ABSTRACT
Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing drug resistance, caused by mutations and/or activation of alternative cellular pathways. To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that regulates the disease. The BioModelAnalyzer (BMA) is a user-friendly computational tool that allows us to do exactly that. We used BMA to build a CML network-model composed of 54 nodes linked by 104 interactions that encapsulates experimental data collected from 160 publications. While previous studies were limited by their focus on a single pathway or cellular process, our executable model allowed us to probe dynamic interactions between multiple pathways and cellular outcomes, suggest new combinatorial therapeutic targets, and highlight previously unexplored sensitivities to Interleukin-3.
Subject(s)
Computational Biology/methods , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Algorithms , Apoptosis/drug effects , Computer Simulation , Fusion Proteins, bcr-abl/antagonists & inhibitors , Fusion Proteins, bcr-abl/metabolism , Gene Knockout Techniques , Gene Regulatory Networks , Humans , Imatinib Mesylate/pharmacology , Interleukin-3/antagonists & inhibitors , Interleukin-3/metabolism , Interleukin-6/antagonists & inhibitors , Interleukin-6/metabolism , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology , Models, Biological , bcl-X Protein/genetics , bcl-X Protein/metabolism , ras Proteins/genetics , ras Proteins/metabolismABSTRACT
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.
Subject(s)
Membrane Glycoproteins/genetics , Nucleocapsid Proteins/genetics , RNA, Viral/genetics , Severe Acute Respiratory Syndrome/virology , Severe acute respiratory syndrome-related coronavirus/genetics , Viral Envelope Proteins/genetics , Amino Acid Substitution/genetics , Coronavirus Nucleocapsid Proteins , Genome, Viral , Humans , Mutation, Missense , Point Mutation , Polymorphism, Genetic , RNA, Viral/isolation & purification , Severe acute respiratory syndrome-related coronavirus/isolation & purification , Spike Glycoprotein, CoronavirusABSTRACT
A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to rapidly detect the severe acute respiratory syndrome-associated coronavirus (SARS-CoV). The assay, based on multiple primer and probe sets located in different regions of the SARS-CoV genome, could discriminate SARS-CoV from other human and animal coronaviruses with a potential detection limit of <10 genomic copies per reaction. The real-time RT-PCR assay was more sensitive than a conventional RT-PCR assay or culture isolation and proved suitable to detect SARS-CoV in clinical specimens. Application of this assay will aid in diagnosing SARS-CoV infection.