Peptidoglycan and Fosfomycin

Most fun paper I've read yet! Sorry I can't put the pdf on here. I haven't figured that out yet.


Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, 

an enzyme essential for the synthesis of bacterial 

peptidoglycan, complexed with substrate UDP-N- 

acetylglucosamine and the drug fosfomycin 

Tadeusz Skarzynski*, Anil Mistry†, Alan Wonacott, Susan E Hutchinson, 

Valerie A Kelly and Kenneth Duncan 

Structure15 December 1996, 4:1465–1474

Knock knock

Have you ever thought about life without a method to knock on doors? If knuckles weren't so painless and universal and effective, how would we know when our dear friends are at our doorstep or we on theirs? Here's to knocking on doors. So convenient.

Unless the Lord builds the house, those who build it labor in vain.  Unless the Lord watches over the city, the watchman stays awake in vain. Psalm 127:1

We put the fun in fungus

Tonight, this is entertainment side of my homework. It's pretty neat.

N. crassa ascospores

Of course, I don't know that I'm interested in fungus long-term, but I have an incredible opportunity to learn an incredible amount about single-gene deletion, genomic defense, gene regulation, and gene expression in eukaryotes. I absolutely love this class. We gather round a dark wood conference table to drink coffee, ask questions with an experienced and engaged Ph.D., and hypothesize about the functional genomics of fungus.

News to you, ya?

Antarctica penguins have suction cups on their feet and this is what keeps them from falling off the earth.

What else would it be? Gravity?

South pole penguin problems.

George Müller on seeking God's will, paraphrased

1. Seek at the beginning to get your heart into such a state that it has no will of its own in regard to a given matter.

2.  Having done this, do not leave the result to feeling or simple impression. (This leads to great delusions).

3.  Seek the Will of the Spirit of God through, or in connection with, the Word of God. The Spirit and the Word must be combined.  If you look to the Spirit alone without the Word, you lay yourself open to great delusions.  If the Holy Ghost guides us at all, He will do it according to the Scriptures and never contrary to them.

4.  Take into account providential circumstances.  These often plainly indicate God's will in connection with His Word and Spirit.

5.  Ask God in prayer to reveal His will to you aright.

6.  Thus, through prayer to God, the Study of the Word, and reflection, you come to a deliberate judgment according to the best of your ability and knowledge, and if your mind is thus at peace, and continues so after two or there more petitions, proceed accordingly.

The following things lead to mistakes:
Lacking honesty of heart
Lacking uprightness before God
Impatience to wait for God
Preferring the counsel of men over the declarations of Scripture

Too Soon?

Soundtrack of the day:

It isn't entirely too soon. What do you think Hailie? Is it ever too soon?

It you think it is too soon, be encouraged that this is a one-day Christmas music fix. Not to return until November.

November comes next week!

The hydrogen atom....

In P-chem we just finished a unit on the hydrogen atom and the shrodinger equation.  It is the mathematics of atomic electrons- their location, momentum, and energy.

I learned that the hydrogen atoms' electrons have no angular momentum!! Do you know what this means? This means that the electron does not move in a circle, like previously supposed by Bohr.

LIES

Instead, the electron moves towards the nucleus, and then away from the nucleus over and over again. In and out. In and out. Without going sideways at all.

It has a pathlength that looks more like this:

Take that sixth-grade science. 

AND, the lack-of-angular-momentum applies to the lowest energy orbital of every atom.  How cool.

By this all men will know that you are my disciples, if you have love for one another.    John 13:35

So Pretty

These are my favorite flowers. 

White Gardenias

Camellias

Hydrangeas

Aren't they beautiful??

Oh there are so many things to blog. School has started up again and I'm three weeks in. I'm taking a research-based class, Fungal Functional Genomics, and I know it sounds smart. It is smart. We learn cool things every day and I thought, hey, this would be perfect for the blog. Too bad I haven't updated it since July and maybe more current things should come first. Like, what has bailey been doing for the past month and a half? Well, lots of things. Lots and lots of things. Ooooo suspense. Maybe I'll tell you later.

I was going to tell you about adenine scanning to find knockout mutations. Want to learn? Yes? No? I'll tell you about it soon.

Things going on now:
I'm in a house! A beautiful house with the best roommates ever.
I bike everywhere. Yay toned legs.
I'm taking self-defense.
I get to cook things.
My pchem prof is a quantum mechanics stud, and he looks like batman's butler.
I'm reading the Cost of Discipleship, again.
I'm a still creek mentor and tutor.
Joel's doing great. He is in grad school, and way smarter than me. Also, he's probably your best friend.
I can't wait to go to ICF and have international students over for dinner.
I know who my grandlittle is. grandleetle!
I get to go to bible study tomorrow.
I'm in a hope group- like a home church in addition to classic church.
I have a bunch of homework. That isn't news.
I'm waiting to call American hospice to be a part of the start-up here. I love elderly people.
I'm (kind of) keeping up with current events, and have the opportunity to see past the headlines via Joel and my dad.
I'm getting enough sleep.
God is good. That isn't news either.

Fungal Functional Genomics lecture (FFG) always serves coffee, so I'm pretty awake. Coffee, biking, punching things, and drinking water wake you up.

Teddy Says

"You're either a flashy fishing vessel 

or a speedbump."

A bow for a beau

Guess what? I learned how to tie a bow tie today. After I made one! This bow tie is a columbia blue, but the color might not show in this picture. Can you tell it is blue?

I'm a tad proud of it. My first bow tie. How charming.

Hurricanes always win

Hurricanes are waaaaayyy cooler than tornadoes.

