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At least 91 records · Page 5Linked to original sources
PubMed2007

Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

Systematic genetic interaction studies have illuminated many cellular processes. Here we quantitatively examine genetic interactions among 26 Saccharomyces cerevisiae genes conferring resistance to the DNA-damaging agent methyl methanesulfonate (MMS), as determined by chemogenomic fitness profiling of pooled deletion strains. We constructed 650 double-deletion strains, corresponding to all pairings of these 26 deletions. The fitness of single- and double-deletion strains were measured in the presence and absence of MMS. Genetic interactions were defined by combining principles from both statistical and classical genetics. The resulting network predicts that the Mph1 helicase has a role in resolving homologous recombination-derived DNA intermediates that is similar to (but distinct from) that of the Sgs1 helicase. Our results emphasize the utility of small molecules and multifactorial deletion mutants in uncovering functional relationships and pathway order.

DEAD-box RNA Helicases↗
PubMed1995

Pathway analysis of radiation-sensitive meiotic mutants of Coprinus cinereus.

We have isolated 37 radiation-sensitive mutants of the basidiomycete Coprinus cinereus. Each mutation is recessive, and the collection defines at least ten complementation groups for survival of gamma irradiation. Four complementation groups define the genes rad3, rad9, rad11 and rad12, which are required both for survival of gamma irradiation and for meiosis. Mutants in each of these four groups fail to complete meiosis and produce mushrooms with greatly reduced numbers of viable spores. Propidium iodide staining of meiotic nuclei showed a characteristic terminal appearance for each mutant: few cells of any of the meiotic mutants progress beyond prophase I, and both condensation and fragmentation or dispersal of meiotic chromatin are frequently observed. Scanning electron micrographs showed that the meiotic mutants make varying numbers (0-6) of basidiospore initials and that few of these initials develop into mature spores. When initials are present they are always symmetrically arrayed on the basidium, regardless of initial number. In quantitative measurements of gamma ray sensitivity, double mutants of every tested combination of rad3, rad9, rad11 and rad12 consistently showed the same gamma ray sensitivity as the more sensitive single mutant parent of the cross. Therefore, these four genes are in the same pathway for the repair of gamma radiation damage, and this pathway also represents one or more functions essential for meiosis.

Coprinus↗
PubMed1990

[Dorsal root potential evoked by stimulation of periaqueductal gray and its efferent pathway analysis in rats].

When periaqueductal gray (PAG) was stimulated with concentric electrodes, a steady negative potential called PAG-DRP was recorded from L5 dorsal root. PAG-DRP with properties of spatial and temporal summation propagates decrementally along the dorsal root and is inhibited by picrotoxin. Lesions of NRM had no effect on the PAG-DRP evoked by stimulation of dorsal PAG, but showed obvious reduction up to about 40% on the PAG-DRP evoked by stimulation of ventral PAG. It is suggested that the descending inhibition of PAG includes some presynaptic inhibition and that the ventral PAG-DRP is relayed partly via NRM while the dorsal PAG-DRP is not associated with NRM.

Animals↗
PubMed1998

A role for the insulin-interleukin (IL)-4 receptor motif of the IL-4 receptor alpha-chain in regulating activation of the insulin receptor substrate 2 and signal transducer and activator of transcription 6 pathways. Analysis by mutagenesis.

