Showing posts from March, 2015

CRISPR/Cas9 gene editing

The hot new technique in molecular biology is CRISPR/Cas9.

The URL has a longer form explanation with diagrams.

The really short description is as follows:

The CRISPR/Cas9 technique takes advantage of a particular way bacteria chop up foreign DNA. This mechanisms has been adapted to facilitate disruption of targeted sequences in model organisms such as mice and zebrafish.

Let's say one wants to disrupt gene P.

Research findings have identified rules that govern the location of the targeting such that one can design a short sequence of DNA that will bind to a specific target site within gene P. In the design, in addition to the target sequence, a guide sequence that will bind the Cas9 enzyme is included contiguously.

Thus, this sequence (1) binds to the target site on gene P and (2) permits the guide sequence to tether Cas9 to that target and Cas9 cuts the target DNA sequence.

After the sequence is cut, DNA repair enzymes enter the picture to fix the lesion. The repair is not perfec…

Liverpool team stats from Man U loss to Man U loss - not yet ready to "move up in weight class?"

There is no question that Liverpool improved in recent months compared to their dismal start to the EPL season. It has often been said by experts that the 3-4-3 formation instituted in the 3-0 loss to Man U at Old Trafford last December was the start of the good run of form for the team.

Last Sunday's loss to Man U at Anfield marked a return to concern about the team. And indeed, they do have issues going forward with Gerrard out due to the red card banishment and what appears to be a likely retroactive red card sanctions for Skrtel. The loss of Skrtel is probably the more substantive concern as he has been a key defender in the back three. Giving Gerrard a proper send off to retirement was already tricky to navigate given that there are some match ups where the team would benefit or at least not be hindered by his presence. But there are possible other situations where he could be a liability. In a way, not having the option of plugging him into the next three games might actual…

Installing GNU Octave 3.8.0 on Mac OS 10.10.2

In the lab, I occasionally run Matlab scripts through Octave for some scientific calculations pertaining to my work on vitamin D. With a new desktop in the lab running OS 10.10 Yosemite, I had to reinstall Octave. The previous desktop was running 10.6 (snow leopard).

I fetched GNU Octave 3.8.0 from SourceForge and attempted to install. Unfortunately, the system didn't want to install it since it didn't come from the Apple App Store.

I opened the README.txt file in the install window and found this advice:
You may need to override Gatekeeper to allow installation of GNU Octave 3.8.0 on OSX 10.9 (Mountain Lion). You may find instructions about how to do this on this page: in the section labeled "How to open an app from a unidentified developer and exempt it from Gatekeeper".

I figure OS 10.10 might have the same work around. Indeed, that was the case.

I opened up the recommended Apple support page.

Control-mouse clicked on the GNU Octa…

Let's go Bruins!

With the loss to Arizona in the semi-finals, I figured UCLA was NIT-bound. But the NCAA committee figured their strength-of-schedule and the "eye" test said they were good enough to get in.

Armed with an 11-seed and a Looney getting used to the face-mask, I thought it would be 50-50 they could sneak past SMU. And indeed, it came down to the final minute and a controversial call to put UCLA over the top.

UCLA was expected to beat UAB and indeed, UCLA pounded it inside and UAB never got closer than six after UCLA established the lead.

Now, it is a rematch against Gonzaga.

Gonzaga easily won the first time they met this year in the non-conference part of the season. They will undoubtedly be favored again. They have a strong inside-outside game and stopping both will be difficult. Coach Alford may have to pick his poison and either collapse in on Gonzaga's bigs and hope the outside shooting is off. On the other hand, they can go out on the shooters but risk getting torn up i…

Fifth Sunday In Lent

John 12:20-33 (NRSV)  Now among those who went up to worship at the festival were some Greeks. They came to Philip, who was from Bethsaida in Galilee, and said to him, "Sir, we wish to see Jesus." Philip went and told Andrew; then Andrew and Philip went and told Jesus. Jesus answered them, "The hour has come for the Son of Man to be glorified. Very truly, I tell you, unless a grain of wheat falls into the earth and dies, it remains just a single grain; but if it dies, it bears much fruit. Those who love their life lose it, and those who hate their life in this world will keep it for eternal life. Whoever serves me must follow me, and where I am, there will my servant be also. Whoever serves me, the Father will honor. "Now my soul is troubled. And what should I say--' Father, save me from this hour'? No, it is for this reason that I have come to this hour. Father, glorify your name." Then a voice came from heaven, "I have glorified it, and I will …

