NYCU-Taipei IGEM Team

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2024 iGEM NYCU-Taipei team團隊招募來囉!👀✨想要對合成生物學的應用有更多了解、在大學生涯裡獲得更多實作經驗嗎?或是想要對iGEM這個競賽有更多的了解嗎?那你絕對不能錯過今天的iGEM NYCU-Taipei tea...
05/12/2023

2024 iGEM NYCU-Taipei team團隊招募來囉!👀✨
想要對合成生物學的應用有更多了解、在大學生涯裡獲得更多實作經驗嗎?或是想要對iGEM這個競賽有更多的了解嗎?

那你絕對不能錯過今天的iGEM NYCU-Taipei team招生說明會🔥
歡迎各位同學一起加入iGEM這個大家庭!

活動資訊🔎
地點:陽明校區 守仁樓 104教室
時間:2023/12/14(星期四)19:00-21:00

🔎聯絡資訊
張菁芬 老師
janechang. [email protected]

🔎活動報名連結

https://docs.google.com/forms/d/e/1FAIpQLSdLWv0FSdGalh1B2Tx0iseYrMDoI7cyQzyKDCqdY3FhWNgCTA/viewform

(現在備有pizza哦🍕)

生物系統模擬是了解這些系統如何隨時間運作必不可少的事。細菌已經發展出專門的訊號傳遞系統,能夠對環境變化做出適應性反應。其中最簡單的系統之一涉及兩個蛋白質成分,被稱為雙組分系統(TCS),在我們的實驗裡是SaeS和SaeR。我們使用了一個在D...
28/10/2023

生物系統模擬是了解這些系統如何隨時間運作必不可少的事。細菌已經發展出專門的訊號傳遞系統,能夠對環境變化做出適應性反應。其中最簡單的系統之一涉及兩個蛋白質成分,被稱為雙組分系統(TCS),在我們的實驗裡是SaeS和SaeR。

我們使用了一個在DH5α大腸桿菌株中基因上的pSB1C3中的phla-mCerluean(BBa_K4822007)來研究Sae系統的動態變化,以便在不同濃度的鋅離子情況下找出最佳表現量。為此,我們採用了(Gayer 2014)模型中的常微分方程式,並模擬鋅離子濃度的變化如何影響螢光蛋白。

根據我們的實際實驗結果,只有在鋅離子濃度超過1mM時,我們才能觀察到螢光蛋白基因表達被鋅離子抑制。未來,我們計劃繼續增加數據集,以提高趨勢線的可靠性並減少誤差。

The use of mathematical models to study biological systems is a crucial step in gaining insight into how these systems function over time.Bacteria have developed specialized signal transduction systems that allow them to respond adaptively to environmental changes. One of the simplest types of these systems involves two protein components, known as two-component systems (TCS), which are SaeS and SaeR in our case.

We studied the dynamics of the Sae system using a phla-mCerluean generator (BBa_K4822007) in the pSB1C3 backbone in a DH5α E. coli strain. We wanted to find out the dynamic range of our promoter that gives optimal expression with respect to different concentrations of zinc ions. For this purpose we’ve used ordinary differential equations adopted from (Gayer 2014) model and demonstrate how change in zinc ions concentration affects the FP.

According to our empirical findings, it is only when the concentration of zinc ions exceeds 1 mM that we can observe the inhibition of fluorescent protein gene expression. In the future, we plan to continue increasing the dataset to enhance the reliability of the trend line and reduce errors.

