Otsuka Y.,Nara Institute of Science and Technology |
Muto A.,Nara Institute of Science and Technology |
Takeuchi R.,Nara Institute of Science and Technology |
Okada C.,Mitsubishi Group |
And 21 more authors.
Nucleic Acids Research | Year: 2015
Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the longterm goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. © The Author(s) 2014.
PubMed | Okinawa Sangyo Shien Center, University of Miami, Purdue University, University of Oklahoma and 6 more.
Type: Journal Article | Journal: Nucleic acids research | Year: 2015
Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.
News Article | November 8, 2016
HAYWARD, CA--(Marketwired - November 08, 2016) - Biolog, Inc., a leader in the field of High Resolution Cell Phenotyping, announced that it has expanded its team by adding two veterans of the life sciences tools space. In August, Biolog elected David Weber to its Board of Directors. David has over 35 years of commercial experience across the life sciences industry with companies such as Pharmacia Biotech, Amersham Biosciences, Chemdex, Stratagene, and Eksigent Technologies. Prior to its recent acquisition by Thermo Fisher Scientific, David served as Executive Vice President and Chief Commercial Officer for Affymetrix and was instrumental in the company's turnaround. Today, Biolog announces the appointment of Richard Mabe to the position of Vice President of Sales and Marketing. Richard has had an extensive career in the life sciences industry with companies such as DuPont, Amersham International, GE Healthcare, and Sequenom. Richard's long track record of success in building and developing commercial teams will have significant impact on Biolog's business. "I am confident that the appointment of two industry veterans like David and Richard will enhance our already successful business and position Biolog for rapid and sustained growth," said Barry Bochner Ph.D., Biolog's Chief Executive Officer. "I am thrilled to welcome them into Biolog." Biolog is embarking on the release of exciting new products in the areas of microbial identification and characterization, and human cell and mitochondrial analysis. This is triggering an expansion and focus on the company's commercial initiatives. Biolog is a privately-held company based in Hayward, CA, that continues to lead in the development of powerful new cell analysis tools for solving critical problems in biological, pharmaceutical, and biotechnological research and development. It is the world leader in phenotypic cell profiling. Biolog products are available worldwide, either directly from the company or through its extensive network of international distributors. Further information can be obtained at Biolog's website, www.biolog.com.
Bochner B.R.,Biolog Inc. |
Siri M.,Biolog Inc. |
Siri M.,University of Colorado at Denver |
Huang R.H.,Biolog Inc. |
And 5 more authors.
PLoS ONE | Year: 2011
Background: To elucidate metabolic changes that occur in diabetes, obesity, and cancer, it is important to understand cellular energy metabolism pathways and their alterations in various cells. Methodology and Principal Findings: Here we describe a technology for simultaneous assessment of cellular energy metabolism pathways. The technology employs a redox dye chemistry specifically coupled to catabolic energy-producing pathways. Using this colorimetric assay, we show that human cancer cell lines from different organ tissues produce distinct profiles of metabolic activity. Further, we show that murine white and brown adipocyte cell lines produce profiles that are distinct from each other as well as from precursor cells undergoing differentiation. Conclusions: This technology can be employed as a fundamental tool in genotype-phenotype studies to determine changes in cells from shared lineages due to differentiation or mutation. © 2011 Bochner et al.
Bochner B.,Biolog Inc. |
Gomez V.,Biolog Inc. |
Ziman M.,Biolog Inc. |
Yang S.,Oak Ridge National Laboratory |
Brown S.D.,Oak Ridge National Laboratory
Applied Biochemistry and Biotechnology | Year: 2010
In this study, we developed a Phenotype MicroArray™ (PM) protocol to profile cellular phenotypes in Zymomonas mobilis, which included a standard set of nearly 2,000 assays for carbon, nitrogen, phosphorus and sulfur source utilization, nutrient stimulation, pH and osmotic stresses, and chemical sensitivities with 240 inhibitory chemicals. We observed two positive assays for C-source utilization (fructose and glucose) using the PM screen, which uses redox chemistry and cell respiration as a universal reporter to profile growth phenotypes in a high-throughput 96-well plate-based format. For nitrogen metabolism, the bacterium showed a positive test results for ammonia, aspartate, asparagine, glutamate, glutamine, and peptides. Z. mobilis appeared to use a diverse array of P-sources with two exceptions being pyrophosphate and tripolyphosphate. The assays suggested that Z. mobilis uses both inorganic and organic compounds as S-sources. No stimulation by nutrients was detected; however, there was evidence of partial inhibition by purines and pyrimidines, NAD, and deferoxamine. Z. mobilis was relatively resistant to acid pH, tolerating a pH down to about 4.0. It also tolerated phosphate, sulfate, and nitrate, but was rather sensitive to chloride and nitrite. Z. mobilis showed resistance to a large number of diverse chemicals that inhibit most bacteria. The information from PM analysis provides an overview of Z. mobilis physiology and a foundation for future comparisons of other wild-type and mutant Z. mobilis strains. © Humana Press 2009.
