocorrem devido às alterações nos padrões de expressão gênica nos diferentes estádios de amadurecimento, cujo controle e coordenação decorrem da ação combinada de hormônios vegetais, principalmente do etileno. Como a ação deste hormônio na regulação da expressão gênica ainda é elusiva, a presente dissertação buscou abordar a análise global do transcriptoma em um amplo estudo dos processos moleculares envolvidos no amadurecimento de mamões tratados e não tratados com etileno. Os fatores de transcrição relacionados com a síntese e a sinalização do etileno tiveram sua atividade aumentada perante o tratamento exógeno com etileno. Consequentemente, as enzimas reguladas por esse hormônio tiveram seus genes de codificação expressos diferencialmente, como foi o caso de genes relacionados à síntese de carotenoides, linalool e vitaminas, que atuam no aumento da cor, aroma e atividade antioxidante, respectivamente. Vias metabólicas relacionadas com à síntese de açúcares foram reprimidas enquanto genes codificantes da enzima responsável pela síntese de sacarose mantiveram uma expressão basal, evidenciando que o acúmulo de açúcares ocorre antes do processo de amadurecimento. A firmeza da casca e da polpa dos frutos foram fortemente influenciadas pelo tratamento com etileno e pelo tempo de experimento, sofrendo ação de inúmeras enzimas relacionadas com a degradação da parede celular. A principal enzima responsável pelo amolecimento da polpa foi a poligalacturonase, em conjunto com a atividade de outras pectinases e celulases. Em contraste com a necessidade da ação pré-climatérica da pectato liase e da pectinesterase relatada em outras frutas carnosas, como tomates e morangos, o mamão não apresentou uma diferença significativa na expressão das mesmas. A meta-análise de diversos transcriptomas do amadurecimento do mamão reafirmaram o perfil de expressão observado no RNA-seq, além de prover enriquecimento estatístico às narrativas biológicas. Por fim, o presente estudo reuniu uma gama de informações robustas sobre a regulação gênica do processo de amadurecimento do mamão papaia, o que abrange a possibilidade para futuras abordagens de análise transcriptomica e valida o uso do mamão como modelo para tais estudos

Graph-based and constraint-based heterologous metabolic pathway design methods and application / 生物工程学报

It is among the goals in metabolic engineering to construct microbial cell factories producing high-yield and high value-added target products, and an important solution is to design efficient synthetic pathway for the target products. However, due to the difference in metabolic capacity among microbial chassises, the available substrate and the yielded products are limited. Therefore, it is urgent to design related metabolic pathways to improve the production capacity. Existing metabolic engineering approaches to designing heterologous pathways are mainly based on biological experience, which are inefficient. Moreover, the yielded results are in no way comprehensive. However, systems biology provides new methods for heterologous pathway design, particularly the graph-based and constraint-based methods. Based on the databases containing rich metabolism information, they search for and uncover possible metabolic pathways with designated strategy (graph-based method) or algorithm (constraint-based method) and then screen out the optimal pathway to guide the modification of strains. In this paper, we reviewed the databases and algorithms for pathway design, and the applications in metabolic engineering and discussed the strengths and weaknesses of existing algorithms in practical application, hoping to provide a reference for the selection of optimal methods for the design of product synthesis pathway.

Discussion on Relevance and Studies of Prescription Compatibility in Chinese Medicine / 中国结合医学杂志

With Chinese medicine (CM) gaining popularity in recent years, researchers and clinicians have put in much interest and effort into the makings and effects of it, especially after the recent announcement of World Health Orgnitation's incorporation of CM into mainstream medical compendium. Individual herb has complex properties, coming from its pharmacological properties and the Chinese medical principles of organ-directed, taste and dynamic orientational behaviours. The use of individual herb in CM is rare, where various herbs/ingredients are mostly found in a prescribed formula. To fully reveal the effects of CM is a great challenge. The complexity of various herbs in combined effect, the absorption and utility rate by the body, uniqueness of individual physique, sub-types of pathological behaviors and time-line progression of the healing process add on to the complication of understanding the full effect of CM. Various theories such as pathophysiology guidance, pharmacokinetic-pharmacodynamic compatibility method, and Global Systems Biology for Integrative Genomics, Proteomics and Metabolomics, which interactively provide a wider scope, more details, with the consideration of development timeline, may shed more light to revealing the full picture of the effects of compatibility prescription.

