SEPARATE

By the way here's a schematic representation of a normal serum protein electrophoresis gel, in case you wondered.

IT'S ENOUGH ALREADY

I WILL CALL YOU TOMORROW FLOW JO AND I HOPE YOU HAVE SOME MUFFINS PREPARED OR SOMETHING BECAUSE THIS HAS GONE TOO FAR REALLY. I CAN'T AFFORD THIS ANYMORE. YOU SHOULD PROVIDE ME WITH AN ANALYTIST WHO CAN DO THE WORK FOR ME.
GATES WERE ERASED FROM THE PLOTS AGAIN WHEN I OPENED UP MY WORKSPACE TODAY, IN ADDITION TO THE FACT THAT PLOTS OF FILES I HAD ARRANGED ON THE LAYOUT WERE REPLACED 50% OF THEM WITH DATA.001.

I HAVE TO LEAVE THE OFFICE NOW BEFORE MY COMPUTER EXPLODES.

REFLECTIONS

Different aspects of work processes appear each day for me.Going to work can be so much more than taking pictures of my feet on the tram. There are openings in places I didn't see before, including the places inside myself.

I think I should buy myself a bike.

Tram station Sahlgrenska Hospital.

IT'S EASY

To blog.

Aaooow!! It hurts!
G. D. did you have to infect my spine too HSV-2?


Really. It hurts.

You don't believe me? Take a look.
I told you.

POURQUOI

this life is for herpes, not for me

you managed big time, more than I could ever have imagine

but today I thank the Lord for reminding me what it means to be healthy

and for putting food on my table

Really. I do.

V AS IN HERPES

Virion polypeptides

HSV-1 virions has been suggested  to contain at least 30 distinct proteins.
They were designated VP and given serial numbers.
All of the virion proteins were made after infection, and no host proteins could be detected in virion preparations.
At least 11 are on the surface of the virion (accessable to antibody) and at least 10 are glycosylated.


GLYCOSYLATION - the enzymatic process that links saccharides to produce glycans, attached to proteins, lipids, or other organic molecules.This enzymatic process produces one of the fundamental biopolymers found in cells (along with DNA, RNA, and proteins). 

Glycosylation is a form of co-translational and post-translational modification. ^1] 
The majority of proteins synthesized in the rough ER undergo glycosylation.
It is an enzyme-directed site-specific process, as opposed to the non-enzymatic chemical reaction of glycation. 
Glycosylation is also present in the cytoplasm and nucleus as the O-GlcNAc modification. 

Five classes of glycans are produced:

• N-linked glycans attached to a nitrogen of asparagine or arginine side chains;
• O-linked glycans attached to the hydroxy oxygen of serine, threonine, tyrosine, hydroxylysine, or hydroxyproline side chains, or to oxygens on lipids such as ceramide;
• phospho-glycans linked through the phosphate of a phospho-serine;
• C-linked glycans, a rare form of glycosylation where a sugar is added to a carbon on a tryptophan side chain;
• glypiation, which is the addition of a GPI anchor that links proteins to lipids through glycan linkages.

The carbohydrate chains attached to the target proteins serve various functions.^[2]
For instance, some proteins do not fold correctly unless they are glycosylated first.^[1]

Also, polysaccharides linked at the amide nitrogen of asparagine in the protein confer stability on some secreted glycoproteins.
Experiments have shown that glycosylation in this case is not a strict requirement for proper folding, but the unglycosylated protein degrades quickly.
Glycosylation may play a role in cell-cell adhesion (a mechanism employed by cells of the immune system), as well.

 

N-linked glycosylation

N-linked glycosylation is important for the folding of some eukaryotic proteins.
The N-linked glycosylation process occurs in eukaryotes and widely in archaea, but very rarely in bacteria.

In Eukaryotes, most N-linked oligosaccharides begin with addition of a 14-sugar precursor to the asparagine in the polypeptide chain of the target protein. 
The structure of this precursor is common to most eukaryotes, and contains 3 glucose, 9 mannose, and 2 N-acetylglucosamine molecules.
A complex set of reactions attaches this branched chain to a carrier molecule called dolichol, and then it is transferred to the appropriate point on the polypeptide chain as it is translocated into the ER lumen.
There are three major classes of N-linked saccharides resulting from this core: high-mannose oligosaccharides, complex oligosaccharides and hybrid oligosaccharides.^[2]

• High-mannose is, in essence, just two N-acetylglucosamines with many mannose residues, often almost as many as are seen in the precursor oligosaccharides before it is attached to the protein.

• Complex oligosaccharides are so named because they can contain almost any number of the other types of saccharides, including more than the original two N-acetylglucosamines.

