Difference between revisions of "Template:Jilin China/Modle C.js"

(Created page with "→‎* * * @authors lhx * @date 2019-05-30 16:25:38 * @version 1.1: var content_alpha = { prospect:{ title:"Model" }, part: [{ title: "Overview", para:...")
 
Line 295: Line 295:
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "In our Human Practices, we have seriously considered the benefit our project bring to world and whether our works followed scientifically valid methods. How we investigated these issues and the methods we engaged with communities are demonstrated on the Human Practices Page. Besides, what we have gained and what we have thought are also laid out. <a href=\"https://2019.igem.org/Team:Jilin_China/Human_Practices\">Click here for more details about our Human Practices.</a>",
+
cont: "The bare DNA molecule is considered as a one-dimensional lattice with numerous free binding sites. One can consider the lattice very long and therefore neglect end effects(sup)[4](suped).",
 
class: "np5"
 
class: "np5"
 
},
 
},
 +
{
 +
type: "word",
 +
cont: "In the same system, the length of a DNA molecule is linearly correlated with the number of EB molecules combined on it.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "4. Result",
 +
class: "np2"
 +
},
 +
{
 +
type: "word",
 +
cont: "In the same system, the following equations can be obtained.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "We can get C(sub)DNA(subed) from the known marker concentration C(sub)Marker(subed).",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "The parameters involved in the above equation are as follows:",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "In order to analyze the gray level of the image, we use computer to recognize the brightness of the image, and express the brightness as the ordinate in the 3D model.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 5. First of all, the image data is imported into matlab and the brightness value is specified between 1-255. Next we convert the pixel points in the image into a double precision numerical matrix according to the brightness, and use the matrix to generate a 3D histogram, which can intuitively reflect the brightness of different parts of the rubber chart.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 6. By directly clicking the point on the model, we can get the coordinates of x, y and z represented by this point. The x and y represent the position of the point in the matrix, and z represents the brightness of the point.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 6. By directly clicking the point on the model, we can get the coordinates of x, y and z represented by this point. The x and y represent the position of the point in the matrix, and z represents the brightness of the point.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 7. In order to calculate the average brightness of a DNA strip, the following algorithm is designed. First, input the approximate x, y coordinate range of the strip to be calculated into the program, so that the selected range is a rectangular area. Then calculate the brightness value Ф of the center point of the selected area by computer, and specify a fluctuation value μ. Other points of which brightness Φ(sub)n(subed) in the selected area meets the requirement of Ф-μ<Ф(sub)n(subed)<Ф+μ will be added to the queue. Next we calculate the average value of the brightness at the midpoint of all queues, which can represent the strip brightness.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 8. For example, if we want to find the average brightness of the above DNA bands, we select the region and output the region matrix with D (:, 211:231) and D (203:215,:). Select the center luminance value 208.5 and set the up fluctuation value 40 and down fluctuation value 10. Pick out the data that meet the conditions, then average the values. The red area is the center point data, and the area within the red box is the data that meet the conditions.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Figure 9. Finally, the average value can be output, which represents the average value of brightness in this area. The brightness of the selected DNA bands can reflect the amount of combined ethidium bromide. The DNA content of the bands can also be reflected, so as to carry out other analysis and verification.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "After obtaining the brightness of the target fragment: Ф(sub)DNA(subed) =220.4, we use the same method to obtain the brightness of the target strip with the size of 3000bp of 1kb DNA ladder: Ф(sub)Marker(subed) = 903.41, and we know that L(sub)DNA(subed)= 6092 bp, V(sub)DNA= 3 μL, V(sub)Marke(subed)r= 5 μL, C(sub)Marker(subed)= 20 ng/μL, and bring the above data into the equation:",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "We can reach that C(sub)DNA(subed)=16.51 ng/μL.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Next the data we obtained could be used in other experiments such as DNA connection and this model offerred great help to our experiments.",
 +
class: "np5"
 +
},
 +
 
 
 
 
 
 
Line 305: Line 381:
 
