iGEM 2020 — Team BIT

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# Team:BIT/Notebook

* Home
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* Project
  + [Description](https://2020.igem.org/Team%3ABIT/Description)
  + [Bio](https://2020.igem.org/Team%3ABIT/Bio)
  + [Hardware](https://2020.igem.org/Team%3ABIT/Hardware)
  + [Model](https://2020.igem.org/Team%3ABIT/Model)
  + [Engineering](https://2020.igem.org/Team%3ABIT/Engineering)
  + [Implementation](https://2020.igem.org/Team%3ABIT/Implementation)
  + [Proof Of Concept](https://2020.igem.org/Team%3ABIT/Proof_Of_Concept)
  + [Contribution](https://2020.igem.org/Team%3ABIT/Contribution)
* Practice
  + [Overview](https://2020.igem.org/Team%3ABIT/Human_Practices)
  + [Silver](https://2020.igem.org/Team%3ABIT/Silver)
  + [Integrated Practice](https://2020.igem.org/Team%3ABIT/Integrated_Practice)
  + [Education](https://2020.igem.org/Team%3ABIT/Education)
* Judge
  + [Medal](https://2020.igem.org/Team%3ABIT/Medal)
  + [Safety](https://2020.igem.org/Team%3ABIT/Safety)
* Team
  + [Members](https://2020.igem.org/Team%3ABIT/Members)
  + [Collaborations](https://2020.igem.org/Team%3ABIT/Collaborations)
  + [Partnership](https://2020.igem.org/Team%3ABIT/Partnership)
  + [Notebook](https://2020.igem.org/Team%3ABIT/Notebook)
  + [Attributions](https://2020.igem.org/Team%3ABIT/Attributions)
  + [Excellence in Another Area](https://2020.igem.org/Team%3ABIT/Excellence_in_Another_Area)

# NOTEBOOK

The COVID-19 disrupted the BIT team's 2020 arrangements, but we adjusted our plan and continued to work towards our goals.

### 03.31-04.06

We brainstormed and finalized this year’s project, and continue to conduct literature research to add details

### 04.07-07.06

* Conduct literature research, supplement project details, and write project documents.
* Design how to conduct experiments after the epidemic is over.
* The team members interviewed doctors, volunteers and other staff in their hometowns.
* Team BIT conducts data collection on the two platforms of Weibo and bilibili.

### 07.07-08.06

* Team BIT prepared a series of special courses for teammates
* Team BIT and team BIT-China cooperate on personnel training.
* Continue to conduct literature research to supplement project details
* Follow up the latest progress of global research on the COVID-19 and make improvements to the project
* Design experiment

### 08.07-09.06

* Participated in the iGEMer exchange meeting in Beijing and received a lot of suggestions to help our team think about the project
* Make relevant preparations before CCIC and conduct in-depth cooperation on relevant content with the BIT-China team
* Participated in CCIC and received many suggestions to help us improve the project
* Participated in virus Police——From scouting to arresting, and had in-depth exchanges with teams on the same project about the new crown virus
* Improve the project through suggestions
* Conduct data analysis of popular science research reports

### 09.07-10.06

* Continue to expand and modify the content of the project
* Revisit the interviewee
* Visited CapitalBio
* Do some pre-experiments

### 10.07-10.27

* Do experiment for more data
* Completed research reports on popular science publicity work
* Held a series of offline science promotion activities
* Conducted a series of offline lectures in cooperation with the BIT-China team
* Write WIKI
* WIKI freeze!

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# Team:BIT/Engineering

* Home
  + [Home](https://2020.igem.org/Team%3ABIT)
* Project

  + [Desciption](https://2020.igem.org/Team%3ABIT/Description)+ [Bio](https://2020.igem.org/Team%3ABIT/Bio)
    + [Hardware](https://2020.igem.org/Team%3ABIT/Hardware)
    + [Model](https://2020.igem.org/Team%3ABIT/Model)
    + [Engineering](https://2020.igem.org/Team%3ABIT/Engineering)
    + [Implementation](https://2020.igem.org/Team%3ABIT/Implementation)
    + [Proof Of Concept](https://2020.igem.org/Team%3ABIT/Proof_Of_Concept)
    + [Contribution](https://2020.igem.org/Team%3ABIT/Contribution)
* Practice