Part two鑑於這些挑戰,我們提出了第2版本,主要改進是3D打印的外殼。這個版本考慮了比色皿和測量電路的位置,並提供了更方便的設備操作和保護。此外,LED光源和感光元件的佈局由180度變為90度,以有效阻擋激發光。經過分析,我們確定了最...
26/10/2023

Part two
鑑於這些挑戰,我們提出了第2版本,主要改進是3D打印的外殼。這個版本考慮了比色皿和測量電路的位置,並提供了更方便的設備操作和保護。此外,LED光源和感光元件的佈局由180度變為90度,以有效阻擋激發光。經過分析,我們確定了最佳的激發光波長為445nm,這一設計被採納。

為了提升使用者體驗,我們添加了按鈕和OLED屏幕,使使用者可以無需電腦操作設備。最終的設備以低成本、小尺寸、便攜性、高準確性和可定制設計為特點,提供了優良的使用者體驗並帶來無限商機。

In light of these challenges, we proposed the second version, with a major improvement being the 3D-printed casing. This version considered the placement of the cuvette and measurement circuit, offering more convenient device operation and protection. Furthermore, the layout of the LED light source and photosensitive components changed from 180 degrees to 90 degrees to effectively block excitation light. Through analysis, we identified the optimal excitation light wavelength as 445nm, which was adopted.

To enhance the user experience, we added a button and an OLED screen on the device's surface, allowing users to operate the device without a computer. The final device, characterized by low cost, small size, portability, high accuracy, and customizable design, offers an excellent user experience and vast business opportunities.

Part one我們的螢光蛋白量測硬體靈感來自於COVID-19快速檢測試劑盒,這些試劑盒因其便攜性、使用者友好性、即時性、準確性、易用性和價格親民而廣受歡迎。為了應對在人體內檢測早期炎症反應的挑戰,我們提出了一種炎症快速檢測試劑盒的概念,...
26/10/2023

Part one
我們的螢光蛋白量測硬體靈感來自於COVID-19快速檢測試劑盒,這些試劑盒因其便攜性、使用者友好性、即時性、準確性、易用性和價格親民而廣受歡迎。為了應對在人體內檢測早期炎症反應的挑戰,我們提出了一種炎症快速檢測試劑盒的概念,並依照專家意見和反饋制定了以下設計原則:便攜性、提供即時且精確的結果、使用者友好、易於取得且價格實惠、內建感應和記錄功能。
在第1版本中,我們的設備採用了10cm的正方形尺寸,以容納比色皿。外部設計設有一個鉸鏈上蓋,以在測量過程中創造完全的黑暗環境。這種設計消除了需要額外組件如螺絲的需求。為了測量光通量(流明),我們使用光敏電阻器和可變電阻,從而簡化了整個設備。
數據分析方面,第1版本的目標是檢查總光通量(包括激發光和散射光的組合)與純激發光光通量的比率,期望較高的比率能提供更好的結果。然而,第1版本的實驗數據並不足夠可靠,因為無法明確區分激發光強度的變化和散射光的影響。這導致了複雜的數據處理,使得設計變得不切實際。

Our fluorescent protein measurement hardware was inspired by COVID-19 rapid test kits, which have gained acclaim for their portability, user-friendliness, real-time results, accuracy, ease of use, and affordability. Addressing the challenges of detecting early inflammatory responses in the human body, we envisioned an inflammation rapid test kit. Guided by expert insights and feedback, we formulated the following design principles: portability, instant and precise results, user-friendliness, accessibility, affordability, and embedded sensing and recording.
In the first version, our device featured a 10cm square design to accommodate a cuvette. The external design included a hinged cover to create complete darkness during measurements, eliminating the need for additional components like screws. To measure light flux (lumens), we used a light-dependent resistor (LDR) and a variable resistor, simplifying the device.
Regarding data analysis, the primary goal of the first version was to examine the ratio of total light flux (comprising both excitation and scattered light) to pure excitation light flux, with higher ratios expected to yield better results. However, the experimental data from the first version was not reliable enough, as it was challenging to differentiate changes in excitation light intensity from the influence of scattered light. This complexity in data processing rendered the design impractical.