An evolving and flourishing metabolic engineering / 生物工程学报

In 1990s, Bailey and Stephanopoulos put forward the concept of classic metabolic engineering, aiming to use DNA recombination technology to rewire metabolic network to achieve improved cell performance and increased target products. In the last 30 years since the birth of metabolic engineering, life science have flourished, and new disciplines such as genomics, systems biology and synthetic biology have emerged, injecting new connotations and vitality into the development of metabolic engineering. Classic metabolic engineering research has entered into an unprecedented stage of systems metabolic engineering. The application of synthetic biology tools and strategies, such as omics technology, genomic-scale metabolic model, parts assembly, circuits design, dynamic control, genome editing and many others, have greatly improved the design, build, and rewiring capabilities of complex metabolism. The intervention of machine learning and the combination of evolutionary engineering and metabolic engineering will further promote the development of systems metabolic engineering. This paper analyzes the development of metabolic engineering in the past 30 years and summarizes the novel theories, techniques, strategies, and applications of metabolic engineering that have emerged over the past 30 years.

Thirty years development of metabolic engineering: a review / 生物工程学报

Since its establishment 30 years ago, the discipline of metabolic engineering has developed rapidly based on its deep integration with molecular biology, systems biology and synthetic biology successively, which has greatly contributed to advancing and upgrading biotechnology industry. This review firstly analyzes the current status of academic research and China's competence in the area of metabolic engineering according to the data of papers published in SCI-indexed journals in the past 30 years. Subsequently, the article summarizes the development of systems biology methods and enabling technologies of synthetic biology and their applications in metabolic engineering in the past 10 years. Finally, the major challenges and future perspectives for the development of metabolic engineering are briefly discussed.

Biologia de Sistemas de RNAs Não-Codificadores Longos na Vacinação / Systems biology of Long Non-Coding RNAs in vaccination

Entender os mecanismos responsáveis pela proteção induzida por vacinas contribui para o desenvolvimento de novas vacinas. Uma abordagem de pesquisa denominada Vacinologia de Sistemas surgiu para endereçar essa tarefa. A aplicação da Vacinologia de Sistemas gerou informações amplas relacionadas a respostas vacinais e foi aplicada no estudo de diversas vacinas. Apesar de estarem envolvidos em diversos processos imunológicos, RNAs Não-Codificadores Longos (lncRNAs) ainda não foram estudados no contexto da imunidade induzida por vacinas. Neste trabalho, fizemos a análise de mais de 2.000 amostras de transcritoma de sangue periférico, oriundas de 17 diferentes coortes vacinadas, com foco na identificação de lncRNAs potencialmente envolvidos com a resposta induzida por vacinas contra gripe e contra febre amarela. Criamos também um banco de dados online, em que todos os nossos resultados podem ser facilmente acessados. Nossos resultados indicaram que diversos lncRNAs participam de múltiplas vias imunológicas relacionadas a respostas induzidas por vacinas. Entre esses, o transcrito FAM30A se destaca por ter alta expressão em células B e ser correlacionado com a expressão de genes de imunoglobulina localizados no mesmo locus genômico. Identificamos também alterações na expressão de lncRNAs em dados de RNA-seq de uma coorte de crianças imunizadas com uma vacina atenuada contra gripe, o que sugere um papel de lncRNAs na resposta a diferentes vacinas. Nossos achados trazem evidências de que lncRNAs tem um papel significativo na resposta imune induzida por vacinas

Understanding the mechanisms of vaccine-elicited protection contributes to the development of new vaccines. The emerging field of Systems Vaccinology provides detailed information on host responses to vaccination and has been successfully applied in the study of the molecular mechanisms of several vaccines. Long Non-Coding RNAs (lncRNAs) are crucially involved in multiple biological processes, but their role in vaccine-induced immunity has not been explored. We performed an analysis of over 2,000 blood transcriptome samples from 17 vaccine cohorts to identify lncRNAs potentially involved with antibody responses to influenza and yellow fever vaccines. We have created an online database where all results from these analyses can be easily accessed. We found that lncRNAs participate in distinct immunological pathways related to vaccine-elicited responses. Among them, we showed that the expression of lncRNA FAM30A was high in B cells and correlates with the expression of immunoglobulin genes located in its genomic vicinity. We also identified altered expression of lncRNAs in RNA-sequencing (RNA-seq) data from a cohort of children vaccinated with intranasal live attenuated influenza vaccine, suggesting a common role across several diverse vaccines. Taken together, these findings provide evidence that lncRNAs have a significant impact on immune responses induced by vaccination