Proteins can be glycosylated by both types of oligosaccharides on different portions of the protein. Whether an oligosaccharide is high-mannose or complex is thought to depend on its accessibility to saccharide-modifying proteins in the Golgi.
If the saccharide is relatively inaccessible, it will most likely stay in its original high-mannose form.
If it is accessible, then it is likely that many of the mannose residues will be cleaved off and the saccharide will be further modified by the addition of other types of group as discussed above.

The oligosaccharide chain is attached by oligosaccharyltransferase to asparagine occurring in the tripeptide sequence Asn-X-Ser or Asn-X-Thr where X could be any amino acid except Pro.
This sequence is known as a glycosylation sequon.

After attachment, once the protein is correctly folded, the three glucose residues are removed from the chain and the protein is available for export from the ER. 

The glycoprotein thus formed is then transported to the Golgi where removal of further mannose residues may take place.

However, glycosylation itself does not seem to be as necessary for correct transport targeting of the protein, as one might think. Studies involving drugs that block certain steps in glycosylation, or mutant cells deficient in a glycosylation enzyme, still produce otherwise-structurally-normal proteins that are correctly targeted, and this interference does not seem to interfere severely with the viability of the cells.
Mature glycoproteins may contain a variety of oligomannose N-linked oligosaccharides containing between 5 and 9 mannose residues. Further removal of mannose residues leads to a 'core' structure containing 3 mannose, and 2 N-acetylglucosamine residues, which may then be elongated with a variety of different monosaccharides including galactose, N-acetylglucosamine, N-acetylgalactosamine, fucose and sialic acid.
GalNAc, glucose, and rhamnose linked to asparagines have been observed as well, although mostly in less complex organisms or bacteria. Glucose linked to the guanidinium group of arginine in sweet corn amyelogenin is the only reported example of N-linked glycosylation on an amino acid other than asparagine.

O-linked glycosylation

O-N-acetylgalactosamine (O-GalNAc)

O-linked glycosylation occurs at a later stage during protein processing, probably in the Golgi apparatus.

This is the addition of N-acetyl-galactosamine to serine or threonine residues by the enzyme UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41), followed by other carbohydrates (such as galactose and sialic acid). This process is important for certain types of proteins such as proteoglycans, which involves the addition of glycosaminoglycan chains to an initially unglycosylated "proteoglycan core protein." These additions are usually serine O-linked glycoproteins, which seem to have one of two main functions.

One function involves secretion to form components of the extracellular matrix, adhering one cell to another by interactions between the large sugar complexes of proteoglycans.
The other main function is to act as a component of mucosal secretions, and it is the high concentration of carbohydrates that tends to give mucus its "slimy" feel.
Proteins that circulate in the blood are not normally O-glycosylated, with the exception of IgA1 and IgD (two types of antibody) and C1-inhibitor.

HERPES GUIDE

The glycoproteins are:

gB (VP7 and VP8.5)

gC (VP8)

gD (VP17 and VP18)

gE (VP12.3 and VP12.6)

gG

gH

gI

gK

gL

gM

maybe:

gJ (Us5)

gN (Ul49.5)

Virion envelopes also contain at least two and possibly more nonglycosylated intrinsic membrane proteins

DANCE

working as a researcher means to think outside the box

keep an open mind

so this is the place where great ideas are born during reload of energy and pause for the mind to process what it has been fed

Today I dance aerobics under the coreography of Niklas, to make room for new synapses to connect

ART

RESEARCH SHOWS ITS OF COURSE SURPRISING CAMOUFLAGE

IF ALL THE FACS PICTURES WOULD LOOK LIKE THIS... AND STAY, NOT RIDE AWAY INTO SOME UNKNOWN COMPUTER SPACE

(it is acutally a picture of one of the 'herpes' chemokines I am working with)

MAYBE MY PLOTS TOOK OFF TO PSYCHEDLIC SPACE  -  CAN I COME TOO? 

IT'S MY DATA REALLY.

CONCENTRATE, FOCUS, EXECUTE!

FLOW JO ANALYSIS

TRAM WAY HOME

LICENSE TO BLOG

 I am so alive that I can see the DNA helix with my bare eyes, aj!Be careful with the pairs, they can easily break or switch places...

BÄR DITT BARN SOM DEN SISTA DROPPEN VATTEN -
Björn Ranelid
(perhaps it would be something like: 'Carry your child like your last drop of water')

I started a new project, and this project is being executed in the place of Latent Lucia, and
will partly be acknowledged by Holy Olga. How lucky I am, Katarina is first author!

So, the only chance to get approved for new publishing of one self, is to let go of the old.