},
 
},
 
{
 
{
−
title: "Gold",
+
title: "Market Prediction Model",
 
para: [
 
para: [
  
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Integrated Human Practices",
+
cont: "1. Introduction",
 
class: "np2"
 
class: "np2"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "We started from the project itself, discussed and investigated with social professionals, whose suggestions certainly helped us a lot to improve the project to further change the world. Our Integrated Human Practices has greatly guided our project. <a href=\"https://2019.igem.org/Team:Jilin_China/Human_Practices\">Click here for more details about our Human Practices.</a>",
+
cont: "To inquire the public acceptance of our gynecology gel and the relationship between market distribution and age group, a market prediction model was built based on the results we obtained from our Human Practices part.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "After analyzing each question in our questionnaires and selecting all the useful questions, we defined different indicators for each option and calculated the evaluation function by age distribution, then we got the results and plotted a figure to show the results more clearly. ",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Improve a Previous Part / Project",
+
cont: "2. Data Processing",
 
class: "np2"
 
class: "np2"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "We have constructed a BBa_K3078012 part as the improvement of BBa_K2150031. <a href=\"http://parts.igem.org/Part:BBa_K3078012\">Click here for more details about our Parts.</a>",
+
cont: "1. Division of age groups
 +
According to the feedbacks from questionnaires in Human Practices, we divided the age into the following six groups. Mark different Age groups as Age(i), and Age(sub)i(subed) for the number of respondents in each group.
 +
",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "2. Division of age groups",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Model Your Project",
+
cont: "From all the questions in the questionnaires, we selected 6 useful questions, which were named Q(sub)j(subed) (j=1~6). The feedbacks of the subjects on these questions directly determined the potential market share of gynecological gel in all ages. These questions are as follows:",
−
class: "np2"
+
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "We have designed complete and instructive models which not only helped us confirm the project but also made our experiment easier. <a href=\"https://2019.igem.org/Team:Jilin_China/Model\">Click here for more details about our Model.",
+
cont: "Each option of these questions was assigned a certain value according to their effect on the result.",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Demonstration of Your Work",
+
cont: "Take Q(sub)2(subed) (Ever had vaginitis.) for example:",
−
class: "np2"
+
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "There are two options, “Yes” or “No”, assign them to a(sub)1(subed)=1, a(sub)2(subed)=0 respectively.",
 +
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "We have succeeded in proving that our system works with lab data and it’s also clearly demonstrated in the Demonstrate page. <a href=\"https://2019.igem.org/Team:Jilin_China/Demonstrate\">Click here for more details about our Demonstrate.</a>",
+
cont: "For Age (5):",
 
class: "np5"
 
class: "np5"
 
},
 
},
−
+
{
−
]
+
−
 
+
−
},
+
−
 
+
−
{
+
−
title: "Special Awards",
+
−
para: [
+
−
 
+
−
{
+
 
type: "word",
 
type: "word",
−
cont: "Best Education and Public Engagement",
+
cont: "Age(sub)5(subed)=368 means “ The number of respondents aged 36~45 is 368”; ",
−
class: "np2"
+
class: "np5"
 
},
 
},
−
{
+
{
 
type: "word",
 
type: "word",
−
cont: "For education and public participation, we set up many educational tools and public participation activities throughout the project. We established a two-way dialogue with society, realized the value of the project to public and enabled more people to participate in synthetic biology.",
+
cont: "x(sub)1(subed)=141 means “The number of respondents choosing Yes is 141”;",
 
class: "np5"
 
class: "np5"
 
},
 
},
−
{
+
{
 
type: "word",
 
type: "word",
−
cont: "We organized classes, debates and other activities for students of different ages and distributed manuals to enhance students' understanding of synthetic biology. We organized activities like synthetic biology forum, laboratory opening day and campus enrollment promotion day to increase the public's understanding of synthetic biology and let more people join in. We launched an education campaign for children with special needs to give them equal access to synthetic biology education; we set up multi-media tools like official accounts, Facebook to interact with society; we drafted a policy brief to address the problem of the classification of biological waste and appeal for it to be used.",
+
cont: "x(sub)2(subed)=44 means “The number of respondents choosing No is 44”.",
 
class: "np5"
 
class: "np5"
 
