The DNA Network

Brain biomarkers in action [biomarker-driven mental health 2.0]

Posted: 06 Sep 2008 07:37 PM CDT

Image by -kÇ- via Flickr Session 4 of our discussion group, "When Basic Neuroscience Meets Psych Rehab" will meet on Sept 25. This session will cover the topic of 'affect labeling' which is one strategy for managing one's emotions. Did you know there are 3,000+ words you can choose from to describe your feelings ? How many can you name right off the bat ? The discussion seeks to flesh out the way in which basic brain mechanisms of emotional regulation work and how brain-based (and genetic) biomarkers might be used in a clinical therapy/rehabilitation setting. Slides and discussion highlights will be posted to the website.

Tracing the evolutionary history of Sarah Palin: links to a parasitic nematode and the pathogenic fungus Botryotinia fuckeliana [The Tree of Life]

Posted: 06 Sep 2008 03:07 PM CDT

You see, as a total sequence analysis dork, when I see names, I frequently ask whether the letters in the name include only letters which are used as amino acid abbreviations. I started this game when the brilliant notes/letters came out in Science in the early 90s about whether ELVIS was overrepresented in protein sequences. Of course, despite being 20 years old, Science still keeps these under wraps requiring registration to see them (see for example the Stevens letter).

Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).

So - I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide "SARAHPALIN" with all the peptides in the non redundant collection at Genbank).

>ref|XP_001545292.1|  hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1|  predicted protein [Botryotinia fuckeliana B05.10]
Length=383

GENE ID: 5425746 BC1G_16161 | hypothetical protein
[Botryotinia fuckeliana B05.10]

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SARA PALI 
Sbjct  209  SARAQPALI  217

>ref|YP_061725.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
gb|AAT88620.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
Length=451

GENE ID: 2939000 thrA | homoserine dehydrogenase
[Leifsonia xyli subsp. xyli str. CTCB07] (10 or fewer PubMed links)

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI
Sbjct  267  SARVHPALI  275

>ref|ZP_02031476.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
gb|EDN87136.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
Length=299

Score = 26.1 bits (54),  Expect =   340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  3    RAHPALIN  10
            RAHPAL+N 
Sbjct  170  RAHPALVN  177
>ref|XP_567332.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
ref|XP_773201.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|EAL18554.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|AAW45815.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
Length=437

GENE ID: 3254188 CNJ01520 | hypothetical protein
[Cryptococcus neoformans var. neoformans JEC21] (10 or fewer PubMed links)

Score = 26.1 bits (54),  Expect =   340
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI 
Sbjct  415  SARQHPALI  423

>ref|YP_001626035.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
gb|ABY24621.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
Length=386

GENE ID: 5822379 RSal33209_2898 | citrate synthase 
[Renibacterium salmoninarum ATCC 33209]

Score = 25.7 bits (53),  Expect =   456
Identities = 9/11 (81%), Positives = 9/11 (81%), Gaps = 2/11 (18%)

Query  1    SARAHP--ALI  9
            SARAHP  ALI 
Sbjct  218  SARAHPYAALI  228

>ref|YP_001817256.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
gb|ACB73656.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
Length=936

GENE ID: 6208547 Oter_0366 | integral membrane sensor hybrid histidine kinase
[Opitutus terrae PB90-1]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3    RAHPALI  9
            RAHPALI 
Sbjct  256  RAHPALI  262

>ref|YP_001757871.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
Length=331

GENE ID: 6141303 Mrad2831_5232 | putative anti-sigma regulatory factor,
serine/threonine protein kinase [Methylobacterium radiotolerans JCM 2831]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  2    ARAHPALI  9
            ARAHPAL+
Sbjct  299  ARAHPALV  306

>ref|ZP_01466013.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
gb|EAU63211.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
Length=209

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3   RAHPALI  9
           RAHPALI 
Sbjct  79  RAHPALI  85

>ref|YP_001558323.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
gb|ABX41584.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
Length=357

GENE ID: 5743305 Cphy_1206 | glycosyl transferase group 1
[Clostridium phytofermentans ISDg]

Score = 25.2 bits (52),  Expect =   611
Identities = 8/10 (80%), Positives = 8/10 (80%), Gaps = 0/10 (0%)

Query  1    SARAHPALIN  10
            S RAHP LIN 
Sbjct  113  SERAHPLLIN  122

There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.

Of course, anybody who has heard me blather on and on about evolution knows that I am always talking about how blast top hits are not a good measure of relatedness per se (see my NAR paper where I first talked about this in 1995). So - I decided to build a tree of Sarah Palin. I used the NCBI Distance Tree option which you can do from blast searches.

Since most likely you cannot see that in enough detail - here is a zoom in.

That one did not come through on the Blog so well either so I decided to output the tree in Newick format and then I searched for a program that could draw a better figure on the web (we have tools in my lab to do this but I am trying to do this all on the web as an exercise). And I found a web site that makes drawtree available. And I plugged in the Newick format and it made a nicer one.

Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.

So in conclusion - by similarity - SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.

