Cloning dilemma: The “Err” code saga and not-so-quick-ligation

  by   Friday, August 14, 2026   No comments

Remember my cloning dilemma story? Well, it slowly turned into a nightmare. 

I made my way back to campus to continue working on my research. It takes time to readjust to everything I left behind for two weeks, hoping that this time, things would finally fall into place after all my previous cloning attempts.

Coincidentally, the research supplies I had been ordering — new ligation kit, primers for colony PCR, and a few other essentials, had finally arrived from the supplier.

Everything was ready. 
The materials were there.
The experiment was waiting.

So, I decided to give my ligation mixture another shot, this time using  the Quick Ligase from NEB. Everything seemed great. It was quick, just like it was named for — Quick Ligase. It saved me a lot of time, and for once, I thought maybe this cloning experiment was finally going to give me some hope...

The ligation was ready.
The samples were ready.
I was ready. 

When I was about to move on to electroporation, I switched on the electroporator… 

And then — ERR. ERROR. No beep. No warning. 

At that point, I was hoping it was just a minor technical issue. Spoiler alert: it wasn’t.

Yup. The electroporator decided that my cloning experiment was the perfect time to have a problem. And just like that, my supposedly “quick” ligation experiment came to a very un-quick halt.

So, I did what any researcher would do when things suddenly go wrong. Apparently, one of the most important skills in research is learning how to search for answers at 2 am.

1) I went down the rabbit hole of Google and ResearchGate
I tried to find out whether other researchers had experienced the same problem — and to convince myself that someone, somewhere, had already suffered through exactly the same thing.

2) Repaired by my own
What was I thinking? I'm not an engineer or a technician.

3) I contacted the supplier
I reported that faulty electroporator error and asked for their advice.

4) I reported (cried) everything to my supervisor

I started thinking, maybe I should just start all over again using the conventional heat-shock method. Back to basics. No electroporation. No fancy troubleshooting. Just my competent cells, my quick ligation mixture, and a little bit of hope.

But guess what?

The refrigerated centrifuge was at faulty too.

One instrument broke down, then another. Every time I thought I had found an alternative route, something else decided to stand in my way. 

It may not be going according to plan. Instead, I somehow ended up sending away that faulty electroporator for a diagnostic repair and it definitely took longer than I expected.

But hey, better late than never.

HaiNow Part II: Exchange Programme to Shanghai Jiao Tong University

  by   Monday, August 03, 2026   No comments

Let’s continue our HaiNow Part II, beginning with…

THIS!

We made our way from Shanghai Pudong International Airport to Shanghai Jiao Tong University campus at 3 pm.

Well… when I say “we”, phew… I wasn’t travelling solo anymore. Somewhere between the long 6-hour flight, China immigration and figuring out where I supposed to go next, I stumbled upon Rehasri, a fellow postgraduate student from INFORMM, USM.

Yes — a Malaysian whom I had actually met in the KLIA departure hall before heading to Pudong… but I didn’t even have the courage to say hello 😅

Looking back, it was comforting to find another Malaysian stranger in China. Both of us were trying to navigate an unfamiliar Shanghai Pudong International Airport while heavily relied on the WeChat group organised by our host institution for directions and updates. 

Not long after, we were greeted by our PIC. I get to know Rehasri in the middle of our conversation while waiting for the arrival of other participants from the Philliphines.

Rehasri was a final-year PhD student already preparing for her upcoming viva voce, with her research focusing on cervical cancer under the supervision of Assoc. Prof. Dr Venugopal Balakrishnan. What made this connection even more fascinating was our supervisors were both serving on the Malaysian biosafety committee. 

What a small world… I guess.

After the Filipinos arrived, me and Rehasri were taken to our assigned room in the middle of Shanghai Jiao Tong University city campus. 

Oh… the breezy air as winter slowly transitioned to spring by the end of March. Shanghai was much colder than I had expected — the chilly weather instantly made me feel passive (sluggish)... As Malaysian I couldn't say more.

I RISE WITH THE SUN 🌞 

I reached my phone, refreshing the weather updates. Oh, it was around 10°C. OK... I was ready with layer of jackets throughout my stay in Shanghai. 

When I was about to check my Gmail, that was when it hit me... 

My Gmail won't simply load.

Well... Welcome to China, where Google services won't work without VPN.

And guess what?

I didn't get a VPN before coming here... ugh. 

Later, Rehasri asked if I wanted to go out and explored the Shanghai city with the Vietnamese and another Malaysian postgraduate from INFORMM, USM as well. 

That was when I knew we actually had Hugo in our Malaysian group. 