},
 
},
−
{
+
{
 
type: "word",
 
type: "word",
−
cont: "Best Integrated Human Practices",
+
cont: "And we define Result(sub)Qj(Age(i))(subed) as a factor of EvF.",
−
class: "np2"
+
class: "np5"
 
},
 
},
−
 
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Human practices guide our project and enable our project to bring more social influence. By interviewing doctors, patients and analyzing 1700 questionnaires, we found that Vulvovaginal candidiasis (VVC) accounted for 40% of all Vaginitis. The current antifungal treatment has led to drug resistance. Therefore, we designed a new VVC treatment approach. Then, experts in immunology and molecular biology were invited to improve our project. Meanwhile, since our experiment involves fungi, laboratory safety specifications were made with the assistance of laboratory safety experts. In addition, our project involves genetic modification. Thus, the ethics considerations were evaluated by ethical experts. To make it practical, we also visited pharmacies, enterprises and other institutions to get practical application suggestions. The integrated human practices not only guide us to accomplish the project but also make our project more closely related to society and more meaningful. For these advantages, we hope to apply for the best Human Practices.",
+
cont: "Then:",
 
class: "np5"
 
class: "np5"
 
},
 
},
−
  {
+
{
 
type: "word",
 
type: "word",
−
cont: "Best Model",
+
cont: "4. Horizontal analysis:",
 
class: "np2"
 
class: "np2"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "To simulate and predict the curative effect of the therapeutic system, an ODE kinetic framework was built based on cellular and biochemical reactions to model the relationship between the concentration of (ita)C. albicans(itaed) and expression of downstream gene of P(sub)BC(subed). ",
+
cont: "We considered all the questions at a certain age, like Age(5), and defined the evaluation function (EvF) as:",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "To have a simple analysis of the DNA concentration in the electrophoretic band, we built a gray analysis model and combined it with gray-concentration analysis equation during our experiments. For the future application, we built a model to forecast customer acceptance among different age groups. We analyzed and defined multiple indicators in the questionnaire. The model was then built by calculating the evaluation function of these indicators according to the age distribution.Our model not only guides the experiments, but also predicts future application. For these two advantages, we want to apply for the Best Model.",
+
cont: "Take Age(5) for example:",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Dr. Tiejun Gu and Mrs. Xiangyu Meng provided guidance on the use of basic instruments and safety standards for instrument operation. ",
+
cont: "Except for Q(sub)2(subed), the other questions were analyzed by the same way of previous step;",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Best Wiki",
+
cont: "Then:",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "5. Vertical analysis:",
 
class: "np2"
 
class: "np2"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "The original HXT 8.0 automatic typesetting system is adopted. Wiki has added many user-friendly functions, you can try to select a paragraph of text! The text is typeset in two ways. You can switch between settings. There are more features in settings and textlab to discover! Web pages are compatible with mobile phones, tablets and computers.",
+
cont: "After performing horizontal analysis for the other age groups, the EvF of each age group was obtained.",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Best New Basic Part",
+
cont: "Then, we got the market share corresponding to each age group by normalization of EvF(sub)Age(i)(subed) (i=1, 2, ... 6).  ",
−
class: "np2"
+
class: "np5"
 
},
 
},
−
  {
+
{
 
type: "word",
 
type: "word",
−
cont: "Have a look on our favourite basic part: BBa_K3078003",
+
cont: "The result is shown in the following table: ",
 
class: "np5"
 
class: "np5"
 
},
 
},
 
{
 
{
 
type: "word",
 
type: "word",
−
cont: "Best New Composite Part",
+
cont: "6. The relationship between EvF and Age(i) is reflected in the figure below: ",
−
class: "np2"
+
class: "np5"
 
},
 
},
−
    {
+
{
 
type: "word",
 
type: "word",
−
cont: "Have a look on our favourite composite part: BBa_K3078100",
+
cont: "The picture shows that different age groups have different preferences for gynecological gels. People in the 26-55 age group are more receptive to our products. ",
 
class: "np5"
 
class: "np5"
−
}
+
},
−
 
+
−
 
+
 
]
 
]
  