More rain. Bigger clouds. Gulf coast. Predictable. Named. Seen from space.
vs.
Sometimes rain. Smaller clouds. Midwest. Unpredictable. Unnamed (unloved). NOT seen from space.

Super cool hurricane

Mean little tornado that
hurts rainbows

A serious pie and San Gregorio

Have you ever had strawberry basil pie? I have! And it is delicious.

Here is another painting. So far, I've been prolific for two days this summer, and those two days were tuesday and wednesday.

Bruno Zupan's San Gregorio by Bailey Jones

For my thoughts are not your thoughts, nor are 

your ways, my ways...   for as the heavens 

are higher than the earth, so are my ways higher 

than your ways and my thoughts higher 

than your thoughts- says the Lord. 

Isaiah 55:8-9

Things to Do #18930494

Compose something beautiful

James Horner

Search James on grooveshark

choose "Play all"

let your playlist be capped at 1,000

and thank the Lord for ridiculously-skilled composers.

This video won't load directly, so sorry. This is for McKinzie.
I'm beginning to understand what drives your passion.

Things to Do #1:

Sit on the bench:

Blue Flag beach, Littlehampton

It is the longest bench.
This one is low on the list. It is, however, first on the blog.

Don't sit on train tracks

"Even if you are on the right track, you will get run over if you just sit there." -Will Rogers
At this point, I would like someone to tell me this daily.

I finished a sketch-painting of a deer, inspired by a piece in the Hamilton's home. Joel requested "classy art" for his room next year. Completely appropriate.

And I told you I'm studying cooler things...

from Quantitative Chemical Analysis, 7th Ed. by Daniel C. Harris

This was in my quant book! Not ochem, not micro. Quant seems more and more like the math of the life sciences. It is the most in-depth, all-encompassing, applicable chemistry course I never knew existed.

All these good classes end Wednesday (pronounced wends-dee). Finals week is a different kind of overwhelming with large blocks of time and a wide scope of information to digest. It makes me want to learn more than study, discuss cool things with my prof instead of taking the exam, and take a job that relates to my future. None of this happens though- I end up just studying because everyone else is doing it. And for me, this constitutes "just sitting there" as far as good serious learning is defined, so I'll probably get run over like most students when the real world comes rolling down the track.

Does that make sense? If you just study, your education doesn't mean much. You may have all the credits to get the degree, but without courage and drive and the guts to seek out opportunities and truly learn, your school plan will run you over. Stand up and do work.

(This is a pep-talk to myself)

For everyone has sinned; we all fall short of God's glorious standard.  Yet God, with undeserved kindness, declares that we are righteous.   He did this through Christ Jesus when He freed us from the penalty of our sins. Romans 3:23-24

DNA Sequencing + color = pony bead necklace

Next abstract, yes? I haven't painted horses yet... life and friends and school are a bit busy. But this is after the horses!

Before Sun Sinks by Yangyang Pan

And a lecture slide blew my mind yesterday, I'm going to try to explain this:

credit to Dr. Matthew Sachs and Dr. Joseph Sorg,
taken from BIOL 351 lecture slides

The dATP, dGTP, dCTP, and dTTP are nucleotide bases. If you take off the hydroxyl group, you get the corresponding ddATP, ddGTP, ddCTP, and ddTTP, which are chain-terminating nucleotides because the 5' phosphate of the next nucleotide can't bond without that 3' hydroxyl. Researchers marked the dd's with flourescent markers.  If you make many single-strand sequences from the original strand's pattern using the d-nucleotides and flourescent dd-nucleotides, the chains will always end with the chain-terminating dd-nucleotides at random lengths. And these dd's are the nucleotides that fluoresce! So you use electrophoresis to order the synthesized strands by weight (corresponding to length), and you get a colorful sequence. How ingenious is that? I hope you were able to follow.

This sequencing technique can't separate larger fragments due to computer-reading errors, so it isn't as useful for large projects. I'm more interested in the logic behind the process. It makes sense. It deals with chemistry. And it processes genomes. "How neat is that?"

Serve only the Lord your God and fear Him alone. Obey His commands, listen to His voice, and cling to Him.  Deuteronomy 13:4

Have you seen the stars at night?

I would rather be here:

The McDonald Observatory

Looking at these:

photo credit: Zach Schrock Photo Blog

But nonspecific host resistance and intraepidermal lymphocytes are cool too. Thank you, Joel, for making sure I am in tip top studying shape and ready to conquer some tests. And thank you, Mama Russell, for buying good green tea. (I term-dropped the intraepidermal lymphocytes for sympathy, but my real hidden agenda is to make you jealous. I am so positive that everything I am studying is way cooler than whatever you have to study.)

Where shall I go from your Spirit? Or where shall I flee from your presence? If I ascend to heaven, you are there! If I make my bed in Sheol, you are there! If I take the wings of the morning and dwell in the uttermost parts of the sea, even there your hand shall lead me, and your right hand shall hold me. Psalm 139:7-12.

Long live Yossarian

I wouldn't recommend Joseph Heller's Catch-22 to everyone. But I recommend it to myself every ten years and I can't wait for that time to come.
     "Death to all modifiers, he declared one day, and out of every letter that passed
      through his hands went every adverb and every adjective."
     "Clevinger really thought he was right, but Yossarian had proof, because
      strangers he didn't know shot at him with cannons every time he flew up
      into the air to drop bombs on them, and it wasn't funny at all."

And watch out, all you who frequent Oregon.  There is a giant fungus.
It is old news, but interesting nonetheless.

Let all that I am praise the Lord; with my whole heart, I will praise His holy name. Psalm 103:1