The Tale of a Boy in a Coffee Shop #12

The day turned dark because of the clouds by the time that boy reached the coffee shop. He pushed the door and was surprised when he met a stranger instead of the old lady behind the bar. It was a young lady he had never seen before. She looks a little bit older than big brother James, he thought.

"Can I help you, little boy?" She asked from behind the bar.

"I am...looking for the owner. My mother asked me to deliver these eggs and milk for her," He looked rather awkward. There was somebody he didn't know in his sanctuary. He disliked the fact. Even though he was a little boy, he knew nearly every single customer in that cafe.

"Ah, Granny Lisda is out to the post office for a while. You can give it to me," she smiled at him.

"Who are you? I've never seen you before? Sorry, I am not trying to be rude," he said while giving his basket to her.

"Ah, nice to meet you. You are a regular then? I am a new part-timer."

"New part-timer?"

"Yes, I work here starting today. My name is Lynn. Lynn Leslie," she offered her hand to the little boy.

"I am Charlie," he reached her hand.

 

BDC #10 - Satellite Cells

Hello!!! Are missing the BDC series? Relax!! I am still studying, so there will always a new post for this series.

I have a new homework today (d*mn!! I shouldn't take this class!! They give a journal-review-HW every week >.<  hahahaha!!!). This time, it's walking about "Satellite Cells". Hem.... what is that? I only know there 2 things called the satellite cells: the myosatellite cells and satellite glial cells. For now, I will only talk about the first one, Myosatellite Cells.

Myosatellite Cells, or just Satellite Cells, are precursor or progenitor cells for skeletal muscle cells. Precursor or progenitor in cell biological term means "soon to be / going to be", and skeletal muscles are muscles attached to your bones, work for the body movement. So these muscles are not related to internal organs. 

These cells are located between the basal lamina and sarcolemma of the muscle fibers. Basal lamina is a layer of extracellular matrix secreted by epithelial cells, where the epithelium sits. On the other hand, sarcolemma, also called myelomma, is the cell membrane of muscle cells, either the skeletal, cardiac, or smooth muscles. The experts say that it's actually quite easy to distinguish these cells amongst the muscles fibers due to its' unique characters; such as, high nuclear-to-cytoplasmic volume ratio (comparatively small nuclear size), few organelles, and a large quantity of nuclear heterochromatin relative to myonuclei.

These cells was actually founded in 1961 (pretty early, huh?) by Alexander Mauro. During that time, without any solid evidence yet, he already hypothesized that these cells represent a kind of muscle progenitor cells, capable of forming new muscle in response to injury.  The experts indeed confirmed this hypothesis years later. 

While there is an injury on the muscle, satellite cells will proliferate following the muscle trauma and form new myofibers through a process similar to fetal muscle development (fetal = baby). After several cell divisions, the satellite cells begin to fuse with the damaged myotubes and undergo further differentiations and maturation, with peripheral nuclei as in hallmark. 

Upon minimal stimulation, satellite cells in vitro or in vivo might continue to the myogenic differentiation process. However, it looks like the transplanted satellite cells have a limited capacity for migration, and are only able to regenerate muscle in the region of the delivery site.  BUT other cells in the body such as hematopoietic stem cells (HSCs) have all been shown to be able to contribute to muscle repair in a similar manner to the endogenous satellite cell. And the advantage of using these cell types for therapy in muscle diseases is that they can be systemically delivered and migrating to the site of injury by themselves. A successful therapy recently has been the delivery of mesoangioblast cells into the Golden Retriever dog model of Duchenne muscular dystrophy, which effectively cured the disease (link).

By the end, we still don't know exactly how to really implement the stem cells therapy to cure diseases. However, if we keep on being curious and researching, we will definitely find ways!! So... keep trying my fellow researches!!!! 

If you want to learn more about these Satellite Cells, you can try to read this review paper. 

   

The Tale of a Boy in a Coffee Shop #11

The weather was getting wet, it entered the rainy season with wet wind. The boy liked this season a lot, because he could play with water more often than any other time during the year. In contrast, his mother definitely disliked it. She got more clothes to wash but less time to hang it dry. She had to be aware anytime, in case it got raining again while she was hanging them. 

The boy was about to go before his mother called him, "Charlie!!" She shouted from the backyard. He didn't answered, but he dashed to the back door and popped his head out behind the door. He just looked his mother with naughty eyes.

His mother saw him, "Are you going to Granny Lisda's again?" She was hanging a big white bed sheet. The boy came near his mother and nodded. 

"Then, could you please bring some eggs for her? Ah...and also 2 jars of milk. Be careful, OK? Don't break the eggs or the jars." 

"OK!" He ran to the small hut near their kitchen to take 15 eggs and 2 jars of milk as his mother asked him. 