Análise integrada à biologia de sistemas para avaliação de citocinas pró-inflamatórias e anti-inflamatórias na infecção por Zika vírus / Analysis integrated with the systems biology pro-inflammatory and anti-inflammatory cytokine evalution in Zica Virus infection

Objetivo: O presente estudo objetivou analisar as citocinas pró e anti-inflamatórias em pacientes infectados pelo Zika vírus. Métodos: Através da Biologia de Sistemas, que contribuiu de forma a sumarizar os dados quantitativos complexos. Resultados: Observamos em nossa pesquisa a elevação das citocinas IL-7, IL-9, IL-17a, RANTES, IP-10 e IL-1ra dos indivíduos infectados pelo ZIKV na fase aguda, relacionadas à atividade de linfócitos T e B,que indica uma possível proliferação desses tipos celulares mediante a infecção pelo ZIKV.Conclusão: Constatamos que nas infecções pelo ZIKV não ocorre uma grande liberação de citocinas, o que era esperado devido ao caráter benigno da doença.

Objective: The present study objected to analyze the pro and antiinflammatory cytokines in patients infected with zika vírus. Methods: Through the Systems Biology that contributed in a way to summarize the complex quantitative data. Results: In our study, we observed elevation of the cytokines IL-7, IL-9, IL-17a, RANTES, IP-10 and IL-1ra of the infected individuals by ZIKV in the acute phase, related to T and B lymphocyte activity, which indicate a possible proliferation of these cell types through ZIKV infection. Conclusion: We found that in the infections by the ZIKV, does not occur a great release of cytokines, which was expected due to the benign nature of the disease.

Analysis of the transcriptional regulatory mechanisms mediated by microRNAs in Metabolic Syndrome / Análise dos mecanismos regulatórios transcricionais mediados por microRNAs na Síndrome Metabólica

Metabolic Syndrome (MetS) is a combination of diseases interrelated and associated with increased mortality and risk of cardiovascular events. Among the elucidated molecular mechanisms of MetS, there are several genes regulated by miRNAs - small non-coding RNAs. A large number of transcriptomic studies in public databases integrated with new analysis methods can generate new insights. Therefore, this study aimed to identify circulating miRNAs and their target genes in MetS using a Systems Biology approach. For this, we used GEO-NCBI to download and analyse 26 microarray transcriptome studies of MetS and obesity. After preprocessing, the data underwent differential expression (LIMMA method), gene co-expression (CEMiTool), and enrichment (GSEA, Reactome) analyses. We retrieved a gene expression signature for subcutaneous adipose tissue (SAT) for obese individuals that included 291 consistent differentially expressed genes (DEG). This signature had a positive normalized enrichment score (NES) for adaptive immune system activation responses, and negative NES for metabolic pathways. The consensus co-expression network of SAT revealed 3 communities (CM) of densely interconnected genes. These CMs had a high number of up regulated genes and a consistent positive NES among the studies. The co-expressed genes of these 3 CMs were related to neutrophil degranulation, infiltration of immune system cells, and inflammatory processes. Also, a small brazillian cohort (6 individuals with MetS and 6 controls) underwent a seric miRNA profiling using PCR array. From the 222 miRNAs detected in serum, the differential expression analysis identified 4 upregulated miRNAs (miR-30c-5p, miR-421, miR-542-5p and miR-574) in MetS patients (p<0.01). The integrative miRNAs-mRNAs analysis revealed that the circulating upregulated miRNAs had 12 targets in the SAT, 3 targets in the liver; and no targets in the muscle and blood. Many of these target genes are known modulators of proinflammatory pathways. In conclusion, the use of Systems Biology in the analysis of gene networks and circulating miRNAs identified some potential molecular and pathophysiological mechanisms of the Metabolic Syndrome. The circulating miRNAs identified in this study are potential biomarkers and/or therapeutic targets. However, further studies are needed to validate these miRNAs and their target mRNA

