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A biological pathway is mainly composed of metabolic pathway, transcription regulatory pathway and signal transduction pathway. With the development of systems biology, many computational algorithms and systems that used to handle...
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A biological pathway is mainly composed of metabolic pathway, transcription regulatory pathway and signal transduction pathway. With the development of systems biology, many computational algorithms and systems that used to handle and predict biological pathway have been developed by many researchers and organizations in related fields on bioinformatics. By the assistance of these tools and systems, biologists may save tremendous time and money from the traditional wet biological experiments, especially in pathway modeling and drug finding. However, the computational patents on biological pathway mainly focus on mining, storing, modeling and visualizing the biological information, such as DNA sequences, the protein information, compounds and the interactions between them. Furthermore, literature information which is related to biological pathways is also integrated in many patents for the knowledge of pathways. This review summarizes the recent patents on biological pathway and catalogs them into three subdirectories based on their topics. The first is on the pathway prediction and identification patents for predicting the pathways in unknown organisms or identify the elements in pathways. The second includes some patents in modeling the pathways and simulating them to analyze the biological actions. The last one includes other patents constructing pathway databases or providing methods for pathway visualization.
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In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquiti...
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In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also on many other physiological functions in the cell. Recently we characterized a gene induction system that, upon the addition of an inducer, results in near-immediate transcription of a gene of interest under physiological conditions. We used this to perturb levels of single transcription factors during steady-state growth in chemostats, which facilitated distinction of direct from indirect effects of individual factors dynamically through quantification of the subsequent changes in genome-wide patterns of gene expression. We were able to show directly that Cbf1p acts sometimes as a repressor and sometimes as an activator. We also found circumstances in which Met31p/Met32p function as repressors, as well as those in which they function as activators. We elucidated and numerically modeled feedback relationships among the regulators, notably feedforward regulation of Met32p (but not Met31p) by Met4p that generates dynamic differences in abundance that can account for the differences in function of these two proteins despite their identical binding sites.
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The full reactive atmospheric oxidation profile of peroxyacetic acid under high NO conditions was examined using electronic structure calculations at various levels of theory. The three pathways resulting from the reaction of pero...
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The full reactive atmospheric oxidation profile of peroxyacetic acid under high NO conditions was examined using electronic structure calculations at various levels of theory. The three pathways resulting from the reaction of peroxyacetic acid with the hydroxyl radical were (1) addition of OH to the central carbon, (2) abstraction of the acidic hydrogen, and (3) abstraction of the methyl hydrogen. These pathways were followed to terminal product steps, the major products being acetic acid for pathway 1 and formaldehyde for pathways 2 and 3.
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Visceral Leishmaniasis is an infectious disease that affects mainly humans and dogs, with the latter being important reservoirs of the parasite. Conversely, cats are naturally resistant. The immune system can offer important expla...
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Visceral Leishmaniasis is an infectious disease that affects mainly humans and dogs, with the latter being important reservoirs of the parasite. Conversely, cats are naturally resistant. The immune system can offer important explanation to this problematic as there is no evidence on the role that the complement system plays in cats. In this context, effect of the complement system from human, dog and cat sera on Leishmania infantum was evaluated. Activation of the classical, alternative and lectin pathways was assessed through hemolytic and ELISA assays. Lytic activity of the complement on the parasite?s viability was investigated by Transmission Electron Microscopy and Flow Cytometry. Complement proteins were more consumed in dog serum on the classical and alternative pathways, leading to less hemolytic activity, and only in cat serum they were consumed on the lectin pathway when incubated with L. infantum. Lytic activity on the parasite?s surface was more accentuated in human serum, and varied throughout the parasite?s developmental stages.
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Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists co...
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Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations.Contact: brian@monrovian.com.
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Photorespiration is a primary metabolic pathway, which, given its energy costs, has often been viewed as a wasteful process. Despite having reached the consensus that one important function of photorespiration is the removal of to...
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Photorespiration is a primary metabolic pathway, which, given its energy costs, has often been viewed as a wasteful process. Despite having reached the consensus that one important function of photorespiration is the removal of toxic metabolite intermediates, other possible functions have emerged, and others could well emerge in the future. As a primary metabolic pathway, photorespiration interacts with other routes; however the nature of these interactions is not well known. One of these interacting pathways could be the biosynthesis of serine, since this amino acid is synthesised through photorespiratory and non-photorespiratory routes. At present, the exact contribution of each route to serine supply in different tissues and organs, their biological significance and how pathways are integrated and/or regulated remain unknown. Here, we review the non-photorespiratory serine biosynthetic pathways, their interactions with the photorespiratory pathway, their putative role in plants and their biotechnological interest.
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BACKGROUNDColorectal cancer (CRC) is one of the most common cancers in the world. A newly proposed integrated pathway comprising traditional, alternate, and serrated pathways by genetic and epigenetic factors was defined recently ...
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BACKGROUNDColorectal cancer (CRC) is one of the most common cancers in the world. A newly proposed integrated pathway comprising traditional, alternate, and serrated pathways by genetic and epigenetic factors was defined recently and hypothesized to play a role in the pathogenesis of CRC; however, to the authors' knowledge, there is a paucity of information regarding these proposed molecular pathways in different ethnic groups.
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The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference frame...
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The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel "meta-pathway" structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species--human, mouse, Arabidopsis, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction.
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