His family was actually not a farmer family. His father was working in a factory nearby. But, the money was definitely not enough. Therefore his mother did some farming and kept some cattle for daily living which fortunately went really well, she had some talents in it. Sometimes, his mother sold a bit of their stocks to buy other things. The old lady from the coffee shop was one of her loyal buyers.      

The boy kissed his little sister's forehead who was sleeping in the wooden baby cart. Then, he left home, whistling.

Illustration of "Farmer Boy" by Laura Ingalls Wilder

I don't own the picture

 

The Tale of a Boy in a Coffee Shop #10

Suddenly the door was opened. There, stood a young man not even taller than 5'6", looking inside the dim lighted cafe. It looked like he just finished crying and repenting over himself.

"Big Brother James!!!" The boy shouted and jumped down his chair. He rushed and bumped himself to that young man. 

"Oh, hello, Charlie. Long time no see. How are you?" That young man tried to lift that boy up to his shoulder, "Argh... you are so heavy now!!" He put the boy down the floor again.

"Of course, I am already ten!" The boy answered in a proud tone.

The young man smiled and ruffled the boy's hair roughly. He looked down with a tender love like a real older brother, though they weren't blood related at all. The old lady looked at those two while sipping her coffee. Then, the young man lifted up his face, straight to the old lady.

"I am sorry."

An awkward silence floated between them, especially when there was that little boy in the middle. The old lady just smiled sympathetically. It's not like he will back to me anyway, the lady said inside her heart.

"But I am still not going to work here. At least... not now. It's no more about pride, it's just.... I think... I think it's better for me to see the outside more. But I will definitely come back and help you here. Definitely."

"Are you going somewhere, Brother James? Is it going to be long? Will you come back?" The boy clung his hands to the young man.

The young man smiled, "Of course I will. I promise you," He offered his pinky finger to the boy. The boy pouted but reached it back with his pinky finger. 

"Just don't forget to send me a letter. Once a month is good enough," The old lady finally said softly.

The young man looked at her and took off his hat, bowed deeply to his chest. Then he walked away the cafe. The boy followed him until the edge of the door. He didn't see puddle of tears in the corner the old lady's eyes.

       

The Tale a Boy in a Coffee Shop #9

"Does pride really make us ashamed to work at our grandma's place, owner?"

"Do you think it doesn't?" The old lady poured some warm milk into her cup.

"I am not sure, I don't think I will fell ashamed. Does that mean I don't have pride?" He looked at the old lady in front of him. He had questioning expression but with sad eyes.

"Well, let's see... That boy said his grandmother that his friends already started working at other cities. That's why he also had to. Why did you he have to?" 

With puzzled mind, the boy thought carefully. He would like to hit the mark. There was something in the corner of his heart made him to think that he didn't want to lose to this question. "Weird.." He said to himself, "What is this feeling of not wanting to lose?"

 "Is it because, he didn't want to be a laughing matter amongst his friends? He didn't want to lose to his friends?"

She smiled gently to him, "It might be one of the forms. But, it doesn't always have a bad impact, little boy." The old lady rubbed her hand on the boy's head, then she walked away behind the kitchen door, taking something.

And a little seed started to grow in the corner of the boy's heart. But, it wasn't something bad.... yet.

BDC #9 - Kingdom of Franks: Where was it?

I am a little bored in the lab, kinda tired reading scientific journals. My brain need something light to digest. Thus, I randomly typed "Learn something new today" in the Google search bar. And...TADAAA... I clicked one random link. I read some sentences, and my curiosity finally landed on a sentence: Each king in a deck of playing cards represents a great king from history: Spades - King David; Clubs - Alexander the Great;Hearts-Charlemagne and Diamonds - Julius Caesar (link).

 

Interesting... I did listen to this several times, but 've never really given a special attention until today. Is there anything interesting for you? 

For me, it's the King Charlemagne... to be totally honest.. I've never heard any great king named Charlemagne (well, it's probably just me, pardon my ignorance >.< ). Well, as usual, I searched it...and it turns out that Charlemagne is also known as Charles the Great (German: Karl der Große, Latin: Carolus or Karolus Magnus) or Charles I, was the King of the Franks from 768, the King of Italy from 774, the first Holy Roman Emperor, and the first emperor in western Europe since the collapse of the Western Roman Empire three centuries earlier. 

WOW!!! I thought... OK, next question.. Where was the Kingdom of Franks? Since there is a German name for this Great King... I assume that it might be around Germany (my mind immediately jumped to Frankfurt for no reason). Well, I didn't guess it very wrong, but it was actually a lot bigger than Germany. As we could see in the given image below, the original territory was indeed around the current Germany, but as the kings ruled, they expanded the territory until it covered nearly all region of Western Europe by the end of King Charlemagne's period.  

We could talk a very long conversation about the history of this kingdom from the very beginning they supported the Roman Kingdom, until how they got their own authority and territory... BUT I will skip that. Instead, I am more interested of how was the end of this huge kingdom. As usual, every kingdom has their own inheritance problem which usually lead to the downfall, include Kingdom of Frank. 