Fourth Sunday In Lent

John 3:14-21 (NRSV) And just as Moses lifted up the serpent in the wilderness, so must the Son of Man be lifted up, that whoever believes in him may have eternal life. For God so loved the world that he gave his only Son, so that everyone who believes in him may not perish but may have eternal life. Indeed, God did not send the Son into the world to condemn the world, but in order that the world might be saved through him. Those who believe in him are not condemned; but those who do not believe are condemned already, because they have not believed in the name of the only Son of God. And this is the judgment, that the light has come into the world, and people loved darkness rather than light because their deeds were evil. For all who do evil hate the light and do not come to the light, so that their deeds may not be exposed. But those who do what is true come to the light, so that it may be clearly seen that their deeds have been done in God. In an iTunes U talk I heard recently, Fred…

Liverpool in the hunt

Liverpool kept pace with Manchester United with a 1-0 win over Swansea. This sets up a showdown with their dreaded rivals to the east on Sunday. A win by Liverpool allows them to jump to 4th while a Man U win gives them a stronger grip on 4th.

Here is an article praising manager Rodgers for his tactical smarts in the second half and overall praise for turning the team around after a dismal start.

Excerpt about the shift in formation he drew up:
"It would have been easy for him to just match what Swansea were doing and gone "like for like." After all, Liverpool did that to great effect during last season's title run. That would have meant reverting to a back four, however; their recent defensive improvement has been largely due to playing with three defenders. So Rodgers, ever the innovator, kept his three at the back but set up a diamond in the middle of the park. It is not a system often seen in the league and it was similar to how the great Ajax side of the mid 199…

Third Sunday in Lent

John 2:13-22 (NRSV) The Passover of the Jews was near, and Jesus went up to Jerusalem. In the temple he found people selling cattle, sheep, and doves, and the money changers seated at their tables. Making a whip of cords, he drove all of them out of the temple, both the sheep and the cattle. He also poured out the coins of the money changers and overturned their tables. He told those who were selling the doves, "Take these things out of here! Stop making my Father's house a marketplace!" His disciples remembered that it was written, "Zeal for your house will consume me." The Jews then said to him, "What sign can you show us for doing this?" Jesus answered them, "Destroy this temple, and in three days I will raise it up." The Jews then said, "This temple has been under construction for forty-six years, and will you raise it up in three days?" But he was speaking of the temple of his body. After he was raised from the dead, his disc…

Second Sunday in Lent

Mark 8:31-38 (NRSV) Then he began to teach them that the Son of Man must undergo great suffering, and be rejected by the elders, the chief priests, and the scribes, and be killed, and after three days rise again. He said all this quite openly. And Peter took him aside and began to rebuke him. But turning and looking at his disciples, he rebuked Peter and said, "Get behind me, Satan! For you are setting your mind not on divine things but on human things." He called the crowd with his disciples, and said to them, "If any want to become my followers, let them deny themselves and take up their cross and follow me. For those who want to save their life will lose it, and those who lose their life for my sake, and for the sake of the gospel, will save it. For what will it profit them to gain the whole world and forfeit their life? Indeed, what can they give in return for their life? Those who are ashamed of me and of my words in this adulterous and sinful generation, of them …

Post-Gerrard Era?

Gerrard signed a deal to go to the LA Galaxy after the end of the Premier League season. Thus, the team needed to prepare for the post-Gerrard era.

Well, due to injury, the team is finding out what life might be like as Gerrard has been out since he was substituted 2/3 of the way through Liverpool vs. Tottenham(2/10).

Since that time, Liverpool defeated Crystal Palace, Southampton, and Manchester City in convincing fashion.

The two legs against Beskitas were probably the most difficult games for Liverpool in this stretch. Liverpool got a one goal lead in leg one and were trying to hold on in leg two. Would Gerrard's presence have made a difference in that leg two away match in rowdy Istanbul site of one of his past glories?

Perhaps, he would have helped them get a second goal in the first half changing the complexion of the game. As it stands, the team missed some opportunities which ultimately came back to haunt them. Would Gerrard have made a difference? Perhaps, so.

But clearly…