Misc

Constructing metabolic profiles of 60 cancer cell lines by integrating metabolomics and systems biology revealed increased glycine consumption in highly proliferative cancer cells.

In Table 2, the mean (10th-90th range)a of Rice for Male should be (250-680). Please see the correct Table 2 here. (Table Presented).

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal epithelial surface form polymicrobial biofilms. In the last decade, it has been widely reported that gut microbial biofilms and gut microbiota-derived products, such as metabolites and bacterial membrane vesicles, not only directly affect the host intestinal environment, but also indirectly influence the health of the host. In this review, we discuss the most recent findings from human and animal studies on the interactions between the gut microbiota and hosts, and their associations with various disorders, including inflammatory diseases, atopic dermatitis, metabolic disorders, and psychiatric and neurological diseases. The integrated approach of metabologenomics together with biofilm imaging may provide valuable insights into the gut microbiota and suggest remedies that may lead to a healthier society.

How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation. © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

5. Conclusions: In April 2001, Keio University established the Institute for Advanced Biosciences, which specializes in Systems Biology, in Tsuruoka City (Yamagata Prefecture), Japan. The ultimate objective of the research at this institute is to construct a computer model of the cellular metabolism, and it has given high priority to metabolome research since its opening. As of 2005, the institute is equipped with the following world-class instrumentation for metabolome analysis: 19 CE systems, six LC systems, two GC/MS systems, nine quadrupole MS systems, four ion-trap MS systems, two Triple QMS/MS systems, six electrospray ionization time-of-flight mass spectrometers (ESI-TOF-MS), one Q-TOF-MS and one nuclear magnetic resonance (NMR) spectrometer. The major projects being conducted at the Institute include: E. coli Modeling Project funded by the New Energy and Industrial Technology Development Organization (NEDO) of the Ministry of Economy, Trade and Industry of Japan, with the ultimate aim of designing useful microorganisms; Leading Project for Biosimulation funded by the Ministry of Education, Culture, Sports, Science and Technology (Monbusho), which is performing metabolome analysis and simulation of red blood cells; and the Grants for Scientific Research and Scientific Research of Priority Areas (funded also by the Ministry of Education, Culture, Sports, Science and Technology), and 21st Century COE program at Keio University entitled The Understanding and Control of Life's Function via Systems Biology, which are developing the basic technologies for metabolomics and cell simulation. In addition, the Faculty of Medicine at the University of Tokyo, Japan, established the Center for Metabolome in February 2003. This group is focusing primarily on lipid metabolomics using LC/MS technology. Finally, Keio University and its partners invested in the establishment of a bio-venture company, Human Metabolome Technologies (HMT) Inc., in Tsuruoka City in July 2003. Utilizing the metabolome technology of the Institute for Advanced Biosciences of Keio University, HMT is now conducting joint research with major food companies, to understand bacterial metabolism of fermentation used in the food industry. Their future plan is to apply this technology to the fields of medical sciences through collaborations with drug companies.