Tag Archives: RE22

qPCR – Taylor Water Filter DNA Extracts from Yesterday

Ran qPCR on the Taylor water filter DNA extracts from yesterday using V.tubiashii 16s primers (SR IDs: 455, 456). Used RE22 DNA as a positive control, provided by Elene. Master mix calcs are here. All samples were run in duplicate. Plate layout, cycling params, etc can be found in the qPCR Report (see Results).

Results:

qPCR Data File (CFX96)

qPCR Report (PDF)

All samples amplified, including the negative controls. Negative controls exhibited very weak, late amplification. Additionally, many of the samples have a “shoulder” or apparent double-peak present in the melt curves. Will repeat to see if I can eliminate amplification in negative control samples.

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qPCR – cDNA from 20120208

Performed qPCR on all 12 samples. Used the following primers, provided by Elene, to detect V.tubiashii expression:

  • rseA_F/R
  • VtpA_F/R
  • VtpR_F/R

Used RE22 DNA (provided by Elene) as a positive control. Master mix calcs are the same as yesterday’s qPCR, but using the primers mentioned above. Plate layout, cycling params, etc. can be found in the qPCR Report (see Results). All samples were run in duplicate.

Results:

qPCR Data File (CFX96)

qPCR Report (PDF)

Positive control worked in all primer sets. All no template controls were clean for all primer sets.

Only one sample (#411) produced any amplification. Amplification was detected in the vtpA primer set (mean Cq = 38.06). However, there was also amplification detected in one of the two replicates for sample #411 in the rseA primer set (Cq = 39.09).

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SOLiD Sequencing Submission

Submitted the following 8 samples for SOLiD sequencing at HTGU:

 

SB unmeth C.gigas C.gigas gill pool gDNA
SB meth C.gigas C.gigas gill pool gDNA
MA Mercenaria mercenaria gill pool polyA(x2)
BX Mercenaria mercenaria gill pool polyA(x2)
Vt RE22 Vibrio tubiashii (RE22) gDNA
Vt STRAIN Vibrio tubiashii (ATCC 19106) gDNA

 

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Gigas Bacterial Challenge – 1hr & 3hr Challenges with Vibrio vulnificus

400mL O/N culture (1x LB+1% NaCl, 37C, 150RPM, 1L flask) of V.vulnificus (STRAIN??) and V.tubiashii (Strain: RE22) were pelleted (4300RPM, 25C, Sorvall ST-H750 rotor). Supe was removed and pellets were each resuspended in 50mL sea water. 1mL was taken from each to use for dilutions to determine colony forming units (CFU).

Two containers were set up with each containing 16 C.gigas, and air stone and 8L of sea water. The entire 50mL of V.vulnificus was added to one of the containers. 8 oysters were sampled (gill and mantle tissue) from each container at 1hr and 3hrs after the addition of V.vulnificus culture and immediately frozen on dry ice. Samples were stored @ -80C in the “Gigas Vibrio Exposure 1,3hrs 1/11/11″ box. Additionally, 1mL samples of the water were taken at each time to determine CFU in the water.

In addition to the samples taken above, the following tissues were taken from 5 control oysters at the 3hr time point and treated/stored in the same fashion as the others, specifically for assessment of cyclooxygenase tissue distribution analysis: muscle, digestive gland/gonad (difficult to differentiate)

All oysters were measured. Morphometric data is here.

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qPCR – V.tubiashii primers test (Vpt A and Vt IGS)

Utilized to sets of primers obtained from the Friedman Lab: VptA (referred to as “Hasegawa”, even though the reference article calls the primers Vtp A) and Vt IGS (referred to as “Lee” primers, presumably from a published article). For template, used “RE22 DNA” that was given to me by Elene. Tube is dated 9/10/09 and has no indication of concentration. Performed qPCR on a set of 10-fold dilutions. Plate layout/qPCR set up is here, along with dilution series used.

Results:

The VptA primer set generated a nice looking set of dilutions with appropriate spacing (~3.2 Ct/10-fold dilution). HOWEVER, the raw fluorescence signal is very low (only 0.4 units; good signal is usually 3-5-fold higher) AND the melting curve doesn’t look that great. The melting curve could look poor due to the low signal, since it doesn’t come up much higher than background levels.

It should be noted that the low fluorescence levels generated could simply be due to the amplicon size generated by these primers. The amplicon size is only 63bp. An amplicon of this size might not be able to incorporate significant amounts of dye to generate a “normal” level of fluorescence (1.25 – 2 units).

The Vt IGS primers failed to generate any product.

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