Preparation for ASM and ANAS with Deinococcus sonorensis


This week the top priority of the lab was to make sure that everyone had presentable posters for the ANAS and ASM conferences. My role in this week was to finalize my poster and then help other groups to finish theirs as well in terms of the writing, graphics, and the design. Although a very busy week, all of the posters were completed as well as another attempt at sequencing of four samples on Illumina. The first flow cell malfunctioned somehow, so this time before leaving for Las Vegas we pooled and diluted B81, D, caeni, D. pimenis, and D. grandis leaving out P65. These samples were prepared similarly to the last attempt with the exception of pooling 5 ul of each sample rather than 4 ul to make up the total 20 ul of volume necessary for library loading on the sequencer. Next week work will begin to analyze the electron microscopy images of D. sonorensis that were received, as well as preparing to potentially transform this specie for gene editing purposes. 

 Below is a copy of the poster I presented at ASM Las Vegas, and my presentation that I prepared for the judging of the poster. 




This presentation included an overview of the bioinformatic data attained and processed using CV-BRC from a novel sequence acquired using Illumina short read technology. The best current representative of the biofilm capabilities of the Deinococcus genus, or at least the most well studied so far, is D. geothermalis. This species forms biofilms on abiotic surfaces described in paper mills that are hypothesized to be a glycosylated type IV pili system. The coding sequences in D. sonorensis revealed genetic parallels to D. geothermalis in having an abundance of type IV pili genes, as well as PelA and glycosyl transferases that are tied to binding to extracellular bodies to surfaces. D. sonorensis has a large amount of equipment beyond was D. geothermalis has in order to build a very tough hearty biofilm like that we have observed in the plaque formations previously. More work will need to be done in imagine and chemical analysis to see what of these genes are being expressed in sonora, and what the difference in biofilm is between different nutrient densities. 

Comments

Post a Comment

Popular posts from this blog

Investigating Production of AHL-Acylase and AHL-Lactonase in Deinococcus radiodurans

Image
 Introduction     Deinococcus radiodurans  is a gram negative extremophilic bacterial species that is frequently recognized for being able to withstand environmental conditions with high levels of radiation. It is also recently found to be one of the few, potentially only, species that produces both AHL-acylase and AHL-lactonase in order to degrade AHLs. AHL, or N-acyl homoserine lactones, are signal molecules produced by cells, typically in a biofilm community, in order to alter gene expression in the recipient cells. The communication between cells is described as quorum sensing, a survival strategy that regulates the behavior of a community of cells. Most cells that have enzymes that degrade AHLs have either AHL-acylase or AHL-lactonase, but it has been found that Deinococcus radiodurans has genes to synthesize both enzymes, which is incredibly unusual. AHL-acylase is a protein that hydrolyzes the amide bond between the lactone ring and the acyl chain of...
Read more

Evaluating Phycocyanin Extraction and Purification Methods

 Introduction:      Previous experiments have so far established that analyzing phycocyanin extraction requires two major components; approximately 1:10 dilutions of sample in appropriate buffer or deionized water, and repeated readings which can be assessed in averages. Values for purity and concentration in the past few weeks have been consistent between each other, although much lower than anticipated. The previous semester produced crude extracts that were supposedly above even food grade purity requirements,  but the authenticity of  that data is now being questioned. This week primarily focuses on comparing the exact sonication practices from the previous semester, which was primarily ultrasonic bath sonification, while also comparing data from samples centrifuged for different durations of time.  Methods:      Arturo prepared the crude extract using 40 grams of dried spirulina and 400 ml of deionized water, with the...
Read more

Evaluating Methods for Optimal Phycocyanin Extraction and Purification

 Introduction:      Attempts to purify crude extracts produced of the phycobiliprotein phycocyanin (C-PC) found in the microalgae Spirulina plantesis have been previously unsuccessful. The test results have shown that charcoal and chitosan adsorption methods for as purification purposes so far have only a negative effect on purity values, opposite to what is expected. Further testing was done in an attempt to differentiate between purification methods more in depth, beginning with primary method of purification, the charcoal adsorption column. Variations that were of interest included the use of a frit, or potentially filter paper, as well as suspending the charcoal in the crude extract as opposed to just adding charcoal to the column. It is crucial for optimal phycocyanin extraction to be able to purify crude extracts in an efficient and productive manner.  Methods:        Two tubes with one gram of spirulina and ten milliliters of deionized...
Read more