  + [Overview](https://2020.igem.org/Team%3ABIT/Human_Practices)
  + [Silver](https://2020.igem.org/Team%3ABIT/Silver)
  + [Integrated Practice](https://2020.igem.org/Team%3ABIT/Integrated_Practice)
  + [Education](https://2020.igem.org/Team%3ABIT/Education)
* Judge

  + [Medal](https://2020.igem.org/Team%3ABIT/Medal)
  + [Safety](https://2020.igem.org/Team%3ABIT/Safety)
* Team

  + [Members](https://2020.igem.org/Team%3ABIT/Members)
  + [Collaborations](https://2020.igem.org/Team%3ABIT/Collaborations)
  + [Partnership](https://2020.igem.org/Team%3ABIT/Partnership)
  + [Notebook](https://2020.igem.org/Team%3ABIT/Notebook)
  + [Attributions](https://2020.igem.org/Team%3ABIT/Attributions)
  + [Excellence
    in Another Area](https://2020.igem.org/Team%3ABIT/Excellence_in_Another_Area)

CONNECT WITH US

---

email: igem\_bit@outlook.com

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BOOKMARK

---

* [1.Nucleic acid aptamer replacement system applied to sample pretreatment](#1)

* [2.Application of nucleic acid amplification method to signal amplification](#2)

* [3.Temperature control for stable control of nucleic acid amplification](#3)

* [4.Application of test strips in optical signal detection](#4)

* [5.Fingertip gyroscope is used in centrifugal chip drive](#5)

* [6. Application of applet development to the detection of optical results](#6)

# Engineering

## 1.Nucleic acid aptamer replacement system applied to sample pretreatment

In this project, a nucleic acid aptamer replacement system is used to design an aptamer
replacement system for the N protein of the new coronavirus to convert protein signals into
nucleic acid signals. Use biotin-streptavidin to bind magnetic beads on one end of the nucleic
acid aptamer, which can be fixed by a magnet, and the aptamer can bind to its complementary
chain through the hydrogen bond force of complementary base pairing. The target protein is
stored in the aptamer, and the protein will bind to the aptamer. Since the force between the
protein and the aptamer is greater than the hydrogen bond force, the complementary chain is
released, thereby achieving the purpose of converting the protein signal into a nucleic acid
signal. This method is simpler and easier to operate, and the cost is much more considerable,
and the detection accuracy is more accurate than only nucleic acid detection, which reduces
false — the probability of negative or false positive. Aiming at the binding length of the aptamer
and the complementary chain, we designed the complementary chain S1 and S2 in the experiment.
The long chain complementary chain S2 reacts well after competing with CKMB. Its length is 25
bp and its sequence is 5' -FAM-CCCAACCCCCTAAAAGCATCCTCCG, this result proves that the nucleic
acid aptamer has been successfully obtained.

## 2.Application of nucleic acid amplification method to signal amplification

In this step, we use RCA and HCR technology to amplify the complementary strands obtained from
the previous step of nucleic acid aptamer replacement. We finally use colloidal gold to detect
the experimental products. We also successfully carried out the amplification experiment and got
the ideal result.

The RCA amplification products obtained in this experiment are as follows: The products of this
RCA experiment were characterized by 2% agarose gel electrophoresis. D2000 was used as the marker
for this experiment. During agarose gel electrophoresis, the lanes 1-6 from left to right next
to D2000 Maker were: blank, sample , Sample, sample, sample, blank, the experimental results
are shown in Figure 1. According to the experimental results, we can conclude that because RCA
amplified long chains, the bands at the opening of lanes 2-5 can prove the success of this RCA
amplification.

![](https://static.igem.org/mediawiki/2020/9/97/T--BIT--engineering_1.png)

#### Figure 1. RCA experiment result graph

According to the experimental results, we can conclude that there are electrophoresis bands
because the long strands of nucleic acid have been amplified from HCR, which proves that the
HCR amplification is successful.

