Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension

This paper demonstrates how to create an HFPNe (hybrid functional Petri net with extension) model, using the lac operon gene regulatory mechanism and glycolytic pathway as an example. Using this example, readers can then model other biopathways of interest. Simulations of the HFPNe model were performed using the software package Genomic Object Net.     

Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes

Modelling and simulation of complex cellular transactions involve development of platforms that understand diverse mathematical representations and are capable of handling large backend computations. Grid Cellware, an integrated modelling and simulation tool, has been developed to precisely address these niche requirements of the modelling community. Grid Cellware implements various pathway simulation algorithms along with adaptive Swarm algorithm for parameter estimation. For enchanced computational productivity Grid Cellware uses grid technology with Globus as the middleware.     

Genomic Markers for Differentiation of Francisella tularensis subsp. tularensis A.I and A.II Strains

Tularemia is caused by two subspecies of Francisella tularensis, F. tularensis subsp. tularensis (type A) and F. tularensis subsp. holarctica (type B). F. tularensis subsp. tularensis is further subdivided into two genetically distinct populations (A.I and A.II) that differ with respect to geographical location, anatomical source of recovered isolates, and disease outcome. Using two human clinical isolates, suppression subtractive hybridization was performed to identify 13 genomic regions of difference between A.I and A.II strains. Two PCR assays, one to identify A.I and A.II as well as to discriminate between F. tularensis subsp. holarctica and F. novicida and another specific for A.I, were developed. This is the first report to identify and characterize conserved genomic differences between A.I and A.II.     

Manuo-ocular coordination in target tracking. I. A model simulating human performance

During eye tracking of a self-moved target, human subjects' performance differs from eye-alone tracking of an external target. Typical latency between target and eye motion onsets is shorter, ocular smooth pursuit (SP) saturation velocity increases and the maximum target motion frequency at which the SP system functions correctly is higher. Based on a previous qualitative model, a quantitative model of the coordination control between the arm motor system and the SP system is presented and evaluated here. The model structure maintains a high level of parallelism with the physiological system. It contains three main parts: the eye motor control (containing a SP branch and a saccadic branch), the arm motor control and the coordination control. The coordination control is achieved via an exchange of information between the arm and the eye sensorimotor systems, mediated by sensory signals (vision, proprioception) and motor command copy. This cross-talk results in improved SP system performance. The model has been computer simulated and the results have been compared with human subjects' behavior observed during previous experiments. The model performance is seen to quantitatively fit data on human subjects. Received: 6 March 1997 / Accepted in revised form: 15 July 1997     

GIV: A Tool for Genomic Islands Visualization

A Genomic Islands (GI) is a chunk of DNA sequence in a genome whose origin can be traced back to other organisms or viruses. The detection of GIs plays an indispensable role in biomedical research, due to the fact that GIs are highly related to special functionalities such as disease-causing GIs - pathogenicity islands. It is also very important to visualize genomic islands, as well as the supporting features corresponding to the genomic islands in the genome. We have developed a program, Genomic Island Visualization (GIV), which displays the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs. GIV was implemented in C++, and was compiled and executed on Linux/Unix operating systems.

Availability

GIV is freely available for non-commercial use at http://www5.esu.edu/cpsc/bioinfo/software/GIV     

InSatDb: A Genomic Tool for Insect Geneticists

Microsatellites show tremendous variation between genomes in terms of their occurrence and composition. Availability of whole genome sequences allows us to study microsatellite characteristics of fully sequenced insect genomes to understand the evolution and biological significance of microsatellites. InSatDb is an insect microsatellite database that provides an interactive interface to query information on microsatellites annotated with size (in base pairs and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%). Here, we present a snap shot of the distribution and composition of microsatellites in introns and exons of insect genomes. The data present interesting observations regarding the microsatellite life-cycle and genome flux.     

Control of human eye movements: I. modelling of extraocular muscle

The properties of extraocular muscle are important in consideration of the control of human eye movements. A proposed model for human extraocular muscle is based on the anatomical and physiological evidence; it considers both the static and dynamic properties of active and passive muscle. The passive parallel elasticity was determined from the length-tension curves for passive muscle, while the active series elasticity was defined utilizing quick stretch results for active muscle. The characteristics of active muscle as the tension generator were computed from length-tension data; the force-velocity relationship was used to describe the viscosity of active muscle. Simulations using the muscle model accurately depicted the quick stretch experiments of both active and passive muscle as well as the isometric development of muscle force to a state of tentanus. The model will be incorporated into an overall representation of the extraocular plant mechanism in the immediately suceeding paper.     

Performance of membrane fixed biocatalyst reactors. I: Membrane reactor systems and modelling

Enzymatic membrane reactors are discussed according to the state of biocatalyst and driving force of reaction. Particular attention is given to the Capillary Membrane Fixed Enzyme Reactor (CAMFER) for its favorable characteristics. It is shown that, for a practical range of operation conditions, both kinetic and mass transfer effects must be considered simultaneously. Three modes of operation were investigated in detail using enzymatic lactose hydrolysis as a model reaction: Diffusional reactor, Recycle reactor, and Backflush reactor. In the comparison, superior performance of the CAMFER in diffusional mode was clearly demonstrated.     