As any other kings, Charlemagne also had several sons, but only one survived him. The son was Louis the Pious. He followed his father as the ruler of this united empire. But when Louis died in 840, they adhered to the custom of partible inheritance, and after a brief civil war between the three sons, they made an agreement in 843, the Treaty of Verdun, which divided the empire in three:

1. Louis' eldest surviving son Lothair I became Emperor in name but de facto only the ruler of the Middle Frankish Kingdom, or Middle Francia, known as King of the Central or Middle Franks. His three sons in turn divided this kingdom between them into Lotharingia (centered on Lorraine), Burgundy, and (Northern) Italy Lombardy. These areas with different cultures, peoples and traditions would later vanish as separate kingdoms, which would eventually become Belgium, the Netherlands, Luxembourg, Lorraine, Switzerland, Lombardy and the various departments of France along the Rhone river drainage basin and Jura massif.
2. Louis' second son, Louis the German, became King of the East Frankish Kingdom or East Francia. This area formed the kernel of the later Holy Roman Empire by way of the Kingdom of Germany enlarged with some additional territories from Lothair's Middle Frankish Realm: much of these territories eventually evolved into modern Austria, Switzerland and Germany. 
3. His third son Charles the Bald became King of the West Franks, of the West Frankish Kingdom or West Francia. This area, most of today's southern and western France, became the foundation for the later France under the House of Capet. 

This was the territory after the treaty

 
After this disseverance, each part of the kingdom kept on dividing or re-uniting until they established as individual kingdoms.

Well, at least it was one huge kingdom. I understand now, why Charlemagne was once called a Great King.

BDC #8 - SHED: Stem cells from human exfoliated deciduous teeth

I've just finished having a regular lab meeting. And as usual, I don't get that much information due to language barrier... Yup, I am still having problem with my Japanese. But fortunately, I am not alone. There is a Brazilian guy came at the same time as me, who also doesn't understand a single thing in the meeting. Thus, he brought a paper to read during the meeting (well, don't follow this fellas...not a good example though....)

Anyway, his paper was about SHED.. WAIT!!! What is that??!! I also have no idea at all. Thus, I checked on the internet and found a very interesting definition. AND... I dedicate this topic to my very best friend who is struggling with her master thesis.

It turns out that SHED is an abbreviation of Stem Cells from Human Exfoliated Deciduous Teeth. I am completely dumbfounded with the term deciduous...what is that???

Terminologically, deciduous means "falling off out of maturity" or "tends to fall out". Thus, deciduous teeth is actually milk teeth, baby teeth, temporary teeth, primary teeth...well, you can say it anything. It's the teeth we had once we were little and fell out when we started turning 6 or 7 years old.
Exfoliated means..well, obviously peeled.. we do remember all of those exfoliation mask etc, right? But in this term, it means those milk tooth which are already fallen off (naturally). 

Now, these SHED are obtained from the inner part of the teeth, which is pulp region. then, how does it different with Dental Pulp Stem Cells (DPSCs)? Well, I am not very sure either, but it looks like the difference is only the fact that DPSCs are obtained from Adult Teeth. Yes... I am not joking. You can't confirm from several papers like this one or this one.

Well, it's just a quick preview to satisfy my curiosity. Happy reading fellas!!!

The Tale of a Boy in a Coffee Shop #8

"I think it's wiser if I tell a story before we discuss about pride," she moved a little bit to the left, filling her cup with her usual blend coffee. The boy was ready, his eyes kept moving, following the old lady's every movement, while eating his breakfast.

"One day, there was a boy. He had no mother anymore. He lived with his father, but....since his father was very busy with his job, travelling around the country, that boy basically grew up by his grandmother's side." She took a deep breath before continuing.

"Ever since he was 7, he was practically living in his grandmother's place. His grandmother opened a small coffee shop on a busy street in the middle of a town. He was happy, until he reached 15."

There was still no reaction from the boy, he kept following the story undoubtedly.

"He said to his grandmother, "I am already 15. I don't want to keep on living here. My every friend already start working on their own to different cities. I have to work too!" But his grandmother was basically lonely without him, she wasn't getting any younger as the time flows. Therefore she said to her one and only grandson, "Why don't you work here, then? I will pay you the same wage as the part-timers.""

"And then, did that boy work at his grandma's?" the boy finally reacted.

"What do you think little boy?" She smiled sadly to him.

"Well, I would love to... working in a coffee shop, I can also get lots of free meals, right?" He grinned from ear to ear.

The old lady smiled again with soft chuckles, "Well, if only that boy thought the same as you. But.. No, unfortunately not. He didn't want to. He was to proud as a young man."

"Is it shameful to work at his grandma's shop, Owner?"

"If you have as high pride as that young man, well it might be, little boy."