 
},
 
},
 +
 
 
 +
{
 +
title: "References",
 +
para: [
  
 +
{
 +
type: "word",
 +
cont: "[1] Prieto M A, Garcia J L. Identification of the 4-hydroxyphenylacetate transport gene of Escherichia coli W: construction of a highly sensitive cellular biosensor[J]. FEBS Lett, 1997, 414(2): 293-7.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "[2] Buchler N E, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits[J]. Proc Natl Acad Sci U S A, 2005, 102(27): 9559-64.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "After analyzing each question in our questionnaires and selecting all the useful questions, we defined different indicators for each option and calculated the evaluation function by age distribution, then we got the results and plotted a figure to show the results more clearly. ",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "[3] Tscherner M, Giessen T W, Markey L, et al. A Synthetic System That Senses Candida albicans and Inhibits Virulence Factors[J]. ACS Synth Biol, 2019, 8(2): 434-444.",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "[4] Rocha M S. Revisiting the neighbor exclusion model and its applications[J]. Biopolymers, 2010, 93(1): 1-7.
 +
 +
 +
",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "2. Division of age groups",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "From all the questions in the questionnaires, we selected 6 useful questions, which were named Q(sub)j(subed) (j=1~6). The feedbacks of the subjects on these questions directly determined the potential market share of gynecological gel in all ages. These questions are as follows:",
 +
class: "np5"
 +
},
 +
{
 +
type: "word",
 +
cont: "Each option of these questions was assigned a certain value according to their effect on the result.",
 +
class: "np5"
 +
},
 +
 +
 +
]
 +
 +
},
  
  

Revision as of 23:25, 21 October 2019

/** 

* 
* @authors lhx 
* @date    2019-05-30 16:25:38
* @version 1.1
*/



var content_alpha = { prospect:{ title:"Model" }, part: [{ title: "Overview", para: [

{ type: "word", cont: "A good model can not only facilitate and conduct experiments, but also guide the project from design to application. Jilin_China has designed three models this year, which guide our project from different aspects.", class: "np5" }, { type: "word", cont: "1. We established an ODE model to show the relationship between the concentration of (ita)C. albicans(itaed) and the expression of downstream proteins of the P(sub)BC(sub) promoter. The model can also provide guidance for experiments on sensing system. According to this model, the theoretical curative effect of our product can be predicted. It also makes it possible for comparisons between Guardian of Rose and existing therapies. For more about our (ita)C. albicans(itaed) Sensing Model.", class: "np5" }, { type: "word", cont: "2. Based on the results from HP, we established a market prediction model to predict the public acceptance of our gynaecological gel and the relationship between market distribution and age groups. Questions in the questionnaire were analyzed and each option was defined in different indicators and assigned. Then we calculated the evaluation function according to the age distribution to get the results. For more about our Market Prediction Model.", class: "np5" }, { type: "word", cont: "3. In the process of molecular cloning experiments, it’s often a big problem for the semi-quantitative analysis of the target gene concentration through the results of electrophoresis. We need this data to carry out the following experiments such as the vector construction. Therefore, the gray analysis model was devised and combined with gray-concentration analysis equation during our experiments. This model will greatly facilitate and guide our experiments. For more about our Gene Concentration Prediction Model.", class: "np5" },



]

