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14 January 2009 @ 08:23 pm
Oops, I guess I got a little carried away yesterday with the lj-ing and forgot about how annoying long posts were, so now I must relearn the way of the lj-cut. But there's a time and a place for everything and I'm too tired to figure out how to do that now.

Mass spec class/lab went well today! I feel like I learned a lot, ITRAQ and ICAT make a lot of sense now :) I don't know how can describe what my day was like without feeling like a text book or an instruction manual, so I think I can sum it up with two moments:

Professor 1: "You mean 'Make like a hockey stick and get the puck out of here' right? Something like that?"
Professor 2: "Well I was thinking make like a milliliter and discharge from the pipette, or make like a picomole and get the fentomole out" or something like that... Hmm... it was a lot funnier at the time--okay, nevermind.

Techie: "It forms a fine spray of charged adducts, has an orbital ion trap, can run MS and MS/MS, can be used with ITRAQ and ICAT, is attached to a High Performance Liquid Chromatography system being able to separate proteins and peptides based on isoelectric point as well as mass AND can make lightly-buttered popcorn!" I added that last part...

Two more days at home and then I'm moving into the dorms O_O I'm REALLY excited, because I have a single :) You never really appreciate the joys of alone time until you're forced to live with other people for a year, especially if it's 3 in a ten by ten room (and a cat--don't ask). Don't get me wrong, I love bus travel--but it would be nice living a little bit less out of the rucksack.

Other then lab, lab and everyday life not much is really going on lately. I just found out that Ashleigh is gone until next christmas (you douche) but it's k, you're never really separated from a friend as long as facebooking and text-fighting is still unconsidered electronic stocking. *** I just saw an ad for naked bike riding, my first thought 'ouch' my second 'where can I sign up?' *** I've got to figure out how this thing works, livejournal I mean. Because I kinda want to upload lots of pics and videos and stuff, cause I think that's cool and neat and jigglypuff and all that, I just need to find stuff to upload... At the moment all I have are PDB screenshots of hemoglobin and cytochrome c oxidase (aka ETC complex iv)--so I was debating whether or not to have a weekly enzyme to dedicate my life to, I really like carbonic anhydrase personally, but that's just me. The humility of how the enzyme seems to help our bodies quickly carry out naturally occuring inorganic conversions of carbon dioxide to bicarbonate and vice versa in a wonderfully unappreciated example of the Bohr effect (also seen in hemoglobin with respect to oxygen and carbon dioxide transportation). Or should I dedicate my weekly life to a pathogen? Ebola what would we do--okay, I'm not even going to go there, karma and all, don't want no fruit bats to appear in my closet tonight... ... Okay, now I'm creeped out. But the thought persists and will be reflected upon and initiated me thinks. Yes, plans will be initiated on Sunday, as plans and new beginnings so often are, and unless my schedule proves to be one full of nonstrategic procrastination I believe this day will remain the initial for further assignments. This is excellent! It gives me time to plan :) To prepare! I must be off, and discover at my own pace. It will be a long and frugal journey through many tens of wikipages and scriptual diagrams.

Kk, thanks for reading, but I should probably go because I obviously have nothing to say :P And Kiko's calling :) As is bed.

Video of the day: Clip from Die Zäuberflöte (Mozart)

Thanks for reading :)
Current Mood: tiredtired
13 January 2009 @ 10:37 pm

Crazy stuff in this world of ours.
Current Mood: predatorypredatory
13 January 2009 @ 09:12 pm
Today was the first day of my 4-day long laboratory course in Mass Spectroscopy, it is a joy I must say. I took a Mass spec. workshop over the summer (in August) and expected this to be the same (as it is taught by the same people) but it's actually different, they added an extra day, and I have to present a research paper. So here's what we have to choose from:


Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma

Paul H. Huang*, Akitake Mukasa†, Rudy Bonavia†, Ryan A. Flynn*, Zachary E. Brewer*, Webster K. Cavenee†,‡,§, Frank B. Furnari†,‡,§, and Forest M. White*,§,¶
+Author Affiliations

*Department of Biological Engineering and
¶Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139; and
†Ludwig Institute for Cancer Research, San Diego Branch, and
‡Department of Medicine and Cancer Center, University of California at San Diego, La Jolla, CA 92093-0660
Contributed by Webster K. Cavenee, June 1, 2007 (received for review May 14, 2007)