     

BDC #7 - Attention Deficit-Hyperactivity Disorder (ADHD)

Talking about OCPD and OCD yesterday, made me remember about one of my bestiests. She claimed that she might be has and ADHD just recently. Coincidentally, I am currently following an online class about Introduction of ADHD, though I don't understand more than half of the classes. But again, another twist by the universe.

So, let's discuss a bit about what is ADHD. It is an abbreviation of Attention Deficit-Hyperactivity Disorder. It is defined as a psychiatric disorder and/or neurobehavioural disorder characterized by significant difficulties of paying attention (inattention) or hyperactivity and/or impulsiveness. Basically, it's a condition where somebody couldn't really paying attention on something more than ...well, let's say 5 minutes. People with ADHD are mostly restless, impulsive, lack of focus, having difficulty in prioritizing things, and even in worse cases, have low memory ability.   

There are at least 3 potential classifications of ADHD - based on the symptoms: predominantly inattentive type, predominantly hyperactive-impulsive type, or the combined type.

Based on the U.S. National Institute of Mental Health, predominantly inattentive type symptoms may include:

•  easily distracted, miss details, forgetful, and frequently switch from one activity to another without finishing the earlier one.
• have difficulty in maintaining focus on one task and get easily bored in a task within a few minutes.
• have difficulty in learning something new due to lack of focus.
• don't really listen to a conversation.
• daydreaming and move slowly.
• have difficulty in processing information and struggling to follow instructions.

Meanwhile, the hyperactive-impulsive type symptoms may include:

• nonstop talking and cannot seat still.
• impatient and tend to blurt out inappropriate comments without really think it in advance.
•  having difficulty in doing quiet or motionless task
• well...basically they can't stop moving around, dashing around, moving anywhere.

What is basically the cause of ADHD? Some of the latest researches revealed that ADHD is highly related to a defect in the signal system in the brain, dopamine transporter to be more exact. Dopamine is one of neurotransmitter in the brain. generally, neurotransmitters are chemicals acted as signals in the brain and body. Dopamine plays important roles especially in motor control, motivation, reasoning, and reward, and arousal. Therefore, problems in the dopamine signalling system will lead to motor control and motivation rationality as seen in ADHD.   

Now...are you really an ADHD patient? 

  

The Tale of a Boy in a Coffee Shop #7

They walked into the shop, and the lady led him to one of high chairs in front of the bar.

"What do you want for breakfast, boy?"

The boy blinked his eyes several times, put his right index finger near the corner of his lips, he was thinking hard, trying to decide his menu.

"I will have an iced cocoa milk with omelette for today," He smiled cheerfully, simply forgetting his earlier question.

The lady served him his requests just under 5 minutes. He instantly dug into a plate full of omelette. The lady always gave him something extra. This time he had a pile of french fries on the edge of his plate.

"So boy, what do you want to know about pride?" She resurfaced the typical question back to him.

The boy looked at her in a blank face, he was trying to remember, why exactly did he ask it. While munching his potato, suddenly a light came to his face, as if it was enlighten.

"You said big brother James has too much pride. Why is that? What is pride?"

She was unnerved by his question. Not very sure, where should she start it. She believed, she had to be careful, not to make a false understanding about what was actually happened between her and her grandson. The awkward silence started to float.  

BDC #6 - Obsessive Compulsive Personality Disorder (OCPD) vs Obsessive Compulsive Disorder (OCD)

I have been wondering since years ago, am I the only one who is kinda curious with what kind of mental illness spectrum that I have? Is there anybody other than me who have ever checked their possibly-mental illness?

So, out of curiosity, I tried some online tests, which credibility might be questionable, but that's not a real matter to me. I was just curious. It turned out I have a light-medium symptoms of Obsessive Compulsive Personality Disorder (OCPD). I bet some you actually familiar with this psychological term. 

So, what is OCPD actually? Is it the same as OCD? The answer is NO, it's not the same between OCPD and OCD.

OCPD is a personality disorder characterized by patterns of preoccupation with orderliness, perfectionism, mental and interpersonal control at the expense of flexibility and efficiency. On the other hand, OCD is basically an anxiety disorder characterized by intrusive or tedious thoughts that produce uneasiness, apprehension, fear, etc. The repetitive behaviours were aimed to reduce the anxiety.

So let's have an example. The most commonly well-known example is the over-clean behaviour. OCD people seem to be germphobic. They will repetitious wash their hand to reduce the anxiety. They can't stand the habit to over-think about the germs on their hands. In contrast, OCPD people actually don't necessarily need to the perform the repetitive rituals. As I said, people with OCPD tend to be more perfectionist. Instead of being distressed by the repetitive actions, OCPD people find pleasure and enjoy perfecting a task. However, indeed, the symptoms are highly interloping each other which make it very difficult to be distinguished. Especially because people with OCPD tend to have OCD too.

