Posts

THE FINAL POST: A BITTER SWEET ENDING

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     THE QUESTION      In my last two blog posts, I've posed a series of questions that I thought might potentially be interesting to explore into given the research data we've been collecting. This week, I intend to explore one of those questions and the question I've selected is... drum roll, please! Do starters with fruits classified as "bitter", have microbial compositions that differ from fruits that are classified as "sweet"?       With this question, I intended to explore if fruits that have differing tastes also have microbial communities with differing compositions. THE HYPOTHESIS     Now, with every research project, no matter how big or small, it is important to have a hypothesis. I always find that coming up with a hypothesis helps me to better understand the question that's being asked (when I'm not the one coming up with it) even more.     In this case, I hypothesize that starters containing fruits ...

MY FIRST TIME USING CLC

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     It's definitely been a while since I've updated my blog (I've been very busy over the past two weeks as the semesters about to start reaching its closing point). But, about a week-and-a-half ago, I started working a little bit with CLC (a genomics workbench used to analyze the microbial species present in our sourdough starters). MY EXPERIENCE     The process of working through the protocols in CLC was actually a bit easier than I expected. I noticed that the direction said that it would take a while and it might be pretty challenging, so a part of me was definitely worried that it would be too difficult for me to figure out. However, by making sure that I was following the directions (and by doing exactly what was happening in the screenshots), everything went smoother than I expected it would.     While the process was definitely easier than I expected, it took just about the amount of time I thought it would. I worked o...

THE PROCESS OF SEQUENCING THE STARTERS AND POTENTIAL RESEARCH QUESTIONS

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      Now that we've finished our starters, they're in the process of being sequenced, and we know a little bit more about DNA sequencing, we're going to hop into what exactly we're sequencing and what kind of research questions we can answer with what we're sequencing. SO, WHAT ARE WE SEQUENCING EXACTLY?      We're sequencing specific regions of the genomic DNA, called the 16S rRNA, which is typically used when sequencing bacteria, and the ITS region, which is typically used when sequencing fungi and other eukaryotic organisms. The method by which we're only sequencing these two regions is referred to as amplicon-based metagenomic sequencing (where amplicons are just little pieces of the DNA).       If we had sequenced the entirety of the DNA of the starters, then we would've performed shotgun metagenomic sequencing, which leads to wondering, why did we choose the method we did to sequence our DNA? THE ENTIRE DN...

A START TO BETTER UNDERSTANDING DNA SEQUENCING

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  WHAT'S THE POINT IN ALL THIS DNA SEQUENCING?     Now that I've finished growing my starters and I've turned in samples of each of them for DNA sequencing, its time to get an even closer look at what made these starters behave in the way they did. Before we can hop into this though, it's important to understand why DNA sequencing is important.     One of the broader purposes of this experiment is to gather data to determine if certain fruit starters grow faster/slower than our control starters and/or other groups of fruits.       Now, it's important to understand that a starter isn't made up of a single organism, rather it a whole community of microbial organisms, meaning that the smell, texture, etc. that were describe isn't for just one organism, but rather a plethora of organisms.     DNA sequencing will enable us to determine what types of microbes are the most common in which starters. Once we are able to determine t...

DIVING INTO MY RISING EXPERIMENTS AND THE BREADS BEHIND THE CULTURES THAT BROUGHT US PEACHES AND LEMONS

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  THE END OF A YEASTY JOURNEY  (SEPTEMBER 14TH-21ST, 2020):        The last week of growing my sourdough starters was a journey in its own way, but not because there were any real challenges. In fact, all of my sourdough starters this week were still consistent  with the results of last week (they were all brownish-white in color, they all smelled fermented (yeasty), and they each rose every day) .     The most adventurous part of this week was the fact that I made a second batch of each of the sourdough starters by taking out a scoop from the old starter (as I usually do each time I feed them) and then putting them each in their own new cup. I then fed them, alongside my original starters, with 1.5 scoops of flour and 1 scoop of water for a span of three days (I started on Friday, September 11th, 2020 and finished at 12:48 AM on Monday, September 14th, 2020).      On Monday, September 14th, 2...