Cell Control Mechanism Of A Model Genetic Terminator System Case Study

Better Essays
Aim: To understand cell control mechanism of a model genetic terminator system and to develop potential termination strategies through computational modelling .

Motivation:
The aim of IGEM- IISER Pune team is to develop a rapid, cost effective, sensitive and portable device for detection of tuberculosis. We adopt a three component tuberculosis diagnosing device consisting of
1 Hijacking Module which would take over cell cycle control inducing rapid replication
2 Detection module which forces targeted cells to produce a visual reporter in form of a pigment.
3 A termination module to self destruct cells or cease further replication to prevent uncontrolled growth.

Objective: To use computational modelling to gain insights
…show more content…
The equations descibing the model are given as:
N
Cell density at given point of time
Nm
Carrying capacity k Growth rate constant
E
Concentration of toxin
A
Concentration of AHL kE Production rate of toxin dE Degradation rate of toxin kA Production rate of AHL dA Degradation rate of AHL d*E Death rate of cells

Here the first equation is a modified logistic curve with an added death rate term(dEN).
The second equation describes the productin of toxin(E) as linearly proportinal to the AHL concentration and the third assumes that AHL(A) formed is proportional to the no of cells.
Both AHL and killer protein are assumed to degrade by first order kinetics with given rate constants.

Assuming the constitutive promoter of same strength as the IPTG inducible one there would be no change in KA .
We thus solve the ODEs for the initial condition (t=0) [N=1250 , A=0 ,E=0] .
The following values of parameters were used:
Parameter
Value
Unit
d
4.0E-03
nM-1h-1 dE 2 h-1 kA
4.8E-07
nM ml h-1 kE 5 h-1 Table 1: Parameters for termination model1

Two sets of values of k , NM ,dA were used in different simulations.

Value for pH 6.2
Value for pH 6.6
Unit
…show more content…
The results shown (in Results section) for Approach 1 are for the values of k , NM , dA given in pH 6.6 column
Approach 2: Delayed termination
Based on the results of Approch 1 a delay term was introduced to allow the population to reach significant numbers initially . This was incorporated as “T” the time at which the terminator module is switched on.
T is an arbitarily time after population close to Nm is reached.
It was expected that by switching it onn at a later time T(when the population is saturated) we would get better population growth initially(tT) :Terminator circuit is switched on . This is same as the the original problem with xinit=Nm
Merging the solutions leads to the full solution

The same values of parameters in Table 1 used in Aprroach 1 are used for this simulation.
The results shown are for the values of k , NM , dA given in pH 6.2 column in Table 2.

Approach 3: Pigment initiated termination.

Looking at the results of Approach 2 where the delayed termination was seen to be more effective , we decided to couple it with the detection module such that the killer gene is activated when a certain concentration of pigment is

Related Documents

  • Decent Essays

    Aim 3. Validation of transcriptional drivers and therapeutic combinations in CRPC. Rationale and strategy: To experimentally validate computationally predicted drivers of CRPC, we will use loss- and gain-of-function approaches for in vitro (i.e., cell lines) and in vivo (i.e., xenograft models) experimental validation to determine whether these genes are essential for drug-resistance. Computationally inferred drug combinations will be validated for their effect on MRs’ activity and ability to govern drug resistance and tumorigenicity. Furthermore, inferred drug combinations will be analyzed using RNA sequencing of treated tumors for their synergistic action and potential benefits for patients with castration-resistant prostate cancer.…

    • 1661 Words
    • 7 Pages
    Decent Essays
  • Decent Essays

    Algorithm isolate the most relevant group of feature and then to class individual that have the considered disease according to these association. Operator to allow GA to explore the search space. GA plays crucial role in disease diagnosis .The dimension of data reduced using GA algorithm techniques. The supervised feature selection of disease used in GA (GA-BN Algorithm combined with SVM (Support vector machine)).The hybrid structure of GA-NN implemented for better performance…

    • 1062 Words
    • 5 Pages
    Decent Essays
  • Decent Essays

    Aiming to develop a highly cost-effective colorimetric assay for pathogenic DNA detection, D. Saikrishnan et al. were able to immobilize sulfhydryl-modified oligonucleotide probes complementary to a segment of pathogenic bacterial DNA sequence IS6110 from Mycobacterium tuberculosis on the surface of tosyl…

