Courtney Dever and Jennifer Lopez: Difference between revisions
Line 275: | Line 275: | ||
[[Image:Gel_electrophoresis.jpeg|thumb|left|Gel electrophoresis]] | [[Image:Gel_electrophoresis.jpeg|thumb|left|Gel electrophoresis]] | ||
• Soil Map | |||
o worksheet inserted into notebook | |||
• Soil collection data | |||
o worksheet inserted into notebook | |||
• Master Patch | |||
o entry about procedure and any mistakes, problems, etc | |||
• Test Patch | |||
o entry about procedure and any mistakes, problems, etc | |||
• Streak plate for isolation | |||
o (entry about procedure and any mistakes, problems, etc) | |||
• Repeat test for antimicrobial properties | |||
• Colony morphology: Description of isolated organism | |||
• Cellular arrangement | |||
• Gram reaction | |||
• Capsule stain | |||
• Endospore stain | |||
• Motility results | |||
• Phenol Red Broth | |||
o Theory | |||
Substrate and possible end products | |||
o Results | |||
• Starch Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Casein Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Gelatin Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• DNA Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Lipid Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Methyl Red | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Voges Proskauer | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Citrate Test | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• SIM Tests (3 in 1) | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Nitrate Reduction Test | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Urea Hydrolysis | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• Triple Sugar Iron Agar | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Results | |||
• PCR | |||
o Procedure performed in class | |||
• Gel Electrophoresis | |||
o Procedure | |||
o Picture of results | |||
• Oxidase | |||
o Theory | |||
Substrate | |||
Enzyme | |||
o Application | |||
o Results | |||
• Eosin Methylene Blue Agar | |||
o Theory | |||
Substrate | |||
pH indicator | |||
o Application | |||
o Results | |||
• Hektoen Enteric Agar | |||
Revision as of 11:43, 17 April 2016
Classification
Kingdom Bacteria
Phylum Firmicutes
Class Bacilli
Order Bacillales
Family Paenibacillaceae
[Others may be used. Use NCBI link to find]
Species
NCBI: Taxonomy |
Genus species Brevibacillus laterosporus
Habitat Information
Describe the location and conditions under which the organism was isolated.
Two tablespoons of an unknown soil organism were collected at a depth of approximately 1” below the soil surface on January 1, 2016 at 11:53 am from (latitude, longitude) and placed in a plastic Ziploc baggie at room temperature. Below is a picture of the area, and also a picture of the exact location where the soil was taken at the time of retrieval.
Weather conditions on January 1, 2016 at 11:53 am were as follows (source: w1.weather.gov):
Wind: S14
Visibility: 10
Weather: A few clouds
Sky conditions: FEW 200
Temperature:
• Air temperature: 73°F
• Dewpoint: 34
• 6 hour max: 73
• 6 hour min: 32
Relative humidity: 24%
Pressure:
• Altimeter (in): 30.06
• Sea level (mb): 1017.8
• Precipitation (in): 0
Weather conditions also included (source: texaset.tamu.edu):
ET0 or PET: 0.10 in.
Temperature max: 76 °F
Temperature min: 36°F
RH min: 17%
Solar radiation: 17.55 MJm2
Rain: 0 in.
Wind 4 am: 0.12 mph
Wind 4 pm: 6.13 mph
Soil conditions included (source: websoilsurvey.sc.egov.usda.gov):
Map Unit Name: Travis soils and urban land, 1 to 8 percent slopes
Acres in AOI: 0.1
Percent of AOI: 100%
Description and Significance
Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism, and why the organism might be significant.
