Let's get this bread

  Sequencing the starters What are we sequencing?  We are sequencing the starters to find what nucleotide sequences and microorganisms are present. Specifically we are sequencing the 16S rRNA gene which is bacterial and the ITS region which is fungal. https://ncsu.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2288bbf2-6cd8-4faf-885b-acd8010517c2&start=15.579365    Amplicon-based metagenomic sequencing This type of DNA sequencing has pros and cons. When looking at the pros, this type of sequencing is frequently used for exactly what we are looking for, identifying microbial species. Cons to this type of sequencing is that it can be very time consuming with all the different tubes and containers and markers that are put in the samples to be able to tell which is which. It seems to me that the shotgun metagenomic sequencing would be easier because you don’t have to worry about doing everything that you do with amplicons before sequencing, you can just look at all the DNA without hav

Update on the starters On Wednesday the starters were submitted for sequencing! Last feeding of the starters: Control- smells like a fresh loaf of bread Banana- not much of a smell but lots of bubbles today Lime- still smells like spoiled milk, also has lot of bubbles R

 Rising rate experiment Time measurement was taken Experimental time point  Control starter height from bottom of cup (cm) Banana starter height from bottom of cup (cm) Lime starter height from bottom of cup (cm) 10:00 am 0 min 2.2 cm 1.9 cm 1.8 cm 1:15 pm 195 min 2.2 cm 2.2 cm 2.2 cm 4:05 pm 365 min 2.2 cm 2.3 cm 3 cm 7:00 pm 540 min 2.2 cm 2.5 cm 3.5 cm 10:00 pm 715 min 2.3 cm 2.8 cm 3.8 cm 7:45am (day 2) 1305 min 3.2 cm 3.2 cm 3.5 cm 11:00 am 1500 min 3.2 cm 3.2 cm 3.5 cm 1:30 pm 1650 min 3.2 cm 3.2 cm 3.5 cm

 What happened this week!? February 15: Starters took a trip to Winston-Salem for a day Other than the quick trip home and back, the starters have remained pretty consistent. Some days the smell got really bad, but nothing unbearable. They had bubbles most of the week and all are still showing signs of rising and falling. The starters have been growing since January 26, so on Friday it will have be 25 days! Stayed tuned to hear about the rising rate experiment!

BREAD!   Last week we determined that bananas were thought to originate in Southeast Asia. The top 7 most popular breads made here are roti canai, papparoti, roti sardin, pinagong, roti durian, roti bawang, and nan bya. https://www.tasteatlas.com/most-popular-breads-in-southeast-asia The most popular bread, roti canai, do not use yeast but instead whole wheat flour. Papparoti on the other hand does use yeast. It is not the same fermented culture as sourdough so the two have different textures. Papparoti is a soft bun while sourdough is crusty/chewy type texture. As we know, lime originated from Indonesia. A couple types of bread they make there are roti gambang and roti isi keju. Roti gambang is a cinnamon flavored bread that is biscuit-like and uses flour. Roti isi keju is a bread bun with cheese filling and uses yeast to grow. http://www.indonesiancooking101.com/catalog/?category_id=19 The texture is more like pita bread, so not very similar to sourdough.

Meet the starters!! Control- LITTLE BREAD RIDING HOOD Banana- MAN OF PEEL Lime- OPTIMUS LIME

  Bananas originate from Southeast Asia and may have been the first fruit on earth according to https://www.bananalink.org.uk/all-about-bananas/#:~:text=Their%20origin%20is%20placed%20in,the%20Arab%20for%20'finger '. They are grown in over 150 countries and are of huge economic importance all over the world. Bananas are eaten in a variety of ways by different cultures. In the Philippines: banana cue and as a condiment, in England: Banoffee pie, in Peru: roasted banana, in Indonesia: dumplings https://www.chiquita.com/blog/how-bananas-are-eaten-around-the-world/ . The possibilities are endless. Fun fact: the highest average per capita consumption of bananas in the world is in Ecuador where they eat an average of 218 pounds of bananas per year per person! https://thebananapolice.com/fun-facts/#:~:text=The%20highest%20average%20per%20capita,food%E2%80%9D%20and%20%E2%80%9Cbanana.%E2%80%9D . Another fun fact: My mom has made me eat a banana every day since I was in high school and I

 It's been a pretty smooth week other than the fact that the starters are a little messy. I will be trying harder to make sure the sides are scraped as well as possible to avoid messing up the experiment.