}, { title: "(ita)C. albicans(itaed) Sensing Model ", para: [

{ type: "word", cont: "1. Principle", class: "np12 }, { type: "word", cont: "(ita)C. albicans(itaed) secrete 4-HPA (4-hydroxyphenylacetic acid), which can enter the cell through the transport protein HpaX on the cell membrane and bind to the protein HpaA to form a complex. After binding to the downstream inducible P(sub)BC(subed) promoter, the complex can activate the transcription of P(sub)BC(subed) downstream genes. Click here to know our design of sensor.", class: "np5" }, { type: "word", cont: "2. Introduction", class: "np2" }, { type: "word", cont: "In order to explore the relationship between inducer 4-HPA and the expression of P(sub)BC(subed) downstream genes, we established an ordinary differential equation model.", class: "np5" }, type: "word", cont: "This model can provide guidance for our experiments in designing the sensing system. In addition, we can also predict the theoretical curative effect of the therapeutic system in our project, which makes it possible to compare the curative effect of Guardian of Rose with existing therapies.", class: "np5" }, { type: "word", cont: "3. Assumption", class: "np2" }, { type: "word", cont: "In order to ensure the solvability and analytical capability of the model, the complex system is assumed as follows:", class: "np5" }, { type: "word", cont: "1. HpaA and HpaX are both overexpressed in (ita)E. coli(itaed);", class: "np5" }, { type: "word", cont: "2. Extracellular 4-HPA concentration remains constant;", class: "np5" }, { type: "word", cont: "3. The catabolism of 4-HPA in (ita)E. coli(itaed) is ignored;", class: "np5" }, { type: "word", cont: "4. DNA degradation is ignored;", class: "np5" }, { type: "word", cont: "5. The maximum transcription rate of P(sub)BC(subed) promoter is 2 nt/s;", class: "np5" }, { type: "word", cont: "6. The binding of 4-HPA to HpaA and their complex to P(sub)BC(subed) promoter are instantaneous processes;", class: "np5" }, { type: "word", cont: "7. A single ribosome is involved in translation.", class: "np5" }, {go type: "word", cont: "4. Biochemical Reactions", class: "np2" }, { type: "word", cont: "Based on the working principle of the sensing system and assumptions above, the following biochemical reaction equations can be deduced as follows:", class: "np5" }, { type: "word", cont: "(1) The 4-HPA secreted by (ita)C. albicans(itaed) enters the cell membrane by the way of diffusion and passive transport which is functioned by transporter HpaX;", class: "np5" }, { type: "word", cont: "(2) The 4-HPA that enters the cell binds to HpaA and forms Complex1;", class: "np5" }, { type: "word", cont: "(3) Complex1 binds to P(sub)BC(subed) promoter immediately and transcribes the downstream target gene;", class: "np5" }, { type: "word", cont: "(4) The mRNA is translated into GFP;", class: "np5" }, { type: "word", cont: "(5) The degradation of mRNA and GFP exists in the previous step.", class: "np5" },