I have to put it aside, it is no longer my baby. You really, really need to get it OUT of your system,
otherwise there will never be anything called new, let alone inventive.

DROP YOUR OLD AS YOUR LAST DROP OF WATER -
Latent Lucia.
And we look forward to seeing my name on many publications to come...

AMEN.

REFLECTIONS

KÄRA GULDHEDSGATAN

Hur ska man kunna skilja sig från denna plätt? På väg hem idag tog jag 43 bilder men som vanligt, blir det bara typ två som är OK. Dessa togs med min moble phone (not iPhone) och jag är rätt glad för det.

                   

Rainy evening - thank god number 6 came when I called it.

Tram goes really quickly, I had to hold on to the chair not to fall down on the disgusting floor.

Are there two directions?!

And what do u know, all of a sudden I find myself at good old Järntorget.

Back and forth, back and forth. Why doesn't people protest to this blessed every day life?

Don't you get tired going back and forth and back?

What if herpes would go back and forth, back and forth up down the ganglion highway?

Oh...
Don't you just die from lack of variation, of knowledge, of new people to look at, of new buildings to see, new streets to walk, new air to breath, new latte to hunt for??

I do.

What can you do?

Just take another step in the forward direction.

Once you decide to walk there is no going back.

Sorry.

This picture is extremely annoying, and the reason to why I put it up. It is my leg yes, but that is not important here. I was trying to catch something from a different angle (?) but people were pushing me from behind, screaming at me to stop taking pictures, hitting me on the head with their big Liseberg-won DAJM. Aj!

That's how annoying it is. I didn't manage to make anything from this.

CONFIRM KOBE

Dear Ms. Katarina Antonsdotter,

 

We are pleased to announce your presentation time and place as follows. We have assigned a presentation number to your abstract. This number will appear in the congress program, book of abstracts and elsewhere.

 

Presentation Number: not yet public for the blog...

Abstract Title:  not yet public for the blog...

 

 

POSTER PRESENTATION:

Presentation Number of your Poster: not yet public for the blog...

Session Number: not yet public for the blog...

Session Title: Immunity to virus infection (excluding retroviruses)

Presentation Format: Poster

Session Start Date and Time (month/day/year time): 8/24/2010 5:00:00 PM

Session End Date and Time (month/day/year time):: 8/24/2010 6:00:00 PM

 

Location: Kobe International Exhibition Hall

 

For presentation instructions, please visit our website.

http://www.ici2010.org/s_program.html#workshops

 

 GLASS PÅ JOBBET FRÅN ABBOTT:

ER LOGO SER JU NÄSTAN UT SOM GLASS?

KAT'S WORK F.EX

B-logg of 14th of June Monday:

Migrationassay set up:

100608                        Mice arrived.

100616                        Depo-Provera treatment of  5 mice

100621                        HSV-2 infection 5 mice

100628                        Day 7 take blood from 5 mice at 8:00 am.

Timepoint planning preliminary.
Ja dates changed! 2 days ahead. So,

100618                        Depo-Provera treatment of  5 mice

100623                        HSV-2 infection 5 mice

100630                        Day 7 take blood from 5 mice at 8:00 am.

Today:

Analysis of FACS continued.
Another lay out has been done named TEST analysis for each mouse FACS;
in this workspace I try different gatings to find the best one.


Administrative work:
Email about my studyplan.
Email about FACS forum.

Miscellaneous.
Planning of wanted, future confocal microscopy work with guided tour.


Order today:

Fisher Scientific AB (Göteborg)
Product nr:      Product:              Price: 4790kr

37503

Pierce Rapid ELISA Mouse mAb Isotyping Kit Five microplates and sufficient reagents to isotype 60 mouse monoclonal antibodies. Includes: Pre-coated 96-well Isotyping Plates, 5 plates Goat Anti-Mouse IgG+IgA+IgM-HRP Conjugate, 30 ml TMB Substrate, 55 ml Stop Solution, 55 ml 30X Wash Buffer, 200 ml Tris buffered Saline, 2 packs   Call Peter Simon and ask if it is a kit that can be used for determining the concentration of the mAb,  message left on answer machine, try again Tuesday!  Registered also for  webcast: Meeting status:   Not started Starting date:   Wednesday 23 June 2010 Starting time:   14:00,GMT Summer Time (London, GMT+01:00) Duration:   1 hour Meeting number:   705 891 511 Meeting password:   None Teleconference:   Conference Code: 314 943 9336 Standard International +44 207 897 0111 Freephone United States : 1 866 966 1187 Austria : 0800 005 345 Belgium : 0800 40867 Canada : 1 866 663 6623 Denmark : 808 88437 France : 0805 102 182 Italy : 800 969 145 Netherlands : 0800 022 1251 South Africa : 0800 982 906 Sweden : 0200 884 649 United Kingdom : 0800 694 8053 Host's name:   Jeremy Fry  Host's Email:  jfry@proimmune.com

FACS FORUM

Flow Cytometry Forum - Molecular Biology Forum Life Science Forums

Finally, smartest decision of today!