Glioblastoma multiforme (GBM) is the most aggressive brain tumor in adults and remains incurable despite multimodal intensive treatment regimens. EGFRvIII is a truncated extracellular mutant of the EGF receptor (EGFR) commonly found in GBMs that confers enhanced tumorigenic behavior. To gain a molecular understanding of the mechanisms by which EGFRvIII acts, we have performed a large-scale analysis of EGFRvIII-activated phosphotyrosine-mediated signaling pathways and thereby have identified and quantified 99 phosphorylation sites on 69 proteins. Distinct signaling responses were observed as a function of titrated EGFRvIII receptor levels with the phosphatidylinositol 3-kinase pathway being dominant over the MAPK and STAT3 pathways at a high level of EGFRvIII expression. Within this data set, the activating phosphorylation site on the c-Met receptor was found to be highly responsive to EGFRvIII levels, indicating cross-activation of the c-Met receptor tyrosine kinase by EGFRvIII. To determine the significance of this finding, we devised a combined treatment regimen that used a c-Met kinase inhibitor and either an EGFR kinase inhibitor or cisplatin. This regimen resulted in enhanced cytotoxicity of EGFRvIII-expressing cells compared with treatment with either compound alone. These results suggest that the clinical use of c-Met kinase inhibitors in combination with either EGFR inhibitors or standard chemotherapeutics might represent a previously undescribed therapeutic approach to overcome the observed chemoresistance in patients with GBMs expressing EGFRvIII.


Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy*,S

Wei-Jun Qian, David T. Kaleta, Brianne O. Petritis, Hongliang Jiang, Tao Liu, Xu Zhang, Heather M. Mottaz, Susan M. Varnum, David G. Camp, II, Lei Huang, Xiangming Fang¶, Wei-Wei Zhang¶ and Richard D. Smith,||
From the Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, GenWay Biotech, Inc., San Diego, California 92121, and ¶ Acrotics Corp., San Diego, California 92130

The enormous dynamic range of human bodily fluid proteomes poses a significant challenge for current MS-based proteomics technologies as it makes it especially difficult to detect low abundance proteins in human biofluids such as blood plasma, which is an essential aspect for successful biomarker discovery efforts. Here we present a novel tandem IgY12-SuperMix immunoaffinity separation system for enhanced detection of low abundance proteins in human plasma. The tandem IgY12-SuperMix system separates 60 abundant proteins from the low abundance proteins in plasma, allowing for significant enrichment of low abundance plasma proteins in the SuperMix flow-through fraction. High reproducibility of the tandem separations was observed in terms of both sample processing recovery and LC-MS/MS identification results based on spectral count data. The ability to quantitatively measure differential protein abundances following application of the tandem separations was demonstrated by spiking six non-human standard proteins at three different levels into plasma. A side-by-side comparison between the SuperMix flow-through and IgY12 flow-through samples analyzed by both one- and two-dimensional LC-MS/MS revealed a 60–80% increase in proteome coverage as a result of the SuperMix separations, suggesting significantly enhanced detection of low abundance proteins. A total of 695 plasma proteins were confidently identified in a single analysis (with a minimum of two peptides per protein) by coupling the tandem separation strategy with two-dimensional LC-MS/MS, including 42 proteins with reported normal concentrations of 100 pg/ml to 100 ng/ml. The concentrations of two selected proteins, macrophage colony-stimulating factor 1 and matrix metalloproteinase-8, were independently validated by ELISA as 202 pg/ml and 12.4 ng/ml, respectively. Evaluation of binding efficiency revealed that 45 medium abundance proteins were efficiently captured by the SuperMix column with >90% retention. Taken together, these results illustrate the potential broad utilities of this tandem IgY12-SuperMix strategy for proteomics applications involving human biofluids where effectively addressing the dynamic range challenge of the specimen is imperative.


A functional polymorphism of apolipoprotein C1 detected
by mass spectrometry

Matthew S. Wroblewski1, Joshua T. Wilson-Grady1, Michael B. Martinez1, Raj S. Kasthuri2,
Kenneth R. McMillan3, Cristina Flood-Urdangarin4 and Gary L. Nelsestuen1
1 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
2 Department of Medicine, University of Minnesota, Minneapolis, MN, USA
3 American Indian Community Development Corporation, Minneapolis, MN, USA
4 St Mary’s Health Clinics, St Paul, MN, USA
apolipoprotein C1; mass spectrometry;
polymorphism; protein–lipid contact surface
G. L. Nelsestuen, 6–155 Jackson Hall,
321 Church St SE, Minneapolis, MN 55455,
Fax: +612 625 2163
Tel: +612 624 3622
E-mail: nelse002@umn.edu
(Received 7 July 2006, revised 16 August
2006, accepted 18 August 2006)

A survey of plasma proteins in approximately 1300 individuals by
MALDI-TOF MS resulted in identification of a structural polymorphism
of apolipoprotein C1 (ApoC1) that was found only in persons of American
Indian or Mexican ancestry. MS ⁄ MS analysis revealed that the alteration
consisted of a T45S variation. The methyl group of T45 forms part of the
lipid-interacting surface of ApoC1. In agreement with an impact on lipid
contact, the S45 variant was more susceptible to N-terminal truncation by
dipeptidylpeptidase IV in vitro than was the T45 variant. The S45 protein
also displayed greater N-terminal truncation (loss of Thr-Pro) in vivo than
the T45 variant. The S45 variant also showed preferential distribution to
the very-low-density lipoprotein fraction than the T45 protein. These prop-
erties indicate a functional effect of the S45 variant and support a role for
residue 45 in lipid contact and lipid specificity. Further studies are needed
to determine the effects of the variant and its altered N-terminal truncation
on the metabolic functions of ApoC1.