Boccuto L.,Greenwood Genetic Center |
Chen C.-F.,Greenwood Genetic Center |
Pittman A.R.,Greenwood Genetic Center |
Skinner C.D.,Greenwood Genetic Center |
And 5 more authors.
Molecular Autism | Year: 2013
Background: Autism spectrum disorders (ASDs) are relatively common neurodevelopmental conditions whose biological basis has been incompletely determined. Several biochemical markers have been associated with ASDs, but there is still no laboratory test for these conditions. Methods. We analyzed the metabolic profile of lymphoblastoid cell lines from 137 patients with neurodevelopmental disorders with or without ASDs and 78 normal individuals, using Biolog Phenotype MicroArrays. Results: Metabolic profiling of lymphoblastoid cells revealed that the 87 patients with ASD as a clinical feature, as compared to the 78 controls, exhibited on average reduced generation of NADH when tryptophan was the sole energy source. The results correlated with the behavioral traits associated with either syndromal or non-syndromal autism, independent of the genetic background of the individual. The low level of NADH generation in the presence of tryptophan was not observed in cell lines from non-ASD patients with intellectual disability, schizophrenia or conditions exhibiting several similarities with syndromal autism except for the behavioral traits. Analysis of a previous small gene expression study found abnormal levels for some genes involved in tryptophan metabolic pathways in 10 patients. Conclusions: Tryptophan is a precursor of important compounds, such as serotonin, quinolinic acid, and kynurenic acid, which are involved in neurodevelopment and synaptogenesis. In addition, quinolinic acid is the structural precursor of NAD§ssup§+§esup§, a critical energy carrier in mitochondria. Also, the serotonin branch of the tryptophan metabolic pathway generates NADH. Lastly, the levels of quinolinic and kynurenic acid are strongly influenced by the activity of the immune system. Therefore, decreased tryptophan metabolism may alter brain development, neuroimmune activity and mitochondrial function. Our finding of decreased tryptophan metabolism appears to provide a unifying biochemical basis for ASDs and perhaps an initial step in the development of a diagnostic assay for ASDs. © 2013 Boccuto et al.; licensee BioMed Central Ltd.
Lei X.-H.,Biolog Inc. |
Bochner B.R.,Biolog Inc.
PLoS ONE | Year: 2013
Toxin production is a central issue in the pathogenesis of Clostridium difficile and many other pathogenic microorganisms. Toxin synthesis is influenced by a variety of known and unknown factors of genetics, physiology, and environment. To facilitate the study of toxin production by C. difficile, we have developed a new, reliable, quantitative, and robust cell-based cytotoxicity assay. Then we combined this new assay with Phenotype MicroArrays (PM) technology which provides high throughput testing of culture conditions. This allowed us to quantitatively measure toxin production by C. difficile type strain ATCC 9689 under 768 culture conditions. The culture conditions include different carbon, nitrogen, phosphorus, and sulfur sources. Among these, 89 conditions produced strong toxin induction and 31 produced strong toxin repression. Strong toxin inducers included adenine, guanosine, arginine dipeptides, γ-D-Glu-Gly, methylamine, and others. Some leucine dipeptides and the triple-leucine tripeptide were among the strongest toxin repressors. While some results are consistent with previous observations, others are new observations that provide insights into toxin regulation and pathogenesis of C. difficile. Additionally, we have demonstrated that this combined assay technology can be applied broadly to a wide range of toxin producing microorganisms. This study is the first demonstration of simultaneous assessment of a large number of culture conditions influencing bacterial toxin production. The new functional cytotoxin quantitation method developed provides a valuable tool for studying toxigenic microorganisms and may also find applications in clinical and epidemiological research. © 2013 Lei, Bochner.