今年,NYCU-Taipei團隊設計了一個生物性裝置,將改造過後的細菌送入裝置內,以快速檢測發炎反應中的生物標記(biomarker)。我們之所以選擇發炎反應作為我們的研究目標是因為在發炎反應的早期階段,從外部表現出的症狀可能不太明顯,也讓...
24/10/2023

今年,NYCU-Taipei團隊設計了一個生物性裝置,將改造過後的細菌送入裝置內,以快速檢測發炎反應中的生物標記(biomarker)。我們之所以選擇發炎反應作為我們的研究目標是因為在發炎反應的早期階段,從外部表現出的症狀可能不太明顯,也讓人很難區分發炎的嚴重程度。此外,我們希望設計出來的裝置可以達到非侵入性的特質,因此在檢體方面,我們主要針對的是可從唾液與尿液中偵測的生物標記。最後,我們選擇了兩種生物標記,分別是L-Tyrosine與Calprotectin,藉此反映體內發炎反應的情形。

L-Tyrosine在人體內屬於必要胺基酸,同時它與路易氏體失憶症 (Lewy Body Dementia, LBD) 所導致的發炎症狀有關聯。路易氏體失智症是繼阿茲海默症之後,第二常見的神經退化性失智症。在我們設計的檢測裝置內,L-Tyrosine會與TyrR蛋白質結合,透過抑制啟動子去調節下游基因的表現。

Calprotectin是由兩個蛋白質次單元體構成,分別是S100A8跟S100A9。它與類風濕性關節炎、發炎性腸道疾病、系統性紅斑狼瘡等病症具備相關性。我們透過Two-Component System SaeS/R與鋅離子,間接測量Calprotectin的濃度,並調節下游基因。

Our team presents a rapid-reaction bio-device that can detect inflammatory biomarkers with engineered bacteria. We selected two biomarkers based on their relevancy to inflammation reactions. The reason of why we choose the inflammatory response as our target is because that in the early stage of inflammatory response, the outside symptoms might not be apparent and be hard for us to distinguish the severity of inflammation. Beside, another goal of our project is we hope to design a detection device that can be non-invasive. Therefore, the criterion of biomarker selection is that it could be found in saliva or urine, which are samples that are convinient for us to aquire. Based on these two main considerations we narrowed down to two biomarkers which are L-Tyrosine and Calprotectin.

L-tyrosine is an essential amino acid in our bodies and it is associated with inflammation in patients with Lewy Body Dementia (LBD). Lewy Body Dementia is the second most common form of neurodegenerative dementia after Alzheimer's disease.
In the detection system, when tyrosine binds to the TyrR protein, it can regulate downstream genes by inhibiting its downstream promoter.

The other biomarker, Calprotectin, consists of proteins S100A8 and S100A9 that can bind to zinc ions. It's related to diseases like rheumatoid arthritis, systemic lupus erythematosus, and inflammatory bowel disease. For detection, we indirectly measure calprotectin using zinc ions and the Two-Component System (TCS), SaeS/R, to regulate downstream genes.

CCU-Taiwan我們於9月19日與台灣的CCU團隊進行了會面,這也是我們首次合作的團隊。在討論中,他們提出了一些我們認為具有建設性的問題,其中一些也是我們尚未解決的問題。例如,他們問及MIT Inventor是否可以供iOS用戶使用,以...
23/10/2023

CCU-Taiwan
我們於9月19日與台灣的CCU團隊進行了會面,這也是我們首次合作的團隊。在討論中,他們提出了一些我們認為具有建設性的問題,其中一些也是我們尚未解決的問題。例如,他們問及MIT Inventor是否可以供iOS用戶使用,以及我們的檢測的特異性和敏感性。這些問題我們知道在我們的實驗中還有一些缺失,並為我們提供了進展的方向。

UMG-Indonesia
我們於9月27日與印尼的UGM團隊進行了線上合作,這與台灣的CCU團隊不同,這次的討論主要集中在Human Practice。當我們完成了關於我們實驗的介紹後,他們首先問了我們如何在偏遠地區的19到81歲的廣泛範圍內找到受訪者。因為長輩也是我們的目標用戶,他們在使用我們的產品時是否從旁協助是一個很重要的問題。醫院的醫生是否將負責監控測試結果?

