Wednesday, April 30, 2014

Li Ma defense, haplotype, Qing Song lab, Morehouse medical school

Fu and Ma in prep

Teri manlolio,

Schizophrenia, Lee 2012, GWAS

Smemo etal Nature 2014 longrage haplotype FTO IRX3

haplotyping methods
GMP 2001, nat genetics
Qiagen 2005
Polony2006, Nat Genet
Barcode 2009, Nat Method
Fosmid 2011, Nat biotech
HiC 2013, Nat Biotech
Illumina 2014, Nat biotech,

Laser microdissection of chromosomes, take half of 46 chrosomes, by chance we can get some single chromosomes which can be used for haplotyping.
23 chromosome is 3.5pg,  amplified to 5-8ug for highthroughput sequencing.
Use heterozygosity of identify diploid and haploid chromosomes.

HiFi software

Quake Dataset

Sunday, April 27, 2014

How to zoom-in on selected coordinates in UCSC genome browser

To zoom in on a selected region, we can high-light a region and then select zoom-in.

Alternatively, we can type the chromosome number and coordinates into the search window:

In this example, we see introns
The dashed line of MSH2 locus indicate introns.

The blocks in this picture are exons with coding regions,

In the following picture, the circled regions are 5' untranslated regions, i.e., 5'UTR, because this region is at the 5' end of "ATG". Notice that 5'UTR is also in an exon.

Wednesday, April 23, 2014

teaching evaluation form

bio233, student project on antibacterial soap

1/10 dilutions of vwr, decon, and dial soaps. There are very viscous and hard to pipette.
70% ethanol as control.

I grew E coli overnight. Students spread 150 ul of Ecoli culture on LB plates. We then spot 5ul of each 1/10 diluted soap and 70% ethanol.

Tuesday, April 22, 2014

Bio125, go over midterm closed book exams.

2 hours, going over midterm exams. Finished about 30 questions.

Two student presented their project using the research day poster.

Bio233, virus trade off paper discussion

Two student led the discussion on De Paepe and Taddei 2006. The key figure 4 was not emphasized enough, and I jumped in and explained the figures.

Monday, April 21, 2014

Sunday, April 20, 2014

Moodle, regrading

Sometimes, questions are unclear, or wrong choices were picked as correct answer. Regrading is need in this case. After reedit the questions, 'regrade' can be clicked to reassign the grades.

Thursday, April 17, 2014

bio125, western blot and signal detection.

We used 25K dilution of second antibody (jackson lab immuno), which is too high. Dr. Kioko said our Kodak Image System has not been optimized to detect Western blots. We need to optimize it during the summer.

bio233, epidemiology

show a video on john snow. the image is mostly still image, but the conversation is informative.

I asked students to go over wikipedia page on 1854 broad street cholera break. I then give John Snow's map to the students and ask them to draw conclusions. To explain clustering, I gave play dough to students and ask them to randomly drop playdough dots on the map. I then explained null hypothesis and alternative hypothesis, p-value.

I then went through slides with clicker questions inserted.

Class evaluation was administrated at the end of the class.

Bio125, hallmarks of cancer, mutagenic primer design

Western blot video. 

I showed students of Kioko's video on transfer procedures. 

1hr on Hallmarkers of cancer

1 hr on mutagenic primer design exercises.
Students have trouble to count the AA positions in alignment. I used subtraction to locate the positions. Students have trouble with offsets of counting.

Dr. Kioko did a demo on second antibody stain and HRP staining. He showed a chem-illuniance in the tube, and students recognize the light from the glow sticks. Kioko told students that they are mostly generated using the same principle.

Corrected a mistake in online quiz. Most students tried, but some did not. 

Design a mutagenic primer to engineer human C333F mutation to yeast MSH2

Goal: Engineer the human C333F mutation into yeast MSH2.

Link of video tutorial of this exercise:

Video on G548C is

The principle of site specific mutagenesis can be found in this tutorial video. Explanation of cognant sites can be see in this Youtube video.