{ type: "word", cont: "5. ODE:", class: "np2" }, { type: "word", cont: "(1) The entry of 4-HPA into cells through the transporter HpaX is an enzyme-catalyzed reaction and it is known that the maximum rate is V(sub)max(subed) and the apparent Michaelis constant is K(sub)t(subed) (Consider that part of 4-HPA enters through diffusion). According to Michaelis equation, for a constant concentration of 4-HPA outside the cell[4-HPA(ex)], the rate of 4-HPA entering the cell is:", class: "np5" }, { type: "word", cont: "(2) If HpaA is overexpressed in cell, the forming rate of Complex1 at equilibrium, which is formed by 4-HPA and HpaA, depends on the entering rate of 4-HPA. [Com1] represents the concentration of complex1, then:", class: "np5" }, { type: "word", cont: "(3) It is known that the transcription rate of mRNA downstream P(sub)BC(subed) promoter is a, the average copy number of pSB1C3 is C(sub)n(subed), the number of cells in the system is N, and the half-life of mRNA is t(sub)1(subed). [mRNA] is used to express molecule numbers of mRNA. In addition, Hill equation is selected to fit the regulation of Complex1 on P(sub)BC(subed) promoter. The net production rate of mRNA depends on both the production and the degradation rate of mRNA:", class: "np5" }, { type: "word", cont: "(4) Given that the translation rate from each mRNA to GFP is b and the half-life of GFP is t(sub)2(subed), the net production rate of GFP depends on the production and the degradation rate of GFP. The number of GFP molecules is represented by [GFP], then:", class: "np5" }, { type: "word", cont: "(5) There is a linear relationship between the number of GFP molecules [GFP] and fluorescence units (FSU), and the proportional coefficient is d, then:", class: "np5" }, { type: "word", cont: "The parameters involved in the above ODE equations are as follows:", class: "np5" }, { type: "word", cont: "6. Result", class: "np2" }, { type: "word", cont: "The parameters involved in the above ODE equations are as follows:", class: "np5" }, { type: "word", cont: "According to the experiment, we consider that after 12 h, the number of engineered bacteria reaches 1*10(sup)9(suped) and our bacteria stay in the growth plateau until 24 h. Their proliferation after 12 h is ignored and 4-HPA is considered as having fully played its maximum induction effect during this period. So we can assign values to t. According to the curve fit by matlab, we know the relationship between concentration of 4-HPA (nmol/L) and fluorescence units (FSU) when t is valued 12 h, 16 h, 20 h and 24 h. ", class: "np5" }, { type: "word", cont: "7. Analysis", class: "np2" }, { type: "word", cont: "Assuming that the concentration of (ita)C. albicans(itaed) is in linear relationship with that of 4-HPA they secrete, the proportionality constant is k (k=14000nmol/L*mL(sup)[3](suped)), c represents the concentration of (ita)C. albicans(itaed), then:", class: "np5" }, { type: "word", cont: "Considering that pVE5523 will be used as the vector when our project is put into application, which carries sensing system, therapeutic system and suicide system simultaneously, the above ordinary differential equations can be modified as follows:", class: "np5" }, { type: "word", cont: "The parameters involved in the above ODE are as follows:", class: "np5" }, { type: "word", cont: "By solving the above ODE and assigning values to each parameter according to the above table, considering engineered bacteria may exist at a stable concentration in the vagina, we assign t to 12 h, 16 h, 20 h, 24 h and the relationship between (ita)C. albicans(itaed) concentration (mL(sup)-1(suped)) and molecule numbers of tetR [tetR] can be obtained at different time:", class: "np5" }, { type: "word", cont: "It is known that when P(sub)tet(subed) is 100% repressed, [tetR]= e. According to the fact that every four tetR can bind to one P(sub)tet(subed), which will cause the inhibition of promoter transcription, we could know:", class: "np5" }, { type: "word", cont: "According to figure 3, when e=2*10(sup)12(suped) and t=24 h, 20 h, 16 h, 12 h，c=1.943*10(sup)4(suped)/mL, 3.368*10(sup)4(suped)/mL, 6.633*10(sup)4(suped)/mL, 15.99*10(sup)4(suped)/mL respectively.", class: "np5" }, { type: "word", cont: "When the suicide system is just completely inhibited, we could know the concentration of (ita)C. albicans(itaed) in this state from above analysis, which corresponds to the minimum curative effect of our therapeutic system. The therapeutic system will continue working for some time after the suicide system is activated. Therefore, the curative effect should theoretically be better.", class: "np5" }, { type: "word", cont: "When the suicide system is just completely inhibited, we could know the concentration of (ita)C. albicans(itaed) in this state from above analysis, which corresponds to the minimum curative effect of our therapeutic system. The therapeutic system will continue working for some time after the suicide system is activated. Therefore, the curative effect should theoretically be better.", class: "np5" },


]