稻麦轮作FACE系统平台I.系统结构与控制

在稻麦轮作水稻田建立FACE系统 (Free AirCO2 Enrichment) ,即CO2 浓度的控制和监测系统平台 .利用计算机网络系统对平台的CO2 浓度进行监测控制 ,根据大气中的CO2 浓度、风向、风速 ,作物冠层高度的CO2 浓度及昼夜等因素的变化调节CO2 气体的释放速度及方向 ,实现FACE圈的CO2 浓度高于周围大气CO2 浓度 2 0 0 μmol·mol-1.试验表明 ,影响控制精度的主要因素有风速、作物和土壤呼吸作用和扩散层高度 .经过控制方程参数调整 ,在白天 ,控制精度达到 80 %的时间占总时间的白天达到 83% ,夜晚为6 8% .FACE圈内的CO2 分布基本均匀 .平均CO2 设置浓度白天为 5 5 7mol·mol-1,晚上为 6 0 8mol·mol-1.圈内CO2 浓度分布基本上沿放气管对称分布 ,由边沿向中心逐步降低 .2 0 0 1年水稻生长季节平均控制精度 (TAR)达到白天 1.0 3和晚间 1.0 9.     

Genomic and proteomic profiling I: Leiomyomas in African Americans and Caucasians

Background  

Clinical observations indicate that leiomyomas occur more frequently in African Americans compared to other ethnic groups with unknown etiology. To identify the molecular basis for the difference we compared leiomyomas form A. Americans with Caucasians using genomic and proteomic strategies.     

A simple force platform.

The force platform consists of a sandwhich of steel, Rockwool and concrete plates about 900 X 700 mm in surface. Four steel rings were bolted to the under side of the steel plate in each corner. Each steel ring was furnished with only one strain gauge, two of which were placed on the outer- respectively on the inner side of each ring. The four strain gauges were connected to a measuring bridge. Before mounting the rings on the steel plate, the sensitivity to pressure of each ring was adjusted in such a way that they were all similar. Because of this the platform responded with a signal which was independent of where a pressure was applied within the surface of the platform. The platform showed a rectilinear response for static forces up to 500 kp with a stable zero value. In response to dynamic forces the platform showed a resononance frequency of about 50 Hz, with a damping factor of 0.15. Calibration of dynamic forces was carried out by calculation of the forces during a vertical jump compared with what would be expected from the time of flight also registered by the platform-measuring-bridge-ink-writer-set-up. The time of flight was significantly higher (11%) than exected from the time-force relations beforetake-off. This was esplained partly by the relatively low damping factor in the system, partly by the subjects not extending their knees at landing on the platform.     

Genomic and proteomic biomarkers for cancer: A multitude of opportunities

Biomarkers are molecular indicators of a biological status, and as biochemical species can be assayed to evaluate the presence of cancer and therapeutic interventions. Through a variety of mechanisms cancer cells provide the biomarker material for their own detection. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Biomarkers have potential both as diagnostic indicators and monitors of the effectiveness of clinical interventions. Biomarkers are also able to stratify cancer patients to the most appropriate treatment. Effective biomarkers for the early detection of cancer should provide a patient with a better outcome which in turn will translate into more efficient delivery of healthcare. Technologies for the early detection of cancer have resulted in reductions in disease-associated mortalities from cancers that are otherwise deadly if allowed to progress. Such screening technologies have proven that early detection will decrease the morbidity and mortality from cancer. An emerging theme in biomarker research is the expectation that panels of biomarker analytes rather than single markers will be needed to have sufficient sensitivity and specificity for the presymptomatic detection of cancer. Biomarkers may provide prognostic information of disease enabling interventions using targeted therapeutic agents as well as course-corrections in cancer treatment. Novel genomic, proteomic and metabolomic technologies are being used to discover and validate tumor biomarkers individually and in panels.     

A model for simulating cognate recognition and response in the immune system.

We have constructed a model of the immune system that focuses on the clonotypic cell types and their interactions with other cells, and with antigens and antibodies. We carry out simulations of the humoral immune system based on a generalized cellular automaton implementation of the model. We propose using computer simulation as a tool for doing experiments in machine, in the computer, as an adjunct to the usual in vivo and in vitro techniques. These experiments would not be intended to replace the usual biological experiments since, in the foreseeable future, a complete enough computer model capable of reliably simulating the whole immune would not be possible. However a model simulating areas of interest could be used for extensively testing ideas to help in the design of the critical biological experiments. Our present model concentrates on the cellular interactions and is quite adept at testing the importance and effects of cellular interactions with other cells, antigens and antibodies. The implementation is quite general and unrestricted allowing most other immune system components to be added with relative ease when desired.     

Programs simulating a I lost eric and other enzyme kinetics for computer-aided teaching

Two programs have been written in BASIC as a teaching aid for instruction of HNC, HND, and degree students in a strategy of experimentation, taking enzyme kinetics as a particular example. Little prior knowledge is required to use the programs. One of the programs (ENZY) simulates the action of a non-allosteric enzyme as (a) a simple case with or without inhibitors including substrate inhibition (b) a two-substrate case with either random-order or ping-pong kinetics. The other program (ALLO) simulates the action of an allosteric enzyme with or without activators or inhibitors or both. A detailed example of an investigation using ALLO is given.