Amid jetlag, I politely declined the offer. Instead, I decided to take a nap and well-rested for the next day activities. 

Oh, and at 12 am on 17 March 2026, I celebrated my birthday in Shanghai...

with this Chinese mooncake. 

A simple birthday, but definitely the one I will remember. 

Cloning dilemma

  by   Sunday, August 02, 2026   No comments
For once, I wanted to distance myself from everything that happened inside those four walls — the cloning experiments that failed, the endless PCR troubleshooting, and the electrotransformation that didn’t turn out the way I hoped. 

I told myself, this one week-break was supposed to be a time to retrace which protocols I overlooked.

 
Double digestion? Done 

Gel-purification? Done 

Ligation mix? Done 

Electrotransformation? Done 

Recovery of transformed cells? Done 


After 16-18 hours of incubation at 37°C on the selective antibiotic agar plates, I saw…there were colonies. I mean, TRANSFORMED COLONIES…

For a brief moment, I genuinely let myself believe it had finally worked. 

But, science has a way of humbling you. 

I picked the transformed colonies, already anticipating the next steps. Colony PCR first. Restriction digestion after that. 

Then… reality hit. 



No expected PCR band. No plasmid to verify… The colonies were there, but the plasmid wasn’t. I still confused, trying to make sense of these endless questions. 

What went wrong? Did I miss something? 


I need answers! — so, I did what every clueless postgraduate student does — I reported (ok… maybe I literally cried) to my supervisor. After all, he's the only premium researcher adult — An expert sifu who's practically capable of turning these countless failed cloning experiments in the lab into an instant diagnosis of what went wrong. 

“It’s probably AMR. Antimicrobial resistance” 

I blinked. I was fully prepared for a Nobel Prize-level explanation. Instead, I got three letters: AMR… 

“What antibiotics are you using?” he asked. 

“Kanamycin,” I replied. 

“OK… Shewanella is resistant to kanamycin”. 

Oh… that was it? I wasn’t convinced because I was expecting something more complicated — a failed ligation, inefficient electrotransformation, or some hidden experimental mysteries that only an expert researcher adult could decode. 


Then, came the final verdict of this cloning dilemma. 

“Get a new kanamycin from our supplier,” he said. “And get a ligase that works at room temperature. Your ligation most probably failed”. 

Honestly, I couldn’t agree more… I’ll work on it next week.


HaiNow Part I: Exchange Programme to Shanghai Jiao Tong University

  by   Friday, July 31, 2026   No comments

I paused a moment when a single notification popped out from Nabila Ramiza, my Indonesian good friend whom I met in China. 

 “Ting! Nabila Ramiza liked your post story” 

You know that feeling when it’s about a time you suddenly find yourself wandering down a memory lane? 

A day before my birthday, 17 March 2026 is my birthday. I supposed to fly to China from Shanghai Pudong International Airport for an academic exchange programme hosted by Hainan International Medical Center (HMIC). This time as an independent postgraduate student travelling without my supervisor, Dr Wee.

My flight was scheduled at 7.05 am from KLIA. Before my departure time, I was accompanied by my Dad. Together we both looked up a place to get our suhur (سحور). Yes, it was my first-ever solo travelling during Ramadhan… and I was genuinely excited.

Everything seemed to fall perfectly in place that early morning — the peaceful drive before dawn, the little talks with Dad, sharing suhur together, and got to experience the rukhsah of fasting in Shanghai before my arrival to Haikou. All felt surreal in one-combo — nervousness, excitement, and gratitude.

That early morning, I boarded with China Eastern Airlines. My honest expectation was simple. I would probably be seated between the Chinese passengers. So, I quietly kept to myself, minding my own business because starting conversations with strangers has never really been my strongest skill especially in Mandarin.

But life had a different plan.

To my surprise, I found myself sitting next to a friendly, gentleman Malaysian Chinese uncle. He smiled politely and started asking me the typical travel questions.

“U mau pergi mana?”

“U daripada mana?”

"U tinggal mana?"

“U puasa?”

The conversation flowed much more naturally. As a Malaysian, I should have expected this — our Malaysian Chinese uncles are known for their warm and friendly attitudes  — the type of uncles who can easily strike up a conversation with almost anyone, even a complete stranger sitting next to them on a flight 😉

He shared that he was from Puchong, and on his way to Japan, with a transit in Shanghai before heading to Tokyo. His daughter had recently completed a Japanese preparatory programme and was about to begin her Chemical Engineering studies in Kyoto. He was making a visit to help her settle down and move into her new place.