Kind regards,

Ms Flow Jo


Dear Antonsdotter,

Thanks for registering at Molecular Biology Forum Life Science Forums! We are glad you have chosen to be a part of our community and we hope you enjoy your stay.

All the best,
Molecular Biology Forum Life Science Forums

SPINNING ELECTRONS

This add on an electron spin was the closest I came to find one which I understood:

Spin-polarized transport 

Spintronics

Electrons have an electrical charge, which enables them to carry an electrical current. However, electrons also have another property, which is the electron spin. Although the electron spin is from quantum mechanical origin and strictly speaking does not have a classical analog, it can be imagined as a "spinning top" which rotates clockwise ("spin-up") or anti-clockwise ("spin-down"). Due to its spin property the electron behaves like a little magnet, which can orient itself along or opposite to an external magnetic field. In the field of spin-based-electronics or "spintronics" one tries to use the electron spin and its sensitivity for a magnetic field in electrical circuits and sensors.
It is our interest is to explore how the electron spin can affect the electron transport properties when it traverses the path from a ferromagnetic material into a non-magnetic material, e.g. a normal metal, a semi-conductor (2DEG) or a superconductor.

(University of Groningen/Physiscs)

KOBE

How did this end up in my sink? Conference 3017 - I'll be there!

It is time for me to get serious. I have to book hotels in Kobe and flights and start working on my poster. Happy days.


ICI2010   14th International Congress of Immunology, Kobe Japan. August 22-27, during the birthday of Katarina which is onthe 26th of August:

Go to Kobe ICI

Kobe Sannomiya Union
Hotel
(14:00 / 11:00)  

PROF NIKITA'S RESEARCH

Prof Nikita Matsunaga is an Associate Professor in Computational and Physical Chemistry

at the Brooklyn campus of Long Island University.

I had the pleasure of working on one of his projects in the summer of 2001.

My work with him unfortunately ended after I moved back to Sweden after 9/11,

and now looking back at the opportunity I was given, being right in the middle of

adventure, my heart starts beating faster when I read the stuff his doing.

Check this out:

Nikita Matsunagas Webpage 

(proudly find my name on his page Students  -post students... =)

Role of surface crossing

In the undergraduate program, you are taught that a chemical reaction is a 

process that transforms reactants to products via a transition state.

For simple reactions, this is a good picture.

Life is a lot more complicated than man! How does an excited state decay?

How does the spin of an electron get flipped during reaction to get diradicals?

These are the questions we can not answer from the conventional single potential

energy surface picture.

Photochemistry has full of these examples. One of such reactions we are interested in

is called spin-forbidden reaction.

The reaction starts out having all electrons paired (singlet state).

During the reaction, one of the electrons flips its spin to become a diradical state (triplet state).  We need to consider both the singlet and triplet potential energy surfaces.  The most important feature common to both potentials is the lowest energy crossing point between the two states. 

By investigating the minimum energy crossing point, we can learn about what geometry of the molecule the spin is likely to flip as well as probability of the event can be calculated.

 Part of Medicinareberget, Gothenburg.

Unfortunately could not put Nikita's picture of S-T crossing in.

My work place

Guldhedsgatan 10B

Guldhedsgatan 10A

Mina pennor:

An office with a view:

My work bag:

Rheuma's Innergård:

Tram to home:

Rheumatic coffee room lamps:

SMALL TALK

I am so disappointed. Another half an hour passed and did only 2 antibody analysis on two organs.

But, I had a great idea! I pack my PC, buy liquorice on my way home and finish all ten by midnight.

LIQUOR ICE

2 1/2 möss down. 7 1/2 to go och klockan e 20:33. Kl 20:55 har jag gjort 2 1/2 till.

Piggelinen slut, Cola uppdrucken och lakrits beställt i 100-pack från Gottelisa:

http://webshop.gottelisa.se/ovrigt/sot-lakrits.html

What a disappointment!  I heard everything by Chet Baker but not his Cuesta notte-wannabe 'Chetty's Lullaby'...
Do I remember the experimental set up? Or maybe I should show result that,

data.037 is upregulated in the CNS post HSV- infection. <3

This will save time and money.