BUT!!! How could I be sure I am an OCPD instead of OCD? I came to realize on the fact I don't necessarily need the repetitious action. I just do my obsessions once a while to relieve some stresses, but as I said, those are habits of perfectionism. I am not actually obsess in cleanliness or piling up my stuffs (Yep... I am definitely not a hoarder.. I am even quite a cruel person in throwing away my no-longer-needed stuffs). Instead, I am kinda fond of order. Let's say some examples... the money in my wallet is always put in a specific order, I always hang my various types of clothes hangers in specific order, I always.... well, it will be endless. I even get irritated when my housemate put things not in "MY" order and will "fix" the placing.

Anyway, my point is actually.... are you curious with yours?

     

 

The Tale of a Boy in a Coffee Shop #6

It was a bright new day with busy street in from of the coffee shop. The boy was running in small happy steps. Just before he reached the door of his favorite places, it was opened harshly from the inside.

"James!! Wait!!!" A weak shout came out for inside the cafe.

The young guy just walked away in rush, bumping several walkers along the run. The old lady finally reached the door knob and she could only see the faint shadow of that young guy until his shoulder lost in the corner. The old lady just sighed before she threw her head to the left and her eyes bumped with the little boy's eyes. Those little eyes were fidgeting in amazement. Is it a drama in a roll? He thought at heart.

"Ah, sorry boy, you've seen something ugly early in the morning."

The boy shook his head, "Not really." The awkward silents filled the gap between them, "Was he Big Brother James?"

The old lady smiled bitterly, "Yes, he was."

"Were you two fighting? Did you get hurt, owner?"
"No. We just had a little argument. He just simply has such a pride." The lady smiled again.
"Do you want something to drink?" The old lady offered her hand to the boy and he reached it, walked inside the cafe with her.

"Owner, what is pride?"
 

BDC #5 - Somatic-cells Nuclear Transfer (SCNT)

I am in the middle of writing a review for a homework, and nearly snap due to the overload. I need a break!! I need to vent out my frustationt!! Thus, I write this 3rd post for today... (If only I am always this productive in everything I do...  O|‾|_ ) 

So, my homework is related to Somatic-cells Nuclear Transfer (SCNT). Some of you might have heard it before, some other might not be familiar at all. I will just make a quick review, and as usual, give some links to refer to. 

SCNT refers to a technique to generate (at least) a clone cell by transferring  (or injecting or forcefully fusing) somatic DNA material (nucleus) into an emptied egg cell (ovum). The term emptied means that the nucleus (or genetic material) of the egg cell is already removed. The egg cell now containing the somatic-cell nucleus will be stimulated and begin to divide, as if the egg cell has been fertilized by sperm, and develop through mitotic divisions. 

Start to feel familiar with the explanation? Well, if Dolly Sheep might help you to ring a bell...

I attached a picture to give a better explanation.

 NOW...you do remember something ... 

 

What is the good thing over this God-wanna-be experiment??!! WAIT!! Don't start an argument before I finish this writing. I am going to continue to the main point of my writing (and my homework of course).

If you are familiar with the cells or tissue or organ transplantation, you might have heard some researchers to improve the art of stem cells and differentiated cells to overcome the limited-number of organs (or tissues) donors. If so, than you also aware that up to know, they still have problems, include the immune rejection reaction problem. Aside the fact there are also some new super techniques, include the Nobel-prize-winner iPSCs, each of them has their own limitations.

NOW...here comes the novelty of this technique. In early 2000, after the huge success of Dolly in 1996, the researchers really hoped that this technique could help us to generate our very-own personalized stem cells!!! Imagine that by using a cell inserted by our very-own DNA...it will (hopefully) develop into our genetically-identical cells, and could be used as our saviour to cure our disease with cell-transplantation-based therapy. HOWEVER, of course, during that time this technique immediately hemmed in lots of issues, especially ethical issue, like playing God and so on. People afraid that we, human, could re-create our own selves in the future. 

Well, here is the problem, even if the nuclear genetic is identical, BUT AT LEAST the mitochondrial genetic is completely different. Because mitochondria is basically an organelle in the cytoplasm, thus...each cell will only inherits their "mother's" mitochondria. Mother means the cell which gives the cytoplasm. As a note, this is also what happens in the natural fertilization between egg cell and sperm, because the sperm will only fuse the genetic material into the egg cell. (PLEASE!!! I hope I didn't make a mistake here!! Please help me correct it, If I am wrong ^^)   

This mitochondrial genetic material will definitely gives effects to the new clone. Thus, the clone is basically not 100% the same as the "Father".

Anyway,that's actually another matter. What I would like to actually deliver is, just a bit earlier from this post, a research team in Oregon Health and Science University published a paper, claimed that they managed to reduce lots of SCNT weak-points, and even dare to challenge the famous iPSCs in term of usability. Check out the full paper if your curious. 

That's it for today.. I am wrapping this up with ... HAPPY WEEKEND EVERYBODY!!!!