To clear things up, I showed him an offer letter I was carrying in my bag. Seeing the Shanghai Jiao Tong University, School of Medicine, he looked at me and asked,

“Doctor?”

I couldn’t help but laugh.

“No… not yet. I’m just a PhD student.”

For a moment, I think he gave me a little more credit than I actually deserved. After that, the cabin grew quiet again. We both settled back into our seats, enjoying the peaceful flight in our own way. 

Oh, I caught a glance of him, setting up games on his phone to play something similar to Candy Crush — Yes, very typical Asian Dad 😏

As for me?

Well… I’m the type of traveller who treats every flight like an opportunity to catch up on sleep.

So yes, I spent through a good portion of the 6-hour flight... sleeping.

And now, my Part I ended here without the full story how I met Nabila Ramiza in China. Stay tuned. More stories are coming.


Collaboration beyond borders

  by   Thursday, July 30, 2026   No comments

I am a  week away from labwork. 

No PCR. No ligation. No cloning. No colony PCR to think about. Just to take a break from routine that had slowly become exhausting — at least for now hehe… 

Oh, I have an announcement! We finally have a baby nephew! I decided to pay him a visit while I am in KL until next week. Cute little guy is now a month-old :)

From July 28 onward, I was glued to my phone, knowing that my supervisor, Dr Wee whatsapped me during my short escape to Genting Highlands…

“Mana awak?” 

I couldn’t help but putting a nervous smile when I read to his message.

“Dr saya takde”

A simple and straight-forward reply because I assumed he was just checking up on me. No urgency indeed.

That tomorrow morning he sent me a link for S. oneidensis MR-1 mutant strain deposited in the University of Tuebingen, Germany. 

https://www.u-017-s125.v263.uni-tuebingen.de/labor/index.php/Shewanella_oneidensis_MR-1_mutants

My first thought it feels surreal to think that a project which started in our lab could now involve discussions that cross continents. The possibility of working with researchers from another country that I never imagined. 

In our research group, we have made several attempts to establish international collaborations from India, China, Thailand and Japan. Well, many of those ended up halfway, maybe because the projects (which I assume now) were not fully aligned to our research objectives at the time. 

I remember on one occasion when my supervisor invited me to join Zoom meeting with UM and Dr Muammar from University of Tuebingen. The discussion was centered around my project. It was my first opportunity to explain my CRISPR/Cas9 work to Dr Muammar. We exchanged a few ideas and discussed the objectives of our projects. As far as I can recall, his work involved in pyrite minerals, which was quite interesting to me because my junior, Siti also worked on something similar last time. But the session wasn’t very that long because a professor from UM wanted to arrange a more formal follow-up Zoom meeting with the UM Dean. So, we had to continue the discussion another time.

Research has a funny way of bringing people together. Different expertise, different perspectives, and different experiences often lead to better ideas than working alone. That’s what excites me the most about this collaboration for now — not just the science, but the opportunity to build networking from people beyond borders that could eventually support my future plan into postdoctoral research after PhD.

Inspiration in Dr. Tan

  by   Wednesday, July 29, 2026   No comments

Recently, I found myself reading Dr. Tan's writings on his juggling lab life, and I have to admit...

"I was impressed!"

There was something about the way he shared his thoughts, his journey, and his experiences that caught my attention. Yes, I rarely get impressed by people, but this time he humbled me down the earth.

Oh, we met at UTM, Johor Bharu. It was an unexpected encounter because he was one of my evaluators during my first-ever participation in an innovation exhibition and competition. 

And I still remember how humble he was while evaluating my work on molecular experiments — especially when discussing biosafety and ethical considerations. My first impression of him... he looked like a very senior researcher — reserved and serious together with the other two evaluators from UTM and UMPSA.

"Alamak habis la...taknak, taknak, taknak"

And I delivered my presentation nervously... knowing that my project was still at an early stage. I didn't have any fancy prototype, or tangible outcome to showcase yet. All I had were carbon steel corrosion demo in vials — something that probably looked ordinary and, BORING.

But what stayed with me was how Dr. Tan approached my project. He didn't judge it simply based on what was physically in front of him. Instead, he looked deeper into the science, asked meaningful questions, and gave attention to the thought process behind the work I done. I actually forgot the exact details he commented. But it mostly on the CRISPR editing methods and how long my primers were designed. Hmm…

After the evaluation session, I asked him for a photograph, which I wanted to share under Dr. Wee’s biosafety committee network.

So yes, that moment of inspiration stayed with me. And honestly, I'll keep growing and carry the same passion that I saw in Dr. Tan’s.


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