A Síndrome Metabólica (MetS) é um conjunto de doenças inter-relacionadas e associadas ao aumento de mortalidade e risco de eventos cardiovasculares. Entre os mecanismos moleculares elucidados da MetS, existem muitos genes regulados por miRNAs - RNAs pequenos não codificadores. O grande número de estudos transcriptômicos em banco dados públicos integrado a novos métodos de análise podem gerar novas descobertas. Deste modo, o objetivo deste estudo foi identificar miRNAs circulantes e genes alvos na MetS usando a abordagem de Biologia de Sistemas. Para isso, GEO-NCBI foi usado para obter e analisar 26 estudos de transcriptoma por microarray de MetS e obesidade. Após o pré-processamento, realizamos análises de expressão diferencial (método LIMMA), co-expressão gênica (CEMiTool), e enriquecimento (GSEA, Reactome). Identificamos uma assinatura de expressão gênica do tecido adiposo subcutâneo (SAT) de indivíduos obesos, composta por 291 genes consistentemente diferencialmente expressos (DEG). Essa assinatura teve um escore de enriquecimento normalizado (NES) positivo para ativação de respostas do sistema imune adaptativo, e NES negativo para vias de metabolismo. A rede consenso de co-expressão do SAT revelou 3 comunidades (CM) de genes densamente interconectadas. Essas CMs continham muitos genes regulados positivamente e com consistência de NES positivo entre os estudos. Os genes co-expressos dessas 3 comunidades pertenciam a vias de a degranulação de neutrófilos, infiltração de células do sistema imune e processos inflamatórios. Além disso, uma pequena coorte brasileira (6 indivíduos com MetS e 6 controles) foi submetida à dosagem sérica de miRNAs por PCR array. Dos 222 miRNAs detectados no soro, a análise de expressão diferencial identificou 4 miRNAs regulados positivamente (miR-30c-5p, miR-421, miR-542-5p e miR-574) nos pacientes com MetS (p<0.01). A análise integrativa miRNAs-mRNAs revelou que osmiRNAs circulantes superexpressos tinham 12 alvos no SAT, 3 alvos no fígado; e nenhum alvo no músculo e no sangue. Muitos desses alvos são moduladores de vias ró-inflamatórias. Em conclusão, a utilização da Biologia de Sistemas na análise de redes gênicas e miRNAs circulantes identificou alguns potenciais mecanismos moleculares e fisiopatológicos da Síndrome Metabólica. Os miRNAs circulantes identificados neste trabalho são potenciais biomarcadores e/ou alvos terapêuticos. Entretanto, mais estudos são necessários para validar esses miRNAs e seus mRNAs alvos

Application of metabolic network model to analyze intracellular metabolism of industrial microorganisms / 生物工程学报

To quickly and efficiently understand the intracellular metabolic characteristics of industrial microorganisms, and to find potential metabolic engineering targets, genome-scale metabolic network models (GSMMs) as a systems biology tool, are attracting more and more attention. We review here the 20-year history of metabolic network model, analyze the research status and development of GSMMs, summarize the methods for model construction and analysis, and emphasize the applications of metabolic network model for analyzing intracellular metabolic activity of microorganisms from cellular phenotypes, and metabolic engineering. Furthermore, we indicate future development trend of metabolic network model.

Systems biology for industrial biotechnology / 生物工程学报

In industrial biotechnology, microbial cell factories utilize renewable resources to produce energy, materials and chemicals. Industrial biotechnology plays an increasingly important role in solving the resource, energy and environmental problems. Systems biology has shed new light on industrial biotechnology, deepening our understanding of industrial microbial cell factories and their bioprocess from "Black-box" to "White-box". Systems-wide profiling of genome, transcriptome, proteome, metabolome, and fluxome has proven valuable to better unveil network operation and regulation on the genome scale. System biology has been successfully applied to create microbial cell factories for numerous products and derive attractive industrial processes, which has constantly expedited the development of industrial biotechnology. This review focused on the recent advance and applications of omics and trans-omics in industrial biotechnology, including genomics, transcriptomics, proteomics, metabolomics, fluxomics and genome scale modeling, and so on. Furthermore, this review also discussed the potential and promise of systems biology in industrial biotechnology.

TarGo: network based target gene selection system for human disease related mouse models / 한국실험동물학회지

Genetically engineered mouse models are used in high-throughput phenotyping screens to understand genotype-phenotype associations and their relevance to human diseases. However, not all mutant mouse lines with detectable phenotypes are associated with human diseases. Here, we propose the “Target gene selection system for Genetically engineered mouse models” (TarGo). Using a combination of human disease descriptions, network topology, and genotype-phenotype correlations, novel genes that are potentially related to human diseases are suggested. We constructed a gene interaction network using protein-protein interactions, molecular pathways, and co-expression data. Several repositories for human disease signatures were used to obtain information on human disease-related genes. We calculated disease- or phenotype-specific gene ranks using network topology and disease signatures. In conclusion, TarGo provides many novel features for gene function prediction.