  

 

       

The Tale of a Boy in a Coffee Shop #5

"Which one do you prefer, carrot cake or blueberry muffin?" The lady asked him lightly. He only answered her with raising his left eyebrow.
"For breakfast," she emphasized.
"Ah... blueberry muffin, please."

The lady went behind the bar. The boy could hear the sound of the oven while she was heating up the muffin. She came back in a minute with a plate of tantalizing muffin. The boy's eyes widen up. He grabbed a mouthful before he shouted..

"HOT!!"

The lady chuckled, "Eat it slowly, Boy. It won't run away from you."

"This is definitely not warm," He grumbled.

"But, how do you fell in here?" She pressed her forefinger on the middle of his chest.

He touched his chest, looked at his coffee milk and the muffin.

"I feel...happy! And..."
"And?"
"I fell grateful, it's overflowed with joy and love. I am here, sitting in your cafe, drinking your always delicious coffee with this wonderful muffin while chatting with you. Here," He pointed his chest
"I feel... a warmth?"

The lady smiled and went behind the bar for a second round of coffee.

     

BDC #4 - Microhomology Mediated End-Joining (MMEJ)

Hello again!! Thanks for still putting up with my writings ^^

I would to continue, just a little a bit, about the whole DSBR conversation. Completing the earlier 2 pathways, the last one is called the Microhomology Mediated End-Joining (MMEJ), or sometimes it's called as alternative end-joining (altNHEJ). . 

In some occasion, some polypeptides might covalently attached to the end of a broken DNA. Consequently, these DNA ends couldn't be bound by the Ku70/80 complex. and be repaired in the usual NHEJ pathway. As an alternative (thus, it's called alternative end-joining/altNHEJ), these ends will follow a Ku-independent repair pathway.

Basically, in this pathway, the blocked end will be removed by nucleolytic process, and one strand of the end will be resected (or digested or deleted or removed) until "they" find a small region (5-20kb) which is compliment (or homologue) to the other end of the broken strand. The broken ends are stabilized by the base-pairing. That's why it's called "Microhomology". After the base-pairing, the "flapping" (basically the leftovers of each strand) are removed, and the ligation occurs.

Well, in the end, at least 2 of the 3 pathways will definitely make a mutation to the DNA sequence. This is a solid prove by nature that "To prevent a further damage, there is always something in return to be sacrificed" (Oh my goodness!! How wise am I in this post!!! >o<)   

As a comparison, you can check on a brief diagram below. 

Ow, as a note..every picture I put in the posts is directly linked to the original paper, if you click it. Just in case you are curious to learn further ^^

So, Happy Friday everybody!! It might a wonderful TGIF for some people, and just another Friday for another...BUT!! Thanks for reading!!

The Tale of a Boy in a Coffee Shop #4

But the boy wasn't satisfied yet. There was something lacking, there was still a hole in his ego.

"What about the heart you said earlier? What is warmth at heart?" He now looked at the old lady fiercely, straight to her eyes, deep and sharp enough to dig a hole right on her face.

She took another mouthful of her cake, chewed it slowly, indulging the thick flavour melted on her tongue. She swallowed it with joy and blended the taste with her own-special-blend black coffee. She knew the boy wasn't patient enough, but she did it purposely.

"I am feeling it right now."

The boy looked at her with big question mark on his face.

"I am enjoying the warmth in my heart while chewing my cake, sipping my coffee..." she let her words hanging in the air without finishing it.

The boy blinked his eyes twice with blank expression, as blank as a paper white. He completely had no idea, what this funny old lady was talking about. And the lady sipped her coffee again, to the bottom of the cup.

BCD #3 - Non Homologous End-Joining (NHEJ)

Before I continue the last post discussion, I would like to say... INDEED!!! the universe has a funnily mysterious over human lives!!! I had a "General Biology" class today. Of course it was in in-understandable Japanese as always. It was talking about the various control of gene expression. Of course it was a useless lecture which tried to summarized the whole things in only a one and 15 minutes lecture. SO STUPID!!! I mean, how could it be happened??!! The whole process of the gene expression control is like one bible itself. As I expected, even the lecturer was overwhelmed with the whole lecture material, and just delivered us the title and subtitles written in the "Molecular Biology of the Cells" part II chapter 7... (ya!! You may open it by yourself)

But while I was fighting my sleepiness in the class, my eyes and ears caught a glimpse of DNA double breaks and HRR....!! What does it mean??!! Does it mean, I am a good student for starting reviewing it for the last 2 days??!!! I was so happy that I fought the whole forces to sleep in the class and tried as best as I could to listen the lecturer to the end.   

And!!! As I promised, following the previous post about DSBR, I continue the next discussion to the first strategy of DSBR: non homologous end-joining (NHEJ).

If HRR is known as the most assuring way, then NHEJ is more well-known as the most straightforward way to repair DSB. It simply rejoin the broken ends, regardless any genetic sequences at the break. OF COURSE, this pathway leads to alteration (or just say the changing) of the DNA sequences and mutation, which makes it considered as an error-prone. The following picture introduces us to the various factors involved in the pathway.