![](https://static.igem.org/mediawiki/2020/8/83/T--BIT--engineering_2.png)

#### Figure 2. HCR experiment result graph

## 3.Temperature control for stable control of nucleic acid amplification

Our temperature control module can provide our amplification with stable temperature, the
commonly used PCR amplification on the temperature change after heating denaturation and
annealing of two steps, which requires the device in the temperature control needs to have
the ability of rapid heating and cooling, which means you need larger space to provide
equipment heat dissipation of the environment, but also has great power to provide our
equipment.However, because of our need for miniaturization and portability, we did not adopt
PCR as our amplification technology. Instead, we adopted an amplification method with low
requirement for temperature change to meet our demand for portability. This amplification
method only needs to be amplified at constant temperature.

Since the amplification temperature we needed was constant, we initially considered whether we
could use human body to amplify the nucleic acid temperature of our chip. However, considering
the biosafety and stable temperature required for amplification, we looked elsewhere.Finally,
we chose a single chip microcomputer to control our temperature. The temperature control unit
of this project is based on the temperature sensor and automatic control algorithm to achieve
a constant temperature of 37℃.Temperature control circuit of the working mechanism is: the use
of Pt1000 temperature sensors and form A complete set of temperature measuring circuit
temperature signal acquisition temperature control unit, the single-chip computer MSP430 with
A/D sampling module, software control algorithm is used to calculate the control quantity,
and then through the I/O port output power control MOS tube or load switch on and off, output
constant current control hardware circuit, and unit of heating and cooling, heating and rely
on simple control PID algorithm, guarantee the stability of temperature.The following picture
is the image of temperature data fitting using Matlab after the temperature sensor is used to
receive the temperature.

![](https://static.igem.org/mediawiki/2020/3/34/T--BIT--engineering_3.png)

#### Figure 3. Temperature curve of constant temperature process

![](https://static.igem.org/mediawiki/2020/4/45/T--BIT--engineering_4.png)

#### Figure 4. Temperature curve during the heating process

## 4.Application of test strips in optical signal detection

The project uses colloidal gold immunochromatography to carry out accurate control testing
of experimental results, the process of which includes the following three steps: sample
preparation, immune response and colloidal gold detection. We need to add the pre-treated
sample to the specific chamber of the centrifugal chip, make the sample to reach the chamber
where the two kinds of side flow test paper are located by rotating the chip and using the
centrifugal force, capture the samples to the test line of the side flow test paper respectively
through the immune chromatography reaction, and then observe and analyze the color development
results of the colloidal gold chromatography strip ,and analyze the colloidal gold images by
taking pictures with mobile phones to obtain the comparison results of the red chromaticity
in RGB with the standard positive chromaticity. The following is the experimental operation:

① Mix the positive sample, the loading buffer solution and the colloidal gold solution that
have been subjected to the HCR reaction in a 37 ℃ incubator in advance. The volume of the
three solutions is 15 μL, 70 μL and 15 μL, totaling 100 μL. Inject the mixed solution into the
chip chamber, and place the test strip with the capture probe embedded in the specific area;

② Rotate the centrifugal chip to make the mixed liquid enter the test strip area, and the liquid
soaks the entire test strip under capillary action. Observe the condition of the C line and T
line of the test strip. In Figure 5, the strips of the test strip from left to right are the C
line and T line respectively, and double strips appear to prove a positive result;

![](https://static.igem.org/mediawiki/2020/5/53/T--BIT--engineering_5.png)

#### Figure 5. Process of mixing liquid injection and flow into test strip

![](https://static.igem.org/mediawiki/2020/9/99/T--BIT--engineering_6.png)

#### Figure 6. Positive test strip result

③ Repeat the above steps to react the blank control group without positive samples to obtain the
negative band result as shown in Figure 7.

![](https://static.igem.org/mediawiki/2020/2/23/T--BIT--engineering_7.png)

#### Figure 7. Negative test strip result

## 5.Fidget spinner is used in centrifugal chip drive

Centrifugal force drive is a unique technology in microfluidic driving technology, and its
system uses the centrifugal force generated by the chip to make circular motion as the driving
force of the liquid flow. The flow velocity can be adjusted and controlled by changing the
rotation speed of the chip and designing different channel configurations.