Primary rodent neural stem cell lines [Reportergene]

Posted: 06 Sep 2008 05:56 AM CDT

Millipore Corporation's MilliTrace primary rodent neural stem cell (NSC) lines express green fluorescent protein (GFP) constitutively. GFP expression in these stem cells allows researchers to monitor the behavior of specific populations of cells as they proliferate, migrate, and differentiate into various cell lineages, depending on developmental context. The MilliTrace cell lines are the first commercially available, GFP-expressing, karyotypically normal stem cell lines, and are supplied with optimized expansion medium. Millipore Corporation www.millipore.com

source: Biotechniques Weekly

Reporter lines for conditional transgenesis [Reportergene]

Posted: 06 Sep 2008 05:56 AM CDT

The technology of gene inactivation (knockout, KO) has boosted our understanding of the role of numbers of gene in vivo. However, it has been progressively realized that the interpretation of the results may be complicated by the existence of compensatory adaptation throughout redundancies both in cell networks of different tissues that in gene networks of the same cell. One way to avoid some of these problems is to make KO animals in desired tissues or at desired time-points, in order to observe phenotypic KO pictures before development of functional adaptations.

The Cre-loxP system is widely used for making conditional alterations to the mouse genome, and many transgenic lines exist that express Cre recombinase in tissue-specific manner. Cre-mediated recombination is frequently monitored using reporter lines in which Cre expression activates a reporter gene driven by a ubiquitous promoter. The most known test line is the 1999's R26R (Rosa26 lacZ) in which beta-galactosidase is expressed following Cre recombination.

Recently a new reporter line has been described: the IRG mouse. Compared to R26 reporter, IRG adopt insulators instead of locus strategy (see where do you express your transgene?). In this line, a red fluorescent protein (RFP) is expressed ubiquitously prior to Cre-mediated recombination and an enhanced green fluorescent protein (EGFP) following recombination. For instance in the picture, you can see Cre-mediated ricombination in CNS (nestin positive cells) of a 13.5 dpc embryo. Given the distinct advantages of fluorescent reporters over the lacZ staining (without exogenous substrates, fluorescence can be visualized in tissues without fixation artifacts and cells can be isolated using FACS sorting), the IRG mouse will bring soon new adepts to the emerging field of optical imaging.

Soriano, P. (1999). Generalized lacZ expression with the ROSA26 Cre reporter strain. Nature Genetics, 21(1), 70-71. DOI: 10.1038/5007
De Gasperi, R.,[...] Elder, G.A. (2008). The IRG mouse: A two-color fluorescent reporter for assessing Cre-mediated recombination and imaging complex cellular relationships in situ. Genesis, 46, 308-317. DOI: 10.1002/dvg.20400

red fluorescence spectrum from soviet countries? [Reportergene]

Posted: 06 Sep 2008 05:56 AM CDT

Despite years of effort since its cloning in 1992, the GFP of the jellyfish Aequorea victoria (the most known and used green fluorescent reporter) has not been turned red... until now.

A team of Russian researchers started from a blueshifted GFP variant and performed a molecular mutagenesis evolution approach to get, not only shift toward red, but also some clues to the chromophore formation theory. Basically they made libraries of millions of mutants and sent them through a Dako cell sorter to select the best red performances that were mutated once again and analyzed iteratively until they achieved the desired shift to the red fluorescence. The results was a protein, R10-3, that has both red and green fluorescence, so a pure red protein has not derived yet (but the evolutive job is still in progress).
It is not the first time that a Russian team turns to red fluorescent reporters: some months ago we were reading the Nature Methods paper about Katushka and mKate. Is a matter of fact that red color is an innate hue in some countries: are there the basis to make a social association study about scientists, countries and reporter colors?

Mishin, A.S., Subach, F.V., Yampolsky, I.V., King, W., Lukyanov, K.A., Verkhusha, V.V. (2008). The First Mutant of the Aequorea victoria Green Fluorescent Protein That Forms a Red Chromophore. Biochemistry, 47(16), 4666-4673. DOI: 10.1021/bi702130s

In this post you can freshen why red spectrum matter in fluorescence imaging

Nuclear Magnetic Reporters [Reportergene]

Posted: 06 Sep 2008 05:55 AM CDT

With the advantage of tomographical data set and detailed anatomical information, magnetic resonance imaging (MRI) features an unsurpassed space resolution (micrometers!) in the field of in vivo imaging. Conversely, imaging of optical reporters like luciferase and GFP, still suffers from short-sighted resolution, often requiring longer post-mortem analysis (i.e. immunoistochemistry) to identify and deconvolve photon emission sources of in vivo datasets. From this "topological" standpoint it is easy to understand the growing awareness and demand of new "superparamagnetic" reporter genes to be detected according to their "relaxivity". NMR gene expression strategies thus far introduced in recent literature include:

detection of beta-galactosidase activity;
targeting of amide protons of expressed proteins;
expression of natural iron homeostasis proteins such as transferrin, ferritin, MagA.

Nonetheless, those "magnetic" papers had very low followup, and a transgenic paramagnetic reporter mouse still don't exists. MRI reporters classically suffer from low sensitivity (lot of reporter need to be expressed in order to be detected) and low dynamic range (the detection don't discriminate very well different reporter concentrations). It is possible to conceive a reporter gene with high space/time resolution, high sensitivity and high linear range? With multimodality imaging a super reporter mouse can harbour a vector containing more than one reporter (for different imaging modalities). This is very fashionable in leading imaging labs, and lot of cut and paste have been made with reporter sequences. Do you know any super-mouse?

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Saturday, September 6, 2008

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