}, { title: "Gene Concentration Prediction Model", para: [

{ type: "word", cont: "1. Introduction：", class: "np2" }, { type: "word", cont: "Our experiments involved a large number of DNA electrophoresis in order to analyze the length and concentration of different DNA fragments obtained from our experiments. Based on the analysis of the obtained fluorescent images, we established an approximate relationship between the concentration of DNA molecules with different length.", class: "np5" }, { type: "word", cont: "Its significance is reflected in:", class: "np5" }, { type: "word", cont: "It is easier for grayscale analysis model to operate than existing apps. The way of inputting horizontal and vertical coordinates as data locates the area to be analyzed more accurately, and the analysis of brightness is also more accurate.", class: "np5" }, { type: "word", cont: "2. Principle", class: "np2" }, { type: "word", cont: "Ethidium bromide (EtBr) is a conventional intercalator for visualizing DNA, which binds between adjacent base pairs of dsDNA and fluoresces. ", class: "np5" }, { type: "word", cont: "3. Assumption", class: "np2" }, { type: "word", cont: "The bare DNA molecule is considered as a one-dimensional lattice with numerous free binding sites. One can consider the lattice very long and therefore neglect end effects(sup)[4](suped).", class: "np5" }, { type: "word", cont: "In the same system, the length of a DNA molecule is linearly correlated with the number of EB molecules combined on it.", class: "np5" }, { type: "word", cont: "4. Result", class: "np2" }, { type: "word", cont: "In the same system, the following equations can be obtained.", class: "np5" }, { type: "word", cont: "We can get C(sub)DNA(subed) from the known marker concentration C(sub)Marker(subed).", class: "np5" }, { type: "word", cont: "The parameters involved in the above equation are as follows:", class: "np5" }, { type: "word", cont: "In order to analyze the gray level of the image, we use computer to recognize the brightness of the image, and express the brightness as the ordinate in the 3D model.", class: "np5" }, { type: "word", cont: "Figure 5. First of all, the image data is imported into matlab and the brightness value is specified between 1-255. Next we convert the pixel points in the image into a double precision numerical matrix according to the brightness, and use the matrix to generate a 3D histogram, which can intuitively reflect the brightness of different parts of the rubber chart.", class: "np5" }, { type: "word", cont: "Figure 6. By directly clicking the point on the model, we can get the coordinates of x, y and z represented by this point. The x and y represent the position of the point in the matrix, and z represents the brightness of the point.", class: "np5" }, { type: "word", cont: "Figure 6. By directly clicking the point on the model, we can get the coordinates of x, y and z represented by this point. The x and y represent the position of the point in the matrix, and z represents the brightness of the point.", class: "np5" }, { type: "word", cont: "Figure 7. In order to calculate the average brightness of a DNA strip, the following algorithm is designed. First, input the approximate x, y coordinate range of the strip to be calculated into the program, so that the selected range is a rectangular area. Then calculate the brightness value Ф of the center point of the selected area by computer, and specify a fluctuation value μ. Other points of which brightness Φ(sub)n(subed) in the selected area meets the requirement of Ф-μ<Ф(sub)n(subed)<Ф+μ will be added to the queue. Next we calculate the average value of the brightness at the midpoint of all queues, which can represent the strip brightness.", class: "np5" }, { type: "word", cont: "Figure 8. For example, if we want to find the average brightness of the above DNA bands, we select the region and output the region matrix with D (:, 211:231) and D (203:215,:). Select the center luminance value 208.5 and set the up fluctuation value 40 and down fluctuation value 10. Pick out the data that meet the conditions, then average the values. The red area is the center point data, and the area within the red box is the data that meet the conditions.", class: "np5" }, { type: "word", cont: "Figure 9. Finally, the average value can be output, which represents the average value of brightness in this area. The brightness of the selected DNA bands can reflect the amount of combined ethidium bromide. The DNA content of the bands can also be reflected, so as to carry out other analysis and verification.", class: "np5" }, { type: "word", cont: "After obtaining the brightness of the target fragment: Ф(sub)DNA(subed) =220.4, we use the same method to obtain the brightness of the target strip with the size of 3000bp of 1kb DNA ladder: Ф(sub)Marker(subed) = 903.41, and we know that L(sub)DNA(subed)= 6092 bp, V(sub)DNA= 3 μL, V(sub)Marke(subed)r= 5 μL, C(sub)Marker(subed)= 20 ng/μL, and bring the above data into the equation:", class: "np5" }, { type: "word", cont: "We can reach that C(sub)DNA(subed)=16.51 ng/μL.", class: "np5" }, { type: "word", cont: "Next the data we obtained could be used in other experiments such as DNA connection and this model offerred great help to our experiments.", class: "np5" },



]