Total phenolic compounds and antioxidant activity of Stachys turcomanica / Compostos fenólicos totais e atividade antioxidante da Stachys turcomanica

The subject of free radicals and their effects on biological systems is an important problem in Medicine. Antioxidants can protect biological systems against free radicals. In this study, the effect of methanol ratio (0, 20, 50, 80, and 100%) in water on extraction yield of Total phenolic (TP) compounds and antioxidant activity (AA) of Stachys turcomanica extract were evaluated. The amount of TP compounds were determined using Folin-Ciocalteu reagent, and AA measured by 2, 2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP) and betacaroten linoleic acid methods. The results showed extraction of phenolic compounds and their AA were affected by solvent combinations. In addition, there was a good correlation between TP content and AA of Stachys turcomanica extracts. Finally the methanol: water (80:20) was good solvent in extracting of phenolic compounds with highest AA.

O tema dos radicais livres e seus efeitos nos sistemas biológicos é um problema importante na medicina. Os antioxidantes podem proteger os sistemas biológicos contra os radicais livres. Neste estudo, avaliou-se o efeito da proporção de metanol (0, 20, 50, 80 e 100%) na água com o rendimento de extração de compostos fenólicos totais (TP) e atividade antioxidante (AA) do extrato Stachys turcomanica. A quantidade de compostos de TP foi determinada utilizando o reagente de Folin-Ciocalteu, e AA medido por 2, 2-difenil-1-picrilidrazilo (DPPH), poder antioxidante redutor férrico (FRAP) e ácido beta-caroten ácido linoleico. Os resultados mostraram a extração de compostos fenólicos e os seus AA foram afetados por combinações de solventes. Além disso, houve uma boa correlação entre o conteúdo de TP e os extratos de AA de Stachys turcomanica. Finalmente, o metanol: água (80:20) foi bom solvente na extração de compostos fenólicos com AA mais alto.

Conceptos fundamentales en ecología de hongos del suelo: una propuesta pedagógica y de divulgación / Fundamental concepts in ecology of soil fungi: a pedagogic and outreach proposal

El estudio de los procesos biogeoquímicos implica entender cómo los macro y micro nutrientes que componen los seres vivos se mueven de un componente a otro del ecosistema (incluyendo la atmósfera, organismos, suelo, cuerpos de agua, etc.). Usualmente, una mayor diversidad biótica y una mayor complejidad de las interacciones bióticas y abióticas, resultan en una mayor estabilidad ecosistémica. El rol de los hongos en los ciclos biogeoquímicos se suele estudiar superficialmente, no mucho más allá de sus funciones ecosistémicas generales: descomposición, simbiosis mutualista, y parasitismo. Esta revisión tiene por objetivo ilustrar los conceptos base de los roles ecológicos de los hongos del suelo, que debieran enseñarse en tres públicos objetivo: universitario, tomadores de decisiones, y estudiantes de educación secundaria/público general. En estos públicos, se propone abordar cuatro áreas temáticas: introducción al suelo, ecología de comunidades, interacciones de hongos con otros organismos, y biogeoquímica. Aunque los roles ecosistémicos de los hongos del suelo están bien documentados, su estudio debería partir de la base de que estos afectan y son afectados tanto por variables climáticas, como por características físico-químicas del suelo, y por flujos biogeoquímicos. Los roles ecológicos de los hongos del suelo debieran entenderse en un contexto holístico de integración multidisciplinar, y el nivel de especialización del conocimiento debiera darse hacia niveles superiores de la jerarquía biológica, es decir, conocer más en detalle la ecología de ecosistemas y comunidades de hongos que la de poblaciones y organismos, o que sus procesos bioquímicos y edáficos específicos.

The study of biogeochemical processes involves understanding how the macro and micro nutrients that make up living things move from one ecosystem component to another (including the atmosphere, organisms, soil, waterbodies, etc.). Usually, a greater diversity of biotic diversity and a greater complexity of biotic and abiotic interactions, result in a greater ecosystemic stability. The role of fungi in biogeochemical cycles is usually studied superficially, not much beyond their general ecosystem functions: decomposition, mutualistic symbiosis, and parasitism. The objective of this review is to illustrate the basic concepts of the ecological roles of soil fungi, which should be taught in three target audiences: university students, decision makers, and secondary school students / general public. In these audiences, it is proposed to address four thematic areas: introduction to soil, community ecology, interactions of fungi with other organisms, and biogeochemistry. Although the ecosystemic roles of soil fungi are well documented, their study should be based on the fact that they affect and are affected by climatic variables, physical-chemical soil characteristics, and biogeochemical flows. The ecological roles of soil fungi should be understood in an holistic context of multidisciplinary integration, and the level of specialization of knowledge should be given to higher levels of the biological hierarchy, that is, to know more in detail the ecology of ecosystems and communities of fungi than that of populations and organisms, or than that of their specific biochemical and edaphic processes.