I've only read the abstracts so far, but I think I'm liking the last one--not too hard to understand, but very interesting. Although I think the serum analyses described in the second research paper are very interesting too, so we'll see what the group thinks :).

I guess I'm too tired to actually describe what we talked about in "class" today, but it was really just describing the workings of Mass Spec and variations thereof (MALDI-TOF, ES, MS/MS, Quadrapoles, etc.).

Other stuff that's new: BACK FROM EUROPE!!! It was really fun ^^ I should post some of the pictures or/and videos I have from there, it was really fun :)

I saw that Ashleigh was making a book list for the year!! That's über awesome!! I want to make one too, but mine will be much shorter, for I am a VERY slow reader and have little time to spend hours or more on single novella chapters :) But, we all have dreams now, so here are mine:

White Teeth (Zadie Smith) [I'm actually almost done with this one, I'm going to try to finish it before school starts :)]

Norton's Recommendations:

Survival of the Sickest (Dr. Sharon Moalem)

Napoleon's Buttons (Penny LeCouteur)

Flu: The Story of the Great Influenza Pandemic (Gina Kolata)

Kite Runner (Khaled Hosseini)

Devil in the White City (Erik Larson)

Paradise Lost (John Milton)

Okay, I should probably stop now XP because I still have to read the following novels for my english class this semester:

America is in the Heart (Carlos Bulosan)

Bamboo Among the Oaks (Mai Neng Moua)

Crossing into America (Louis Mendoza)

Crossing Over (Ruben Martinez)

How the Other Half Lives (Jacob Riis)

Jasmine (Bharati Mukherjee)

And I left out something that I think is a sort of packet that I can't find on amazon.com :)

Anywho, who exactly is still online and reads this? Does anyone want to RP with me again? That was really fun, and I think it would be nice to practice and warm up those creative writing skills again :) Otherwise I'll probably just be really boring and post stuff about school, and science and life, or HIV!


How the Human Immunodeficiency Virus Exploits the Loopholes of the Immune System

The immune system is built to fortify the body for nearly any pathogen that intends to invade it. It has evolved in a number of different ways in order to create an arsenal of anti-pathogenic products, such as cytokines, antibodies, T cells (derived from the thyroid), B lymphocytes (derived from the bone marrow), and macrophages to name a few. From the ability to shuffle genes within b lymphocytes to create novel antibodies, to the presentation of major histocompatibility complex (MHC)-bound antigenic peptides on infected cells, the immune system seems to have a flawless design with the ability to prevent any infection, any attack from an invading pathogen. But there is a flaw, or—better stated—a loophole. The Human Immunodeficiency Virus (HIV), the Acquired Immunodeficiency Syndrome (AIDS) virus, has exploited this loophole and changed the way scientists think about pathogens. HIV infects cells of the immune system.

HIV is a negative, single-stranded RNA (ssRNA) retrovirus (meaning that it has an RNA genome that must first be transcribed before viral proteins can be expressed). To help jumpstart replication and establish long-term (latent) infection, the AIDS virus has three proteins packaged within its nucleocapsid: a reverse transcriptase, a protease, and an integrase. Reverse transcriptase quickly and sloppily transcribes viral ssRNA into complimentary DNA (cDNA). It is not commonly present in somatic cells, which is why the virus needs to bring it into the host cell with itself. When viral proteins are synthesized, they are expressed as long peptides that need to be cleaved for proper activation, the protease performs this role. The third enzyme, integrase, integrates viral cDNA into the host genome, sealing the host cell’s fate as a long-term virion producer even if active (lytic) infection is not occuring.

The immune cell that HIV infects is the CD4+ helper T-cell. Helper T cells are not involved in direct pathogenic cleansing, but they play many crucial roles in the immune system such as: activation and commencement of cytoxic T cell growth, heightened macrophage and phagocyte response, and b lymphocyte differentiation and immunoglobulin (antibody) production. When infected with the AIDS virus, the helper T cell turns into a factory forced to reroute its own metabolic processes to promote the development of stable virions. These virions bud out from the cell upon maturation and move on to infect new helper T cells. The lack of metabolic attention the helper T cell aliquots to itself inevitably causes the cell to die from nutrient exhaustion and metabolic override, thus decreasing the helper T cell count and weakening the immune system. Infection and control of components of the immune system is the first method HIV employs to evade the host immune system.