}, { title: "Market Prediction Model", para: [

{ type: "word", cont: "1. Introduction", class: "np2" }, { type: "word", cont: "To inquire the public acceptance of our gynecology gel and the relationship between market distribution and age group, a market prediction model was built based on the results we obtained from our Human Practices part.", class: "np5" }, { type: "word", cont: "After analyzing each question in our questionnaires and selecting all the useful questions, we defined different indicators for each option and calculated the evaluation function by age distribution, then we got the results and plotted a figure to show the results more clearly. ", class: "np5" }, { type: "word", cont: "2. Data Processing", class: "np2" }, { type: "word", cont: "1. Division of age groups According to the feedbacks from questionnaires in Human Practices, we divided the age into the following six groups. Mark different Age groups as Age(i), and Age(sub)i(subed) for the number of respondents in each group. ", class: "np5" }, { type: "word", cont: "2. Division of age groups", class: "np5" }, { type: "word", cont: "From all the questions in the questionnaires, we selected 6 useful questions, which were named Q(sub)j(subed) (j=1~6). The feedbacks of the subjects on these questions directly determined the potential market share of gynecological gel in all ages. These questions are as follows:", class: "np5" }, { type: "word", cont: "Each option of these questions was assigned a certain value according to their effect on the result.", class: "np5" }, { type: "word", cont: "Take Q(sub)2(subed) (Ever had vaginitis.) for example:", class: "np5" }, { type: "word", cont: "There are two options, “Yes” or “No”, assign them to a(sub)1(subed)=1, a(sub)2(subed)=0 respectively.", class: "np5" }, { type: "word", cont: "For Age (5):", class: "np5" }, { type: "word", cont: "Age(sub)5(subed)=368 means “ The number of respondents aged 36~45 is 368”; ", class: "np5" }, { type: "word", cont: "x(sub)1(subed)=141 means “The number of respondents choosing Yes is 141”;", class: "np5" }, { type: "word", cont: "x(sub)2(subed)=44 means “The number of respondents choosing No is 44”.", class: "np5" }, { type: "word", cont: "And we define Result(sub)Qj(Age(i))(subed) as a factor of EvF.", class: "np5" }, { type: "word", cont: "Then:", class: "np5" }, { type: "word", cont: "4. Horizontal analysis:", class: "np2" }, { type: "word", cont: "We considered all the questions at a certain age, like Age(5), and defined the evaluation function (EvF) as:", class: "np5" }, { type: "word", cont: "Take Age(5) for example:", class: "np5" }, { type: "word", cont: "Except for Q(sub)2(subed), the other questions were analyzed by the same way of previous step;", class: "np5" }, { type: "word", cont: "Then:", class: "np5" }, { type: "word", cont: "5. Vertical analysis:", class: "np2" }, { type: "word", cont: "After performing horizontal analysis for the other age groups, the EvF of each age group was obtained.", class: "np5" }, { type: "word", cont: "Then, we got the market share corresponding to each age group by normalization of EvF(sub)Age(i)(subed) (i=1, 2, ... 6). ", class: "np5" }, { type: "word", cont: "The result is shown in the following table: ", class: "np5" }, { type: "word", cont: "6. The relationship between EvF and Age(i) is reflected in the figure below: ", class: "np5" }, { type: "word", cont: "The picture shows that different age groups have different preferences for gynecological gels. People in the 26-55 age group are more receptive to our products. ", class: "np5" },

]

},


{ title: "References", para: [

{ type: "word", cont: "[1] Prieto M A, Garcia J L. Identification of the 4-hydroxyphenylacetate transport gene of Escherichia coli W: construction of a highly sensitive cellular biosensor[J]. FEBS Lett, 1997, 414(2): 293-7.", class: "np5" }, { type: "word", cont: "[2] Buchler N E, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits[J]. Proc Natl Acad Sci U S A, 2005, 102(27): 9559-64.", class: "np5" }, { type: "word", cont: "After analyzing each question in our questionnaires and selecting all the useful questions, we defined different indicators for each option and calculated the evaluation function by age distribution, then we got the results and plotted a figure to show the results more clearly. ", class: "np5" }, { type: "word", cont: "[3] Tscherner M, Giessen T W, Markey L, et al. A Synthetic System That Senses Candida albicans and Inhibits Virulence Factors[J]. ACS Synth Biol, 2019, 8(2): 434-444.", class: "np5" }, { type: "word", cont: "[4] Rocha M S. Revisiting the neighbor exclusion model and its applications[J]. Biopolymers, 2010, 93(1): 1-7.


", class: "np5" }, { type: "word", cont: "2. Division of age groups", class: "np5" }, { type: "word", cont: "From all the questions in the questionnaires, we selected 6 useful questions, which were named Q(sub)j(subed) (j=1~6). The feedbacks of the subjects on these questions directly determined the potential market share of gynecological gel in all ages. These questions are as follows:", class: "np5" }, { type: "word", cont: "Each option of these questions was assigned a certain value according to their effect on the result.", class: "np5" },


]

},


]

}