Screening and analysis of key active constituents in Guanxinshutong capsule using mass spectrum and integrative network pharmacology / 中国天然药物

Guanxinshutong capsule (GXSTC) is an effective and safe traditional Chinese medicine used in the treatment of cardiovascular diseases (CVDs) for many years. However, the targets of this herbal formula and the underlying molecular mechanisms of action involved in the treatment of CVDs are still unclear. In the present study, we used a systems pharmacology approach to identify the active ingredients of GXSTC and their corresponding targets in the calcium signaling pathway with respect to the treatment of CVDs. This method integrated chromatographic techniques, prediction of absorption, distribution, metabolism, and excretion, analysis using Kyoto Encyclopedia of Genes and Genomes, network construction, and pharmacological experiments. 12 active compounds and 33 targets were found to have a role in the treatment of CVDs, and four main active ingredients, including protocatechuic acid, cryptotanshinone, eugenol, and borneol were selected to verify the effect of (GXSTC) on calcium signaling system in cardiomyocyte injury induced by hypoxia and reoxygenation. The results from the present study revealed the active components and targets of GXSTC in the treatment of CVDs, providing a new perspective to enhance the understanding of the role of the calcium signaling pathway in the therapeutic effect of GXSTC.

Screening and analysis of key active constituents in Guanxinshutong capsule using mass spectrum and integrative network pharmacology / 中国天然药物

Guanxinshutong capsule (GXSTC) is an effective and safe traditional Chinese medicine used in the treatment of cardiovascular diseases (CVDs) for many years. However, the targets of this herbal formula and the underlying molecular mechanisms of action involved in the treatment of CVDs are still unclear. In the present study, we used a systems pharmacology approach to identify the active ingredients of GXSTC and their corresponding targets in the calcium signaling pathway with respect to the treatment of CVDs. This method integrated chromatographic techniques, prediction of absorption, distribution, metabolism, and excretion, analysis using Kyoto Encyclopedia of Genes and Genomes, network construction, and pharmacological experiments. 12 active compounds and 33 targets were found to have a role in the treatment of CVDs, and four main active ingredients, including protocatechuic acid, cryptotanshinone, eugenol, and borneol were selected to verify the effect of (GXSTC) on calcium signaling system in cardiomyocyte injury induced by hypoxia and reoxygenation. The results from the present study revealed the active components and targets of GXSTC in the treatment of CVDs, providing a new perspective to enhance the understanding of the role of the calcium signaling pathway in the therapeutic effect of GXSTC.

A Systems Biology Approach for Studying Heterotopic Ossification: Proteomic Analysis of Clinical Serum and Tissue Samples / 基因组蛋白质组与生物信息学报·英文版

Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO) and without (HO) heterotopic ossification. The resulting data were then analyzed using a systems biology approach. We found that serum samples from subjects experiencing traumatic injuries with resulting HO have a different proteomic expression profile compared to those from the matched controls. Subsequent quantitative ELISA identified five blood serum proteins that were differentially regulated between the HO and HO groups. Compared to HO samples, the amount of insulin-like growth factor I (IGF1) was up-regulated in HO samples, whereas a lower amount of osteopontin (OPN), myeloperoxidase (MPO), runt-related transcription factor 2 (RUNX2), and growth differentiation factor 2 or bone morphogenetic protein 9 (BMP-9) was found in HO samples (Welch two sample t-test; P < 0.05). These proteins, in combination with potential serum biomarkers previously reported, are key candidates for a serum diagnostic panel that may enable early detection of HO prior to radiographic and clinical manifestations.

Application of network biology on study of traditional Chinese medicine / 中国中药杂志

With the completion of the human genome project, people have gradually recognized that the functions of the biological system are fulfilled through network-type interaction between genes, proteins and small molecules, while complex diseases are caused by the imbalance of biological processes due to a number of gene expression disorders. These have contributed to the rise of the concept of the "multi-target" drug discovery. Treatment and diagnosis of traditional Chinese medicine are based on holism and syndrome differentiation. At the molecular level, traditional Chinese medicine is characterized by multi-component and multi-target prescriptions, which is expected to provide a reference for the development of multi-target drugs. This paper reviews the application of network biology in traditional Chinese medicine in six aspects, in expectation to provide a reference to the modernized study of traditional Chinese medicine.

Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases

Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs.