All 4 entries tagged Biochemistry

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October 29, 2005

Developmental Biology Tutorial No. 2 – The Making of a Vertebrate Limb.

"How is the vertebrate limb patterned?"

If you do not wish to read about vertebrate limb development it is advised you scroll straight down to the kittens strategically placed at the bottom of the page to help you overcome the trauma of momentarily being forced to think about work.

Presentation 1

General Introduction

Presentation 2

The formation of the limb bud and the identity of the fore and hind limbs

(For background interest this is one of the many papers on the role of Tbx5 in genetic disease. It causes Holt-Oram syndrome: A dominantly inherited malformation syndrome with short stature, upper limb anomaly, minor craniofacial anomalies, and absence of TBX5 mutations: Report of a Thai family )

Presentation 3

Induction of the apical ectodermal ridge and limb outgrowth

Allocation to the AER

AER induction

D/V patterning of the outgrowth

Presentation 4

AER function, the roles of FGF's in limb outgrowth

Presentation 5

Development of the antero- posterior axis


In the interest of actually making research that bit more interesting i have developed "ScopusWhacking". Woo and yay. Aim for the search to return only one research article when provided with just one surname and one other word. Usually works 1/3 of the time. At least it does in bio. God i'm bored…


As promised…

Caption anybody? No prizes well, no prizes that involve the consumption of vinegar shots

M xxx

October 25, 2005

Ok, so you want a punchline?

Follow-up to Development Essay 1 Resources from Something Random

An Englishman, and Irishman and a half-Spanish blogger all have to hand their development essays by 2pm on tuesday the 25th of october 2005…

The Englishman has his finished and doublechecked by his tutor by the previous wednesday, strolls onto campus tuesday morning, hands it in and then goes for a big cholo breakfast with his mates.

The Irishman just about finishes it the night before, is forced to cycle onto campus in the rain but manages to hand it in 3 minutes and 27 seconds before the deadline.

The half-Spanish blogger screams at her computer than goes to bed, wakes up at 5am and smashes her alarmclock with the heel of a shoe then proceeds to swear at God, herself, her computer monitor and her empty teacup before resorting to half an hour of primal scream therapy. After waking all 5 of her housemates she breaks down into tears and manic depression and throws the keyboard against the wall permanently damaging the F5 key and a small section of desk. With the keyboard now temporarily out of action she resorts to throwing another shoe. The shoe bounces in a wholly unsatisfactory manner and elicits another scream. Housemate #5 makes a noise that indicates irritation, and blogger hits adjoining wall for good measure.

After a brief pause to catch her breath she fashions a voodoo doll out of socks and declares it to be "Täald"(1), the god of 293-word-essays which she then proceeds to stab. Flashlight interrogation and water torture however, also prove unsuccessful and the essay remains uncompleted. The decorative sheepskin rug on her floor is pulled aside and a rudimentary bonfire is prepared over the pre-existing iron shaped scorch mark with the remenants of wine soaked essay notes. Täald is staked to a biro and told to contemplate the mysteries of life in the few seconds left to him while the cojones curse(2) is recited. A little shoulder devil reminds the half-Spanish blogger that notes although made of wood are unlikely to be too flammable when soaked in wine. She goes through half a dozen matches then is forced to agree. Strapping Täald to her hip with a bandana, she grabs a sharpened bic biro and wades out into the dark hallway to hunt down her furtive essay. Meanwhile her shoulder devil props up the shoulder angel on a chair in some dark recess of her mind, there is a faint odour of chloroform in the air.

She has to be careful, the essay could take almost any form and it has had weeks of practice evading her. Ten minutes later and after much deliberation, she decides that it is not the pot plant, the doorknob or the sofa; nor is it the kettle or the small bag of sugar on the worktop; her analysis of a punnet of cherry tomatoes is inconclusive.

Suddenly there is a knock at the front door. She answers and is faced by a tall thin man. He has very watery eyes and a thin moustache that hovers above slightly skewed lips. She asks if he is her essay. He replies that doesn't recall ever being an essay. The shoulder devil prompts her to poke him. She does, and also throws a teabag at him for good measure lest he be an evil spirit. The strange man takes her to a strange room where they give her tea and mozart. The tea tastes a little funny. She thinks the pictures she draws make the man look a little worried – especially the black one; he doesn't like the black one. This tea is rather strange. All the voices are far away now, they are sinking deep into the soft walls. She falls asleep and thus starts her 20 year journey through mental institutions and the subsequent rehab for dependance on "crazy pills" and a lifelong struggle with mind altering drugs.


Yeah I don't really get the joke either. But I'm pretty sure I've heard it somewhere before…

Oh christwaggons this isn't good...

M xxx


1) It should be mentioned that Täald is also the patron saint of all that shit that creeps into your Ikea shopping trolley when you aren't paying attention only to be discovered as you recover from your Ikea-coma and load everything into the car "WTF?! a shoehorn shaped like a snake and a set of eight novelty placemats shaped like a fornicating octopus?! surely i didn't just pay for all this..."