The interleukin (IL)-4 receptor alpha-chain (IL-4Ralpha) contains a sequence motif (488PLVIAGNPAYRSFSD) termed the insulin IL-4 receptor motif (I4R motif). Mutation of the central Tyr497 to Phe blocks the tyrosine phosphorylation of the insulin receptor substrate 1 (IRS1) and diminishes proliferation in response to IL-4. Recent data suggest that the I4R motif encodes binding sites for several protein tyrosine binding (PTB) domain-containing proteins such as IRS1 and Shc and potentially for the Src homology 2 domain of signal transducer and activator of transcription 6 (STAT6). To analyze the function of the I4R motif in regulating IL-4 signaling, we changed conserved residues upstream and downstream of the central Tyr to Ala in the human IL-4Ralpha. We analyzed the ability of these constructs to signal the tyrosine phosphorylation of IRS2 and STAT6, the induction of DNA binding activity, and CD23 induction in response to human IL-4 (huIL-4) in transfected M12.4.1 cells. Mutagenesis of residues downstream of Tyr497, such as Arg498 or Phe500, to Ala had no effect on any of these responses, suggesting that the I4R motif may not be important for functional Src homology 2 domain interactions. However, mutagenesis of Pro488 to Ala (P488A) greatly diminished the tyrosine phosphorylation of IRS2 and abolished tyrosine phosphorylation of STAT6, induction of DNA binding activity, and CD23 induction in response to huIL-4. By contrast, a P488G mutant signaled these responses to huIL-4. Mutagenesis of hydrophobic amino acids previously shown to contact the PTB domain of IRS1, Leu489 or Ile491, to Ala had only minimal effects on responses to huIL-4. However, changing both Leu498 and Ile491 to Ala greatly diminished the tyrosine phosphorylation of IRS2 and abolished STAT6 activation. Taken together, these results indicate the important role of the I4R motif in regulating IRS docking and suggest that I4R docking to a PTB domain-containing protein regulates activation of the STAT6 pathway.

Alanine↗
PubMedDate not supplied

Snell's Law: optimum pathway analysis.

An analysis is made of the various possible paths traveling from one medium to another. It is demonstrated that the most efficient possible path for traveling in the shortest possible time is the path determined by Snell's Law. Conversely, when light is refracted as it passes from one medium to another, it is completing the trip in the minimum possible time, less time than if it had passed through the various media in a straight line.

Humans↗
PubMed2006

Statistical search space reduction and two-dimensional data display approaches for UPLC-MS in biomarker discovery and pathway analysis.

A new analytical strategy for biomarker recovery from directly coupled ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC Tof MS) data on biofluids is presented and exemplified using a study on hydrazine-induced liver toxicity. A key step in the strategy involves a novel procedure for reducing the spectroscopic search space by differential analysis of cohorts of normal and pathological samples using an orthogonal projection to latent structures discriminant analysis (O-PLS-DA). This efficiently sorts principal discriminators of toxicity from the background of thousands of metabolic features commonly observed in data sets generated by UPLC-MS analysis of biological fluids and is thus a powerful tool for biomarker discovery.

Animals↗
PubMed2003

Equilibrium O2 distribution in the Zn2+-protoporphyrin IX deoxymyoglobin mimic: application to oxygen migration pathway analysis.

Proton spin relaxation induced by the triplet ground state of O(2) in the zinc-containing diamagnetic analogue of sperm whale deoxymyoglobin has been measured as a function of oxygen concentration. As no covalent binding of oxygen to the metal occurs in the zinc species, the relaxation effects of O(2) on the protein (1)H resonances arise exclusively via much weaker noncovalent interactions. The relaxation effects at the amide proton sites are found to be highly localized and are derived almost exclusively from O(2) binding at the four previously identified xenon binding sites. Relative binding constants of 1.0, 0.08, 0.07, and 0.23 were determined for the Xe 1, Xe 2, Xe 3, and Xe 4 sites, respectively. In combination with earlier measurements of the kinetics of the heme binding of oxygen, these equilibria measurements enable a more detailed analysis of models characterizing O(2) entry and egress. A correlation is established between the fraction of O(2) which enters the Fe(2+)-binding site via rotation of the distal histidine side chain (so-called "histidine gate") and the experimentally observable O(2) (or CO) lifetime in the Xe 1 site. A physiological role for these secondary oxygen binding sites is proposed in enhancing the efficiency of the O(2) association reaction by rendering more favorable its competition with water binding in the distal heme pocket.

Animals↗
PubMed2001

Outcome after traumatic brain injury: pathway analysis of contributions from premorbid, injury severity, and recovery variables.