Copy yeast and human MSH2 protein sequences in FASTA format from this link. 

Google "EMBL ClustalW2".  Then, paste the yeast and human MSH2 sequences in FASTA format into ClustalW2 window.

  After "submit", you should see the protein alignment.

Identify the cognant site in yeast MSH2. Human C333 corresponds to yeast C345.

Therefore, human mutation C333F should become C345F mutation in yeast MSH2 gene.

Now, we can design the mutagenic primer based on the DNA coding sequences of the yeast MSH2 (linked here).  You can copy-paste this sequences into ApE.

In the yeast MSH2 ORF sequence, the 345th amino acid position corresponds to 345x3=1035 nucleotide position. So, the codon position is 1033-1035.  We can select these 3 nucleotide in ApE to and double check this codon.

This selected codon should be:
We can verify that  codon TGC is amino acid "C".

To design a mutagenic primer, we will pick 10 bp left to the TGC codon and 10 bp right to the TGC codon, by select from 1023-1045.

Copy the selected sequence into a new ApE window.

At the center of this sequence should be "TGC".

The yeast codon usage table is:

The preferred codon for "F" in yeast is "TTT". 

We can manually change "TGC" to "TTT".

We can save this file in ApE as "C345F_mutagenic_primer.seq".

Tuesday, April 15, 2014

bio125, SDS PAGE gel running, cancer and cell cycle

0.5 hour on protocol, wester blot, probes
1 hour loading gels
1 hour, Cancer and cell cycle, virtual lab on cell cycle and cancer.
MSH2 expression and cell cycle

The SDSPAGE gels were run for 2 hours. Dr. Kioko transfer the gel after the class, and stained with primary antibody.

bio233, ch9, viruses, jeopardy

=> clicker poll on exam logistics
=> Viruses youtube video
=>Viruses Game show rule
=>  Viruses game show. Presentation style can show the next slide, and I can give clues to students.
  The prizes are travel mixer bars.
=>Exam 2 were given back to students.
=> student went through their practical exam on streaking plates. 

I forgot to mention the virus trade off paper discussion. I need to announce in news forum.
=>Virus trade-off paper to read, questions to answer


Thursday, April 10, 2014

BIO125, research day poster on H658Y

FOA plate show that H658Y has as few colonies as potential wildtype MSH2 control. So, H658Y has nearly-normal MMR function. The mutation occurs in ATPase domain, so maybe human MSH2-H658Y just cannot repair as efficiently as the wildtype one, even though its actual repair machinery is normal.

It is also possible that protein expression level of H658Y is lowered.

In Gammie 2007, H658Y was shown to be '-' on MMR. So, our FOA results are not consistent with Gammie07. It is possible that H658Y cells were substantially lower than wildtype MSH2. 

Wednesday, April 9, 2014

Update Snow Leopard to Maverick

I backuped my Snow leopard laptop and then upgraded its osX to Maverick.

After the update, multiple 'mdworker' process heated up the laptop. I used a cold-pad to lower the temperature.  This went on for about 2 hours and 'mdworker' stopped.

Older version of ApE and VirtualBox stopped working, but Mathematica still works.

Console version R is lost. Reinstall R sovles the problem.

Github GUI can be installed now.

Tuesday, April 8, 2014

todo: convert chars to num in ms02

ms02_singlerun_v2() test

The code has trouble to deal with small network with many selfing or redundant pairs. 

Test on 48 states runs OK.

Kilometers versus miles: Does it really matter? 2014 report.

The link between metric systems, scientific literacy and attitude.

The daily life in the U.S.A. is based on customary units separated from the international systems of units (metric system) that are taught in sciences. Does this partition of daily life and scientific understanding hinder the scientific literacy for the American population and impose a negative connotation on science as a whole? These are the questions that we set to investigate. We designed a survey to gauge people’s scientific literacy and acceptance of scientific findings, while taking into account confounding factors such as educational background, gender, country, and age. The survey contains 3 sets of problems: one set on proficiency of the metric system, one set on scientific literacy, and one set on attitude and acceptance toward science. The survey is administrated online and through paper.