The special feature of our centrifugal microfluidic chip is that it does not use a motor, but
uses a pushing hand to drive the microfluidic chip to rotate, so as to construct a simulated
gravity field, that is, the centrifugal field, and the flow is controlled by the volume force
acting on the material in the centrifugal microfluidic chip, so as to get rid of the complicated
laboratory equipment. Centrifugal microfluidic chip can be designed as a closed system, which
means that the centrifugal microfluidic chip can realize the functions of pre-storage, release,
mixing and reaction of reagents or samples, which greatly enhances the convenience of the chip.
One of the characteristics of centrifugal force drive is that the power is applied to all the
liquid flows on the chip. The advantage of centrifugal force is that it can provide the driving
force of all the structural units on the chip at the same time, which is of great significance
for the high-throughput analysis of microfluidic chips; Due to the characteristics of centrifugal
motion, centrifugal microfluidic chips usually build flow channels and chambers on a CD-shaped
disk, and the radian of each part needs to be adjusted or designed according to the rotation
center. In the centrifugal microfluidic chip, the volume force can be controlled by controlling
the rotation speed and angular acceleration, and driven by the volume force, the liquid in the
flow channel will flow by itself, and because there is no other liquid flowing in, the
centrifugal microfluidic chip needs to open a hole to let the air enter the original space of
the substitute liquid, so as to avoid the vacuum force restricting the liquid flow. Therefore,
unlike the continuous liquid flow in other microfluidic chips, the flow in centrifugal
microfluidic chips is mostly gas-liquid two-phase flow.

Based on the previous model construction, we have produced a centrifugal microfluidic chip
prototype, as shown in the figure below. Instead of installing gaskets in this chip, we rotate
directly with a solid center shaft. Preliminary tests show that the chip can maintain a
basically stable rotation and speed with the handheld center shaft. The following is the
experimental operation:

①In order to simulate the fluid flow during the actual rotation of the centrifugal chip, we
injected 100μL of pigment into the amplification chamber of the chip, and placed a test strip
in the chip test strip area in advance. It is evaluated by visually observing the pigment flow.
Figure 8 shows that the pigment can be injected normally without entering the test strip area;

![](https://static.igem.org/mediawiki/2020/0/09/T--BIT--engineering_8.png)

#### Figure 8. Pigment injection

②Turn the chip upside down to deposit the pigment in the amplification chamber on the other
side of the chip chamber, and at the same time turn the centrifugal chip to rotate around the
central axis. The liquid in the amplification chamber enters the test strip chamber under the
action of centrifugal force, and covers the entire test strip under the capillary action of the
test strip. By observing the liquid flow during the rotation process and the pigment diffusion
of the test strip, it can be proved that the centrifugal force provided by the toggle chip can
drive the liquid in the amplification chamber into the detection area of the test strip.

![](https://static.igem.org/mediawiki/2020/7/7f/T--BIT--engineering_9.png)

#### Figure 9. Actual driving situation

## 6.Application of mini program development to the detection of optical results

Through the construction of the Mini Program, we have completed the following functions:
reading images, fitting image features and solution concentration, output image, output
predictive concentration.

Software interaction module: based on the development of WeChat Mini Program, extract image
color (RGB) and other features, use the least squares method to linearly fit to obtain the
relationship between feature and concentration.

The least squares method (also known as the least square method) is a mathematical optimization
technology. It matches the best function of finding data by minimizing the square of the error.
The least squares method can be used to easily find unknown data and minimize the sum of the
error between the obtained data and the actual data.

Software interaction process: the mobile phone takes multiple images, reads the image in the
small program, manually enters the solution concentration, image processing, fittings the
relationship between the image characteristics and the solution concentration, inputs new
images in the small program, and outputs and predicts the concentration.

![](https://static.igem.org/mediawiki/2020/2/20/T--BIT--engineering_10.png)

#### Figure 10. WeChat mini program operation interface

Description of WeChat Mini Program:

1.Enter the concentration value and click Upload Image to upload the picture. Click Color
Feature1 to extract color features, you can upload at least 2 to 5 samples;

2.Upload a new image to extract new features, use the least square method to fit and output
the predicted concentration.

Created By Beijing Institute of Technology

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# Team:BIT/Experiments

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

If you made Parts this year, please remember to put all information, characterization, and measurement data on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).

### What should this page contain?

* Protocols
* Experiments

### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:BIT/Results

# Results

You can describe the results of your project and your future plans here.

### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

### Describe what your results mean

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember **all measurement and characterization data must also be on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).** Otherwise these data will not be in consideration for any medals or part awards!
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)