    • 911 Words
    • 4 Pages
    Decent Essays
  • Decent Essays

    Tempkin Isotherm Essay

    • 982 Words
    • 4 Pages

    The values of k2 for removal of iron by Tribulus Terrestris adsorbents was calculated from the slopes of the respective linear plots of t/Qt vs. t (Figure.10).The correlation coefficients, R2 was 0.994 for Tribulus Terrestris respectively suggest a strong relationship between the parameters and also explain that the process follows pseudo second order kinetics (Table 6 ). Elovich kinetic model Elovich model suggests that the chemisorptions, i.e. a chemical reaction, is probably the Mechanism that controls the rate of adsorption. This model can be applied with success in liquid solution and the linear form of the Elovich equation is: Q_t= 1/β ln⁡αβ+ 1/β ln⁡t ..................................8 Where, α (mg g-1) is the initial sorption rate and β (g mg-1) is the desorption constant. The values of α and β can be calculated from the slope and intercept of the plot of Qt versus ln t…

    • 982 Words
    • 4 Pages
    Decent Essays
  • Decent Essays

    PDAC biomarker identification and validation. Biomarkers in ex vivo expanded CTCs will be recognized by stringent statistical analysis and subjected to further characterization in three studies. First, we will confirm the association of biomarkers with CTCs and CTC-PDX models. Second, the biomarkers will be validated for correlation with clinical PDAC metastasis and therapeutic resistance. Finally, we will retrospectively test the application of selected biomarkers in PDAC diagnosis, treatment evaluation and disease prognosis.…

    • 1048 Words
    • 4 Pages
    Decent Essays
  • Decent Essays

    T Cells Essay

    • 1316 Words
    • 6 Pages

    Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is an essential immune-regulatory molecule (showed on triggered T cells and a portion of regulatory T cells) able to down-regulate T cell activation. Blockade of CTLA-4 has been shown in animal models to improve the effectiveness of cancer immunotherapy (citation). This study founded that CTLA-4 is a valuable molecule regulating the resistance to “self” antigens in humans and recommends a role for CTLA-4 blockade in crumbling its tolerance to human cancer antigens for cancer immunotherapy. Furthermore, known that CTLA-4 is not existent on resting T cells but is up regulated for two to three days after T cell activation (citation). Since CTLA-4 seems to impair T cell initiation, efforts have been made to obstruct the antigen-4 activity in murine models of cancer immunotherapy.…

    • 1316 Words
    • 6 Pages
    Decent Essays
  • Decent Essays

    Tumor cells often take advantage of these mechanisms by using immunological brakes or checkpoints to escape the immune system. Cytotoxic T -lymphocyte-associated antigen 4 (CTLA-4) and Programmed death 1 (PD-1) are targets for cancer treatment. CTLA-4 is a protein found on surface of T cells that binds to B7 family molecules expressed by dendritic cells through an inhibitory pathway, thus preventing CD28 from binding to B7 (Pardoll 2012). This pathway leads to suppression of T cell activation freeing cancer cells from immunosurveilance. Researchers have developed monoclonal antibodies (drugs) for CTLA-4 to activate the CD28/B7 T cell activation and elicit an immune response against tumors (Alegre & Fallarino 2006).…

    • 1172 Words
    • 5 Pages
    Decent Essays
  • Decent Essays

    In this experiment, bacteria will be used in an attempt to perform genetic transformation, “Naturally competent bacteria are able to take up exogenous DNA and undergo genetic transformation.” Dubnau, David. 2004. DNA uptake during bacterial transformation. Nature Reviews Microbiology. 2,…

    • 1643 Words
    • 7 Pages
    Decent Essays
  • Decent Essays

    Analysis Of HCV DNA

    • 975 Words
    • 4 Pages

    Using Primer Express version 2 (Applied Biosystems) software, CrossLife Technologies (CLT) will design the PNA probe sets targeting several highly conserved regions within the HCV. In Phase 1, only probes to HCV will be synthesized and tested. The other probes will be synthesized and tested in Phase 2 when we develop the multiplex detection test for HCV, HBV, HDV, and HEV. PNAs can be easily synthesized and functionalized, are more stable, and are more responsive to point-mutations than their DNA counterpart. Several PNA probe combinations will be evaluated experimentally to determine the most efficient combination.…

    • 975 Words
    • 4 Pages
    Decent Essays
  • Decent Essays

    2.5. Statistical analysis Multivariate analysis was performed using two algorithms: PCA and 2-D HCA heat map. The PCA, based on the correlation matrix, was performed using XLStat-Pro 2015 software. The 2-D HCA heat map was carried out with the ArrayTrack, and the Ward's minimum-variance method was used for runs and hydrocarbons clustering. A probability level of p=0.05 was considered as significant difference.…

    • 2062 Words
    • 9 Pages
    Decent Essays