OBJECTIVE: To examine the relationship of premorbid variables, injury severity, and cognitive and functional status to outcome 1 year after traumatic brain injury (TBI) and to assess the feasibility of multivariate path analysis as a way to discover those relationships. DESIGN: Prospective, longitudinal. SETTINGS: Level I trauma center, acute inpatient rehabilitation hospital. PATIENTS: One hundred seven subjects (87 men, 20 women; mean age, 33.91 +/- 14.2 yr) who had experienced severe TBI, typically from motor vehicle crashes. INTERVENTIONS: Acute medical and rehabilitation care. MAIN OUTCOME MEASURES: Disability Rating Scale, Community Integration Questionnaire, and return to employment. Evaluated in acute rehabilitation, and at 6 and 12 months' postinjury. RESULTS: Path analyses revealed that premorbid factors had significant relationships with injury severity, functional skills, cognitive status, and outcome; injury severity affected cognitive and functional skills; and cognitive status influenced outcome. No significant relationships were found between injury severity and emotional status, injury severity and outcome, emotional status and outcome, and functional skills and outcome. CONCLUSIONS: Multivariate analysis is important to understanding outcome after TBI. Injury severity, as measured in this study, is less important to 12-month outcome than the premorbid status of the person and the difficulties (particularly cognitive deficits) exhibited at follow-up 6 months after the trauma.

Adult↗
PubMed2006

The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis.

Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid/ that allows users to browse, search, and blast Alliance for Cellular Signaling plasmids. The collection primarily contains murine signaling ORFs with an emphasis on kinases and G protein signaling genes. Here we describe the cloning, databasing, and application of this proteomics resource for large scale subcellular localization screens in mammalian cell lines.

Animals↗
PubMed2005

Kinetic studies and biochemical pathway analysis of anaerobic poly-(R)-3-hydroxybutyric acid synthesis in Escherichia coli.

Poly-(R)-3-hydroxybutyric acid (PHB) was synthesized anaerobically in recombinant Escherichia coli. The host anaerobically accumulated PHB to more than 50% of its cell dry weight during cultivation in either growth or nongrowth medium. The maximum specific PHB production rate during growth-associated synthesis was approximately 2.3 +/- 0.2 mmol of PHB/g of residual cell dry weight/h. The by-product secretion profiles differed significantly between the PHB-synthesizing strain and the control strain. PHB production decreased acetate accumulation for both growth and nongrowth-associated PHB synthesis. For instance under nongrowth cultivation, the PHB-synthesizing culture produced approximately 66% less acetate on a glucose yield basis as compared to a control culture. A theoretical biochemical network model was used to provide a rational basis to interpret the experimental results like the fermentation product secretion profiles and to study E. coli network capabilities under anaerobic conditions. For example, the maximum theoretical carbon yield for anaerobic PHB synthesis in E. coli is 0.8. The presented study is expected to be generally useful for analyzing, interpreting, and engineering cellular metabolisms.

Anaerobiosis↗
PubMed2001

Recovering filter-based microarray data for pathways analysis using a multipoint alignment strategy.

The use of commercial microarrays is rapidly becoming the method of choice for profiling gene expression and assessing various disease states. Research Genetics has provided a series of biological and software tools to the research community for these analyses. The fidelity of data analysis using these tools is dependent on a series of well-defined reference control points in the array. During the course of our investigations, it became apparent that in some instances the reference control points that are required for analysis became lost in background noise. This effectively halted the analysis and the recovery of any information contained within that experiment. To recover this data and to increase analytical veracity, the simple strategy of superimposing a template of reference control points onto the experimental array was developed. The utility of this tool is established in this communication.

Filtration↗
PubMed2006

From genome to phenome--RNAi library screening and hit characterization using signaling pathway analysis.

Comprehensive, high-throughput analysis of gene function using RNA interference (RNAi)-based screens is emerging as a significant step forward for preliminary drug-target identification. Until quite recently drug target identification depended heavily on the analysis of changes in gene expression, which in turn needed to be correlated with gene function. The promise of obtaining preliminary 'gene to phenotype' information using a single high-throughput platform is propelling major investment in this area by biotechnology and pharmaceutical companies. This review discusses recent developments in the use of RNAi library screens, and the various assay formats and techniques currently in use for data analysis downstream of such screens.

Animals↗