UNC-ChapelHill
我們於9月28日與北卡羅來納大學教堂山分校的團隊進行了線上合作。在整個會議中,我們討論了Dry Lab所選擇的材料,以及我們選擇的生物標記的特異性和敏感性。由於這兩個團隊的項目都涉及快速檢測,我們在討論中找到了許多共同點,因此交流了許多想法,並從中學到很多東西。

CCU-Taiwan
We met up with CCU-Taiwan on September 19, they are also the first team we have collaborated with. During the discussion, they bring up some questions that we think are constructive and some of them are also problems that we haven’t solved yet. For example, they asked a question about whether MIT Inventor can be used by ios users, and also about the specificity and the sensitivity of our detection, these questions we know that we still have parts missing in our experiment, and give us the direction of progress.

UMG-Indonesia
We have an online collaboration with the UGM-Indonesia team on September 27, which is different from team CCU-Taiwan, our discussion this time focuses mainly on Human Practice. When we finished our presentation about our experiment, they first asked us how we could find people in the wide range( range of 19 to 81) in our survey in rural areas. Because elders are also our target users, whether we take any action to support them while they use our product will be a crucial question. And is the doctor at the hospital the one who is going to monitor the test result?

UNC-ChapelHill
Meeting up with team UNC-ChapelHill, we did a virtual collaboration with them on September 28. Throughout the meeting, we discussed material chosen for the dry lab, and also the sensitivity and specificity of the biomarker we have chosen. Since both of the team’s projects are about fast detection, we found many common points throughout the discussion, so we exchanged lots of ideas, and learned from each presentation.

張菁芬 博士 (Jane老師)Dr. Ching-Fen Chang (Dr. Jane)張菁芬老師擁有分子醫學博士學位,自2013年開始擔任 NYCU-Taipei iGEM 團隊的指導老師。在準備 iGEM 的過程中,她總是利用在基因與...
03/09/2023

張菁芬 博士 (Jane老師)
Dr. Ching-Fen Chang (Dr. Jane)

張菁芬老師擁有分子醫學博士學位,自2013年開始擔任 NYCU-Taipei iGEM 團隊的指導老師。在準備 iGEM 的過程中,她總是利用在基因與合成生物學方面的專長提供我們許多見解與方向,另外也協助我們設計實驗並學習解決問題。在教學、研究之餘,Jane老師也一直是支持著我們的後盾,時時給予大家能量並照顧每位隊員。我們都很感謝老師對我們的關心💓

下周,我們將介紹我們團隊的創團元老:張傳雄教授!

Dr. Ching-Fen Chang holds a Ph.D. in Molecular Medicine and has been primary investigator of the NYCU-Taipei iGEM team since 2013. Ever since the start of our iGEM journey, Dr. Jane has been providing us valuable advice by using her experience and expertise in the field of genomics and synthetic biology. Thanks for Dr. Jane for helping us with our research project design and giving us kind suggestions on how to troubleshoot our experiments. Besides the “scientific” work, Dr. Jane is also a heart-warming teacher who never forgets to take care for our safety and well-being💓

Next week, we will introduce the founding elder of our team: Prof. Chuan-Hsiung Chang

我們這次的計畫同時涵蓋的檢測和治療兩個方面,並且與橙皮素有大的關連。根據最新的研究發現,橙皮素與炎症、氧化還有癌症等疾病的治療有相關。關於偵測方面,我們的目標是從唾液上面取得橙皮素相關疾病的生物標誌物,再檢測到生物標誌物的大概含量後將檢測結...
20/08/2023

我們這次的計畫同時涵蓋的檢測和治療兩個方面,並且與橙皮素有大的關連。根據最新的研究發現,橙皮素與炎症、氧化還有癌症等疾病的治療有相關。關於偵測方面,我們的目標是從唾液上面取得橙皮素相關疾病的生物標誌物,再檢測到生物標誌物的大概含量後將檢測結果導出至電腦及行動裝置。接著,我們會將部分細菌擁有的電子傳遞的系統移至大腸桿菌中。當偵測到生物標誌物時,該細菌就會放出電子、我們再去捕捉電訊號,就能夠達到非侵入且檢測快速的效果了!在治療方面,因為每個人身體合成橙皮素的效率不一樣,所以我們會設計一個益生菌去提高人體生產橙皮素的效率。

下一週,我們會介紹我們的指導老師:張菁芬老師。請繼續關注我們喔!