• Soil Map o worksheet inserted into notebook • Soil collection data o worksheet inserted into notebook • Master Patch o entry about procedure and any mistakes, problems, etc • Test Patch o entry about procedure and any mistakes, problems, etc • Streak plate for isolation o (entry about procedure and any mistakes, problems, etc) • Repeat test for antimicrobial properties • Colony morphology: Description of isolated organism • Cellular arrangement • Gram reaction • Capsule stain • Endospore stain • Motility results • Phenol Red Broth o Theory Substrate and possible end products o Results • Starch Hydrolysis o Theory Substrate Enzyme o Results • Casein Hydrolysis o Theory Substrate Enzyme o Results • Gelatin Hydrolysis o Theory Substrate Enzyme o Results • DNA Hydrolysis o Theory Substrate Enzyme o Results • Lipid Hydrolysis o Theory Substrate Enzyme o Results • Methyl Red o Theory Substrate Enzyme o Results • Voges Proskauer o Theory Substrate Enzyme o Results • Citrate Test o Theory Substrate Enzyme o Results • SIM Tests (3 in 1) o Theory Substrate Enzyme o Results • Nitrate Reduction Test o Theory Substrate Enzyme o Results • Urea Hydrolysis o Theory Substrate Enzyme o Results • Triple Sugar Iron Agar o Theory Substrate Enzyme o Results • PCR o Procedure performed in class • Gel Electrophoresis o Procedure o Picture of results • Oxidase o Theory Substrate Enzyme o Application o Results • Eosin Methylene Blue Agar o Theory Substrate pH indicator o Application o Results • Hektoen Enteric Agar
• Soil Map o worksheet inserted into notebook • Soil collection data o worksheet inserted into notebook • Master Patch o entry about procedure and any mistakes, problems, etc • Test Patch o entry about procedure and any mistakes, problems, etc • Streak plate for isolation o (entry about procedure and any mistakes, problems, etc) • Repeat test for antimicrobial properties • Colony morphology: Description of isolated organism • Cellular arrangement • Gram reaction • Capsule stain • Endospore stain • Motility results • Phenol Red Broth o Theory Substrate and possible end products o Results • Starch Hydrolysis o Theory Substrate Enzyme o Results • Casein Hydrolysis o Theory Substrate Enzyme o Results • Gelatin Hydrolysis o Theory Substrate Enzyme o Results • DNA Hydrolysis o Theory Substrate Enzyme o Results • Lipid Hydrolysis o Theory Substrate Enzyme o Results • Methyl Red o Theory Substrate Enzyme o Results • Voges Proskauer o Theory Substrate Enzyme o Results • Citrate Test o Theory Substrate Enzyme o Results • SIM Tests (3 in 1) o Theory Substrate Enzyme o Results • Nitrate Reduction Test o Theory Substrate Enzyme o Results • Urea Hydrolysis o Theory Substrate Enzyme o Results • Triple Sugar Iron Agar o Theory Substrate Enzyme o Results • PCR o Procedure performed in class • Gel Electrophoresis o Procedure o Picture of results • Oxidase o Theory Substrate Enzyme o Application o Results • Eosin Methylene Blue Agar o Theory Substrate pH indicator o Application o Results • Hektoen Enteric Agar
Genome Structure
• Soil Map o worksheet inserted into notebook • Soil collection data o worksheet inserted into notebook • Master Patch o entry about procedure and any mistakes, problems, etc • Test Patch o entry about procedure and any mistakes, problems, etc • Streak plate for isolation o (entry about procedure and any mistakes, problems, etc) • Repeat test for antimicrobial properties • Colony morphology: Description of isolated organism • Cellular arrangement • Gram reaction • Capsule stain • Endospore stain • Motility results • Phenol Red Broth o Theory Substrate and possible end products o Results • Starch Hydrolysis o Theory Substrate Enzyme o Results • Casein Hydrolysis o Theory Substrate Enzyme o Results • Gelatin Hydrolysis o Theory Substrate Enzyme o Results • DNA Hydrolysis o Theory Substrate Enzyme o Results • Lipid Hydrolysis o Theory Substrate Enzyme o Results • Methyl Red o Theory Substrate Enzyme o Results • Voges Proskauer o Theory Substrate Enzyme o Results • Citrate Test o Theory Substrate Enzyme o Results • SIM Tests (3 in 1) o Theory Substrate Enzyme o Results • Nitrate Reduction Test o Theory Substrate Enzyme o Results • Urea Hydrolysis o Theory Substrate Enzyme o Results • Triple Sugar Iron Agar o Theory Substrate Enzyme o Results • PCR o Procedure performed in class • Gel Electrophoresis o Procedure o Picture of results • Oxidase o Theory Substrate Enzyme o Application o Results • Eosin Methylene Blue Agar o Theory Substrate pH indicator o Application o Results • Hektoen Enteric Agar
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Include S Ribosomal sequence that you obtained from PCR and sequencing here.