We previously reported our findings using 200 participants. The survey received 300 responses recently, and enabled us to analyze the link of proficiency of metric systems to scientific literacy and attitude toward science. 

First, we found the scientific literacy is significantly associated with proficiency of metric system (Figure 1), which is perhaps not a surprise because science is taught in the metric system. This correlation suggests that people that are familiar with scientific knowledge are also more proficient at metric usage.

Second, we found that attitude toward science is significantly associated with proficiency of metric usage (Figure 2). Attitude toward science is also directly associated with scientific literacy (data not sure), but this association disappears if the metric proficiency is controlled in regression (data not shown). This partial correlation suggests that metric proficiency is the causal factor for both scientific literacy and attitude (Figure 3). Updated on April 8, 2014. Attitude toward science correlated significantly with both metric proficiency and scientific literacy, even when age is controlled.

Third, we found that attitude toward science is significantly associated with age, suggesting that old people tend to have better attitude toward science, even when metric proficiency is controlled (Figure 3).  Because the current survey involved many faculty, it is not clear whether this association is due to our biased samples or not.  When educational degree is controlled, age is still significantly correlated with attitude toward science, and this correlation persists when people with Ph.D. are excluded from the analysis. This might mean another bias: People participated in the online survey tend to be more inclined toward science. On-campus survey were often done by papers, and target students that are not interested in science. This bias can only be mitigated by targeting a broader population.

Figure 1.  Scientific literacy correlates with metric proficiency.

Figure 2.  Science attitude correlates with metric proficiency and age. 

Figure 3. Science attitude correlates with age. 

Ages of Participants by gender

Figure.  Metric proficiency is significantly influenced by educations. 

We need a large data and more broad sampling scale to make this survey more meaningful.  Please help us persuade more people to take this on-line survey.

The current R code and survey data are deposit into Hong Qin's GibHub repository


Things to do: 
Some further analysis that I want to do. If people choose 'yes' for "My religious views are more important than scientific views", would answers to the rest of the attitude questions become predictably negative on science? 

Note on 2013 Nov 15, I may use interaction and auto-correlation to address the sampling bias.

bio233, microbial systematics, phylogeny, evolution

Student went through their practical exams: Plate images,



Play-dough on trees, rooted and unrooted trees

The earth history calculation and play dough on tree seem to engage most students. The BLAST slides simply eluded most of them. Some of them probably worked for other courses in front of they computers.

On board exercise: If the earth history becomes 1 day, how long will the human history become?

Playdough exercise:
  How to root unrooted trees.


Upgrade mactower to Maverick

Upgraded mactower to Maverick. This take a few hours.

I backedup all data before the upgrade.

After the upgrade, it looks the all of data files are still there.   Good.
The network configuration also seems unchanged.

The shell link of "R" disappeared, even though the Rgui is still in /Applications/.  I re-installed R3.0.3 and 'which R' points to '/usr/bin/R'.


pathogenic yeast, note, 2014 April 8

interesting ones


non-informative ones

bio125, protein extraction

I spent 50 minutes to explain the protocol on board. Students were given spundown cells in eppendorf tubes, and begin with adding 160 lysis buffer.  The protein extraction took 1 hours and finished around 3:10pm. I used the rest of the time for course evaluation.


yeast cell wall, membrane, nuclear envelope

Nuclear and cytosol

beta mecaptal ethanol


Protocol on board: 

After adding blue ESB to the protein pellet, the TCA will turn ESB into yellow. Use Tris to adjust the color back to blue.

Add DSB to pellet
Changed to yellow. 
Adjusted to blue. 

MSH2 expression, cell cycle, log-phase
hMSH2 has no putative NLS signal, but MSH6 have 3.
co-import is supported.

MSH2 deficient,