 

The basic explanation for the NHEJ pathway is as the next picture follows. The DNA breaks are recognized by the Ku70/80 complex. This recognition will promotes the recruitment of DNA-dependent kinase catalytic subunit (DNAPKcs). Afterward, it will induce the DNA end processing enzymes (in the form of kinase activity). This kinase activity will contributes to the phosphorylation of some histones and thus promotes the ligation process.   

However, not all broken DNA ends could immediately be ready for ligation. One or more of the ends might have an abnormal structure. Therefore, these abnormal ends need to be trimmed. In a low eukaryote cells such as yeast, the MRE11, Rad50, and NBS1 will make an M-R-N complex with endo- and exonucleolytic activities might share an important role in trimming these ends. However, in higher eukaryote cells, another nuclease named Artemis is recruited to the phosphorylated and activated DNA breaks by DNAPKcs. This nuclease will trim the overhang ends and prepare the DNA to be ligated by DNA ligase IV-XRCC4-XLF complex.  

That's it!! I hope I explained it quite simple to be understood!!

See you on the next post... I am studying the MMEJ right now... hope I could post it ASAP ^^

Thanks for reading, and of course, comments and discussion are highly welcomed!!

The Tale of a Boy in a Coffee Shop #3

"Doesn't it depend on how you feel? Whether physically or at heart?" The lady finally took him seriously. She started digging on the carrot cake she made earlier.
"Depends on how I feel? Physically or at heart?"
"Doesn't it?"
"What does it mean?"

The lady dropped her fork, what a cute question, she thought.

"Isn't it obvious? How does you feel on your cup of coffee milk? Is it too hot?"
"Not really, in fact, it's warm enough. The weather is suitable for this."
"How about if today was in a mid-summer, the sun shone so brightly, you were sitting with sweats dripping out your skin. Would you say that coffee is warm enough?"

The boy looked at the old lady for a while before finally saying, "No, I don't think so. I think it would be too hot for a cup of coffee under summer heat. I would prefer a glass of ice coffee instead."

And suddenly the boy's eyes widen up with enthusiasm. She understood what did it mean.

"Then, that's it," she took another mouthful of her cake.

BDC #2 - Homology Dependent DNA Repair (HDR)

I’ve finally finished the paper from yesterday’s topic about X-SCID this afternoon, and my eyes landed on 2 keywords, DSBR and IL2rg. OK, what are those things? Easy… I am not going to discuss both of them today. Even 1 topic is already long enough to be discussed in a day.

For today, I decided to look a bit deeper on the first keyword, DSBR.

So, what is DSBR? It’s an abbreviation of DNA double-strand break repair. Double-strand break itself reveres to the condition where both strands of the double helix are severed (or mutated), and DSBR means the effort to repair this condition. There are (at least…not very sure, haven’t finished digging up >.<) 3 mechanisms exist to repair the double-strand breaks (DSBs): non-homologous end joining (NHEJ), microhomology end joining (MMEJ), and Homologous Recombination.

WAIT!! Have I ever learned these things??As a note, I have a Bachelor of Biotechnology degree, so AT LEAST I’ve ever read it somewhere. Why I don’t remember any of it? I mean, during undergraduate, we learned for (at least!!) 5 semesters (equal to 2 and a half years) of DNA technology and all the necessary things. BUT!!! Why couldn’t I recall any of these?! I even argued some seniors via twitter whether our lecturers taught us of these or not…

Well, anyway, I dug deeper and got addicted as the papers passed my eyes page by page.

For now, I will discuss a bit about the “might be the simplest” one first. I will talk about the Homologous Recombination Repair (HRR). This strategy is also well-known as might the best explanation for the DNA recombination during meiosis stage of the cells. Basically, it requires the presence of an identical (or nearly identical) sequence to be used as the template to repair the break. This path allows a damages set of DNA (let’s say, chromosome) to be repaired by using a sister chromatid or a homologous chromosome as their template. Out of the strategies, this pathway might be the most “error-free” DNA repair mechanism with an almost 100% guarantee there will be no mistake during repairing process.  

So, let’s imagine it in a simpler way. Let’s say you spoiled a page of a journal presented in your lab’s journal club today by a cup of coffee. CRAP, you really need that page!! So, you just borrowed the same journal from your friend who also attended the club, and copied it. Voila!! You got your spoiled page back!! 

BUT!! This simplicity is not the actual HRR. The experts prefer to call this pathway as Synthesis Dependent Strand Annealing (SDSA) Repair system. The HRR will happen if there is cross-over through the holliday junction. What is cross-over? As the word says, if the template and the broken DNA cross over each other, there is a possibility that the DNA strands interlope and switch over. Now, this is the real combination we are talking about!! The picture will be not as simple as given above, but now there is a small branch as this one.

Now, the HRR is on the left side and the SDSA is on the right side.