BLAST Search from DNA sequencing results:
Cell Structure, Metabolism and Life Cycle
Interesting features of cell structure; how it gains energy; what important molecules it produces.
Physiology and Pathogenesis
Biochemical characteristics, enzymes made, other characteristics that may be used to identify the organism; contributions to environment (if any).
If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
Biochemical Characteristics:
Phenol Red Broth:
•Glucose fermentation: (+) result; broth was yellow indicating glucose fermentation
•Lactose fermentation: (-) result; broth was red—no change in broth??
•Sucrose fermentation: (-) result; broth was red—no change in broth??
problems encountered during procedure:
Starch Hydrolysis: (+) result; clearing was present on starch agar media; soil organism produces the α-amylase enzyme
Casein Hydrolysis: (-) result; no clearing in skim milk agar; soil organism does not produce the casease enzyme
Gelatin Hydrolysis: (+) result; solid broth turned to liquid; soil organism produces the gelatinase enzyme
DNA Hydrolysis: (+) result; clearing in agar; soil organism produces the DNase enzyme
Lipid Hydrolysis: (-) result; no clearing in Tributyrin agar; soil organism does not produce the Lipase enzyme
Methyl Red: (-) result; broth is orange in color; soil organism does not use the mixed acid fermentation pathway, and does not produce mixed acid end-products????
Voges Proskauer (+) result; broth is red in color; soil organism utilizes the butylene glycol pathway, produces acetoin, and produces neutral end-products???
Citrate Test: (-) result, slant is green in color; soil organism does not utilize citrate as a carbon source
SIM Tests:
•Motility (+) result; soil organism is motile as entire tube is pink
•Indole () result; media??? is ???; soil organism [is or is not???] able to produce indole????
•Sulfur () result; media?? Is ???; soil organism [can or cannot???] reduce sulfur to hydrogen sulfide
Nitrate Reduction Test: (+) result; soil organism is able to reduce Nitrate to ammonia or molecular nitrogen???; zinc was added---procedure notes here
Urea Hydrolysis: (-) result; broth is salmon in color; soil organism does not produce the urease enzyme
Triple Sugar Iron: (K/A) result; slant is red in color, butt is orange in color; glucose fermentation with acid production; peptones/proteins catabolized aerobically (in the slant) with alkaline products (reversion)
Decarboxylation:
•Arginine (-) result; broth is yellow; soil organism does not produce arginine decarboxylase and does not ferment ????
•Lysine (-) result; broth is yellow; soil organism does not produce lysine decarboxylase ????
•Ornithine (-)result; broth is yellow; soil organism does not produce ornithine decarboxylase ????
Oxidase Test: (?) result; soil organism [can or cannot] produce Cytochrome c oxidase
Eosin Methylene Blue Agar : (-) result;
Hektoen Enteric Agar (HE): (-) result;
MacConkey Agar (MAC): (-) result;
Decarboxylation: (?) result;
Phenylalanine Deaminase: (?) result;
Catalase Test: (?) result;
Blood Agar: (gamma) result; no clearing in the media; soil organism does not produce hemolysins
Mannitol Salt Agar : (?) result;
Phenylethyl Alcohol Agar (PEA): (+) result; growth, but really slow growth;
Bile Esculin: (+) result; slant is dark brown in color;
6.5% Salt Tolerance: () result;
Bacitracin/Optochin: () result;
Antimicrobial Sensitivity/Kirby-Bauer Test:
•() to Triple Sulfa;
•() to Azlocillin;
•() to Ceftazidime;
•() to Bacitracin
problems encountered during procedure:
Disinfectant sensitivity:
•() to lavendar
•() to clove
•() to rosemary
•() to oregano
problems encountered during procedure:
References
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
Author
Page authored by Courtney Dever and Jennifer Lopez, students of Prof. Kristine Hollingsworth at Austin Community College.