In order to initiate the translation of proteins, HIV needs to reverse-transcribe its RNA genome into cDNA. Because one virus can lead to many thousands of progeny virions, extremely accurate replication is not an important requirement to ensure the continuance of the viral infection within the host. The inaccuracy of the reverse-transcriptase enzyme promotes the production of progeny with slight alterations due to mutations of the viral genome arising from transcription of the cDNA. As with all newly experienced pathogenic compounds, the immune system needs time to develop a strong response and will be delayed in stopping new infection by novel viral progeny. The heightened mutational rate of HIV is a second method of immune evasion.

The third and possibly most crucial method HIV uses to maintain its foothold on the host is integration into the host genome. Upon infection of a helper T cell, the integrase enzyme will cleave off ends of a viral cDNA genome leaving “sticky ends” and shuttle it to the nucleus for host genome integration. When a suitable DNA sequence is found, the host DNA is cleaved in a similar fashion and the viral genome is ligated into the host’s. The viral genome now acts as host DNA, and most importantly is replicated with the host’s genome where it can sit inactive in the lysogenic phase for years before “rebirth” in multiple “healthy” cells and entry into the lytic growth phase. The ability of HIV to integrate a copy (or even multiple copies) of its genome into that of the host is a third important mode of immune system evasion.

Unlike the majority of pathogens that can only evade the immune system long enough to be transmitted to another host, the AIDS virus has evolved multiple methods of immune system evasion. By infecting the CD4+ helper T cells, generating a wide variety of virions and integrating into the host genome, HIV has been able to exploit fundamental loopholes of the human immune system.

While the immune system appears to be unable to maintain control of HIV, scientists are working on ways to fill the loopholes that the virus uses to its advantage. Research on the AIDS virus takes many routes including: investigation of Antiretroviral Therapy and Highly-active Antiretroviral Therapy (ART and HAART respectively), which both involve a cocktail of drugs that hinder various components of the HIV proteome (inhibiting reverse transcriptase, integrase, and GP120 binding, for example); evolutionary advantage studies involving the CCR5 delta 32 HIV-resistance mutation (a mutant allele occurring in about 10% of people with European ancestry involving a lack of the CCR5 protein on CD4+ cells which aids in HIV GP120 surface receptor binding,); and APOBEC3G research, a naturally occurring human antiviral protein that is controlled by the viral vif protein and degraded by the host cell’s own components. With the combined effort of scientific initiative and natural co-evolution with the AIDS virus (as has happened with many animal-immunodeficiency viruses; Feline-IV and Simian-IV for example), the outlook on the AIDS epidemic looks bright; although the method by which the epidemic will be overcome remains unclear.


I told you it was coming... I wrote that for my second genetics essay last semester, it's pretty interesting stuff :)

I really want to put pictures up--and by put up I mean steal them off other websites and link them to appear on here, but I don't want to offend any copyrights or however that works, i t'would make things look a lot prettier around here though, I'll think about that... And the porn thing, can I not post pictures of topless women on here? Even if it's artwork? I'm not saying I'm going to, or that I even have any at all, but I was just seeing if I *could* if it came up. I'm thinking udders... I suppose she can have a bikini top at the moment, don't want to go offending those crack-whore puritans out there.

PROP 8 ads (A bit of a set back for the gay community :/, but I thought the ads were interesting)

The "yes" ads seem to be more highly funded then the "no" ads just by looking at them, but I guess the money input was actually the other way around ($35.8 million and $37.6 million respectively). I don't know why I care though because it is all the way in California--well, maybe I do.
Current Mood: coldcold
12 January 2009 @ 11:10 am
Whoa, this is weird, I totally just started thinking about the blogging life again, and totally want to start this up again!! Who's still on?? I saw that Ashleigh, you just made a 2009 book list!! FUN!!! Ok, let's see how long I can keep this going, I'll post pictures and stuff, as well as life update, why not? Maybe some homework assignments :)

Let the blogging begin!!

I'm actually at work right now though, so I need to start working on my lab presentation... :)

Current Mood: excitedexcited
03 September 2006 @ 05:08 pm
I've finally made the new lj that I've been intending to for so long, and here it is... It shall be friends only, and I won't bother cloggin up my friends page with any lj groups that are not created by people that are meaningful to me. This way I can stay in contact with my friends, while making sure not to miss a so much after not going on for a day or two, if I have forgotten to add you, or would like to be added, please comment in this message, thank you!
Current Mood: accomplishedaccomplished
Current Music: Shostakovich