  NGS technology This video was a tough one to understand. The only parts I really got were cluster generation and sequencing. For the bit on cluster generation I didn’t understand what she was talking about but I could see through the pictures/animation that clonal amplification was taking place, but I am not sure what was happening on the scientific level. The only part about sequencing I understood was that the fluorescent bases were competing to match with the original strand. The part of the video that confused me the most was sample prep and how the bridge is formed. I was also struggling with forward and reverse and why the strands were in the order that they were and what the significance of that was.

  February 4 Control- still smells like cardboard. Thicker consistency Banana- smells like rotting banana Lime- starting to smell bad like feet Feeding time: 8:45pm Starters all have dried flour/water mixture stuck on the sides. I’ve been scraping the sides everyday but it has just been building up since the beginning.

  Sequencing the starters What are we sequencing?  We are sequencing the starters to find what nucleotide sequences and microorganisms are present. Specifically we are sequencing the 16S rRNA gene which is bacterial and the ITS region which is fungal. https://ncsu.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2288bbf2-6cd8-4faf-885b-acd8010517c2&start=15.579365    Amplicon-based metagenomic sequencing This type of DNA sequencing has pros and cons. When looking at the pros, this type of sequencing is frequently used for exactly what we are looking for, identifying microbial species. Cons to this type of sequencing is that it can be very time consuming with all the different tubes and containers and markers that are put in the samples to be able to tell which is which. It seems to me that the shotgun metagenomic sequencing would be easier because you don’t have to worry about doing everything that you do with amplicons before sequencing, you can just look at all the DNA without hav

  What have I learned? Using the resources provided by my professors ( https://moodle-courses2021.wolfware.ncsu.edu/course/view.php?id=6573&section=3 ) I was able to see key differences between Sanger sequencing and NGS. Sanger sequencing is much faster and cost effective for less than 20 target sequences because it can only sequence one strand at a time. NGS can sequence many strands all at the same time. It is quicker and cost effective for sequencing more than 20 targets. It is also advantageous because it requires less sample input and can read lower allele frequencies than Sanger sequencing which allows for more DNA to be sequenced in a shorter amount of time.

  DNA sequencing I have not previously learned about DNA sequencing but I am familiar with parts of the method. In my AP Biology class in high school we learned about gel electrophoresis and performed the technique. I knew that gel electrophoresis separates the DNA segments by size using an electrode. I have heard of Sanger sequencing but have not previously learned about it in depth and I had never heard of NGS before this course.

February 3 Lots of changes today. The smells of the starters are all over the place day to day. Starters have definitely risen since last night. Bubbles in the lime starter. Control- still smells like cardboard. Smelled like bread after feeding Banana- smells faintly of corn and cardboard. Bubbles on the surface after stirring Lime- smells fresh, almost lemony. Thinner consistency than other starters Feeding time: 9:15 am

 February 2 Starters got moved today. They are now sitting on top of a cabinet in the kitchen because no one wants growing yeast at the dinner table!

  Why are we sequencing our starters? By sequencing our starters we will be able to see what species of microbes are present. This will allow us to connect the genotype and phenotype of our starters to the different types of microbes we discover. By the end we will be able to “link fruit, microbes, and bread using genetics”. https://youtu.be/DfX5kwtLry0

February 1, 2021 Time to start feeding twice a day!! None of the starters had the holes but they all had a thin clear layer on top. Control- smells grainy, but more on the side of cardboard Banana- smells like grainy bread Lime- smells like corn and lime mixture Feeding time: 8:00 pm