Amardeep Kaur March 5, 2020 Dis 1B Week 9 Thursday Questions from Tuesday Lecture 1. What are examples of multi-species microbial communities that form during production of fermented foods? Cheese shows to have many microbial communities. Some other types of cheese are made through fermentation of milk by lactic acid bacteria. During aging, a biofilm, which is termed rind, develops on the surface and it is largely what contributes to the flavor of cheese. Rind biofilm can have a subset of mixed eukaryotic and prokaryotic bacterial communities. Some meats have fermentation going on by lactic acid bacteria. An example includes salami. Yeast and bacteria colonize the surface and are usually visible as white and yellow colonies. There are some liquid fermented foods, such as fermented tea. Yogurt is also fermented with bacterial communities. 2. How does the microbiome relate to lung disease? Microbiome is important for healthy lungs. Studies have shown that certain lung diseases have different microbiota than healthy lungs. For example, chronic obstructive pulmonary disease research found that global changes of microbiome can be associated with this disease. Microbiome of COPD patients may have different bacterial species present compared to health individuals. Other lung diseases that follow this path include cystic fibrosis, asthma, idiopathic pulmonary fibrosis, and lung cancer. Week 9 Thursday Paper 1 1. How are metaproteomics, microbial community proteomics, and microbial community proteogenomics similar or different? Explain. All of these terms can be used interchangeably as some researchers say. They are all emerging fields of technology in the genomics world. However, there are some differences. Metaproteomics is used to classify experimental systems and results that are complex and genes that are identified using this system cannot be binned into a certain species type or organism. Microbial community proteomics is used when experiments have identifiable proteins. Microbial community proteogenomics is going a bit further with microbial community proteomics. It is identifying the protein at the peptide level. 2. What does microbial proteomics mostly rely on? Explain. Microbial proteomics makes use of gel based and gel independent liquid chromatography which relies on mass spectrometry based peptide identification. In gel based approaches, the intact proteins are separated before enzymatic digestion happens to generate proteolytic peptides. Liquid based chromatography does not use intact proteins. Instead, there is a shotgun approach. This stage involves three stages including sample preparation, liquid based mass spec analysis, and proteome informatics. All three stages are important for application. Week 9 Thursday Paper 2 1. How did the researchers test if some peptide sequences could have been missed because of evolutionary divergence of amino acids? The researchers generated aligned sequences that were from chicken collagen a1t1, which is the most closely related sequence of ostrich. They compared it to that of frogs and newt. For the fragments where one or more of three taxa diverged at one or more residue, a set of theoretical protein sequences were generated that included the same sequence in regions where all three species were identical as well as different combinations of the observed variant amino acids at residues where all the species diverged. The researchers predicted an ostrich peptide based on relatedness. 2. What is point assisted mutation and how did researchers use it? Point assisted mutation is replacing a single amino acid in the primary structure of a protein to another amino acid. Point assisted mutation matrices predict changes in amino acid residue through evolution. The researchers used it for additional sequencing for misaligned residues. With this technique, the researchers found six additional collagen peptide sequences that were unique to an extant ostrich and was missed in comparison in the public data that was recovered earlier in the study. Amardeep Kaur 3/5/20 Dis 1B Guest Speaker Rachel Loo How does enhanced filter aided sample preparation provide efficient ways to extract proteins and purify them?