2) A fearsome spanish curse that involves tying a gods cojones in a knot until a certain offending object is returned to you. In this case it also involves large amounts of warpaint


p.s. the F5 key doesn't control anything vital does it?

October 24, 2005

Development Essay 1 Resources

links to all the research papers

(you may need your athens account details to access them)

Talk 1

Talk 2
Setting up the initial asymmetries in the embryo.

  1. Early patterning of the C. elegans embryo.

  2. Axis determination in _C. elegans: initiating and transducing polarity.

  3. Heads or tails: Cell polarity and axis formation in the early _Caenorhabditis elegans embryo.

  4. Polarization of the C. elegans zygote proceeds via distinct establishment and maintainance phases. (for pictures of localisation)

Talk 3
Skn-1 and EMS development.

  1. Skn-1 a maternally expressed gene required to specify the fate of ventral blastomeres in the early _C. elegans embryos.

  2. Formation of a monomeric DNA binding domain by Skn-1 bZIP and homeodomain elements.

  3. The maternal gene skn-1 encodes a protein that is distributed unequally in early _C. elegans embryos.

Talk 4
Germline development pie-1 and mex-1 genes; transcriptional silencing.

  1. The pie-1 and mex-1 genes and maternal control of blastomere identity in early _C. elegans embryos.

  2. The PIE-1 protein and germline specification in C. elegans embryos.

  3. Repression of gene expression in the embryonic germ lineage of C. elegans.

  4. The C. elegans MEX-1 protein is present in germline blastomeres and is a P granule component. (only need abstract)

  5. Launching the germline in Caenorhabditis elegans: regulation of gene expression in early germ cells.

  6. PIE-1 is a bifunctional protein that regilates maternal and zygotic gene expression in the embryonic germ line of Caenorhabditis elegans.

  7. Germ plasm: protein degradation in the soma.

Talk 5
The C. elegans maternal Notch system.

  1. The maternal genes apx-1 and glp-1 and establishement of dorsal-ventral polarity in the early _C. elegans embryo.

  2. Translational control of maternal glp-1 mRNA establishes asymmetry in the _C. elegans embryo.

  3. Translational control of maternal glp-1 mRNA by POS-1 and its interacting protein SPN-4 in Caenorhabditis elegans.

  4. An inductive interaction in 4-cell stage embryos involves APX-1 expression in the signalling cell

  5. Time dependant responses to glp-1 mediated inductions in early C. elegans embryos.


It's taken me just over 2 (goddamn) hours to find these links.

They make me hurt all over.

I think my eyes may be bleeding
I may never smile again…

oooh a rabbit!!

M xxx

October 07, 2005

Stem cells

Writing about web page

WARNING: this is Biochemistry related. You have permission to run away screaming from your monitor.

ok useful sites i found:

These sites should all refer to stem cell maintainance in vitro. maybe. havn't read them in full yet


A bit on maintaining stem cells.

When used in vitro for research, it is vital that the stem cells used retain their "stemness" or "pluripotency". Without the correct stimulation the cells quicky differentiate into somatic cells, losing their "repopulating capacity"(1). Firstly, the normal procedure for maintaining the culture of cells is as a suspension. The cells must be kept disaggregated; This can be done manually or by nonenzymatic "CDB"(cell dissociation buffer) or enzymatic "CT"(collagenase/trypsin) cell passaging(2). However the CT and CDB methods were found to promote the development of abnormal karyotypes in the cultured stem cells (such as trisomy - particularly of chr17 and 20)

The conclusions were that up to 15 passages with CDB/CT could be used and still mantain a high fidelity to the normal stem cell karyotype(2).

The "cell passaging" seems to refer to the replacement to the medium in which the cells are suspended. Does anyone have a more precise definition?

"hESC"(human embryonic stem cell) cultures are generally grown in conjunction with feeder cells. These cells seem to secrete soluble factors that maintain the stem cells in their undifferentiated state – however the particular factors in question remain unidentified. "mESC"(mouse embryonic stem cells)

1. cDNA cloning of FRIL, a lectin from Dolichos lablab, that preserves hematopoietic progenitors in suspension culture

2. Activin A Maintains Pluripotency of Human Embryonic Stem Cells in the Absence of Feeder Layers

Maintenance of Pluripotency in Human Embryonic Stem Cells Is STAT3 Independent


these are the speakers for the International symposium on Germ Cells, Epigenetics and Embryonic Stem Cells. I've included mention of where they seem to be focused mostly on one specific area. (The links are just google scholar links to any of their stem cell papers)

Oh and a kitten. But why kittens and stem cells?

That's right.
Because I say so. I love that answer.

*sigh* i know how it feels…

EDIT: Biochemisty is damaging to your mental health. I just found a malformed gummibear in my hairibo and caught myself thinking "I wonder what genetic defect it has? Looks like the morphogen gradient-induced cell differentiation went wrong..." AAaaarrrgggh! development overload. :s

M xxx

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