Our project this time encompasses both detection and treatment aspects, closely related to hesperetin. According to the latest research, hesperetin is associated with the treatment of diseases such as inflammation, oxidation, and cancer. Regarding detection, our goal is to sense biomarkers related to diseases associated with hesperetin from saliva. Once we detect the approximate content of these biomarkers, we will export the detection results to computers and electronic devices. Subsequently, we plan to transfer the electron transfer system found in certain bacteria to E. coli. When a disease is detected, electrons will be released from the engineered bacteria. By capturing these electronic signals, we can achieve non-invasive and rapid detection! In terms of treatment, as the efficiency of hesperetin synthesis varies among individuals, we are designing a probiotic to enhance the body's efficiency in producing hesperetin.
Next week, we will introduce our PI, Ms. Jane. Please stay tuned for more updates from us!

大家好~我們是NYCU-Taipei 2023 iGEM team。NYCU-Taipei iGEM團隊由陽明交大生物醫學資訊研究所張傳雄教授白手起家創立,是台灣第一個參加iGEM的隊伍。從2007年參賽至今,總共於國際合成生物學競賽拿下一...
17/08/2023

大家好~我們是NYCU-Taipei 2023 iGEM team。
NYCU-Taipei iGEM團隊由陽明交大生物醫學資訊研究所張傳雄教授白手起家創立,是台灣第一個參加iGEM的隊伍。從2007年參賽至今,總共於國際合成生物學競賽拿下一次環境類組世界冠軍、全球前六名、亞洲第三名以及12金2銀2銅、無數的特別獎項的佳績,屢次在iGEM大賽的舞台發光發熱。
今年我們團隊由生命科學系、醫學系、醫工系所組成,19位來自不同系的學生,透過不斷的腦力激盪,藉由彼此的專業,決定出我們今年的主題:VigilaGuard。下一篇貼文將會介紹我們的計畫,還請繼續關注我們!
Hello everyone! We are the NYCU-Taipei 2023 iGEM team.
The NYCU-Taipei iGEM team was founded from scratch by Professor Chuan-Hsiung Chang from the Institute of Biomedical Informatics at National Yang Ming Chiao Tung University. We are the first team from Taiwan to participate in iGEM. Since our participation in 2007, we have achieved exceptional results in the International Genetically Engineered Machine (iGEM) competition. Our accomplishments include winning the world championship in the environmental category, ranking among the top six globally, achieving third place in Asia, and earning an impressive total of 12 gold, 2 silver, and 2 bronze medals, along with numerous special awards. We have consistently shone on the iGEM stage.
This year, our team is composed of students from the Department of Life Science, the School of Medicine, and the Department of Biomedical Engineering. With 19 members from these three departments, we have engaged in continuous brainstorming and leveraged each other's expertise to decide on this year's theme: VigilaGuard. Our next post will introduce our project, so please continue to follow and support us!

Breaking News: The NYCU-Taipei iGEM team won GOLD in the 2022 Grand Jamboree!Thanks to everyone who instructed us and ga...
04/12/2022

Breaking News: The NYCU-Taipei iGEM team won GOLD in the 2022 Grand Jamboree!

Thanks to everyone who instructed us and gave us kind support among the journey!

After 300 days of hard work, our project- E. COLOR has gone through leaps and bounds, and finally, we are able to demonstrate our accomplishments with everyone. Throughout the process, we have been working on the development of fluorescent microbial growth status indicators as well as "BaGroBot", a remote monitoring device, and NYCU-Taipei made it by applying basic concepts of synthetic biology.

So...you mean it's the end? Of course not!
The development of synthetic biology, as well as the spirit of iGEM is still on the rise, and every year, iGEMers worldwide are continuously putting effort in making broader applications in this field!

We are NYCU-Taipei, and see you again in iGEM 2023!

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