A little extra explanation, is the point (or the place..oh well it's a junction) where the 2 strands of sister chromatids or chromosomes interlope over each other. This holliday junction is the thing which makes the cross-over possible. The cross-over might lead to a "Branch Migration" or a "Double Crossing Over". Now, the picture will get a little more detail into this one.

That's all for this topic. I will discuss another things for the next post. ^^

If you are interested to learn more, I could suggest you to check on this online article of “Homologous Recombination from a Molecular Perspective”, or read some papers, like this one as an example. 

Happy exploring!!! ^^

    

The Tale of a Boy in a Coffee Shop #2

The lady stared at the boy for a moment, then continue drinking the black coffee on her hand.

"What do you think" the lady asked back.

That boy disliked it when people answered him with another question.

"Normally, it's about temperature, right? It's a condition when the temperature feels a bit higher than the normal, but not to the point it's too hot, " he answered lightly.

The lady just smiled faintly, "It might be right, if we are talking about warm as an adjective. But is it warmth? And, how hot or cold is normal temperature, anyway?" 

The boy glared at the owner. He had been bitten by his own question.

"I don't know, I just blabbered I guess. That's why I asked you, come to the beginning, owner."

The boy threw his eyes through the window, looking at the rain drops which started falling down.  

BDC #1 - Severe Combined Immunodeficiency (SCID)

Severe Combined Immunodeficiency (SCID) is a genetic disorder with a severe immunodeficiency case and characterized by complete inability of the adaptive immune system to maintain the immune response in the body. It is called severe because it is fatal, typically due to the absent of T or/and B lymphocytes.  Some people give a name of "bubble boy" disease, as the patients might need a complete "clinical isolation" to prevent any lethal infection. I believe we could easily imagine a person rolling inside a huge plastic bubble, since there are quite some adds using it.

Now the question is, why do I discuss it? 

Well, I had a journal club in the lab today, and though they spoke in mostly in-understandable Japanese, my eyes landed on as text on the paper "X-linked SCID (X-SCID) mice". If you work in animal or cells or genetic research, I assume you understand that the X-linked means the genetic defect is linked or occur in the X chromosome, and as a note, SCIDs are mostly X-linked. If you ever learned about genetic even just a little bit, you would understand that The incidence of X-SCID is 3X higher in males than females, due to the fact that male on has 1 "X"-chromosome, meanwhile female has 2 "X"-chromosomes.  

Then, it's definitely a horrible condition which better never occur in the beginning, isn't it?!

Well, indeed it is not to ever happened on people. However in term of medical research, X-SCID animals are extensively used as hosts for normal and malignant tissue transplant. Malignant in this term are mostly related to tumor and cancer cells. Those X-SCID animals has low or even no rejection reaction towards the transplant due to the weak or nearly no immune response.

I would like to discuss more about it, but since this is my first quite-scientifiic-post, I don't want to complicate it.

By any cases, if you are interested a bit more, you can try reading some of these pages

https://en.wikipedia.org/wiki/Severe_combined_immunodeficiency

https://www.inkling.com/read/janeways-immunobiology-kenneth-murphy-8th/chapter-5/case-5

http://download.cell.com/cell-reports/pdf/PIIS2211124712002343.pdf?intermediate=true

The Tale of a Boy in a Coffee Shop #1

It was a cloudy day with strong wind blowing outside the door. A boy just sat at the nearest set of chairs and a table to the window, looking through the clear glass with his mind flying in the air.

The cafe owner, a wise old lady, came, pulled the chair across the boy and sat in front of him. The owner put 2 cups of coffee on the table, one for each. The boy took a quick glance and reached his share which mixed with lots of milk. With an adult-wanna-be style, he sipped the warmth inside. Suddenly, he stopped his hand in the mid-air.

"Say it owner, what is warmth actually?"

It wasn't 9 o'clock yet in the morning, and the old lady got her first questions of the day.

Welcome!! to the whole mess in my mind ^^

Hello, nice to meet you!!

Welcome!! to the whole mess in my mind!!

I don't know how you could end up reading this silly blog, but anyway, thanks for starting reading this thing!! This blog will be my aid to keep my sanity from the whole mess in my own brain.

Starting today, I promise myself to keep on writing, at least 1 post daily.

There will be at least 2 series that I will keep on posting.

The first one will be titled "Brain Damage Control" or I will label it as BDC. In this series I will write about anything I learned in that day. It might be mostly about Biotechnological term, since I am a Biotech Grade Student, but I will keep it easy to read, easy to understand. It's a practice for me too ^^

The other one will be titled "The Tale of a Boy in a Coffee Shop". This will be a micro-novel series. YAY!!! Enjoy the might-be-not-a-very-new-but-I-like-it-this-way experience while reading it. I hope I could keep writing it in an interesting way. Of course, issues suggestions or requests are highly welcomed!!

So!!!

Enjoy!!